27 Works

2019 NSF Workshop on Connecting Large Facilities and Cyberinfrastructure

Ewa Deelman, Ilya Baldin, Brian Bockelman, Adam Bolton, Patrick Brady, Tom Cheatham, Laura Christopherson, Rafael Ferreira da Silva, Tom Gulbransen, Kate Keahey, Marina Kogan, Anirban Mandal, Angela Murillo, Jarek Nabrzyski, Valerio Pascucci, Steve Petruzza, Mats Rynge, Susan Sons, Dan Stanzione, Chaudhuri Surajit, Daryl Swensen, Alexander Szalay, Douglas Thain, John Towns, Charles Vardeman … & Jane Wyngaard

Understanding the role of clay minerals in the three-dimensional fossilization of erniettomorphs from the Ediacaran Wood Canyon Formation, Nevada

James Hall, Emmy Smith, Nobumichi Tamura, Sirine Fakra & Tanja Bosak
Three-dimensionally preserved Ediacaran fossils occur within globally distributed sandstone beds. Sandy mass flow deposits of the Ediacaran Wood Canyon Formation in the Montgomery Mountains, Nevada, contain two different examples of erniettomorphs, soft-bodied organisms with uncertain taxonomic affinities. One type exhibits mm-scale ridges, the other one is flattened and lacks any smaller diagnostic features, including a distinct lower boundary. We explore the cast-and-mould preservation of both fossil types by petrography, Raman spectroscopy, X-ray microprobe and X-ray...

Social relationships, social status, and survival in wild baboons: A tale of two sexes

Fernando Campos, Francisco Villavicencio, Elizabeth Archie, Fernando Colchero & Susan Alberts
People who are more socially integrated or have higher social status live longer, and recent studies on aging and social environments in mammals show some striking convergences with this human pattern. Nonhuman primates are especially valuable models of aging, and studies of several populations of wild primates have shown parallel results to human studies. Specifically, greater numbers and strength of social bonds and/or higher social dominance rank predict longer lifespan in females of several nonhuman...

Tensor Product Decomposition Networks: Uncovering Representations of Structure Learned by Neural Networks

Richard T. McCoy, Tal Linzen, Ewan Dunbar & Paul Smolensky

Extending adaptor grammars to learn phonological alternations

Canaan Breiss & Colin Wilson

Neural network learning of the Russian genitive of negation: optionality and structure sensitivity

Natalia Talmina & Tal Linzen

Mass ratio effects underlie ecosystem responses to environmental change

Melinda Smith, Sally Koerner, Alan Knapp, Meghan Avolio, Francis Chaves, Elsie Denton, John Dietrich, David Gibson, Jesse Gray, Ava Hoffman, David Hoover, Kimberly Komatsu, Andrea Silletti, Kevin Wilcox, Qiang Yu & John Blair
1. Random species loss has been shown experimentally to reduce ecosystem function, sometimes more than other anthropogenic environmental changes. Yet, controversy surrounds the importance of this finding for natural systems where species loss is non-random. 2. We compiled data from 16 multi-year experiments located at a single site in native tallgrass prairie. These experiments included responses to 11 anthropogenic environmental changes, as well as non-random biodiversity loss - either the removal of uncommon/rare plant species...

Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

Michael D. Martin, Elizabeth A. Zimmer, Morten T. Olsen, Andrew D. Foote, M. Thomas P. Gilbert & Grace S. Brush
Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North...

Data from: Suppression and facilitation of human neural responses

Michael-Paul Schallmo, Alexander M. Kale, Rachel Millin, Anastasia V. Flevaris, Zoran Brkanac, Richard A.E. Edden, Raphael A. Bernier, Scott Murray, Alexander M Kale, Anastasia V Flevaris, Scott O Murray, Raphael A Bernier & Richard AE Edden
Efficient neural processing depends on regulating responses through suppression and facilitation of neural activity. Utilizing a well-known visual motion paradigm that evokes behavioral suppression and facilitation, and combining 5 different methodologies (behavioral psychophysics, computational modeling, functional MRI, pharmacology, and magnetic resonance spectroscopy), we provide evidence that challenges commonly held assumptions about the neural processes underlying suppression and facilitation. We show that: 1) both suppression and facilitation can emerge from a single, computational principle - divisive...

Data from: Vocal turn-taking in a nonhuman primate is learned during ontogeny

Cecilia P. Chow, Jude F. Mitchell, Cory T. Miller & C. T. Miller
Conversational turn-taking is an integral part of language development, as it reflects a confluence of social factors that mitigate communication. Humans coordinate the timing of speech based on the behaviour of another speaker, a behaviour that is learned during infancy. While adults in several primate species engage in vocal turn-taking, the degree to which similar learning processes underlie its development in these non-human species or are unique to language is not clear. We recorded the...

Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dörner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio De Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, PANGEA Consortium, _ & Rakai Health Sciences Program, _
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from...

Data from: Testing conceptual models of early plant succession across a disturbance gradient

Cynthia C. Chang, Charles B. Halpern, Joseph A. Antos, Meghan L. Avolio, Abir Biswas, James E. Cook, Roger Del Moral, Dylan G. Fischer, Andrés Holz, Robert J. Pabst, Mark E. Swanson & Donald B. Zobel
1.Studies of succession have a long history in ecology, but rigorous tests of general, unifying principles are rare. One barrier to these tests of theory is the paucity of longitudinal studies that span the broad gradients of disturbance severity that characterize large, infrequent disturbances. The cataclysmic eruption of Mount St. Helens (Washington, USA) in 1980 produced a heterogeneous landscape of disturbance conditions, including primary to secondary successional habitats, affording a unique opportunity to explore how...

Data from: Cherry-picking by trialists and meta-analysts can drive conclusions about intervention efficacy

Evan Mayo-Wilson, Tianjing Li, Nicole Fusco, Lorenzo Bertizzolo, Joseph K. Canner, Terrie Cowley, Peter Doshi, Jeffrey Ehmsen, Gillian Gresham, Nan Guo, Jennifer A. Haythornthwaite, James Heyward, Hwanhee Hong, Diana Pham, Jennifer L. Payne, Lori Rosman, Elizabeth A. Stuart, Catalina Suarez-Cuervo, Elizabeth Tolbert, Claire Twose, Swaroop Vedula & Kay Dickersin
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN SUBSEQUENT PUBLICATIONS. PLEASE SEE http://dx.doi.org/10.1016/j.jclinepi.2017.05.007 FOR MORE INFORMATION. Objectives The objective of this study was to determine whether disagreements among multiple data sources affect systematic reviews of randomized clinical trials (RCTs). Study Design and Setting Eligible RCTs examined gabapentin for neuropathic pain and quetiapine for bipolar depression, reported in public (e.g., journal articles) and nonpublic sources (clinical study reports [CSRs] and individual participant data [IPD]). Results...

Data from: Measuring couple relationship quality in a rural African population: validation of a couple functionality assessment tool in Malawi

Allison Ruark, Rachel Chase, John Hembling, Valerie Rhoe Davis, Paul Clayton Perrin & Dorothy Brewster-Lee
Available data suggest that individual and family well-being are linked to the quality of women’s and men’s couple relationships, but few tools exist to assess couple relationship functioning in low and middle-income countries. In response to this gap, Catholic Relief Services has developed a Couple Functionality Assessment Tool (CFAT) to capture valid and reliable data on various domains of relationship quality. This tool is designed to be used by interventions which aim to improve couple...

Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

Meredith M. Doellman, Gregory J. Ragland, Glen R. Hood, Peter J. Meyers, Scott P. Egan, Thomas H.Q. Powell, Peter Lazorchak, Mary M. Glover, Cheyenne Tait, Hannes Schuler, Daniel A. Hahn, Stewart H. Berlocher, James J. Smith, Patrik Nosil, Jeffrey L. Feder, Daniel Hahn, Stewart Berlocher, James Smith, Meredith Doellman, Peter Meyers, Scott Egan, Mary Glover, Jeffrey Feder, Glen Hood, Thomas Powell … & Gregory Ragland
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a...

Data from: Substance P signalling in primary motor cortex facilitates motor learning in rats

Benjamin Hertler, Jonas Aurel Hosp, Manuel Buitrago Blanco, Andreas R. Luft & Andreas Rüdiger Luft
Among the genes that are up-regulated in response to a reaching training in rats, Tachykinin 1 (Tac1) - a gene that encodes the neuropeptide Substance P (Sub P) - shows an especially strong expression. Using Real-Time RT-PCR, a detailed time-course of Tac1 expression could be defined: a significant peak occurs 7 hours after training ended at the first and second training session, whereas no up-regulation could be detected at a later time-point (sixth training session)....

Data from: Phylogenetic, ecological, and allometric correlates of cranial shape in Malagasy lemuriforms

Karen L. Baab, Jonathan M. G. Perry, F. James Rohlf & William L. Jungers
Adaptive radiations provide important insights into many aspects of evolution, including the relationship between ecology and morphological diversification as well as between ecology and speciation. Many such radiations include divergence along a dietary axis, although other ecological variables may also drive diversification, including differences in diel activity patterns. This study examines the role of two key ecological variables, diet and activity patterns, in shaping the radiation of a diverse clade of primates, the Malagasy lemurs....

Data from: Protein synthesis inhibition in the peri-infarct cortex slows motor recovery in rats

Maximilian Schubring-Giese, Susan Leemburg, Andreas R. Luft, Jonas A. Hosp, Andreas Rüdiger Luft & Jonas Aurel Hosp
Neuroplasticity and reorganization of brain motor networks are thought to enable recovery of motor function after ischemic stroke. Especially in the cortex surrounding the ischemic scar (i.e., peri-infarct cortex), evidence for lasting reorganization has been found at the level of neurons and networks. This reorganization depends on expression of specific genes and subsequent protein synthesis. To test the functional relevance of the peri-infarct cortex for recovery we assessed the effect of protein synthesis inhibition within...

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, A. Vachani, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Data from: Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies

Meredith M. Doellman, Scott P. Egan, Gregory J. Ragland, Peter J. Meyers, Glen R. Hood, Thomas H.Q. Powell, Peter Lazorchak, Daniel A. Hahn, Stewart H. Berlocher, Patrik Nosil, Jeff L. Feder, Jeffrey L. Feder & Thomas H. Q. Powell
Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer if standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency...

Data from: A 2.6‐g sound and movement tag for studying the acoustic scene and kinematics of echolocating bats

Laura Stidsholt, Mark Johnson, Kristian Beedholm, Lasse Jakobsen, Kathrin Kugler, Signe Brinkløv, Angeles Salles, Cynthia F. Moss, Peter T. Madsen & Peter Teglberg Madsen
1. To study sensorimotor behaviour in wild animals, it is necessary to synchronously record the sensory inputs available to the animal, and its movements. To do this, we have developed a biologging device that can record the primary sensory information and the associated movements during foraging and navigating in echolocating bats. 2. This 2.6 -gram tag records the sonar calls and echoes from an ultrasonic microphone, while simultaneously sampling fine-scale movement in three dimensions from...

Data from: EDAPHOLOG monitoring system: automatic, real-time detection of soil microarthropods

Miklós Dombos, Oxána Bánszegi, Katalin Szlávecz & Andrés Kosztolányi
Soil microarthropods as organic matter decomposers play an important role in soil functioning thus providing ecosystem services. However, ecosystem scale investigations on their abundance and dynamics are scarce because their high spatio-temporal heterogeneity requires huge sample size. Processing and identifying large number of individuals are extremely labour-intensive. We prototyped a device called EDAPHOLOG monitoring system that consists of (1) a probe that catches and detects microarthropods and estimates their body size; (2) a data logger...

Data from: Fisher’s geometric model predicts the effects of random mutations when tested in the wild

Frank W. Stearns & Charles B. Fenster
Fisher's Geometric Model of Adaptation (FGM) has been the conceptual foundation for studies investigating the genetic basis of adaptation since the onset of the neo Darwinian synthesis. FGM describes adaptation as the movement of a genotype toward a fitness optimum due to beneficial mutations. To date, one prediction of FGM, the probability of improvement is related to the distance from the optimum, has only been tested in microorganisms under laboratory conditions. There is reason to...

Data from: A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda

François Blanquart, Mary Kate Grabowski, Joshua Herbeck, Fred Nalugoda, David Serwadda, Michael A. Eller, Merlin L. Robb, Ronald Gray, Godfrey Kigozi, Oliver Laeyendecker, Katrina A. Lythgoe, Gertrude Nakigozi, Thomas C. Quinn, Steven J. Reynolds, Maria J. Wawer, Christophe Fraser, Maria J Wawer, Katrina A Lythgoe, Thomas C Quinn & Steven J Reynolds
Evolutionary theory hypothesizes that intermediate virulence maximizes pathogen fitness as a result of a trade-off between virulence and transmission, but empirical evidence remains scarce. We bridge this gap using data from a large and long-standing HIV-1 prospective cohort, in Uganda. We use an epidemiological-evolutionary model parameterised with this data to derive evolutionary predictions based on analysis and detailed individual-based simulations. We robustly predict stabilising selection towards a low level of virulence, and rapid attenuation of...

Data from: Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish

Stefan Dennenmoser, Fritz J. Sedlazeck, Michael C. Schatz, Janine Altmüller, Matthias Zytnicki & Arne W. Nolte
Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through non-allelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genome-wide distribution of transposon insertions in a young hybrid lineage (“invasive...

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