663 Works

Data from: Phylogenetic Congruence and Discordance Among One Morphological and Three Molecular Data Sets from Pontederiaceae

Sean W. Graham, Joshua R. Kohn, Brian R. Morton, James E. Eckenwalder & Spencer C.H. Barrett
A morphological data set and three sources of data from the chloroplast genome (two genes and a restriction-site survey) were used to reconstruct the phylogenetic history of the Pickerelweed family Pontederiaceae. The chloroplast data are converging to a single tree, presumably the true chloroplast phylogeny of the family. Unrooted trees estimated from the three chloroplast data sets were identical or extremely similar in shape to each other, mostly robustly supported and there was no evidence...

Data from: Reproductive aging patterns in primates reveal that humans are distinct

Susan C. Alberts, Jeanne Altmann, Diane K. Brockman, Marina Cords, Linda M. Fedigan, Anne Pusey, Tara S. Stoinski, Karen B. Strier, William F. Morris & Anne M. Bronikowski
Women rarely give birth after approximately 45 years of age, and they experience the cessation of reproductive cycles – menopause – at approximately 50 years of age, after a fertility decline lasting almost two decades. Such reproductive senescence in mid-lifespan is an evolutionary puzzle of enduring interest because it should be inherently disadvantageous. Further, comparative data on reproductive senescence from other primates, or indeed other mammals, remains relatively rare. Here we carried out the first...

Data from: Environmental gradients and the evolution of successional habitat specialization: a test case with 14 Neotropical forest sites

Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H. S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander DeFrancesco, Juan M. Dupuy, Bryan Finegan … & G. Bruce Williamson
1. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late successional stages in wet forest. 2....

Data from: The multivariate association between genomewide DNA methylation and climate across the range of Arabidopsis thaliana

Thomas E. Keller, Jesse R. Lasky & Soojin V. Yi
Epigenetic changes can occur due to extracellular environmental conditions. Consequently, epigenetic mechanisms can play an intermediate role to translate environmental signals to intracellular changes. Such a role might be particularly important in plants, which often show strong local adaptation and have the potential for heritable epigenetic states. However, little is currently known about the role of epigenetic variation in the ecological mechanisms of adaptation. Here, we used multivariate redundancy analyses to examine genomewide associations between...

Data from: Selection, constraint and the evolution of coloration in African starlings

Rafael Maia, Dustin R. Rubenstein & Matthew D. Shawkey
Colorful plumage plays a prominent role in evolution of birds, influencing communication (sexual/social selection) and crypsis (natural selection). Comparative studies have focused primarily upon these selective pressures, but the mechanisms underlying color production can also be important by constraining the color gamut upon which selection acts. Iridescence is particularly interesting to study the interaction between selection and color-producing mechanisms because a broad range of colors can be produced with a shared template, and innovations to...

Data from: A curated and standardized adverse drug event resource to accelerate drug safety research

Juan M. Banda, Lee Evans, Rami S. Vanguri, Nicholas P. Tatonetti, Patrick B. Ryan & Nigam H. Shah
Identification of adverse drug reactions (ADRs) during the post-marketing phase is one of the most important goals of drug safety surveillance. Spontaneous reporting systems (SRS) data, which are the mainstay of traditional drug safety surveillance, are used for hypothesis generation and to validate the newer approaches. The publicly available US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) data requires substantial curation before they can be used appropriately, and applying different strategies for...

Data from: Understanding past population dynamics: Bayesian coalescent-based modeling with covariates

Mandev S. Gill, Philippe Lemey, Shannon N. Bennett, Roman Biek & Marc A. Suchard
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman's coalescent process enables inference of past population dynamics directly from molecular sequence data, and researchers have developed a number of flexible coalescent-based models for Bayesian nonparametric estimation of the effective population size as a function of time. Major goals of demographic reconstruction include identifying driving factors of effective population size, and...

Data from: Invasion of two tick-borne diseases across New England: harnessing human surveillance data to capture underlying ecological invasion processes

Katharine S. Walter, Kim M. Pepin, Colleen T. Webb, Holly D. Gaff, Peter J. Krause, Virginia E. Pitzer & Maria A. Diuk-Wasser
Modelling the spatial spread of vector-borne zoonotic pathogens maintained in enzootic transmission cycles remains a major challenge. The best available spatio-temporal data on pathogen spread often take the form of human disease surveillance data. By applying a classic ecological approach—occupancy modelling—to an epidemiological question of disease spread, we used surveillance data to examine the latent ecological invasion of tick-borne pathogens. Over the last half-century, previously undescribed tick-borne pathogens including the agents of Lyme disease and...

Data from: A hierarchical model of whole assemblage island biogeography

Jesse R. Lasky, Timothy H. Keitt, Brian C. Weeks & Evan P. Economo
Island systems have long played a central role in the development of ecology and evolutionary biology. However, while many empirical studies suggest species differ in vital biogeographic rates, such as dispersal abilities, quantitative methods have had difficulty incorporating such differences into analyses of whole-assemblages. In particular, differences in dispersal abilities among species can cause variation in the spatial clustering and localization of species distributions. Here, we develop a single, hierarchical Bayes, assemblage-wide model of 252...

Data from: Global terrestrial Human Footprint maps for 1993 and 2009

Oscar Venter, Eric W. Sanderson, Ainhoa Magrach, James R. Allan, Jutta Beher, Kendall R. Jones, Hugh P. Possingham, William F. Laurance, Peter Wood, Balázs M. Fekete, Marc A. Levy & James E.M. Watson
Remotely-sensed and bottom-up survey information were compiled on eight variables measuring the direct and indirect human pressures on the environment globally in 1993 and 2009. This represents not only the most current information of its type, but also the first temporally-consistent set of Human Footprint maps. Data on human pressures were acquired or developed for: 1) built environments, 2) population density, 3) electric infrastructure, 4) crop lands, 5) pasture lands, 6) roads, 7) railways, and...

Data from: Using matrix and tensor factorizations for the single-trial analysis of population spike trains

Arno Onken, Jian K. Liu, P. P. Chamanthi R. Karunasekara, Ioannis Delis, Tim Gollisch & Stefano Panzeri
Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike...

A chemically-triggered transition from conflict to cooperation in burying beetles

Bo-Fei Chen, Mark Liu, Dustin R. Rubenstein, Syuan-Jyun Sun, Jian-Nan Liu & Sheng-Feng Shen
Although interspecific competition has long been recognized as a major driver of trait divergence and adaptive evolution, relatively little effort has focused on how it influences the evolution of intraspecific cooperation. Here we identify the mechanism by which the perceived pressure of interspecific competition influences the transition from intraspecific conflict to cooperation in a facultative cooperatively breeding species, the Asian burying beetle Nicrophorus nepalensis. We not only found that beetles are more cooperative at carcasses...

Data from: Area 2 of primary somatosensory cortex encodes kinematics of the whole arm

Raeed Chowdhury, Joshua Glaser & Lee Miller
Proprioception, the sense of body position, movement, and associated forces, remains poorly understood, despite its critical role in movement. Most studies of area 2, a proprioceptive area of somatosensory cortex, have simply compared neurons' activities to the movement of the hand through space. By using motion tracking, we sought to elaborate this relationship by characterizing how area 2 activity relates to whole arm movements. We found that a whole-arm model, unlike classic models, successfully predicted...

Clinical recommendations to guide physical therapy practice for Huntington disease

Nora Fritz, Lori Quinn, Deb Kegelmeyer, Anne Kloos, Ashwini Rao & Monica Busse
Objective In the past decade, an increasing number of studies have examined the efficacy of physical therapy interventions in people with Huntington disease (HD). Methods We performed a mixed-methods systematic review using Joanna Briggs Institute (JBI) methodology and included experimental and observational study designs. The search resulted in 23 quantitative studies and 3 qualitative studies from which we extracted data using JBI standardized extraction tools. Results of this review suggested that physical therapy interventions may...

Cortical encoding of melodic expectations in human temporal cortex

Giovanni Di Liberto, Claire Pelofi, Roberta Bianco, Prachi Patel, Ashesh D Mehta, Jose L Herrero, Alain De Cheveigné, Shihab A Shamme & Nima Mesgarani
Humans engagement in music rests on underlying elements such as the listeners’ cultural background and interest in music. These factors modulate how listeners anticipate musical events, a process inducing instantaneous neural responses as the music confronts these expectations. Measuring such neural correlates would represent a direct window into high-level brain processing. Here we recorded cortical signals as participants listened to Bach melodies. We assessed the relative contributions of acoustic versus melodic components of the music...

The Million Song Dataset

Thierry Bertin-Mahieux, Daniel P.W. Ellis, Brian Whitman & Paul Lamere
We introduce the Million Song Dataset, a freely-available collection of audio features and metadata for a million contemporary popular music tracks. We describe its creation process, its content, and its possible uses. Attractive features of the Million Song Database include the range of existing resources to which it is linked, and the fact that it is the largest current research dataset in our field. As an illustration, we present year prediction as an example application,...

Data from: Neurologic manifestations in an infant with COVID-19

Nischay Mishra, Rachelle Dugue, Karla C. Cay-Martínez, Kiran Thakur, Joel A. Garcia, Lokendra V. Chauhan, Simon H. Williams, Thomas Briese, Komal Jain, Marc Foca, Danielle K. McBrian, Jennifer M. Bain & W. Ian Lipkin
Currently, there are over 1.9 million confirmed cases of Coronavirus disease 2019 (COVID-19) globally with over 590,000 cases in the United States.1 The number of COVID-19 positive children in the United States is unknown. A report summarizing 72,314 COVID-19 cases from the Chinese Center for Disease Control and Prevention noted 416 COVID-19 positive children under 10.2 An observational study at Wuhan Children's Hospital noted 31 COVID-19 positive children under 1 year with the youngest confirmed...

Data from: First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

Howard C. Rosenbaum, Francine Kershaw, Martin Mendez, Cristina Pomilla, Matthew S. Leslie, Ken P. Findlay, Peter B. Best, Timothy Collins, Michel Vely, Marcia H. Engel, Robert Baldwin, Gianna Minton, Michael Meyer, Lillian Florez-Gonzalez, M. Michael Poole, Nan Hauser, Claire Garrigue, Muriel Brasseur, John Bannister, Megan Anderson, Carlos Olavarria & C. Scott Baker
The description of genetic population structure over a species’ geographic range can provide insights into its evolutionary history and also support effective management efforts. Assessments for globally distributed species are rare, however, requiring significant international coordination and collaboration. The global distribution of demographically discrete populations for the humpback whale Megaptera novaeangliae is not fully known, hampering the definition of appropriate management units. Here, we present the first circumglobal assessment of mitochondrial genetic population structure across...

Data from: Interannual variations in needle and sapwood traits of Pinus edulis branches under an experimental drought

Marceau Guerin, Dario Martin-Benito, Georg Von Arx, Laia Andreu Hayles, Kevin L. Griffin, Rayann Hamdan, Nate G. McDowell, Robert Muscarella, Will Pockman, Pierre Gentine, William Pockman & Laia Andreu-Hayles
1) In the Southwest United States, recent large-scale die-offs of conifers raise the question of their resilience and mortality under droughts. To date, little is known about the interannual structural response to droughts. 2) We hypothesized that piñon pines (Pinus edulis) respond to drought by reducing the drop of leaf water potential in branches from year to year through needle morphological adjustments. We tested our hypothesis using a seven-year experiment in central New Mexico with...

Data From: Contrasting physiological traits of shade tolerance in Pinus and Podocarpaceae native to a tropical Vietnamese forest: Insight from an aberrant flat-leaved pine

Stephanie Schmiege, Brendan Buckley, Dennis Stevenson, Truong Cuong, Le Nam & Kevin Griffin
The absence of pines from tropical forests is a puzzling biogeographical oddity potentially explained by traits of shade intolerance. Pinus krempfii, a flat-leaved pine endemic to the Central Highlands of Vietnam, provides a notable exception as it seems to successfully compete with shade-tolerant tropical species. Here, we test the hypothesis that successful conifer performance at the juvenile stage depends on physiological traits of shade tolerance by comparing the physiological characteristics of P. krempfii to coexisting...

Personalized Policy Learning Using Longitudinal Mobile Health Data

Xinyu Hu, Min Qian, Bin Cheng & Ying Kuen Cheung
Personalized policy represents a paradigm shift one decision rule for all users to an individualized decision rule for each user. Developing personalized policy in mobile health applications imposes challenges. First, for lack of adherence, data from each user are limited. Second, unmeasured contextual factors can potentially impact on decision making. Aiming to optimize immediate rewards, we propose using a generalized linear mixed modeling framework where population features and individual features are modeled as fixed and...

Always Together: A Digital Diasporic Elegy

Tzarina T. Prater
This essay takes up the question of how diasporic Caribbean subjects deal with death, dying, and grieving in online spaces. With a focus on the genre of *digital diasporic elegy*, the author argues that by analyzing the digital life of a Sino-Caribbean diasporic cultural text, a digital diasporic elegiac practice emerges. This practice allows for consideration of the very code that enables our traversal between digital nodes, thereby allowing for a more nuanced understanding of...

Teaching without a Text: Close Listening to Kamau Brathwaite's Digital Audio Archive

Jacob Edmond
New media technologies—from the tape recorder to the computer—enabled Kamau Brathwaite's revolutionary poetic approach; digital technologies likewise enable us to study and teach his groundbreaking work in new ways. This essay argues that teaching and studying Brathwaite should begin with the audible word not the written text and that digital audio archives and platforms can play a key role in enabling this approach. Digital audio archives such as PennSound and the Poetry Archive allow students...

Data from: Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

Pengcheng Zhou, Shanna L. Resendez, Jose Rodriguez-Romaguera, Jessica C. Jimenez, Shay Q. Neufeld, Andrea Giovannucci, Johannes Friedrich, Eftychios A Pnevmatikakis, Garret D. Stuber, Rene Hen, Mazen A. Kheirbek, Bernardo L. Sabatini, Robert E. Kass & Liam Paninski
In vivo calcium imaging through microendoscopic lenses enables imaging of previously inaccessible neuronal populations deep within the brains of freely moving animals. However, it is computationally challenging to extract single-neuronal activity from microendoscopic data, because of the very large background fluctuations and high spatial overlaps intrinsic to this recording modality. Here, we describe a new constrained matrix factorization approach to accurately separate the background and then demix and denoise the neuronal signals of interest. We...

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  • Columbia University
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  • Chinese Academy of Medical Sciences & Peking Union Medical College
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  • University of Chinese Academy of Sciences
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  • Chinese Academy of Sciences
  • Nanjing Medical University
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