557 Works

Data from: The representational dynamics of perceived voice emotions evolve from categories to dimensions

Bruno L. Giordano, Caroline Whiting, Nikolaus Kriegeskorte, Sonja A. Kotz, Joachim Gross & Pascal Belin
Long-standing affective science theories conceive the perception of emotional stimuli either as discrete categories (for example, an angry voice) or continuous dimensional attributes (for example, an intense and negative vocal emotion). Which position provides a better account is still widely debated. Here we contrast the positions to account for acoustics-independent perceptual and cerebral representational geometry of perceived voice emotions. We combined multimodal imaging of the cerebral response to heard vocal stimuli (using functional magnetic resonance...

Data from: An MRI measure of degenerative and cerebrovascular pathology in Alzheimer’s disease

Adam M. Brickman, Giuseppe Tosto, Jose Gutierrez, Howard Andrews, Yian Gu, Atul Narkhede, Batool Rizvi, Vanessa Guzman, Jennifer J. Manly, Jean Paul Vonsattel, Nicole Schupf & Richard Mayeux
Objective: To develop, replicate, and validate an MRI-based quantitative measure of both cerebrovascular and neurodegeneration in Alzheimer’s disease for clinical and potentially research purposes. Methods. We used data from a cross-sectional and longitudinal community-based study of Medicare-eligible residents in northern Manhattan followed every 18-24 months (N=1,175, mean age=78 years). White matter hyperintensities, infarcts, hippocampal volumes, and cortical thicknesses were quantified from MRI and combined to generate an MRI measure associated with episodic memory. The combined...

Data from: Genome-wide assessment of diversity and divergence among extant Galápagos giant tortoise species

Joshua M. Miller, Maud C. Quinzin, Danielle L. Edwards, Deren A.R. Eaton, Evelyn L. Jensen, Michael A. Russello, James P. Gibbs, Washington Tapia, Danny Rueda, Adalgisa Caccone & Deren A R Eaton
Genome-wide assessments allow for fuller characterization of genetic diversity, finer-scale population delineation, and better detection of demographically significant units to guide conservation compared to those based on “traditional” markers. Galapagos giant tortoises (Chelonoidis spp.) have long provided a case study for how evolutionary genetics may be applied to advance species conservation. Ongoing efforts to bolster tortoise populations, which have declined by 90%, have been informed by analyses of mitochondrial DNA sequence and microsatellite genotypic data,...

Supplemental material for this article is available online.

Qian Nie, Chunyan Yang, Meg Stomski, Zhanfeng Zhao, Zhaojun Teng & Cheng Guo
Supplemental Material for Longitudinal Link Between Bullying Victimization and Bullying Perpetration: A Multilevel Moderation Analysis of Perceived School Climate by Qian Nie, Chunyan Yang, Meg Stomski, Zhanfeng Zhao, Zhaojun Teng and Cheng Guo, in Journal of Interpersonal Violence

Supplemental material for this article is available online.

Keith L. Kaufman, David S. Lee, Jeffrey J. Milroy, Anita Raj, Qian Nie, Chunyan Yang, Meg Stomski, Zhanfeng Zhao, Zhaojun Teng & Cheng Guo
Supplemental Material for Longitudinal Link Between Bullying Victimization and Bullying Perpetration: A Multilevel Moderation Analysis of Perceived School Climate by Qian Nie, Chunyan Yang, Meg Stomski, Zhanfeng Zhao, Zhaojun Teng and Cheng Guo, in Journal of Interpersonal Violence

Data from: Population-specific genetic modification of Huntington's disease in Venezuela

Michael J. Chao, Kyung-Hee Kim, Jun Wan Shin, Diane Lucente, Vanessa C. Wheeler, Hong Li, Jared C. Roach, Leroy Hood, Nancy S. Wexler, Laura B. Jardim, Peter Holmans, Lesley Jones, Michael Orth, Seung Kwak, James F. Gusella, Marcy E. MacDonald & Jong-Min Lee
Modifiers of Mendelian disorders can provide insights into disease mechanisms and guide therapeutic strategies. A recent genome-wide association (GWA) study discovered genetic modifiers of Huntington's disease (HD) onset in Europeans. Here, we performed whole genome sequencing and GWA analysis of a Venezuelan HD cluster whose families were crucial for the original mapping of the HD gene defect. The Venezuelan HD subjects develop motor symptoms earlier than their European counterparts, implying the potential for population-specific modifiers....

Data from: Ion microprobe measured stable isotope evidence for ammonite habitat and life mode during early ontogeny

Benjamin J. Linzmeier, Neil H. Landman, Shanan E. Peters, Reinhard Kozdon, Kouki Kitajima & John W. Valley
Ammonites have disparate adult morphologies indicative of diverse ecological niches, but ammonite hatchlings are small (~1 mm diameter), which raises questions about the similarity of egg incubation and hatchling life mode in ammonites. Modern Nautilus is sometimes used as a model organism for understanding ammonites, but despite their outward similarities, the groups are only distantly related. Trends in ammonite diversity and extinction vulnerability in the fossil record contrast starkly with those of nautilids, and embryonic...

Data from: Legume abundance along successional and rainfall gradients in neotropical forests

Maga Gei, Danaë M. A. Rozendaal, Lourens Poorter, Frans Bongers, Janet I. Sprent, Mira D. Garner, T. Mitchell Aide, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Pedro H.S. Brancalion, George A. L. Cabral, Ricardo Gomes César, Robin L. Chazdon, Rebecca J. Cole, Gabriel Dalla Colletta, Ben De Jong, Julie S. Denslow, Daisy H. Dent, Saara J. DeWalt, Juan Manuel Dupuy, Sandra M. Durán, Mário Marcos Do Espírito Santo, G. Wilson Fernandes, Yule Roberta Ferreira Nunes … & Jennifer S. Powers
The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen (N)-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest-inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area...

Brewster angle optical reflection observation of self-limiting nanoparticle monolayer self-assembly at a liquid/liquid interface

Jiayang Hu, Brady Pan, Takuma Makihara, Roy D. J. Garcia & Irving P. Herman
Real-time optical reflection of incident p-polarized light near Brewster’s angle shows that after drop-casting iron oxide nanoparticles (NPs) in heptane on top of a diethylene glycol (DEG) liquid substrate, an iron oxide NP layer forms at the DEG/heptane interface, and it self-limits to a monolayer even when there are excess NPs dispersed in the upper heptane phase. Most modes of NP self-assembly do not self-limit growth after the formation of a single monolayer. Observations are...

Data from: Effect of aerobic exercise on cognition in younger adults: a randomized clinical trial

Yaakov Stern, Anna MacKay-Brandt, Seonjoo Lee, Paula McKinley, Kathleen McIntyre, Qolamreza Razlighi, Emil Agarunov, Matthew Bartels & Richard P. Sloan
Objective: To determine efficacy of aerobic exercise for cognitive function in younger healthy adults. Methods: In a randomized, parallel-group, observer-masked, community-based clinical trial, 132 cognitively normal individuals aged 20-67 with below median aerobic capacity were randomly assigned to one of two 6-month, four-times-weekly conditions: aerobic exercise and stretching/toning. Efficacy measures included: aerobic capacity; cognitive function in six domains (executive function, episodic memory, processing speed, language, and attention), everyday function, BMI and cortical thickness. Results: Aerobic...

Data from: Social density, but not sex ratio, drives ecdysteroid hormone provisioning to eggs by female house crickets (Acheta domesticus)

Katherine C. Crocker, Mark Hunter & Mark D. Hunter
Social environment profoundly influences the fitness of animals, affecting their probability of survival to adulthood, longevity, and reproductive output. The social conditions experienced by parents at the time of reproduction predict the social environments that offspring will face. Despite clear challenges in predicting future environmental conditions, adaptive maternal effects provide a mechanism of passing environmental information from parent to offspring, and are now considered pervasive in natural systems. Maternal effects have been widely studied in...

Differentially-expressed mRNAs, microRNAs and long noncoding RNAs in intervertebral disc degeneration identified by RNA-sequencing

Zhimin Li, Yu Sun, Maolin He & Jianwei Liu
The underlying molecular mechanisms of intervertebral disc degeneration (IDD) remain unclear. This study aimed to identify the crucial molecules and explore the function of noncoding RNAs and related pathways in IDD. We randomly selected three samples each from an IDD and a spinal cord injury group (control) for RNA-sequencing. We identified 463 differentially-expressed long noncoding RNAs (lncRNAs), 47 differentially-expressed microRNAs (miRNAs), and 1,334 differentially-expressed mRNAs in IDD. Three hundred fifty-eight lncRNAs as cis-regulators could potentially...

Data from: High-order thalamic inputs to primary somatosensory cortex are stronger and longer lasting than cortical inputs

Wanying Zhang & Randy M. Bruno
Layer (L) 2/3 pyramidal neurons in the primary somatosensory cortex (S1) are sparsely active, spontaneously and during sensory stimulation. Long-range inputs from higher areas may gate L2/3 activity. We investigated their in vivo impact by expressing channelrhodopsin in three main sources of feedback to rat S1: primary motor cortex, secondary somatosensory cortex, and secondary somatosensory thalamic nucleus (the posterior medial nucleus, POm). Inputs from cortical areas were relatively weak. POm, however, more robustly depolarized L2/3...

Data from: Concerted evolution reveals co-adapted amino acid substitutions in Na+K+ ATPase of frogs that prey on toxic toads

Shabnam Mohammadi, Lu Yang, Arbel Harpak, Santiago Herrera-Álvarez, María Del Pilar Rodríguez-Ordoñez, Julie Peng, Karen Zhang, Jay Storz, Susanne Dobler, Andrew Crawford & Peter Andolfatto
Gene duplication is an important source of evolutionary innovation, but the functional distinction between duplicates can be opposed by ongoing gene conversion between them. Here we document a tandem duplication of Na+,K+-ATPase subunit α1 (ATP1A1) sharedby frogs in the genus Leptodactylus,a group of species that feeds on toxic toads. One ATP1A1 paralog evolved resistance to toad toxins while the other paralog retained ancestral susceptibility. Frequent non-allelic gene conversion homogenized most of the paralog sequences,yet the...

Data from: Restriction-site-associated DNA sequencing reveals a cryptic viburnum species on the North American coastal plain

Elizabeth L. Spriggs, Deren A.R. Eaton, Patrick W. Sweeney, Caroline Schlutius, Erika J. Edwards, Michael J. Donoghue & Deren A R Eaton
Species are the starting point for most studies of ecology and evolution, but the proper circumscription of species can be extremely difficult in morphologically variable lineages, and there are still few convincing examples of molecularly-informed species delimitation in plants. We focus here on the Viburnum nudum complex, a highly variable clade that is widely distributed in eastern North America. Taxonomic treatments have mostly divided this complex into northern (V. nudum var. cassinoides) and southern (V....

Data from: The return to water in ancestral Xenopus was accompanied by a novel mechanism for producing and shaping vocal signals

Ursula Kwong-Brown, Martha L. Tobias, Damian O. Elias, Ian C. Hall, Coen P.H. Elemans, Darcy B. Kelley & Coen PH Elemans
Listeners locate potential mates using species-specific vocal signals. As tetrapods transitioned from water to land, lungs replaced gills, allowing expiration to drive sound production. Some frogs then returned to water. Here we explore how air-driven sound production changed upon re-entry to preserve essential acoustic information on species identity in the secondarily aquatic frog genus Xenopus. We filmed movements of cartilage and muscles during evoked sound production in isolated larynges. Results refute the current theory for...

Feasibility Study on the Creation of a Virtual Center for Copyright Education for Professionals in Libraries, Archives, and Museums

Kristin Kelly & Rina Elster Pantalony
$30,000 to Columbia University Libraries to conduct a feasibility study to determine the viability and sustainability of a copyright education center for libraries, archives and museums.

Long-term measures of climate unpredictability shape the avian endocrine stress axis

Sarah Guindre-Parker & Dustin R. Rubenstein
The vertebrate glucocorticoid stress response is an important mechanism facilitating pleiotropic phenotypic adjustments for coping with environmental change and optimizing fitness. Although circulating glucocorticoid hormones are mediators of plasticity that individuals can adjust rapidly in response to environmental challenges, they are also shaped by ecological selection. It remains unclear, however, how environmental variation on different timescales influences glucocorticoids. Here, we use an intraspecific comparative approach to determine how variation in precipitation on different timescales (months,...

Data from: Genomic signatures of spatially divergent selection at clownfish range margins

Rene Clark, Matthew Aardema, Peter Andolfatto, Paul Barber, Akihisa Hattori, Jennifer Hoey, & Malin Pinsky
Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species’ range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow, and genetic drift in the...

Data from: Native forest cover safeguards stream water quality under a changing climate

Pedro Piffer
This dataset contains water quality data from 286 water monitoring stations in the state of São Paulo, Brazil, used in the paper: “Piffer, P.R., Tambosi, L.R., Ferraz, S.F., Metzger, J.P. & Uriarte, M. (2021) Native forest cover safeguards stream water quality under a changing climate. Ecological Applications”. The data was obtained from the São Paulo State Environmental Agency and is publicly available at https://sistemainfoaguas.cetesb.sp.gov.br for download. More information on the dataset, analysis and results can...

Data from: Encephalization and longevity evolved in a correlated fashion in Euarchontoglires but not in other mammals

Alex R. DeCasien, Nicole A. Thompson, Scott A. Williams & Milena R. Shattuck
Across mammals, encephalization and longevity show a strong correlation. It is not clear, however, whether these traits evolved in a correlated fashion within mammalian orders, or when they do, whether one trait drives changes in the other. Here, we compare independent and correlated evolutionary models to identify instances of correlated evolution within six mammalian orders. In cases of correlated evolution, we subsequently examined transition patterns between small/large relative brain size and short/long lifespan. In four...

De novo genome assembly of Leptodactylus fuscus

Lu Yang, Peter Andolfatto, Andrew Crawford, Santiago Herrera-Álvarez, Maríadel Pilar Rodríguez-Ordoñez, Julie Peng, Shabnam Mohammadi, Jay Storz, Arbel Harpak & Susanne Dobler
This presents a de novo genome assembly of Leptodactylus fuscus. High molecular weight DNA was extracted from a L. fuscus embryo which had been preserved in ethanol upon collection in Garzón, Huila, Colombia. The library was prepared and sequenced with 10X Genomics Chromium. Linked reads were processed by Long Ranger basic v2.2.2 and assembled with Supernova v2.1.1. The assembled genome is 2.42 Gb with 16,530 scaffolds >=10 kb, and scaffold N50 = 363 kb. The...

Fiscal and Monetary Stabilization Policy at the Zero Lower Bound: Consequences of Limited Foresight

Yinxi Xie & Michael Woodford
"We consider the effectiveness of stabilization policy when the zero lower bound (ZLB) is a relevant constraint on conventional monetary policy by relaxing the assumption of rational expectations. In particular, we assume bounded rationality in terms of limited foresight—people can plan for only a finite distance into the future when they deductively reason about the economy's future evolution. We examine how the degree of foresight affects the outcomes of fiscal and monetary stabilization policy. We...

Associations between infant sex and DNA methylation across umbilical cord blood, artery, and placenta samples

Anne K. Bozack, Elena Colicino, Allan C. Just, Robert O. Wright, Andrea A. Baccarelli, Rosalind J. Wright & Alison G. Lee
DNA methylation (DNAm) is vulnerable to dysregulation by environmental exposures during epigenetic reprogramming that occurs in embryogenesis. Sexual dimorphism in environmentally induced DNAm dysregulation has been identified and therefore it is important to understand sex-specific DNAm patterns. DNAm at several autosomal sites has been consistently associated with sex in cord blood and placental foetal tissues. However, there is limited research comparing sex-specific DNAm across tissues, particularly differentially methylated regions (DMRs). This study leverages DNAm data...

Tracing Carbonate Formation, Serpentinization, and Biological Materials with Micro-/Meso-Scale Infrared Imaging Spectroscopy in a Mars Analog System, Samail Ophiolite, Oman

Ellen K. Leask, Bethany L. Ehlmann, Rebecca N. Greenberger, Patrick Pinet, Yves Daydou, Georges Ceuleneer & Peter Kelemen
This dataset underlies the following publication, which must be cited with use of the dataset: Leask, E. K., B. L. Ehlmann, R. N. Greenberger, P. Pinet, Y. Daydou, G. Ceuleneer, and P. Kelemen (accepted), Tracing carbonate formation, serpentinization, and biological materials with micro-/meso-scale infrared imaging spectroscopy in a Mars analog system, Samail ophiolite, Oman, Earth and Space Science. Data used in each figure or analysis presented in the paper are archived here. Data are atmospherically...

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