486 Works

Data from: Distinct neural and neuromuscular strategies underlie independent evolution of simplified advertisement calls

Elizabeth C. Leininger & Darcy B. Kelley
Independent or convergent evolution can underlie phenotypic similarity of derived behavioural characters. Determining the underlying neural and neuromuscular mechanisms sheds light on how these characters arose. One example of evolutionarily derived characters is a temporally simple advertisement call of male African clawed frogs (Xenopus) that arose at least twice independently from a more complex ancestral pattern. How did simplification occur in the vocal circuit? To distinguish shared from divergent mechanisms, we examined activity from the...

Data from: Key ornamental innovations facilitate diversification in an avian radiation

Rafael Maia, Dustin R. Rubenstein & Matthew D. Shawkey
Patterns of biodiversity are often explained by ecological processes, where traits that promote novel ways of interacting with the environment (key innovations) play a fundamental role in promoting diversification. However, sexual selection and social competition can also promote diversification through rapid evolution of ornamental traits. Because selection can operate only on existing variation, the tendency of ornamental traits to constrain or enable the production of novel phenotypes is a crucial but often overlooked aspect of...

Data from: Low plant density enhances gene dispersal in the Amazonian understory herb Heliconia acuminata

Marina Corrêa Côrtes, María Uriarte, Maristerra R. Lemes, Rogério Gribel, W. John Kress, Peter E. Smouse & Emilio M. Bruna
In theory, conservation genetics predicts that forest fragmentation will reduce gene dispersal, but in practice, genetic and ecological processes are also dependent on other population characteristics. We used Bayesian genetic analyses to characterize parentage and propagule dispersal in Heliconia acuminata L. C. Richard (Heliconiaceae), a common Amazonian understory plant that is pollinated and dispersed by birds. We studied these processes in two continuous forest sites and three 1-ha fragments in Brazil's Biological Dynamics of Forest...

Data from: Asymmetric dispersal and colonization success of Amazonian plant-ants queens

Emilio M. Bruna, Thiago J. Izzo, Brian D. Inouye, Maria Uriarte & Heraldo L. Vasconcelos
Background: The dispersal ability of queens is central to understanding ant life-history evolution, and plays a fundamental role in ant population and community dynamics, the maintenance of genetic diversity, and the spread of invasive ants. In tropical ecosystems, species from over 40 genera of ants establish colonies in the stems, hollow thorns, or leaf pouches of specialized plants. However, little is known about the relative dispersal ability of queens competing for access to the same...

Data from: Elevated substitution rates estimated from ancient DNA sequences

Simon Y. W. Ho, Sergios-Orestis Kolokotronis, Robin G. Allaby & Simon Y.W Ho
Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, which are not directly accessible via modern DNA. They are particularly suitable for the estimation of substitution rates because their ages provide calibrating information in phylogenetic analyses, circumventing the difficult task of choosing independent calibration points. The substitution rates obtained from such datasets have typically been high, falling between the rates estimated from pedigrees and species phylogenies. Many of these estimates have...

Data from: Quantifying the human impacts on Papua New Guinea reef fish communities across space and time

Joshua A. Drew, Ruth A. Hufbauer & Kathryn L. Amatangelo
Describing the drivers of species loss and of community change are important goals in both conservation and ecology. However, it is difficult to determine whether exploited species decline due to direct effects of harvesting or due to other environmental perturbations brought about by proximity to human populations. Here we quantify differences in species richness of coral reef fish communities along a human population gradient in Papua New Guinea to understand the relative impacts of fishing...

Data from: Effects of fertilizer on inorganic soil N in East Africa maize systems: vertical distributions and temporal dynamics

Katherine L. Tully, Jonathan Hickman, Madeline McKenna, Christopher Neill & Cheryl A. Palm
Fertilizer applications are poised to increase across sub-Saharan Africa (SSA), but the fate of added nitrogen (N) is largely unknown. We measured vertical distributions and temporal variations of soil inorganic N following fertilizer application in two maize (Zea mays L.)-growing regions of contrasting soil type. Fertilizer trials were established on a clayey soil in Yala, Kenya, and on a sandy soil in Tumbi, Tanzania, with application rates of 0–200 kg N/ha/yr. Soil profiles were collected...

Data from: Publication and reporting of clinical trial results: cross sectional analysis across academic medical centers

Ruijun Chen, Nihar R. Desai, Joseph S. Ross, Weiwei Zhang, Katherine H. Chau, Brian Wayda, Karthik Murugiah, Daniel Y. Lu, Amit Mittal & Harlan M. Krumholz
Objective: To determine rates of publication and reporting of results within two years for all completed clinical trials registered in ClinicalTrials.gov across leading academic medical centers in the United States. Design: Cross sectional analysis. Setting: Academic medical centers in the United States. Participants: Academic medical centers with 40 or more completed interventional trials registered on ClinicalTrials.gov. Methods: Using the Aggregate Analysis of ClinicalTrials.gov database and manual review, we identified all interventional clinical trials registered on...

Data from: Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes

Brenna R. Forester, Matthew R. Jones, Stéphane Joost, Erin L. Landguth & Jesse R. Lasky
The spatial structure of the environment (e.g., the configuration of habitat patches) may play an important role in determining the strength of local adaptation. However, previous studies of habitat heterogeneity and local adaptation have largely been limited to simple landscapes, which poorly represent the multi-scale habitat structure common in nature. Here, we use simulations to pursue two goals: (1) we explore how landscape heterogeneity, dispersal ability, and selection affect the strength of local adaptation, and...

Data from: Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

Zachary Baker, Molly Schumer, Yuki Haba, Lisa Bashkirova, Chris Holland, Gil G Rosenthal & Molly Przeworski
Studies of highly diverged species have revealed two mechanisms by which meiotic recombination is directed to the genome—through PRDM9 binding or by targeting promoter-like features—that lead to dramatically different evolutionary dynamics of hotspots. Here, we identify PRDM9 orthologs from genome and transcriptome data in 225 species. We find the complete PRDM9 ortholog across distantly related vertebrates but, despite this broad conservation, infer a minimum of six partial and three complete losses. Strikingly, taxa carrying the...

Data from: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria

Olatunji Kolawole, Michael Oguntoye, Tina Dam & Rumi Chunara
Objective: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical (hospital) surveillance in Nigeria. Results: Children were selected via convenience sampling from communities and a tertiary care center (n = 91) during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority (79.1%) of subjects were under 6 years...

Data from: Multiple benefits of alloparental care in a fluctuating environment

Sarah Guindre-Parker & Dustin R. Rubenstein
Although cooperatively breeding vertebrates occur disproportionately in unpredictable environments, the underlying mechanism shaping this biogeographic pattern remains unclear. Cooperative breeding may buffer against harsh conditions (hard life hypothesis), or additionally allow for sustained breeding under benign conditions (temporal variability hypothesis). To distinguish between the hard life and temporal variability hypotheses, we investigated whether the number of alloparents at a nest increased reproductive success or load-lightening in superb starlings (Lamprotornis superbus), and whether these two types...

Harlem Education History

Ansley Erickson

Data from: Abundance-dependent effects of neighborhood dissimilarity and growth rank reversal in a Neotropical forest

Yuxin Chen, María Natalia Umaña, María Uriarte & Shixiao Yu
Why tropical forests harbor an exceptional number of species with striking differences in abundances remains an open question. We propose a theoretical framework to address this question in which rare species may have different extirpation risks depending on species ranks in tree growth and sensitivities to neighborhood interactions. To evaluate the framework, we studied tree growth and its responses to neighborhood dissimilarity (ND) in traits and phylogeny for 146 species in a Neotropical forest. We...

Data from: Trends in anesthesiology research: a machine learning approach to theme discovery and summarization

Alexander Rusanov, Riccardo Miotto & Chunhua Weng
Objectives: Traditionally, summarization of research themes and trends within a given discipline was accomplished by manual review of scientific works in the field. However, with the ushering in of the age of “big data”, new methods for discovery of such information become necessary as traditional techniques become increasingly difficult to apply due to the exponential growth of document repositories. Our objectives are to develop a pipeline for unsupervised theme extraction and summarization of thematic trends...

Data from: Catechol-O-Methyltransferase moderates effect of stress mindset on affect and cognition

Alia J. Crum, Modupe Akinola, Bradley P. Turnwald, Ted J. Kaptchuk & Kathryn T. Hall
There is evidence that altering stress mindset— the belief that stress is enhancing vs. debilitating —can change cognitive, affective and physiological responses to stress. However individual differences in responsiveness to stress mindset manipulations have not been explored. Given the previously established role of catecholamines in both placebo effects and stress, we hypothesized that genetic variation in catechol-O-methyltransferase (COMT), an enzyme that metabolizes catecholamines, would moderate responses to an intervention intended to alter participants’ mindsets about...

Data from: Nusinersen in later-onset spinal muscular atrophy: long-term results from the phase 1/2 studies

Basil T. Darras, Claudia A. Chiriboga, Susan T. Iannaccone, Kathryn J. Swoboda, Jacqueline Montes, Laurence Mignon, Shuting Xia, C. Frank Bennett, Kathie M. Bishop, Jeremy M. Shefner, Allison M. Green, Peng Sun, Ishir Bhan, Sarah Gheuens, Eugene Schneider, Wildon Farwell & Darryl C. De Vivo
Objective: Report results of intrathecal nusinersen in children with later-onset spinal muscular atrophy (SMA). Methods: Analyses included children from the phase 1b/2a study (ISIS-396443-CS2; NCT01703988) who first received nusinersen during that study and were eligible to continue treatment in the extension study (ISIS-396443-CS12; NCT02052791). The phase 1b/2a study was a 253-day, ascending dose (3, 6, 9, 12 mg), multiple-dose, open-label, multicenter study that enrolled children with SMA aged 2 to 15 years. The extension study...

Data from: Entropic bonding of the type 1 pilus from experiment and simulation

Fabiano Corsetti, Alvaro Alonso-Caballero, Simon Poly, Raul Perez-Jimenez & Emilio Artacho
The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing β-strands. Its strength and structural stability are critical for its anchoring function in uropathogenic Escherichia coli bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations [A. Alonso-Caballero et al., Nature Commun. 9, 2758...

Variable prediction accuracy of polygenic scores within an ancestry group

Hakhamanesh Mostafavi, Arbel Harpak, Ipsita Agarwal, Dalton Conley, Jonathan Pritchard & Molly Przeworski
Fields as diverse as human genetics and sociology are increasingly using polygenic scores based on genome-wide association studies (GWAS) for phenotypic prediction. However, recent work has shown that polygenic scores have limited portability across groups of different genetic ancestries, restricting the contexts in which they can be used reliably and potentially creating serious inequities in future clinical applications. Using the UK Biobank data, we demonstrate that even within a single ancestry group (i.e., when there...

Making Your Way Through Grey: Metadata, MARC and User Tools

Meagan Cooke & Sean
Columbia International Affairs Online (CIAO) is the largest online collection of grey literature on international relations. Online since 1997, CIAO has grown to encompass both grey literature and published materials from over 200 contributing institutions. Currently the database contains over 10,000 papers and, as with anything of this magnitude, the challenge is not only continued growth in terms of content aggregation but also achieving successful user experiences and wider integration with other services. Our metadata...

Statistical data from: Cholinergic modulation of hippocampally mediated attention and perception

Nicholas Ruiz, Monica Thieu & Mariam Aly
Attention to the relations between visual features modulates hippocampal representations. Moreover, hippocampal damage impairs discrimination of spatial relations. We explore a mechanism by which this might occur: modulation by the acetylcholine system. Acetylcholine enhances afferent input to the hippocampus and suppresses recurrent connections within it. This biases hippocampal processing toward environmental input, and should improve externally-oriented, hippocampally mediated attention and perception. We examined cholinergic modulation on an attention task that recruits the hippocampus. On each...

Social rank modulates how environmental quality influences cooperation and conflict within animal societies

Mark Liu, Bo-Fei Chen, Dustin Rubenstein & Sheng-Feng Shen
Although dominance hierarchies occur in most societies, our understanding of how these power structures influence individual investment in cooperative and competitive behaviors remains elusive. Both conflict and cooperation in animal societies are often environmentally-regulated, yet how individuals alter their cooperative and competitive investments as environmental quality changes remains unclear. Using game theoretic modeling, we predict that individuals of all ranks will invest more in cooperation and less in social conflict in harsh environments than individuals...

Genetic Adaptation in New York City Rats

Arbel Harpak, Nandita Garud, Noah Rosenberg, Dmitri Petrov, Pleuni Pennings & Jason Munshi-South
Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthropocentric environment and taking advantage of human resources and by-products. From the human perspective, rats are a chronic problem that causes billions of dollars in damage to agriculture, health and infrastructure. Did genetic adaptation play a role in the spread of rats in cities? To approach this question, we collected whole-genome sequences from 29 brown rats from New York City (NYC) and scanned for...

Data from: Daily protein prioritization and longterm nutrient balancing in a dietary generalist, the blue monkey

Maressa Takahashi & Marina Cords
Animals must make dietary choices to achieve adequate nutrient intake, however it is challenging to study in the field such nutritional strategies in wild populations. We explored the nutritional strategy of a generalist social primate, the blue monkey (Cercopithecus mitis). We hypothesized that females balance the intake of nutrients, specifically non-protein energy and available protein (hereafter, protein), both on a daily and long-term basis. When balancing was not possible, we expected subjects to prioritize constant...

Slave Movement -- Records of Slave Ship Movement Between Africa and the Americas, 1817-1843

Philip D. Curtin & Herbert S. Klein

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  • Columbia University
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