225 Works

Disentangling interactions among mercury, immunity, and infection in a Neotropical bat community

Daniel Becker, Kelly Speer, Jennifer Korstian, Dmitriy Volokhov, Hannah Droke, Alexis Brown, Catherene Baijnauth, Ticha Padgett-Stewart, Hugh Broders, Raina Plowright, Thomas Rainwater, Brock Fenton, Nancy Simmons & Matthew Chumchal
Contaminants such as mercury are pervasive and can have immunosuppressive effects on wildlife. Impaired immunity could be important for forecasting pathogen spillover risks, as many land-use changes that generate mercury contamination also bring wildlife into close contact with humans and domestic animals. However, the interactions among contaminants, immunity, and infection are difficult to study in natural systems, and empirical tests of possible directional relationships remain rare. We capitalized on extreme mercury variation in a diverse...

Data from: Strength of selection on Trpc2 gene predicts accessory olfactory bulb form in bat vomeronasal evolution

Laurel R. Yohe & Liliana M. Davalos
Vestigial characters are common across the tree of life, but the underlying evolutionary processes shaping phenotypic loss are poorly understood. The mammalian vomeronasal system, which detects social chemical cues important to fitness, is an impressive example of a sensory system lost multiple times. Three times more losses are inferred among bats than in other mammalian orders. We characterized the relationship between amino acid substitutions in a gene tightly linked to vomeronasal function (Trpc2) and the...

Data from: Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens

Rafael J. Hernandez, Elze Hesse, Andrea J. Dowling, Nicola M. Coyle, Edward J. Feil, Will H. Gaze & Michiel Vos
Climate change, changing farming practices, social and demographic changes and rising levels of antibiotic resistance are likely to lead to future increases in opportunistic bacterial infections that are more difficult to treat. Uncovering the prevalence and identity of pathogenic bacteria in the environment is key to assessing transmission risks. We describe the first use of the Wax moth larva Galleria mellonella, a well-established model for the mammalian innate immune system, to selectively enrich and characterize...

Data from: A comprehensive analysis of autocorrelation and bias in home range estimation

Michael J. Noonan, Marlee A. Tucker, Christen H. Fleming, Tom S. Akre, Susan C. Alberts, Abdullahi H. Ali, Jeanne Altmann, Pamela C. Antunes, Jerrold L. Belant, Dean Beyer, Niels Blaum, Katrin Böhning-Gaese, , Rogerio De Paula Cunha, Jasja Dekker, Jonathan Drescher-Lehman, Nina Farwig, Claudia Fichtel, Christina Fischer, Adam T. Ford, Jacob R. Goheen, René Janssen, Florian Jeltsch, Matthew Kauffman, Peter M. Kappeler … & Justin M. Calabrese
Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of...

Data from: Fires in protected areas reveal unforeseen costs of Colombian peace

Dolors Armenteras, Laura Schneider & Liliana María Dávalos
Armed conflict, and its end, can have powerful effects on natural resources, but the influence of war and peace on highly biodiverse tropical forests remains disputed. We found a sixfold increase in fires in protected areas across biodiversity hotspots following guerrilla demobilization in Colombia, and a 52% increase in the probability of per-pixel deforestation within parks for 2018. Peace requires urgent shifts to include real-time forest monitoring, expand programmes to pay for ecosystem services at...

Data from: Evaluating the target‐tracking performance of scanning avian radars by augmenting data with simulated echoes

Samuel Urmy & Joseph Warren
1. Small scanning radars have been used for many years to track the movements of insects, birds, and bats. While the ability to track multiple flying animals simultaneously has numerous applications in basic ecology and applied conservation, translating radar tracks into accurate animal densities and fluxes requires estimates of detection and tracking probabilities. These can be challenging to determine, especially in environments with variable background clutter. 2. In order to assess radar tracking probabilities, we...

Data from: Characterization of the abiotic drivers of abundance of nearshore Arctic fishes

Noah Khalsa, Kyle Gatt, Trent Sutton & Amanda Kelley
Fish are critical ecologically and socioeconomically for subsistence economies in the Arctic, an ecosystem undergoing unprecedented environmental change. Our understanding of the responses of nearshore Arctic fishes to environmental change is inadequate because of limited research on the physicochemical drivers of abundance occurring at a fine scale. Here, high-frequency in-situ measurements of pH, temperature, salinity, and dissolved oxygen were paired with daily fish catches in nearshore Alaskan waters of the Beaufort Sea. This dataset includes...

Raw data for: Biomechanical demands of percussive techniques in the context of early stone toolmaking

Robin Macchi, Guillaume Daver, Michel Brenet, Sandrine Prat, Laurent Hugueville, Sonia Harmand, Jason Lewis & Mathieu Domalain
Recent discoveries in archaeology and palaeoanthropology highlight that stone stool knapping could have emerged first within the genera Australopithecus or Kenyanthropus rather than Homo. To explore the implications of this hypothesis determining the physical demands and motor control needed for performing the percussive movements during the oldest stone toolmaking technology (i.e. Lomekwian) would help. We analysed the joint-angle patterns and muscle activity of a knapping expert using three stone tool replication techniques: unipolar flaking on...

Data from: Separation of realized ecological niche axes among sympatric tilefishes provides insight into potential drivers of co‐occurrence in the NW Atlantic

Jill A. Olin, Oliver Shipley, Robert Cerrato, Paul Nitschke, Cedric Magen & Michael Frisk
Golden and Blueline Tilefish (Lopholatilus chamaeleonticeps and Caulolatilus microps) are keystone taxa in northwest (NW) Atlantic continental shelf‐edge environments due to their biotic (trophic‐mediated) and abiotic (ecosystem engineering) functional roles combined with high‐value fisheries. Despite this importance, the ecological niche dynamics (i.e., those relating to trophic behavior and food‐web interactions) of these sympatric species are poorly understood, knowledge of which may be consequential for maintaining both ecosystem function and fishery sustainability. We used stable isotope...

Sound velocities and P-V-T data of phase A obtained at GSECARS beamline 13-ID-D

Nao Cai, Xintong Qi, Ting Chen, Siheng Wang, Tony Yu, Yanbing Wang, Toru Inoue, Duojun Wang & Baosheng Li
The sound velocities and lattice parameters for sample in the under review paper, "Enhanced visibility of subduction slabs by the formation of dense hydrous phase A", submitted to the journal 'Geophysical Research Letters', are published. The high pressure and high-temperature experiment was conducted in the 1000-ton Kawai type large volume apparatus (T-25) installed at the GSECARS beamline 13-ID-D of Advanced Photon Source, Argonne National Laboratory. The datasets were obtained at conditions up to 11 GPa...

CAM Global RCE simulations TC track, radial profiles, and filtered precipitation files

Alyssa Stansfield & Kevin Reed
This dataset includes processed output from the Community Atmosphere Model (CAM), version 5, the atmospheric component of the Community Earth System Model (CESM2). CAM was run in a global rotating radiative convective equilibrium (RCE) aquaplanet configuration for 2 years, with the first 2 months discarded to allow for spin-up. The globally-uniform sea surface temperature (SST) was varied from 295 to 305 K in 1 K increments, producing a total of 11 model simulations. More details...

Supplemental dataset from: Initial acoustoelastic measurements in olivine: Investigating the effect of stress on P- and S-wave velocities

Taryn Traylor, Pamela Burnley & Matthew Whitaker
It is well known that elasticity is a key physical property in the determination of the structure and composition of the Earth and provides critical information for the interpretation of seismic data. This study investigates the stress-induced variation in elastic wave velocities, known as the acoustoelastic effect, in San Carlos olivine. A recently developed experimental ultrasonic acoustic system, the Directly Integrated Acoustic System Combined with Pressure Experiments (DIASCoPE), was used with the D-DIA multi-anvil apparatus...

The biogeography of community assembly: latitude and predation drive variation in community trait distribution in a guild of epifaunal crustaceans

Collin Gross, Collin Gross, J Duffy, Kevin Hovel, Melissa Kardish, Pamela Reynolds, Christoffer Boström, Katharyn Boyer, Mathiew Cusson, Johan Eklöf, Aschwin Engelen, Klemens Eriksson, Joel Fodrie, John Griffin, Clara Hereu, Masakazu Hori, A Randall Hughes, Mikhail Ivanov, Pablo Jorgensen, Claudia Kruschel, Kun-Seop Lee, Jonathan Lefcheck, Karen McGlathery, Per-Olav Moksnes, Masahiro Nakaoka … & Jay Stachowicz
While considerable evidence exists of biogeographic patterns in the intensity of species interactions, the influence of these patterns on variation in community structure is less clear. Using a model selection approach on measures of trait dispersion in crustaceans associated with eelgrass (Zostera marina) spanning 30º of latitude in two oceans, we found that dispersion strongly increased with increasing predation and decreasing latitude. Ocean and epiphyte load appeared as secondary predictors; Pacific communities were more overdispersed...

Additional file 6 of Novel trends of genome evolution in highly complex tropical sponge microbiomes

Joseph B. Kelly, David E. Carlson, Jun Siong Low & Robert W. Thacker
Additional file 6: Table S1. Taxonomy, statistics, source metadata, and CSG occurrence in MAGs that passed QC and dereplication steps and were used in the final analyses. The archaeal MAGs and the Trichodesmium MAG that did not meet the completeness threshold are included.

Additional file 9 of Novel trends of genome evolution in highly complex tropical sponge microbiomes

Joseph B. Kelly, David E. Carlson, Jun Siong Low & Robert W. Thacker
Additional file 9: Table S4. The top BLASTn hits for representative CSGs.

Additional file 7 of Novel trends of genome evolution in highly complex tropical sponge microbiomes

Joseph B. Kelly, David E. Carlson, Jun Siong Low & Robert W. Thacker
Additional file 7: Table S2. Table of relative abundances of Synechococcus MAGs in Ircinia, inferred via CoverM.

Additional file 10 of Novel trends of genome evolution in highly complex tropical sponge microbiomes

Joseph B. Kelly, David E. Carlson, Jun Siong Low & Robert W. Thacker
Additional file 10: Data File S1. Fasta-formatted CSGs found in bacterial symbionts of Ircinia.

Nonparametric Prediction Distribution from Resolution-Wise Regression with Heterogeneous Data

Jialu Li, Wan Zhang, Peiyao Wang, Qizhai Li, Kai Zhang & Yufeng Liu
Modeling and inference for heterogeneous data have gained great interest recently due to rapid developments in personalized marketing. Most existing regression approaches are based on the conditional mean and may require additional cluster information to accommodate data heterogeneity. In this article, we propose a novel nonparametric resolution-wise regression procedure to provide an estimated distribution of the response instead of one single value. We achieve this by decomposing the information of the response and the predictors...

From Black Box to Shining Spotlight: Using Random Forest Prediction Intervals to Illuminate the Impact of Assumptions in Linear Regression

Andrew J. Sage, Yang Liu & Joe Sato
We introduce a pair of Shiny web applications that allow users to visualize random forest prediction intervals alongside those produced by linear regression models. The apps are designed to help undergraduate students deepen their understanding of the role that assumptions play in statistical modeling by comparing and contrasting intervals produced by regression models with those produced by more flexible algorithmic techniques. We describe the mechanics of each approach, illustrate the features of the apps, provide...

From Black Box to Shining Spotlight

Andrew J. Sage, Yang Liu & Joe Sato
We introduce a pair of Shiny web applications that allow users to visualize random forest prediction intervals alongside those produced by linear regression models. The apps are designed to help undergraduate students deepen their understanding of the role that assumptions play in statistical modeling by comparing and contrasting intervals produced by regression models with those produced by more flexible algorithmic techniques. We describe the mechanics of each approach, illustrate the features of the apps, provide...

Supplemental Material, original_data - Effectiveness of Continuous Positive Airway Pressure Versus Mandibular Advancement Device in Severe Obstructive Sleep Apnea Patients With Mandibular Retrognathia: A Prospective Clinical Trial

Haichun Lai, Wei Huang, Wei Chen & Desheng Wang
Supplemental Material, original_data for Effectiveness of Continuous Positive Airway Pressure Versus Mandibular Advancement Device in Severe Obstructive Sleep Apnea Patients With Mandibular Retrognathia: A Prospective Clinical Trial by Haichun Lai, Wei Huang, Wei Chen and Desheng Wang in Ear, Nose & Throat Journal

Additional file 1 of Inconsistency analysis between metagenomic next-generation sequencing results of cerebrospinal fluid and clinical diagnosis with suspected central nervous system infection

Jin Wang, Jun Ye, Liqi Yang, Xiangfeng Chen, Haoshu Fang, Zhou Liu, Guomei Xia, Yafei Zhang & Zhenhua Zhang
Additional file 1: The results of next generation sequencing of cerebrospinal fluid.

Additional file 2 of Inconsistency analysis between metagenomic next-generation sequencing results of cerebrospinal fluid and clinical diagnosis with suspected central nervous system infection

Jin Wang, Jun Ye, Liqi Yang, Xiangfeng Chen, Haoshu Fang, Zhou Liu, Guomei Xia, Yafei Zhang & Zhenhua Zhang
Additional file 2: Comparison of the etiological results between conventional detection methods and next-generation sequencing technology.

A Unified Framework for Specification Tests of Continuous Treatment Effect Models

Wei Huang, Oliver Linton & Zheng Zhang
We propose a general framework for the specification testing of continuous treatment effect models. We assume a general residual function, which includes the average and quantile treatment effect models as special cases. The null models are identified under the unconfoundedness condition and contain a nonparametric weighting function. We propose a test statistic for the null model in which the weighting function is estimated by solving an expanding set of moment equations. We establish the asymptotic...

IL-27 overexpression alleviates inflammatory response in allergic asthma by inhibiting Th9 differentiation and regulating Th1/Th2 balance

Peng Xiong, Tonglin Liu, Hao Huang, Yi Yuan, Wendi Zhang, Lina Fu & Yu Chen
To investigate the effect of IL-27 on Th9 differentiation and Th1/Th2 balance. C57BL/6 (B6) mice were treated with ovalbumin to establish an allergic asthma (AA) model and subjected to IL-27 overexpression (OV) and empty vector (EV). Hematoxylin-eosin (HE) staining was performed to observe lung tissue inflammation. Flow cytometry was carried out to evaluate the percentage of Th9, Th1, and Th2 cells. The expression of IL-27, IL-27R, IL-9, T-bet, IFN-γ, and IgE was evaluated by quantitative...

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