121 Works

Data for: Characterizing individual tree-level snags using airborne lidar-derived forest canopy gaps within closed-canopy conifer forests

Jessica M. Stitt, Andrew T. Hudak, Carlos Alberto Silva, Lee A. Vierling & Kerri T. Vierling
1. Airborne lidar is often used to calculate forest metrics about trees but it may also provide a wealth of information about the space between trees. Forest canopy gaps are defined by the absence of vegetative structure and serve important roles for wildlife, such as facilitating animal movement. Forest canopy gaps also occur around snags, keystone structures that provide important substrates to wildlife species for breeding, roosting, and foraging. 2. We wanted to test a...

Numbers of individuals and endemicity for birds in three study sites of the Himalayas-Hengduan mountains of China

Yiming Hu, Brett Scheffers, Xinyuan Pan, Huijian Hu, Zhixin Zhou, Dan Liang, Cheng Wenda, Zhixin Wen & Luke Gibson
1. Describing the patterns and revealing the underlying mechanisms responsible for variations in community structure remains a central focus in ecology. However, important gaps remain, including our understanding of species abundance. Most studies on abundance-based relationships are from either temperate ecosystems or tropical ecosystems, and few have explicitly tested abundance-based relationships across a temperate to tropical ecotone. 2. Here, we use a comprehensive dataset of breeding birds across elevation spanning a temperate to subtropical gradient...

Identification of a 3-gene signature based on differentially expressed invasion genes related to cancer molecular subtypes to predict the prognosis of osteosarcoma patients

Yue Wan, Ning Qu, Yang Yang, Jing Ma, Zhe Li & Zhenyu Zhang
Invasion is a critical pathway leading to tumor metastasis. This study constructed an invasion-related polygenic signature to predict osteosarcoma prognosis. We initially determined two molecular subtypes of osteosarcoma, Cluster1 (C1) and Cluster2 (C2).. A 3 invasive-gene signature was established by univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression analysis of the differentially expressed genes (DEGs) between the two subtypes, and was validated in internal and two external data sets (GSE21257...

Local canopy disturbance as an explanation for long-term increases in liana abundance

Stefan Schnitzer, David DeFilippis, Marco Visser, Sergio Estrada-Villegas, Rigoberto Rivera-Camaña, Boris Bernal, Salomé Peréz, Abelino Valdéz, Seberino Aguilar, James Dalling, Eben Broadbent, Angelica Almeyda Zambrano, Stephen Hubbell & Maria Garcia-Leon
Canopy disturbance explains liana abundance and distribution within tropical forests and thus may also explain the widespread pattern of increasing liana abundance; however, this hypothesis remains untested. We used a 10-year study (2007 – 2017) of 117,100 rooted lianas in an old-growth Panamanian forest to test whether local canopy disturbance explains increasing liana abundance. We found that liana density increased 29.2% and basal area 12.5%. The vast majority of these increases were associated with clonal...

Lack of neophobic responses to color in a jumping spider that uses color cues when foraging (Habronattus pyrrithrix)

Michael Vickers, Madison Heisey & Lisa Taylor
Chemically defended prey often advertise their toxins with bright and conspicuous colors. To understand why such colors are effective at reducing predation, we need to understand the psychology of key predators. In bird predators, there is evidence that individuals avoid novelty - including prey of novel colors (with which they have had no prior experience). Moreover, the effect of novelty is strongest for colors that are typically associated with aposematic prey (e.g., red, orange, yellow)....

A Case Study on the Medical Library Association’s 2019 Communities Transition Qualitative Data Set

Kathryn Houk, Kelsa Bartley, Jane Morgan-Daniel & Elaina Vitale
In 2019, the Medical Library Association (MLA) adopted a new model of community governance and participation, referred to as the MLA Communities Transition. The Communities Transition was the culmination of long-ranging plans by MLA to support two of its strategic goals: Diversity and Inclusion, and Communities. The reorganization aimed to strengthen MLA member communities, better support programming, reduce administrative overhead, and attract new members. The 2019 - 2020 MLA Rising Stars cohort was tasked to...

In the eye of the beholder: Is color classification consistent amongst human observers?

Kim Valenta, Sally Bornbusch, Yan-Daniel Jacques & Omer Nevo
Colorful displays have evolved in multiple plant and animal species as signals to mutualists, antagonists, competitors, mates, and other potential receivers. Studies of color have long relied on subjective classifications of color by human observers. However, humans have a limited ability to perceive color compared to other animals, and human biological, cultural, and environmental variables can influence color perception. Here, we test the consistency of human color classification using fruit color as a model system....

Comparative analysis of circRNA expression profile and circRNA-miRNA-mRNA regulatory network between palmitic and stearic acid-induced lipotoxicity to pancreatic β cells

Yunjin Zhang, Qingrui Zhao, Shenghan Su, Lingfeng Dan, Xuebei Li, Yu Wang, Yuqing Lin, Zhen Tian, Changhao Sun & Huimin Lu
Chronic exposure to high concentrations of circulating palmitic acid and stearic acid leads to impaired β cell function, which accelerates the development of type 2 diabetes. However, differences in the mechanisms underlying this process between these two saturated fatty acids remain largely unknown. In this study, we screened for potential circular RNAs (circRNAs) and their associated regulatory pathways in palmitic acid- and stearic acid-induced mouse β-TC6 cell dysfunction. CircRNA high-throughput sequencing, gene ontology enrichment and...

Comparative analysis of circRNA expression profile and circRNA-miRNA-mRNA regulatory network between palmitic and stearic acid-induced lipotoxicity to pancreatic β cells

Yunjin Zhang, Qingrui Zhao, Shenghan Su, Lingfeng Dan, Xuebei Li, Yu Wang, Yuqing Lin, Zhen Tian, Changhao Sun & Huimin Lu
Chronic exposure to high concentrations of circulating palmitic acid and stearic acid leads to impaired β cell function, which accelerates the development of type 2 diabetes. However, differences in the mechanisms underlying this process between these two saturated fatty acids remain largely unknown. In this study, we screened for potential circular RNAs (circRNAs) and their associated regulatory pathways in palmitic acid- and stearic acid-induced mouse β-TC6 cell dysfunction. CircRNA high-throughput sequencing, gene ontology enrichment and...

Data from: Developmental origins of the crocodylian skull table and platyrostral face

Zachary S. Morris, Kent A. Vliet, Arhat Abzhanov & Stephanie E. Pierce
The dorsoventrally flattened skull typifies extant Crocodylia perhaps more than any other anatomical feature and is generally considered an adaptation for semi-aquatic feeding. Although the evolutionary origins have been extensively studied, the developmental origins of craniofacial flattening have yet to be explored. To understand how the skull table and platyrostral snout develop, we quantified embryonic development and post-hatching growth (ontogeny) of the crocodylian skull in lateral view using geometric morphometrics. Our dataset (n=103) includes all...

Convergence of undulatory swimming kinematics across a diversity of fishes

Elsa Goerig, Valentina Di Santo, Dylan K. Wainwright, Theodore Castro-Santos, James Liao, Otar Akanyeti & George Lauder
Fishes exhibit an astounding diversity of locomotor behaviors, from classic swimming with their body and fins to jumping, flying, walking, and burrowing. Fishes that use their body and caudal fin (BCF) during undulatory swimming have been traditionally divided into modes based on the length of the propulsive body wave and the ratio of head:tail oscillation amplitude: anguilliform, sub-carangiform, carangiform and thunniform. This classification was first proposed based on key morphological traits, such as body stiffness...

Plant and bird phenology and plant occurrence from 1851 to 2020 (non-continuous) in Thoreau’s Concord, Massachusetts

Elizabeth R. Ellwood, Amanda S. Gallinat, Caitlin McDonough MacKenzie, Tara Miller, Abraham Miller-Rushing, Caroline Polgar & Richard B. Primack
Concord, Massachusetts, USA has served as an active location for phenological observations since philosopher and naturalist Henry David Thoreau began recording plant and animal occurrence and phenology in 1851. Since that time, numerous naturalists, scientists, and researchers have continued this tradition, creating an invaluable time series of 758 species in a single location. A total of 13,441 phenological records, spanning 118 years, now exist, with observations of many species ongoing. Relative abundance data for an...

Kearney 2021 Lateral Pinch Data

Kalyn Kearney, Jennifer Nichols & Joel Harley
Datasets representing variations in lateral pinch thumb-tip force due to changes in maximum isometric force, as simulated with OpenSim v4.0. Each dataset includes outputs from forward dynamics, with thumb-tip force provided via joint reactions analyses. We also include muscle activations from computed muscle control which were used to drive these forward dynamic simulations. See the included ReadMe file and the following publication for more details: Kearney KM, Harley JB, Nichols JA. “Classifying muscle parameters with...

Automated audio recording as a means of surveying Tinamous (Tinamidae) in the Peruvian Amazon

Reid Rumelt, Arianna Basto & Carla Mere Roncal
The use of machine learning technologies to process large quantities of remotely-collected audio data is a powerful emerging research tool in ecology and conservation. We applied these methods to a field study of tinamou (Tinamidae) biology in Madre de Dios, Peru, a region expected to have high levels of interspecies competition and niche partitioning as a result of high tinamou alpha diversity. We used autonomous recording units to gather environmental audio over a period of...

Molecular investigation of infection sources and transmission chains of brucellosis in Zhejiang, China

Heng Wang, Wei-min Xu, Kuang-ji Zhu, Su-juan Zhu, Hong-fang Zhang, Jia Wang, Yang Yang, Feng-yao Shao, Neng-ming Jiang, Zhen-yang Tao, Hang-yi Jin, Yi Tang, Liang-liang Huo, Fang Dong, Zhen-jun Li, Hua Ding & Zhi-guo Liu
In the present study, a total of 7793 samples from 5 different types of hosts were collected and tested, with a seroprevalence of 2.4% (184/7793). Although the seroprevalence of human and animal brucellosis is relatively low, numbers of human brucellosis cases reported have increased continuously from 2004 to 2018. A total of 118 Brucella strains containing 4 biotypes were obtained, including Brucella melitensis bv.1 (n = 8) and bv.3 (n = 106), Brucella abortus bv.3...

Hippocampal spectral degradation

Yuchen Zhou, Alex Sheremet, Kennedy Jack, Dicola Nicholas, Maciel Carolina, Burke Sara & Maurer Andrew
The hippocampal local field potential (LFP) exhibits a strong correlation with behavior. During rest, the theta rhythm is not prominent, but during active behavior, there are strong rhythms in the theta, theta harmonics, and gamma ranges. With increasing running velocity, theta, theta harmonics and gamma increase in power and in cross-frequency coupling, suggesting that neural entrainment is a direct consequence of the total excitatory input. While it is common to study the parametric range between...

Power for balanced linear mixed models with complex missing data processes

Kevin P. Josey, Brandy M. Ringham, Anna E. Barón, Margaret Schenkman, Katherine A. Sauder, Keith E. Muller, Dana Dabelea & Deborah H. Glueck
When designing repeated measures studies, both the amount and the pattern of missing outcome data can affect power. The chance that an observation is missing may vary across measurements, and missingness may be correlated across measurements. For example, in a physiotherapy study of patients with Parkinson’s disease, increasing intermittent dropout over time yielded missing measurements of physical function. In this example, we assume data are missing completely at random, since the chance that a data...

Experimentally elevated testosterone shortens telomeres across years in a free-living songbird

Britt Heidinger, Samuel Slowiniski, Aubrey Sirman, Nicole Gerlach & Ellen Ketterson
Reproductive investment often comes at a cost to longevity, but the mechanisms that underlie these long-term effects are not well understood. In male vertebrates, elevated testosterone has been shown to increase reproductive success, but simultaneously decrease survival. One factor that may contribute to or serve as a biomarker of these long-term effects of testosterone on longevity is telomeres, which are often positively related to lifespan and have been shown to shorten in response to reproduction....

Macroevolution of dimensionless life history metrics in tetrapods

Cecina Babich Morrow, S.K. Morgan Ernest & Drew Kerkhoff
Life history traits represent organisms’ strategies to navigate the fitness trade-offs between survival and reproduction. Eric Charnov developed three dimensionless metrics to quantify fundamental life history trade-offs. Lifetime reproductive effort (LRE), relative reproductive lifespan (RRL), and relative offspring size (ROS), together with body mass, can be used to classify life history strategies across the four major classes of tetrapods: amphibians, reptiles, mammals, and birds. First, we investigate how the metrics have evolved in concert with...

Tuned inhibition in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior: S4 data, evidence for tuned inhibition in macaque superior colliculus

Megan Peters, Brian Maniscalco, Brian Odegaard, Piercesare Grimaldi, Seong Hah Cho, Michele Basso & Hakwan Lau
This dataset contains online spike-sorted single-unit recordings from one Rhesus macaque who performed a dot-motion discrimination task while neural data was recorded with a 16-channel v-probe from superior colliculus neurons. Full methods for data collection, including description of the stimuli and task, surgical details, ethics statement, funding information, and other relevant details, are available in the above-referenced manuscript, section S4 Text.

Non-linear thresholds in the effects of island area on functional diversity in woody plant communities

Aiying Zhang, Shilu Zheng, Raphael K. Didham, Robert D. Holt & Mingjian Yu
1. Threshold non-linearities in the relationship between island area and species richness can result in dramatic declines in richness with a seemingly small decline in area near the threshold. What is not known, is whether threshold declines in richness are also accompanied by non-linear changes in functional trait space and non-random shifts of trait group composition in response to declining area. 2. Plant species richness was recorded, and four functional diversity (FD) indices calculated based...

When text simplification is not enough: Could a graph-based visualization facilitate consumers’ comprehension of dietary supplement information?

Xing He, Rui Zhang, Jordan Alpert, Sicheng Zhou, Terrence Adam, Aantaki Raisa, Yifan Peng, Hansi Zhang, Yi Guo & Jiang Bian
Background: Dietary supplements are widely used. However, dietary supplements are not always safe. For example, an estimated 23,000 emergency room visits every year in the United States were attributed to adverse events related to dietary supplement use. With the rapid development of the Internet, consumers usually seek health information including dietary supplement information online. To help consumers access quality online dietary supplement information, we have identified trustworthy dietary supplement information sources and built an evidence-based...

Continuous bite monitoring method (GPEP)

Anderson Michel Soares Bolzan, Szymczak, Nadin, Olivier Bonnet, Marcelo Wallau, Anibal De Moraes, Renata Moraes, Alda Monteiro & Paulo Carvalho
Determining herbage intake is pivotal for studies on grazing ecology. Direct observation of animals allows describing the interactions of animals with the pastoral environment along the complex grazing process. The objectives of the study were to evaluate the reliability of the continuous bite monitoring (CBM) method in determining herbage intake in grazing sheep compared to the standard double-weighing technique (DW) method during 45-min feeding bouts; evaluate the degree of agreement between the two techniques; and...

Microarthropod contributions to fitness variation in the common moss Ceratodon purpureus

Erin Shortlidge, Adam Payton, Sarah Carey, Stuart McDaniel, Todd Rosenstiel & Sarah Eppley
The evolution of sustained plant-animal interactions depends critically upon genetic variation in the fitness benefits from the interaction. Genetic analyses of such interactions are limited to a few model systems, in part because genetic variation may be absent or the interacting species may be experimentally intractable. Here we examine the role of sperm-dispersing microarthropods in shaping reproduction and genetic variation in mosses. We established experimental mesocosms with known moss genotypes and inferred the parents of...

Males respond to substrate-borne, not airborne, female chemical cues in the jumping spider, Habronattus pyrrithrix

Ellen Humbel, Rebecca Kimball & Lisa Taylor
Jumping spiders are known for complex courtship displays with both visual and vibratory components, but increasing evidence shows they also use chemoreception in intraspecific communication. We conducted two experiments using Habronattus pyrrithrix (Chamberlin, 1924) to assess male response to substrate-borne or airborne chemical cues produced by virgin females. First, we tested the effect of substrate-borne cues by allowing males to inspect two pieces of filter paper that had either been exposed to a female (thus...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Florida
  • Chinese Academy of Agricultural Sciences
  • Shanghai Jiao Tong University
  • West China Second University Hospital of Sichuan University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Sichuan University
  • University of Electronic Science and Technology of China
  • West China Hospital of Sichuan University
  • Central South University
  • University of Hong Kong