121 Works

Data from: Opportunities to catalyze improved healthcare access in pluralistic systems: a cross-sectional study in Haiti

Molly Klarman, Justin Schon, Youseline Cajusma, Stacey Maples, Valery M Beau De Rochars, Chantale Baril & Eric J Nelson
Introduction. Gains to ensure global healthcare access are at risk of stalling because some old resilient challenges require new solutions. Our objective was to identify determinants of intended versus actual care-seeking behaviors in a pluralistic healthcare system that is reliant on both conventional and non-conventional providers and discover opportunities to catalyze improved healthcare access. Methods. A cross-sectional study was conducted among households with children less than 5 years of age in Haiti. Households were randomly...

The soil microbiome increases plant survival and modifies interactions with root endosymbionts in the field

Corlett Wood, Shaniya Markalanda, Connor McFadden & Steven Cassidy
Evidence is accumulating that the soil microbiome—the community of microorganisms living in soils—has a major effect on plant traits and fitness. However, most work to date has taken place under controlled laboratory conditions and has not experimentally disentangled the effect of the soil microbiome on plant performance from the effects of key endosymbiotic constituents. As a result, it is difficult to extrapolate from existing data to understand the role of the soil microbiome in natural...

Bioinformatics-based identification of SPNS3 (Spinster homolog 3) as a prognostic biomarker of apoptosis resistance in acute myeloid leukemia

Yang Hong, Xiaopeng Tian, Mengmiao Wang, Cheng Chen & Aining Sun
Spinster homolog 3 (SPNS3) belongs to the Spinster (SPNS) family which participates in sphingolipid transportation through the cell membrane. However, the functions of SPNS3 in acute myeloid leukemia (AML) are unknown. This study obtained SPNS3 from a gene set that was related to AML relapse and evaluate whether high SPNS3 expression induced apoptosis resistance in an AML cell line, which is consistent with the role of SPNS3 as a marker of poor prognosis in the...

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...

Body size, trophic position, and the coupling of different energy pathways across a saltmarsh landscape

Friedrich Keppeler, Jill Olin, Paola López-Duarte, Michael Polito, Linda Hooper-Bùi, Sabrina Taylor, Nancy Rabalais, F Joel Fodrie, Brian Roberts, R Eugene Turner, Charles Martin & Olaf Jensen
Here, we listed the bulk stable isotope values (δ13C and δ15N) and body size measurements of organisms that were analyzed in the manuscript "Body size, trophic position, and the coupling of different energy pathways across a saltmarsh landscape", published in Limnology and Oceanography Letters. Our dataset is a compilation of samplings obtained by the Southern Louisiana marsh food webs project within the Coastal Waters Consortium (CWC) II (Lopez-Duarte et al. 2017a [https://doi.org/10.7266/N7XS5SGD], Lopez-Duarte et al....

Attitudes Toward and Impacts of Free-roaming Dogs in Madagascar

Leandra Merz, Akhil Kshirsagar, Radoniaina Rafaliarison, Tsiky Rajaonarivelo, Zach Farris, Kim Valenta & Zoavina Randriana
Free-roaming domesticated dogs interact with humans and wildlife in ways that can exacerbate or mitigate existing conflict. Dogs are known to predate wildlife as well as domestic livestock which contributes to increasing human-wildlife conflict. However, dogs can also mitigate conflict by protecting livestock from native predators or killing invasive pest species. Because attitudes toward dogs vary greatly, conflict often arises between humans over how to manage free-roaming dogs. We conducted surveys to assess attitudes toward...

Moss growth, development, morphology, and physiology dataset and code

Leslie Kollar
A central problem in evolutionary biology is to identify the forces that maintain genetic variation for fitness in natural populations. Sexual antagonism, in which selection favors different variants in males and females, can slow the transit of a polymorphism through a population or can actively maintain fitness variation. The amount of sexually antagonistic variation to be expected depends in part on the genetic architecture of sexual dimorphism, about which we know relatively little. Here, we...

Dataset for: Trade-offs between weapons and testes do not manifest at high social densities

Christine Miller
Social conditions can alter the allocation of resources to reproductive traits. For example, an increase in social density during development is frequently associated with an increase in the testes mass of males. Sperm competition theory assumes that increased investment in testes should come at the expense of investing into precopulatory traits, such as sexually selected weaponry. However, much remains unknown about the role of the social context on the concurrent, relative investment in both testes...

American crocodile captures in South Florida

Venetia Briggs-Gonzalez
The federally threatened American crocodile (Crocodylus acutus) is a flagship species and ecological indicator of hydrologic restoration in the Florida Everglades. we conducted a long-term capture-recapture study on the South Florida population of American crocodiles from 1978 to 2015 to evaluate the effects of restoration efforts to restore historic hydrologic conditions. The study produced 10,040 crocodile capture events of 9,865 individuals and more than 90% of captures were of hatchlings. Body condition and growth rates...

Data from: Hybrid coffee cultivars may enhance agroecosystem resilience to climate change

Emily Pappo, Chris H. Wilson & S. Luke Flory
Anthropogenic climate change is predicted to cause shifts in temperature and precipitation patterns that will be detrimental for global agriculture. Developing comprehensive strategies for building climate resilient agroecosystems is critical for maintaining future crop production. Arabica coffee (Coffea arabica) is highly sensitive to the quantity and timing of precipitation, so alterations in precipitation patterns that are predicted under climate change are likely to be a major challenge for maintaining coffee agroecosystems. We assessed cultivar selection...

Life history and environment predict variation in testosterone across vertebrates

Jerry Husak, Matthew Fuxjager, Michele A. Johnson, Maren Vitousek, Jeremy Donald, Clinton David Francis, Wolfgang Goymann, Michaela Hau, Bonnie Kircher, Rosemary Knapp, Lynn B. Martin, Eliot Miller, Laura Schoenle & Tony Williams
Endocrine systems act as key intermediaries between organisms and their environments. This interaction leads to high variability in hormone levels, but we know little about the ecological factors that influence this variation within and across major vertebrate groups. We study this topic by assessing how various social and environmental dynamics influence testosterone levels across the entire vertebrate tree of life. Our analyses show that breeding season length and mating system are the strongest predictors of...

A target enrichment probe set for resolving the flagellate land plant tree of life

Jesse W. Breinholt, Sarah B. Carey, George P. Tiley, E. Christine Davis, Lorena Endara, Stuart F. McDaniel, Leandro Neves, Emily B. Sessa, Matt Von Konrat, Susan Fawcett, Stefanie M. Ickert-Bond, Paulo H. Labiak, Juan Larraín, Marcus Lehnert, Lily R. Lewis, Nathalie S. Nagalingum, Nikisha Patel, Stefan A. Rensing, Weston Testo, Alejandra Vasco, Juan Carlos Villarreal, Evelyn Webb Williams, J. Gordon Burleigh, Sahut Chantanaorrapint, Leandro G. Neves … & Stefanie M. Ickert‐Bond
Premise of the Study: New sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. Methods and Results: We leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target...

Data from: Invasive grass fuel loads suppress native species by increasing fire intensity and soil heating

Giovanna Tomat-Kelly, Whalen W. Dillon & S. Luke Flory
Non-native invasive grasses are driving intense fires across the globe but the impacts of native versus invader-fueled fires on community assemblages are poorly understood. By increasing fire intensity, grass invasions might increase belowground mortality of heat-sensitive seeds and buds, thereby shifting community composition. We compared fuel loads in native and non-native invasive (cogongrass, Imperata cylindrica) plant dominated areas of pine savannas in Florida. Then, we conducted a field experiment to examine how fuel loads and...

Identification of biomarkers related to Tumor-Infiltrating Lymphocytes (TILs) infiltration with gene co-expression network in colorectal cancer

Rong Liao, Qi-Zhi Ma, Cong-Ya Zhou, Jun-Jun Li, Ning-Na Weng, Yang Yang & Qing Zhu
Colorectal cancer (CRC) is one of the most common tumors, ranking second in the global cause of death from cancer. The prognosis of advanced patients is still very poor. In this study, hub modules with the highest association with tumor-infiltrating immune cells were identified by weighted gene co-expression network analysis based on CRC expression data from the Gene Expression Omnibus database. Next, three hub genes (ADAM8, IL-1A, VAV3) related to infiltrating immune cells were identified...

Disentangling the influence of water limitation and simultaneous above and belowground herbivory on plant tolerance and resistance to stress

Fabiane Mundim, Ernane Vieira-Neto, Hans Alborn & Emilio Bruna
1. Plants face multiple biotic and abiotic stressors simultaneously. Many species can tolerate and resist stress, but countermeasures differ between roots and leaves. Since herbivores and environmental conditions modulate costs and benefits of plant defense traits, stress responses are context-dependent. We examined whole-plant tolerance and resistance responses to individual and combined effects of above and belowground herbivory under variable water conditions. 2. We manipulated water availability and access by two common herbivores (Spodoptera exigua caterpillars...

Cost of step time asymmetry and step length asymmetry in human walking

Jan Stenum & Julia Choi
The metabolic cost of walking in healthy individuals increases with spatiotemporal gait asymmetries. Pathological gait, such as post-stroke, often has asymmetry in step lengths and step times which may contribute to an increased energy cost. But paradoxically, enforcing step length symmetry does not reduce metabolic cost of post-stroke walking. The isolated and interacting costs of asymmetry in step times and step lengths remain unclear, because previous studies did not simultaneously enforce spatial and temporal gait...

Data from: Multiple dimensions of bird beta diversity support that mountains are higher in the tropics

Flavia A. Montaño-Centellas, Bette Loiselle & Christy McCain
Aim We examine latitudinal effects of breeding bird taxonomic, phylogenetic and functional β-diversity (Tβ, Pβ and Fβ, respectively) along elevational gradients to test predictions derived from Janzen’s (1967) classic ideas that tropical mountains represent stronger dispersal barriers than temperate mountains. Location Global Taxon Birds Methods Using a global dataset from 46 mountains, we examine latitudinal patterns of Tβ, Pβ, and Fβ, and their components: β rich and β repl. For each mountain and each dimension...

Data and Code for: An index for measuring functional extension and evenness in trait space

Tao Zhang, Grant M. Domke, Matthew B. Russell & Jeremy W. Lichstein
Most existing functional diversity indices focus on single specific facet of functional diversity. Although they help scrutinize the details of functional diversity from their own angles, they often present some limitations in estimating functional diversity from a broad perspective. Here we presented a functional extension and evenness (FEE) index that encloses two important aspects of functional diversity. This index is based on a straightforward notion that a community has high diversity when its species are...

Exploring the effects of extreme polyandry on estimates of sexual selection and reproductive success

E.V(Ginny) Greenway, Jennifer Hamel & Christine Miller
Multiple mating by females can dramatically alter selection on males by creating indirect interactions between rivals via sperm competition. Exactly how this behavior alters the relationship between male mating and fertilization success depends on multiple factors: re-mating frequency, sperm usage patterns, and mating assortment (the extent to which the most promiscuous individuals mate with each other). Here we explore the role these elements play in determining sexual selection in a highly polygyandrous species, the squash...

Large herbivores transform plant-pollinator networks in an African savanna

Matthew C. Hutchinson, Travis J. Guy, Todd M. Palmer, Robert M. Pringle, Katherine C. R. Baldock, Elisha Kayser, Benjamin Baiser, Phillip P. A. Staniczenko, Jacob R. Goheen, Robert M. Pringle & Todd M. Palmer
Pollination by animals is a key ecosystem service1,2 and interactions between plants and their pollinators are a model system for the study of ecological networks3,4, yet plant-pollinator networks are typically studied in isolation from the broader ecosystems in which they are embedded. The plants visited by pollinators also interact with other consumer guilds that eat stems, leaves, fruits, or seeds. One such guild, large mammalian herbivores, are well-known ecosystem engineers5–7 and may have substantial impacts...

SUVA: splicing site usage variation analysis from RNA-seq data reveals highly conserved complex splicing biomarkers in liver cancer

Chao Cheng, Lei Liu, Yongli Bao, Jingwen Yi, Weili Quan, Yaqiang Xue, Luguo Sun & Yi Zhang
Most of the current alternative splicing (AS) analysis tools are powerless to analyse complex splicing. To address this, we developed SUVA (Splice sites Usage Variation Analysis) that decomposes complex splicing events into five types of splice junction pairs. By analysing real and simulated data, SUVA showed higher sensitivity and accuracy in detecting AS events than the compared methods. Notably, SUVA detected extensive complex AS events and screened out 69 highly conserved and dominant AS events...

SUVA: splicing site usage variation analysis from RNA-seq data reveals highly conserved complex splicing biomarkers in liver cancer

Chao Cheng, Lei Liu, Yongli Bao, Jingwen Yi, Weili Quan, Yaqiang Xue, Luguo Sun & Yi Zhang
Most of the current alternative splicing (AS) analysis tools are powerless to analyse complex splicing. To address this, we developed SUVA (Splice sites Usage Variation Analysis) that decomposes complex splicing events into five types of splice junction pairs. By analysing real and simulated data, SUVA showed higher sensitivity and accuracy in detecting AS events than the compared methods. Notably, SUVA detected extensive complex AS events and screened out 69 highly conserved and dominant AS events...

Six-state amino acid recoding is not an effective strategy to offset compositional heterogeneity and saturation in phylogenetic analyses

Alexandra Hernandez & Joseph Ryan
Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of 6-state recoding approaches by comparing the performance of analyses on recoded and non-recoded datasets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches...

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...

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...

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