WaRSwap is a randomization algorithm that for the first time provides a practical network motif discovery method for large multi-layer networks, for example those that include transcription factors, microRNAs, and non-regulatory protein coding genes. The algorithm is applicable to systems with tens of thousands of genes, while accounting for critical...
The Greenland NEEM (North Greenland Eemian Ice Drilling) operation in 2010 provided the first opportunity to combine trace-gas measurements by laser spectroscopic instruments and continuous-flow analysis along a freshly drilled ice core in a field-based setting. We present the resulting atmospheric methane (CH₄) record covering the time period from 107.7...
A stratigraphy-based chronology for the North Greenland Eemian Ice Drilling (NEEM) ice core has been derived by transferring the annual layer counted Greenland Ice Core Chronology 2005 (GICC05) and its model extension (GICC05modelext) from the NGRIP core to the NEEM core using 787 match points of mainly volcanic origin identified...
Soils are globally significant sources and sinks of
atmospheric CO₂. Increasing the resolution of soil carbon
turnover estimates is important for predicting the response of
soil carbon cycling to environmental change. We show that
soil carbon turnover times can be more finely resolved using
a dual isotope label like the...
Complex systems science provides a transdisciplinary framework to study systems characterized by (1) heterogeneity, (2) hierarchy, (3) self‐organization, (4) openness, (5) adaptation, (6) memory, (7) non‐linearity, and (8) uncertainty. Complex systems thinking has inspired both theory and applied strategies for improving ecosystem resilience and adaptability, but applications in forest ecology...
Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus...
Dietary selenium (Se) alters whole-blood Se concentrations in sheep, dependent upon Se source and dosage administered, but little is known about effects on immune function. We used footrot (FR) as a disease model to test the effects of supranutritional Se supplementation on immune function. To determine the effect of Se-source...
Long-term ecological data are crucial in helping ecologists understand ecosystem function and environmental change. Nevertheless, these kinds of data sets are difficult to analyze because they are usually large, multivariate, and spatiotemporal. Although existing analysis tools such as statistical methods and spreadsheet software permit rigorous tests of pre-conceived hypotheses and...
The recovery of a 1.5 million yr long ice core from Antarctica represents a keystone of our understanding of Quaternary climate, the progression of glaciation over this time period and the role of greenhouse gas cycles in this progression. Here we tackle the question of where such ice may still...
This paper presents a particle method designed for high-dimensional state estimation. Instead of weighing random forecasts by their distance to given observations, the method samples an ensemble of particles around an optimal solution based on the observations (i.e., it is implicit). It differs from other implicit methods because it includes...
A major challenge for biodiversity conservation is to mitigate the effects of future environmental change, such as land use, in important areas for biodiversity conservation. In the United States, recent conservation efforts by The Nature Conservancy and partners have identified and mapped the nation's Areas of Biodiversity Significance (ABS), representing...
In some cases a canopy height model (CHM) is the only available source of forest height information. For these cases it is important to understand the predictive power of CHM data for forest attributes. In this study we examined the use of lidar-derived CHM metrics to predict forest structure classes...
The cereal pathogen Fusarium graminearum produces secondary metabolites toxic to humans and animals, yet coordinated transcriptional regulation of gene clusters remains largely a mystery. By chromatin immunoprecipitation and high-throughput DNA sequencing (ChIP-seq) we found that regions with secondary metabolite clusters are enriched for trimethylated histone H3 lysine 27 (H3K27me3), a...
Macromoth diversity, abundance, and community structure in the topographically complex HJ Andrews Experimental Forest and LTER site was studied on the west slope of the Cascade Range, Oregon. Data on 493 macromoth species (62,221 individuals) was sampled eight times/year at 20 locations from 2004 to 2008 and examined using multivariate...
Ongoing greenhouse gas emissions can modify climate processes and induce shifts in ocean temperature, pH, oxygen concentration, and productivity, which in turn could alter biological and social systems. Here, we provide a synoptic global assessment of the simultaneous changes in future ocean biogeochemical variables over marine biota and their broader...
Rapamycin (Rapa) and dietary restriction (DR) have consistently
been shown to increase lifespan. To investigate whether Rapa
and DR affect similar pathways in mice, we compared the effects
of feeding mice ad libitum (AL), Rapa, DR, or a combination of
Rapa and DR (Rapa + DR) on the transcriptome and...
We examined the multivariate life-history trajectories of age 0 and age 1 female Gambusia affinis to determine relative effects of age-based and environment-based cues on reproductive investment. Age 0 females decreased reproductive investment prior to the onset of fall and winter months, while age 1 females increased reproductive investment as...
The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the
application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity
is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the...
Intraspecific assisted migration (ISAM) through seed transfer during artificial forest regeneration has been suggested as an adaptation strategy to enhance forest resilience and productivity under future climate. In this study, we assessed the risks and benefits of ISAM in white spruce based on long-term and multilocation, rangewide provenance test data....
We present high-resolution measurements of carbon monoxide (CO) concentrations from a shallow ice core of the North Greenland Eemian Ice Drilling project (NEEM-2011-S1). An optical-feedback cavity-enhanced absorption spectrometer (OF-CEAS) coupled to a continuous melter system performed continuous, online analysis during a four-week measurement campaign. This analytical setup generated stable measurements...
This paper reviews the current progress in mathematical modeling of anti-reflective subwavelength structures. Methods covered include effective medium theory (EMT), finite-difference time-domain (FDTD), transfer matrix method (TMM), the Fourier modal method (FMM)/rigorous coupled-wave analysis (RCWA) and the finite element method (FEM). Time-based solutions to Maxwell’s equations, such as FDTD, have...
Gold nanoparticles (AuNPs) are increasingly used in biomedical applications, hence understanding the processes that affect their biocompatibility and stability are of significant interest. In this study, we assessed the stability of peptide-capped AuNPs and used the embryonic zebrafish (Danio rerio) as a vertebrate system to investigate the impact of synthesis...
Climate warming is projected to affect forest water yields but the effects are expected to vary. We investigated how forest type and age affect water yield resilience to climate warming. To answer this question, we examined the variability in historical water yields at long‐term experimental catchments across Canada and the...
The regiodivergent O- to C- or N-carboxyl transfer of pyrazolyl carbonates is described, with DMAP giving preferential N-carboxylation and triazolinylidenes promoting selective C-carboxylation (both with up to >99 : 1 regioselectivity). An enantioselective O- to C-carboxyl variant using NHC catalysis is demonstrated (up to 92% ee), while mechanistic and DFT studies outline...
Early‐seral ecosystems make important contributions to regional biodiversity by supporting high abundance and diversity of many plant and animal species that are otherwise rare or absent from closed‐canopy forests. Therefore, the period of post‐fire tree establishment is a key stage in forest stand and ecosystem development that can be viewed...
Foundation species are structurally dominant members of ecological communities that can stabilize ecological processes and influence resilience to disturbance and resistance to invasion. Being common, they are often overlooked for conservation but are increasingly threatened from land use change, biological invasions, and over‐exploitation. The pattern of foundation species abundances over...
The exponential growth of the salmonid farming industry during the last 3 decades has created conditions for massive escapes of these exotic species into natural environments in southern Chile. Here, we review and update information about salmonid escapes from 1993 to 2012 and examine their potential environmental, social, and economic...
Forest understory vegetation is influenced by broad-scale variation in climate, intermediate-scale variation in topography, disturbance and neighborhood interactions. However, little is known about how these multi-scale controls interact to influence observed spatial patterns. We examined relationships between the aggregated cover of understory plant species (%C[subscript U]) and multi-scale controls using...
Radiocarbon is an exceptionally useful tool for studying soil-respired CO₂, providing information about soil
carbon turnover rates, depths of production, and the biological sources of production through partitioning. Unfortunately, little
work has been done to thoroughly investigate the possibility of inherent biases present in current measurement techniques,
like those present...
Southwestern US irrigated landscapes are facing
upheaval due to water scarcity and land use conversion associated
with climate change, population growth, and changing
economics. In the traditionally irrigated valleys of northern
New Mexico, these stresses, as well as instances of community
longevity in the face of these stresses, are apparent....
The West Antarctic Ice Sheet Divide (WAIS Divide, WD) ice core is a newly drilled, high-accumulation
deep ice core that provides Antarctic climate records of
the past ~68 ka at unprecedented temporal resolution. The
upper 2850 m (back to 31.2 ka BP) have been dated using
annual-layer counting. Here we...
This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Hindawi Publishing Corporation. The published article can be found at: http://dx.doi.org/10.1155/2015/169256
RNA-Sequencing (RNA-Seq) has been widely adopted for quantifying gene expression changes in comparative transcriptome analysis. For detecting differentially expressed genes, a variety of statistical methods based on the negative binomial (NB) distribution have been proposed. These methods differ in the ways they handle the NB nuisance parameters (i.e., the dispersion...
The coexistence problem occurs when a single wireless body area network (WBAN) is located within a multiple-WBAN
environment. This causes WBANs to suffer from severe channel interference that degrades the communication performance of each
WBAN. Since a WBAN handles vital signs that affect human life, the detection or prediction of...
In this study we investigated the role of astragaloside IV (AS-IV), one of the major active constituents purified from the Chinese
medicinal herb Astragalus membranaceus, in LPS-induced acute inflammatory responses in mice in vivo and examined possible
underlying mechanisms. Mice were assigned to four groups: vehicle-treated control animals; AS-IV-treated animals...
The reliable simulation of gross primary productivity (GPP) at various spatial and temporal scales is of significance to quantifying the net exchange of carbon between terrestrial ecosystems and the atmosphere. This study aimed to verify the ability of a nonlinear two-leaf model (TL-LUEn), a linear two-leaf model (TL-LUE), and a...
The methods for conducting reductionist ecological science are well known and widely used. In contrast, those used in the synthesis of ecological science (i.e., synthesis science) are still being developed, vary widely, and often lack the rigor of reductionist approaches. This is unfortunate because the synthesis of ecological parts into...
Accurate measurement of the amount and timing of surface runoff at multiple scales is needed to understand fundamental hydrological processes. At the plot-scale (i.e., length scales on the order of 1 to 10 m) current methods for direct measurement of runoff either store the water in a collection vessel, which...
Accurate measurement of the amount and timing of surface runoff at multiple scales is needed to understand fundamental hydrological processes. At the plot scale (i.e., length scales on the order of 1–10 m) current methods for direct measurement of runoff either store the water in a collection vessel, which is...
Submersible pressure transducers have been utilized
for collecting water level data since the early 1960s.
Together with a digital data logger, it is a convenient way
to record water level fluctuations for long-term monitoring.
Despite the wide use of pressure transducers for water level
monitoring, little has been reported regarding...
Submersible pressure transducers have been utilized for collecting water level data since early 1960s. Together with a digital datalogger, it is a convenient way to record water level fluctuations for long-term monitoring. Despite the widely use of pressure transducers for water level monitoring, little has been reported for their accuracy...
Although there is acute concern that insect‐caused tree mortality increases the likelihood or severity of subsequent wildfire, previous studies have been mixed, with findings typically based on stand‐scale simulations or individual events. This study investigates landscape‐ and regional‐scale wildfire likelihood following outbreaks of the two most prevalent native insect pests...
Although there is acute concern that insect‐caused tree mortality increases the likelihood or severity of subsequent wildfire, previous studies have been mixed, with findings typically based on stand‐scale simulations or individual events. This study investigates landscape‐ and regional‐scale wildfire likelihood following outbreaks of the two most prevalent native insect pests...
Error in distributed temperature sensing (DTS) water temperature measurements may be introduced by contact of the fiber optic cable sensor with bed materials (e.g., seafloor, lakebed, streambed). Heat conduction from the bed materials can affect cable temperature and the resulting DTS measurements. In the Middle Fork John Day River, apparent...
Error in Distributed Temperature Sensor (DTS) water temperature measurements may be introduced by contact of the fiber optic cable sensor with bed materials (e.g., seafloor, lakebed, stream bed). Heat conduction from the bed materials can affect cable temperature and the resulting DTS measurements. In the Middle Fork John Day River,...
During the last 3 decades, tagging technology has been used to study different aspects of cetacean ecology. Tags implanted in animal’s blubber, muscle and surrounding tissue have produced successful results, providing information on long-term movements. However, apart from the reports of ‘divots’ (depressions) and swelling at the tag sites in...
The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3...
A large amount of organic carbon is stored in high-latitude soils. A substantial proportion of this carbon stock is vulnerable and may decompose rapidly due to temperature increases that are already greater than the global average. It is therefore crucial to quantify and understand carbon exchange between the atmosphere and...
Large amount of organic carbon is stored in high latitude soils. A substantial proportion of this carbon stock is vulnerable and may decompose rapidly due to temperature increases that are already greater than the global average. It is therefore crucial to quantify and understand carbon exchange between the atmosphere and...
Although there is acute concern that insect-caused tree mortality increases the likelihood or severity of subsequent wildfire, previous studies have been mixed, with findings typically based on stand-scale simulations or individual events. This study investigates landscape- and regional-scale wildfire likelihood following outbreaks of the two most prevalent native insect pests...