The Forest Elevation Snow Transect (ForEST) project is a paired site elevational snow study. It is designed to measure how snow accumulates and ablates under different forest structures across an elevation range. The ForEST project has been ongoing since the winter of 2011-2012 within the McKenzie River Basin of the...
Background: Next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. Despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated...
In an era of political polarization, the possibility of the legalization of recreational marijuana has become a popular topic of controversy. While a few states have passed general legislation, the vast majority still prohibit recreational use. In the interest of understanding why there are so many differences between the states,...
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...
The genetic aspects of population health are critical, but frequently difficult to assess. Of concern has been the genetic constitution of Scandinavian wolves (Canis lupus), which represent an important case in conservation. We examined the incidence of different congenital anomalies for 171 Scandinavian wolves, including the immigrant founder female, born...
Severe droughts occurred in the western United States during recent decades, and continued human greenhouse gas emissions are expected to exacerbate warming and drying in this region. We investigated the role of water availability in shaping forest carbon cycling and morphological traits in the eastern Cascade Mountains, Oregon, focusing on...
Severe droughts occurred in the western United States during recent decades, and continued human greenhouse gas emissions are expected to exacerbate warming and drying in this region. We investigated the role of water availability in shaping forest carbon cycling and morphological traits in the eastern Cascade Mountains, Oregon, focusing on...
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...
Background. The US commercial fishing industry is hazardous, as measured by mortality data. However, research on non-fatal injuries is limited. Non-fatal injuries constitute the majority of occupational injuries and can result in workers' lowered productivity and wages, lost quality of life, and disability. In the United States, a Work Process...
Because animal studies are labor intensive, predictive equations are used extensively for calculating metabolizable energy (ME) concentrations of dog and cat pet foods. The objective of this retrospective review of digestibility studies, which were conducted over a 7-year period and based upon Association of American Feed Control Officials (AAFCO) feeding...
Data management plans (DMPs) are a rich source of information about researchers and their research data management (RDM) knowledge, capabilities, and practices. Systematic analysis of DMPs can uncover important insights about local RDM needs, which can then inform the development or expansion of library RDM services. As part of an...
An analysis of Data Management Plans (DMPs) can offer insight into local data management practices. The IMLS- funded “Data management plans as A Research Tool (DART) Project” has developed an analytic rubric to assist librarians in facilitating and standardizing the review of DMPs. This panel will consist of data specialists...
To provide research data management (RDM) support services, libraries need to develop expertise in data curation and management within the library. Many academic libraries are reorganizing to initiate RDM service structures, but may lack staff expertise in this area. Funding agencies increasingly require a data management plan (DMP) with funding...
The World Health Organization defines food security as “all people at all times have access to sufficient, safe, nutritious food to maintain a healthy and active life.” The reality is that one in six Americans are not food secure, even though the US produces enough food to feed its national...
Funding agencies increasingly require a data management plan (DMP) with funding proposals, which describe how data generated in the proposed work will be managed, preserved and shared. Data management plans are a rich source of information about an institution’s researchers and their research data management (RDM) knowledge, capabilities, and needs....
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...
Ambient ultraviolet-B radiation can harm amphibian eggs, larvae and adults. However, some amphibians avoid UV-B radiation when given the opportunity. The strawberry poison dart frog, Oophaga pumilio, is diurnal and males vocalize throughout the day in light gaps under forest canopies that expose them to solar radiation. Previous studies have...
Heliotropium foliatum and Tournefortia humilis are transferred to Euploca Nutt. respectively as Euploca foliata comb. n. and Euploca humilis comb. n. A collection from Guyana has been recently identified as Euploca humistrata, a species previously considered a Brazilian endemic. A collection from French Guiana documents for the first time the...
This paper explores Jazz music during the Cold War. During the Cold War the U.S. went through a process of becoming more explicitly religious, identifying specifically a Judeo-Christian country. Particularly through foreign policy, the separation between church and state became less and less clear to the point where it seemed...
In a wireless sensor network, sensor nodes are deployed in an ad hoc fashion and they deliver data packets using multihop transmission. However, transmission failures occur frequently in the multihop transmission over wireless media. Thus, a loss recovery mechanism is required to provide end-to-end reliability. In addition, because the sensor...
We develop an approach for measuring in-well fluid velocities using point electrical heating combined with spatially and temporally continuous temperature monitoring using distributed temperature sensing (DTS). The method uses a point heater to warm a discrete volume of water. The rate of advection of this plume, once the heating is...
The hepatic α-tocopherol transfer protein (TTP) is required for optimal α-tocopherol bioavailability in humans; mutations in the human TTPA gene result in the heritable disorder ataxia with vitamin E deficiency (AVED, OMIM #277460). TTP is also expressed in mammalian uterine and placental cells and in the human embryonic yolk-sac, underscoring...
We present the WD2014 chronology for the upper part (0–2850 m; 31.2 ka BP) of the West Antarctic Ice Sheet (WAIS) Divide (WD) ice core. The chronology is based on counting of annual layers observed in the chemical, dust and electrical conductivity records. These layers are caused by seasonal changes...
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...
The VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx) was an international field program designed to make observations of poorly understood but critical components of the coupled climate system of the southeast Pacific. This region is characterized by strong coastal upwelling, the coolest SSTs in the tropical belt, and is home to...
Biomass burning impacts vegetation dynamics, biogeochemical cycling, atmospheric chemistry, and climate, with sometimes deleterious socio-economic impacts. Under future climate projections it is often expected that the risk of wildfires will increase. Our ability to predict the magnitude and geographic pattern of future fire impacts rests on our ability to model...
With the recent advent of commercial laser absorption spectrometers, field studies measuring stable isotope ratios of hydrogen and oxygen in water vapor have proliferated. These pioneering analyses have provided invaluable feedback about best strategies for optimizing instrumental accuracy, yet questions still remain about instrument performance and calibration approaches for multi-year...
With the recent advent of commercial laser absorption spectrometers, field studies measuring stable isotope ratios of hydrogen and oxygen in water vapor have proliferated. These pioneering analyses have provided invaluable feedback about best strategies for optimizing instrumental accuracy, yet questions still remain about instrument performance and calibration approaches for multi-year...
Managing for species using current weather patterns fails to incorporate the uncertainty associated with future climatic conditions; without incorporating potential changes in climate into conservation strategies, management and conservation efforts may fall short or waste valuable resources. Understanding the effects of climate change on species in the Great Plains of...
Phenology is an integrative science that comprises the study of recurring biological activities or events. In an era of rapidly changing climate, the relationship between the timing of those events and environmental cues such as temperature, snowmelt, water availability, or day length are of particular interest. This article provides an...
Plants are constantly exposed to a large and diverse array of microbes; however, most plants are immune to the majority of potential invaders and susceptible to only a small subset of pathogens. The cytoskeleton comprises a dynamic intracellular framework that responds rapidly to biotic stresses and supports numerous fundamental cellular...
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...
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...
Previous game-theoretic studies of vaccination behavior typically have often assumed that populations are homogeneously mixed and that individuals are fully rational. In reality, there is heterogeneity in the number of contacts per individual, and individuals tend to imitate others who appear to have adopted successful strategies. Here, we use network-based...
The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of...
Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely...
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...
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...
Endogenous small interfering RNAs (siRNAs) are a class of naturally occuring regulatory RNAs found in fungi, plants, and animals. Some endogenous siRNAs are required to silence transposons or function in chromosome segregation; however, the specific roles of most endogenous siRNAs are unclear. The helicase gene eri-6/7 was identified in the...
Patterns of β diversity are commonly used to infer underlying ecological processes. In this study, we examined the effect of spatial configuration of habitat capacity on different metrics of β diversity, i.e., β diversity measured as turnover and as variation. For β diversity as turnover, a monotonic species spatial turnover...
A novel role of the dihydroorotatedehydrogenase (DHODH) inhibitor leflunomide as a potential anti-melanoma therapy was recently reported (Nature 471: 518-22, 2011). We previously reported that leflunomide strongly activates the transcriptional activity of the Aryl Hydrocarbon Receptor (AhR). We therefore tested whether the AhR regulates the anti-proliferative effects of leflunomide in...
Seasonal polyphenism demonstrates an organism's ability to respond to predictable environmental variation with alternative phenotypes, each presumably better suited to its respective environment. However, the molecular mechanisms linking environmental variation to alternative phenotypes via shifts in development remain relatively unknown. Here we investigate temporal gene expression variation in the seasonally...
Extracting benthic oxygen fluxes from eddy covariance time series measured in the presence of surface gravity waves requires careful consideration of the temporal alignment of the vertical velocity and the oxygen concentration. Using a model based on linear wave theory and measured eddy covariance data, we show that a substantial...
Extracting benthic oxygen fluxes from eddy covariance time series measured in the presence of surface gravity waves requires careful consideration of the temporal alignment of the vertical velocity and the oxygen concentration. Using a model based on linear wave theory and measured eddy covariance data, we show that a substantial...
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,...
Remains of parasites in vertebrates are rare from the Mesozoic and Paleozoic. Once most parasites that live in - or pass through - the gastrointestinal tract of vertebrates, fossil feces (coprolites) or even intestinal contents (enterolites) can eventually preserve their remains. Here we announce the discovery of a spiral shark...
Background: Barn Swallows (Hirundo rustica) breed almost exclusively in the Northern Hemisphere. However, since the early 1980's, a small disjunct breeding population has become established in eastern Argentina, presumably by birds previously derived from those breeding in North America. Currently, it is unknown where these individuals go following breeding and...
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...
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....
Understanding charge transfer in organic semiconductors is important for developing devices like organic light emitting diodes and flexible electronics. Optical tweezers have been used in many disciplines for trapping, manipulating, and analyzing microscopic objects such as microspheres, micro-organisms, and other colloidal particles. Using optical tweezers, studies have measured the average...
Spawning salmon create patches of disturbance through redd digging which can reduce macroinvertebrate abundance and biomass in spawning habitat. We asked whether displaced invertebrates use non-spawning habitats as refugia in streams. Our study explored how the spatial and temporal distribution of macroinvertebrates changed during a pink salmon (Oncorhynchus gorbuscha) spawning...
As a result of warming temperatures and subsequently declining snowpacks, forest fires are increasing in frequency, intensity and extent across the western USA. In turn, forest fire disturbance affects patterns of snow accumulation and ablation by reducing canopy interception and modifying the snowpack energy balance. Following a 2011, high severity...
Dynein is a motor protein which transports cargo along tracks inside the cell. Like related motor proteins kinesin and myosin, dynein uses cellular energy to take steps with its two foot domains. Unlike kinesin or myosin, dynein’s stepping pattern is highly varied: it can take steps between zero and 60nm...
We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate interactions. (2) Neofunctionalization, in which a mutation leads to a new interaction with some other protein. Since many...
Rangelands are significant providers of ecosystem services in agroecosystems world‐wide. Yet few studies have investigated how different intensities of livestock grazing impact one important provider of these ecosystem services—native bees. We conducted the first large‐scale manipulative study on the effect of a gradient of livestock grazing intensities on native bees...
Selfish DNA poses a significant challenge to genome stability and organismal fitness in diverse eukaryotic lineages. Although selfish mitochondrial DNA (mtDNA) has known associations with cytoplasmic male sterility in numerous gynodioecious plant species and is manifested as petite mutants in experimental yeast lab populations, examples of selfish mtDNA in animals...
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...
Background: Ctip2 is crucial for epidermal homeostasis and protective barrier formation in developing mouse embryos. Selective ablation of Ctip2 in epidermis leads to increased transepidermal water loss (TEWL), impaired epidermal proliferation, terminal differentiation, as well as altered lipid composition during development. However, little is known about the role of Ctip2...
Hydroacoustic data document the occurrence of 5 flare clusters and several single flares from which bubbles rise through the entire water column from an active seep site at 40 m water depth in the central North Sea. We investigated the difference in dissolved methane distributions along a 6 km transect...
We investigated dissolved methane distributions along a 6 km transect crossing active seep sites at 40 m water depth in the central North Sea. These investigations were done under conditions of thermal stratification in summer (July 2013) and homogenous water column in winter (January 2014). Dissolved methane accumulated below the...
Students often struggle with the appropriate use of scholarly sources. Underlying this skill set are complex concepts: scholarship is a conversation, the scholarly community has its own unique perspectives and biases, not all scholarly information is equally credible or appropriate for all situations. This session will address how we discuss...
Mild mutations in BRCA2 (FANCD1) cause Fanconi anemia (FA) when homozygous, while severe mutations cause common cancers including breast, ovarian, and prostate cancers when heterozygous. Here we report a zebrafish brca2 insertional mutant that shares phenotypes with human patients and identifies a novel brca2 function in oogenesis. Experiments showed that...
Nitrogen-fixing lichens (cyanolichens) are an important source of nitrogen (N) in Pacific Northwest forests, but limitation of lichen growth by elements essential for N fixation is poorly understood. To investigate how nutrient limitation may affect cyanolichen growth rates, we fertilized a tripartite cyanobacterial lichen (Lobaria pulmonaria) and a green algal...
The frequency of moderate to heavy rainfall events is projected to change in response to global warming. Here we show that these hydrologic changes may have a profound effect on mosquito population dynamics and rates of mosquito-borne disease transmission. We develop a simple model, which treats the mosquito reproductive cycle...
Cells of the ventrolateral dermomyotome delaminate and migrate into the limb buds where they give rise to all muscles of the limbs. The migratory cells proliferate and form myoblasts, which withdraw from the cell cycle to become terminally differentiated myocytes. The myogenic lineage colonizes pre-patterned regions to form muscle anlagen...
Despite its importance to biodiversity and ecosystem function, patterns and drivers of regional scale variation in forest structure and development are poorly understood. We characterize structural variation, create a hierarchical classification of forest structure, and develop an empirically based framework for conceptualizing structural development from 11,091 plots across 25 million...
Polar ecosystems are sensitive to climate forcing, and we often lack baselines to evaluate changes. Here we report a nearly 50-year study in which a sudden shift in the population dynamics of an ecologically important, structure-forming hexactinellid sponge, Anoxycalyx joubini was observed. This is the largest Antarctic sponge, with individuals...
Sand dunes provide coastal communities critical protection from flooding and erosion, as well as a habitat for a range of species- some threatened or endangered. As such, it is of importance to develop a quantitative understanding of the processes through which these systems evolve at a variety of temporal and...
Temperate nearshore reefs along the Pacific coast of North America are highly valuable to commercial and recreational fisheries yet comprise a small fraction of the seabed. Monitoring fisheries resources in this region is difficult; high-relief structural complexity and adverse sea conditions have led to a paucity of information on temperate...
Many Gram-negative bacteria use the type II secretion (T2S) pathway to deliver proteins that contribute to disease in humans, animals, and plants. Vibrio cholerae, the causative agent of the life-threatening diarrheal disease cholera, utilizes the T2S system for translocation of at least 19 proteins, including the large hexameric protein cholera...
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 endangered western stock of the Steller sea lion (Eumetopias jubatus) - the largest of the eared seals - has declined by 80% from population levels encountered four decades ago. Current overall trends from the Gulf of Alaska to the Aleutian Islands appear neutral with strong regional heterogeneities. A published...
Fibre optic distributed temperature sensing (DTS) is widely applied in Earth sciences. Many applications require a spatial resolution higher than that provided by the DTS instrument. Measurements at these higher resolutions can be achieved with a fibre optic cable helically wrapped on a cylinder. The effect of the probe construction,...
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...
Chmp2b is closely related to Vps2, a key component of the yeast protein complex that creates the intralumenal vesicles of multivesicular bodies. Dominant negative mutations in Chmp2b cause autophagosome accumulation and neurodegenerative disease. Loss of Chmp2b causes failure of dendritic spine maturation in cultured neurons. The homeobox gene Lbx1 plays...
Objective: This study examines obstetrician/gynecologists and family medicine physicians' reported care patterns, attitudes and beliefs and predictors of adherence to postpartum testing in women with a history of gestational diabetes mellitus.
Research Design and Methods: In November-December 2005, a mailed survey went to a random, cross-sectional sample of 683 Oregon...
The phylogeny of ground beetles of supertribe Trechitae is inferred using DNA sequences of genes that code for 28S ribosomal RNA, 18S ribosomal RNA, and wingless. Within the outgroups, austral psydrines are inferred to be monophyletic, and separate from the three genera of true Psydrina (Psydrus, Nomius, Laccocenus); the austral...
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...
Ontogenetic changes in resource use often delimit transitions between life stages. Ecological and individual factors can cause variation in the timing and consistency of these transitions, ultimately affecting community and population dynamics through changes in growth and survival. Therefore, it is important to document and understand behavioral and life history...
Sea-level and ice-sheet databases have driven numerous advances in understanding the Earth system. We describe the challenges and offer best strategies that can be adopted to build self-consistent and standardised databases of geological and geochemical information used to archive palaeo-sea-levels and palaeo-ice-sheets. There are three phases in the development of...
OSU Libraries & Press initiated a pilot Open Access Fund in April 2015 that paid for open access article processing charges for OSU authors who met award criteria. The purpose of the fund was to heighten the visibility and accessibility of OSU scholarship and to support faculty and their student...
The Strategic Agenda for Research Data Services will guide the development of data services at OSU Libraries from January 2013 to June 2014. The Strategic Agenda is informed by best practices in data management at peer universities. Major elements of the Strategic Agenda include an instructional program on data management,...
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...
For ethical and logistical reasons, population-genetic studies of parasites often rely on the non-invasive sampling of offspring shed from their definitive hosts. However, if the sampled offspring are naturally derived from a small number of parents, then the strong family structure can result in biased population-level estimates of genetic parameters,...
Oregon State University Libraries and Press (OSULP) has a long history of digitizing, creating, and curating digital objects. These objects include digital representations of unique items from the Special Collections and Archives Research Center (SCARC) such as the photographs, maps, manuscripts, audio, and video housed in Oregon Digital. The ScholarsArchive@OSU...
We sought to characterize the distribution of juvenile walleye pollock Theragra chalcogramma in an area of intense predator-prey interactions and to describe habitat features that lead to their observed distributions. The distribution of juvenile walleye pollock around the Pribilof Islands in the southeastern Bering Sea in 2008 and 2009 was...
Correction
10 Aug 2012: Klinck H, Mellinger DK, Klinck K, Bogue NM, Luby JC, et al. (2012) Correction: Near-Real-Time Acoustic Monitoring of Beaked Whales and Other Cetaceans Using a Seaglider™. PLOS ONE 7(8): 10.1371/annotation/57ad0b82-87c4-472d-b90b-b9c6f84947f8.
