Oregon State University

About: Oregon State University is a education organization based out in Corvallis, Oregon, United States. It is known for research contribution in the topics: Population & Gene. The organization has 28192 authors who have published 64044 publications receiving 2634108 citations. The organization is also known as: Oregon Agricultural College & OSU.

Collaborative filtering recommender systems

Abstract: One of the potent personalization technologies powering the adaptive web is collaborative filtering. Collaborative filtering (CF) is the process of filtering or evaluating items through the opinions of other people. CF technology brings together the opinions of large interconnected communities on the web, supporting filtering of substantial quantities of data. In this chapter we introduce the core concepts of collaborative filtering, its primary uses for users of the adaptive web, the theory and practice of CF algorithms, and design decisions regarding rating systems and acquisition of ratings. We also discuss how to evaluate CF systems, and the evolution of rich interaction interfaces. We close the chapter with discussions of the challenges of privacy particular to a CF recommendation service and important open research questions in the field.

Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps.

Abstract: Carbonate communities: The activity of anaerobic methane oxidizing microbes facilitates precipitation of vast quantities of authigenic carbonate at methane seeps. Here we demonstrate the significant role of carbonate rocks in promoting diversity by providing unique habitat and food resources for macrofaunal assemblages at seeps on the Costa Rica margin (400–1850 m). The attendant fauna is surprisingly similar to that in rocky intertidal shores, with numerous grazing gastropods (limpets and snails) as dominant taxa. However, the community feeds upon seep-associated microbes. Macrofaunal density, composition, and diversity on carbonates vary as a function of seepage activity, biogenic habitat and location. The macrofaunal community of carbonates at non-seeping (inactive) sites is strongly related to the hydrography (depth, temperature, O2) of overlying water, whereas the fauna at sites of active seepage is not. Densities are highest on active rocks from tubeworm bushes and mussel beds, particularly at the Mound 12 location (1000 m). Species diversity is higher on rocks exposed to active seepage, with multiple species of gastropods and polychaetes dominant, while crustaceans, cnidarians, and ophiuroids were better represented on rocks at inactive sites. Macro-infauna (larger than 0.3 mm) from tube cores taken in nearby seep sediments at comparable depths exhibited densities similar to those on carbonate rocks, but had lower diversity and different taxonomic composition. Seep sediments had higher densities of ampharetid, dorvilleid, hesionid, cirratulid and lacydoniid polychaetes, whereas carbonates had more gastropods, as well as syllid, chrysopetalid and polynoid polychaetes. Stable isotope signatures and metrics: The stable isotope signatures of carbonates were heterogeneous, as were the food sources and nutrition used by the animals. Carbonate δ13Cinorg values (mean = -26.98‰) ranged from -53.3‰ to +10.0‰, and were significantly heavier than carbonate δ13Corg (mean = -33.83‰), which ranged from -74.4‰ to -20.6‰. Invertebrates on carbonates had average δ13C (per rock) = -31.0‰ (range -18.5‰ to -46.5‰) and δ15N = 5.7‰ (range -4.5‰ to +13.4‰). Average δ13C values did not differ between active and inactive sites; carbonate fauna from both settings depend on chemosynthesis-based nutrition. Community metrics reflecting trophic diversity (SEAc, total Hull Area, ranges of δ13C and δ15N) and species packing (mean distance to centroid, nearest neighbor distance) also did not vary as a function of seepage activity or site. However, distinct isotopic signatures were observed among related, co-occurring species of gastropods and polychaetes, reflecting intense microbial resource partitioning. Overall, the substrate and nutritional heterogeneity introduced by authigenic seep carbonates act to promote diverse, uniquely adapted assemblages, even after seepage ceases. The macrofauna in these ecosystems remain largely overlooked in most surveys, but are major contributors to biodiversity of chemosynthetic ecosystems and the deep sea in general.

Reconstructing the early evolution of Fungi using a six-gene phylogeny

Abstract: The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.

Loss of foundation species: consequences for the structure and dynamics of forested ecosystems

Abstract: In many forested ecosystems, the architecture and functional ecology of certain tree species define forest structure and their species-specific traits control ecosystem dynamics. Such foundation tree species are declining throughout the world due to introductions and outbreaks of pests and pathogens, selective removal of individual taxa, and over-harvesting. Through a series of case studies, we show that the loss of foundation tree species changes the local environment on which a variety of other species depend; how this disrupts fundamental ecosystem processes, including rates of decomposition, nutrient fluxes, carbon sequestration, and energy flow; and dramatically alters the dynamics of associated aquatic ecosystems. Forests in which dynamics are controlled by one or a few foundation species appear to be dominated by a small number of strong interactions and may be highly susceptible to alternating between stable states following even small perturbations. The ongoing decline of many foundation species provides a set of important, albeit unfortunate, opportunities to develop the research tools, models, and metrics needed to identify foundation species, anticipate the cascade of immediate, short- and long-term changes in ecosystem structure and function that will follow from their loss, and provide options for remedial conservation and management.

Climatological mean and decadal change in surface ocean pCO2, and net sea–air CO2 flux over the global oceans

Abstract: A climatological mean distribution for the surface water pCO2 over the global oceans in non-El Nino conditions has been constructed with spatial resolution of 4° (latitude) ×5° (longitude) for a reference year 2000 based upon about 3 million measurements of surface water pCO2 obtained from 1970 to 2007. The database used for this study is about 3 times larger than the 0.94 million used for our earlier paper [Takahashi et al., 2002. Global sea–air CO2 flux based on climatological surface ocean pCO2, and seasonal biological and temperature effects. Deep-Sea Res. II, 49, 1601–1622]. A time-trend analysis using deseasonalized surface water pCO2 data in portions of the North Atlantic, North and South Pacific and Southern Oceans (which cover about 27% of the global ocean areas) indicates that the surface water pCO2 over these oceanic areas has increased on average at a mean rate of 1.5 μatm y−1 with basin-specific rates varying between 1.2±0.5 and 2.1±0.4 μatm y−1. A global ocean database for a single reference year 2000 is assembled using this mean rate for correcting observations made in different years to the reference year. The observations made during El Nino periods in the equatorial Pacific and those made in coastal zones are excluded from the database. Seasonal changes in the surface water pCO2 and the sea-air pCO2 difference over four climatic zones in the Atlantic, Pacific, Indian and Southern Oceans are presented. Over the Southern Ocean seasonal ice zone, the seasonality is complex. Although it cannot be thoroughly documented due to the limited extent of observations, seasonal changes in pCO2 are approximated by using the data for under-ice waters during austral winter and those for the marginal ice and ice-free zones. The net air–sea CO2 flux is estimated using the sea–air pCO2 difference and the air–sea gas transfer rate that is parameterized as a function of (wind speed)2 with a scaling factor of 0.26. This is estimated by inverting the bomb 14C data using Ocean General Circulation models and the 1979–2005 NCEP-DOE AMIP-II Reanalysis (R-2) wind speed data. The equatorial Pacific (14°N–14°S) is the major source for atmospheric CO2, emitting about +0.48 Pg-C y−1, and the temperate oceans between 14° and 50° in the both hemispheres are the major sink zones with an uptake flux of −0.70 Pg-C y−1 for the northern and −1.05 Pg-C y−1 for the southern zone. The high-latitude North Atlantic, including the Nordic Seas and portion of the Arctic Sea, is the most intense CO2 sink area on the basis of per unit area, with a mean of −2.5 tons-C month−1 km−2. This is due to the combination of the low pCO2 in seawater and high gas exchange rates. In the ice-free zone of the Southern Ocean (50°–62°S), the mean annual flux is small (−0.06 Pg-C y−1) because of a cancellation of the summer uptake CO2 flux with the winter release of CO2 caused by deepwater upwelling. The annual mean for the contemporary net CO2 uptake flux over the global oceans is estimated to be −1.6±0.9 Pg-C y−1, which includes an undersampling correction to the direct estimate of −1.4±0.7 Pg-C y−1. Taking the pre-industrial steady-state ocean source of 0.4±0.2 Pg-C y−1 into account, the total ocean uptake flux including the anthropogenic CO2 is estimated to be −2.0±1.0 Pg-C y−1 in 2000.