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Institution

Oregon State University

EducationCorvallis, Oregon, United States
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 & Climate change. The organization has 28192 authors who have published 64044 publications receiving 2634108 citations. The organization is also known as: Oregon Agricultural College & OSU.


Papers
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Journal ArticleDOI
TL;DR: Glycinebetaine has been studied extensively as a compatible solute because of the availability of GB-accumulating transgenic plants that harbor a variety of transgenes for GB-biosynthetic enzymes.

553 citations

Proceedings Article
03 Dec 2007
TL;DR: The experiments show that learning from instance labels can significantly improve performance of a basic MI learning algorithm in two multiple-instance domains: content-based image retrieval and text classification.
Abstract: We present a framework for active learning in the multiple-instance (MI) setting. In an MI learning problem, instances are naturally organized into bags and it is the bags, instead of individual instances, that are labeled for training. MI learners assume that every instance in a bag labeled negative is actually negative, whereas at least one instance in a bag labeled positive is actually positive. We consider the particular case in which an MI learner is allowed to selectively query unlabeled instances from positive bags. This approach is well motivated in domains in which it is inexpensive to acquire bag labels and possible, but expensive, to acquire instance labels. We describe a method for learning from labels at mixed levels of granularity, and introduce two active query selection strategies motivated by the MI setting. Our experiments show that learning from instance labels can significantly improve performance of a basic MI learning algorithm in two multiple-instance domains: content-based image retrieval and text classification.

551 citations

Journal ArticleDOI
TL;DR: Authigenic magnesian calcite, dolomite, and aragonite are precipitated in the uppermost terrigenous sediments of the Washington/Oregon accretionary prism by subduction-induced dewatering.
Abstract: Authigenic magnesian calcite, dolomite, and aragonite are precipitated in the uppermost terrigenous sediments of the Washington/Oregon accretionary prism by subduction-induced dewatering. These distinctive carbonates are methane-derived and occur at sites of concentrated pore-water expulsion. Unique biologic communities that subsist, at least indirectly, on methane (Suess et al., 1985) are also found at some of these sites. The methane, which is dominantly biogenic, is carried to the uppermost sediments of the prism by fluids and is oxidized by sulfate reducers before being incorporated into a carbonate cement. Carbonate precipitation occurs below the oxic layer, probably no deeper than several centimetres to a few metres below the seabed. Cementation may be induced by three factors: (1) increased carbonate alkalinity resulting from microbial sulfate reduction, (2) decreased σCO 2 solubility resulting from a pressure decrease when the pore water escapes the prism, and/or (3) the addition of Ca 2+ and Mg 2+ ions from sea water near the sediment/water interface. The convergent margin setting engenders precipitation of authigenic carbonates in several ways. Compressive stresses induce anomalously rapid compaction and dewatering rates, and they may cause overpressuring in migrating pore water, thereby delaying precipitation of carbonates until pressure is released near the sediment-water interface. Structural deformation of the accretionary prism creates pathways (such as fault zones), secondary fracture porosity, and dipping permeable layers (often exposed by mass movement) for efficient advection and expulsion of methane-enriched pore water. These characteristic conditions, which lead to the precipitation of methane-derived carbonates, may be found at other convergent margins.

550 citations

Journal ArticleDOI
13 Feb 2015-Science
TL;DR: The challenges of understanding the role protists play in geochemical cycling in the oceans are reviewed, and researchers must bring the conceptual framework of systems biology into bigger “ecosystems biology” models that broadly capture the geochemical activities of interacting plankton networks.
Abstract: BACKGROUND Marine ecosystems are composed of a diverse array of life forms, the majority of which are unicellular—archaea, bacteria, and eukaryotes. The power of these microbes to process carbon, shape Earth’s atmosphere, and fuel marine food webs has been established over the past 40 years. The marine biosphere is responsible for approximately half of global primary production, rivaling that of land plants. Unicellular eukaryotes (protists) are major contributors to this ocean productivity. In addition to photosynthetic growth, protists exhibit a range of other trophic modes, including predation, mixotrophy (a combination of photosynthetic and predatory-based nutrition), parasitism, symbiosis, osmotrophy, and saprotrophy (wherein extracellular enzymes break down organic matter to smaller compounds that are then transported into the cell by osmotrophy). ADVANCES Sensitive field approaches have illuminated the enormous diversity of protistan life (much of it uncultured) and, coupled with activity measurements, are leading to hypotheses about their ecological roles. In parallel, large-scale sequencing projects are providing fundamental advances in knowledge of genome/gene composition, especially among photosynthetic lineages, many of which are complex amalgams derived from multiple endosymbiotic mergers. Marine protists have yielded insight into basic biology, evolution, and molecular machineries that control organismal responses to the environment. These studies reveal tightly controlled signaling and transcriptional regulation as well as responses to limitation of resources such as iron, nitrogen, and vitamins, and offer understanding of animal and plant evolution. With the formulation of better computational approaches, hypotheses about interactions and trophic exchanges are becoming more exact and modelers more assertive at integrating different data types. At the same time, the impacts of climate change are being reported in multiple systems, of which polar environments are the touchstone of change. OUTLOOK Driven by the need to translate the biology of cells into processes at global scales, researchers must bring the conceptual framework of systems biology into bigger “ecosystems biology” models that broadly capture the geochemical activities of interacting plankton networks. Existing data show that protists are major components of marine food webs, but deducing and quantifying their ecosystem linkages and the resulting influences on carbon cycling is difficult. Genome-based functional predictions are complicated by the importance of cellular structures and flexible behaviors in protists, which are inherently more difficult to infer than the biochemical pathways typically studied in prokaryotes. Alongside the plethora of genes of unknown function, manipulable genetic systems are rare for marine protists. The development of genetic systems and gene editing for diverse, ecologically important lineages, as well as innovative tools for preserving microbe-microbe interactions during sampling, for visual observation, and for quantifying biogeochemical transformations, are critical but attainable goals. These must be implemented in both field work and laboratory physiology studies that examine multiple environmental factors. Expanding genome functional predictions to identify the molecular underpinnings of protistan trophic modes and realistically constrain metabolism will position the field to build reliable cell systems biology models and link these to field studies. By factoring in true complexities, we can capture key elements of protistan interactions for assimilation into more predictive global carbon cycle models.

549 citations

Journal ArticleDOI
TL;DR: This work suggests an alternative approach which allows us to explicitly model a joint environmental technology and gauge performance in terms of increased good output and decreased undesirable output by adopting a directional distance function which may be estimated using the usual linear programming techniques employed in DEA.

548 citations


Authors

Showing all 28447 results

NameH-indexPapersCitations
Robert Stone1601756167901
Menachem Elimelech15754795285
Thomas J. Smith1401775113919
Harold A. Mooney135450100404
Jerry M. Melillo13438368894
John F. Thompson132142095894
Thomas N. Williams132114595109
Peter M. Vitousek12735296184
Steven W. Running12635576265
Vincenzo Di Marzo12665960240
J. D. Hansen12297576198
Peter Molnar11844653480
Michael R. Hoffmann10950063474
David Pollard10843839550
David J. Hill107136457746
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
2023105
2022375
20213,156
20203,109
20193,017
20182,987