Showing papers by "Oregon State University published in 2002"

Efficient Inverse Modeling of Barotropic Ocean Tides

Abstract: A computationally efficient relocatable system for generalized inverse (GI) modeling of barotropic ocean tides is described. The GI penalty functional is minimized using a representer method, which requires repeated solution of the forward and adjoint linearized shallow water equations (SWEs). To make representer computations efficient, the SWEs are solved in the frequency domain by factoring the coefficient matrix for a finite-difference discretization of the second-order wave equation in elevation. Once this matrix is factored representers can be calculated rapidly. By retaining the first-order SWE system (defined in terms of both elevations and currents) in the definition of the discretized GI penalty functional, complete generality in the choice of dynamical error covariances is retained. This allows rational assumptions about errors in the SWE, with soft momentum balance constraints (e.g., to account for inaccurate parameterization of dissipation), but holds mass conservation constraints. Wh...

Cleavage of Scarecrow-like mRNA Targets Directed by a Class of Arabidopsis miRNA

Abstract: Micro-RNAs (miRNAs) are regulatory molecules that mediate effects by interacting with messenger RNA (mRNA) targets. Here we show that Arabidopsis thaliana miRNA 39 (also known as miR171), a 21-ribonucleotide species that accumulates predominantly in inflorescence tissues, is produced from an intergenic region in chromosome III and functionally interacts with mRNA targets encoding several members of the Scarecrow-like (SCL) family of putative transcription factors. miRNA 39 is complementary to an internal region of three SCL mRNAs. The interaction results in specific cleavage of target mRNA within the region of complementarity, indicating that this class of miRNA functions like small interfering RNA associated with RNA silencing to guide sequence-specific cleavage in a developmentally controlled manner.

Views of nature of science questionnaire: Toward valid and meaningful assessment of learners' conceptions of nature of science

Abstract: Helping students develop informed views of nature of science (NOS) has been and continues to be a central goal for kindergarten through Grade 12 (K–12) science education. Since the early 1960s, major efforts have been undertaken to enhance K–12 students and science teachers' NOS views. However, the crucial component of assessing learners' NOS views remains an issue in research on NOS. This article aims to (a) trace the development of a new open-ended instrument, the Views of Nature of Science Questionnaire (VNOS), which in conjunction with individual interviews aims to provide meaningful assessments of learners' NOS views; (b) outline the NOS framework that underlies the development of the VNOS; (c) present evidence regarding the validity of the VNOS; (d) elucidate the use of the VNOS and associated interviews, and the range of NOS aspects that it aims to assess; and (e) discuss the usefulness of rich descriptive NOS profiles that the VNOS provides in research related to teaching and learning about NOS. The VNOS comes in response to some calls within the science education community to go back to developing standardized forced-choice paper and pencil NOS assessment instruments designed for mass administrations to large samples. We believe that these calls ignore much of what was learned from research on teaching and learning about NOS over the past 30 years. The present state of this line of research necessitates a focus on individual classroom interventions aimed at enhancing learners' NOS views, rather than on mass assessments aimed at describing or evaluating students' beliefs. © 2002 Wiley Periodicals, Inc. J Res Sci Teach 39: 497–521, 2002

Anxiety-Related Attentional Biases and Their Regulation by Attentional Control

Abstract: This study examined the role of self-reported attentional control in regulating attentional biases related to trait anxiety. Simple detection targets were preceded by cues labeling potential target locations as threatening (likely to result in negative feedback) or safe (likely to result in positive feedback). Trait anxious participants showed an early attentional bias favoring the threatening location 250 ms after the cue and a late bias favoring the safe location 500 ms after the cue. The anxiety-related threat bias was moderated by attentional control at the 500-ms delay: Anxious participants with poor attentional control still showed the threat bias, whereas those with good control were better able to shift from the threatening location. Thus, skilled control of voluntary attention may allow anxious persons to limit the impact of threatening information.

A knowledge-based approach to the statistical mapping of climate

Abstract: The demand for spatial climate data in digital form has risen dramatically in recent years. In response to this need, a variety of statistical techniques have been used to facilitate the pro- duction of GIS-compatible climate maps. However, observational data are often too sparse and unrepresentative to directly support the creation of high-quality climate maps and data sets that truly represent the current state of knowledge. An effective approach is to use the wealth of expert knowl- edge on the spatial patterns of climate and their relationships with geographic features, termed 'geospatial climatology', to help enhance, control, and parameterize a statistical technique. Described here is a dynamic knowledge-based framework that allows for the effective accumulation, application, and refinement of climatic knowledge, as expressed in a statistical regression model known as PRISM (parameter-elevation regressions on independent slopes model). The ultimate goal is to develop an expert system capable of reproducing the process a knowledgeable climatologist would use to create high-quality climate maps, with the added benefits of consistency and repeata- bility. However, knowledge must first be accumulated and evaluated through an ongoing process of model application; development of knowledge prototypes, parameters and parameter settings; test- ing; evaluation; and modification. This paper describes the current state of a knowledge-based framework for climate mapping and presents specific algorithms from PRISM to demonstrate how this framework is applied and refined to accommodate difficult climate mapping situations. A weighted climate-elevation regression function acknowledges the dominant influence of elevation on climate. Climate stations are assigned weights that account for other climatically important factors besides elevation. Aspect and topographic exposure, which affect climate at a variety of scales, from hill slope to windward and leeward sides of mountain ranges, are simulated by dividing the terrain into topographic facets. A coastal proximity measure is used to account for sharp climatic gradients near coastlines. A 2-layer model structure divides the atmosphere into a lower boundary layer and an upper free atmosphere layer, allowing the simulation of temperature inversions, as well as mid-slope precipitation maxima. The effectiveness of various terrain configurations at producing orographic precipitation enhancement is also estimated. Climate mapping examples are presented.

SAR11 clade dominates ocean surface bacterioplankton communities

Abstract: The most abundant class of bacterial ribosomal RNA genes detected in seawater DNA by gene cloning belongs to SAR11-an alpha-proteobacterial clade. Other than indications of their prevalence in seawater, little is known about these organisms. Here we report quantitative measurements of the cellular abundance of the SAR11 clade in northwestern Sargasso Sea waters to 3,000 m and in Oregon coastal surface waters. On average, the SAR11 clade accounts for a third of the cells present in surface waters and nearly a fifth of the cells present in the mesopelagic zone. In some regions, members of the SAR11 clade represent as much as 50% of the total surface microbial community and 25% of the subeuphotic microbial community. By extrapolation, we estimate that globally there are 2.4 x 10(28) SAR11 cells in the oceans, half of which are located in the euphotic zone. Although the biogeochemical role of the SAR11 clade remains uncertain, these data support the conclusion that this microbial group is among the most successful organisms on Earth.

Endogenous and Silencing-Associated Small RNAs in Plants

Abstract: A large set of endogenous small RNAs of predominantly 21 to 24 nucleotides was identified in Arabidopsis. These small RNAs resembled micro-RNAs from animals and were similar in size to small interfering RNAs that accumulated during RNA silencing triggered by multiple types of inducers. Among the 125 sequences identified, the vast majority (90%) arose from intergenic regions, although small RNAs corresponding to predicted protein-coding genes, transposon-like sequences, and a structural RNA gene also were identified. Evidence consistent with the derivation of small RNAs of both polarities, and from highly base-paired precursors, was obtained through the identification and analysis of clusters of small RNA loci. The accumulation of specific small RNAs was regulated developmentally. We propose that Arabidopsis small RNAs participate in a wide range of post-transcriptional and epigenetic events.

Equations for potential annual direct incident radiation and heat load

Abstract: Estimation of potential annual direct incident radia- tion has traditionally required numerical integration with simu- lation models. As an alternative, we present convenient equa- tions for use in spreadsheet, GIS, and database applications. Input variables are latitude, slope, and aspect. The equations apply to 0-60∞ north latitude, slopes from 0-90∞, and all aspects. By transforming aspect, the equations can also be applied as an index of heat load, symmetrical about a northeast to southwest axis.

Cultivation of the ubiquitous SAR11 marine bacterioplankton clade

Abstract: The alpha-proteobacterial lineage that contains SAR11 and related ribosomal RNA gene clones was among the first groups of organisms to be identified when cultivation-independent approaches based on rRNA gene cloning and sequencing were applied to survey microbial diversity in natural ecosystems. This group accounts for 26% of all ribosomal RNA genes that have been identified in sea water and has been found in nearly every pelagic marine bacterioplankton community studied by these methods. The SAR11 clade represents a pervasive problem in microbiology: despite its ubiquity, it has defied cultivation efforts. Genetic evidence suggests that diverse uncultivated microbial taxa dominate most natural ecosystems, which has prompted widespread efforts to elucidate the geochemical activities of these organisms without the benefit of cultures for study. Here we report the isolation of representatives of the SAR11 clade. Eighteen cultures were initially obtained by means of high-throughput procedures for isolating cell cultures through the dilution of natural microbial communities into very low nutrient media. Eleven of these cultures have been successfully passaged and cryopreserved for future study. The volume of these cells, about 0.01 micro m(3), places them among the smallest free-living cells in culture.

Test case prioritization: a family of empirical studies

Abstract: To reduce the cost of regression testing, software testers may prioritize their test cases so that those which are more important, by some measure, are run earlier in the regression testing process. One potential goal of such prioritization is to increase a test suite's rate of fault detection. Previous work reported results of studies that showed that prioritization techniques can significantly improve rate of fault detection. Those studies, however, raised several additional questions: 1) Can prioritization techniques be effective when targeted at specific modified versions; 2) what trade-offs exist between fine granularity and coarse granularity prioritization techniques; 3) can the incorporation of measures of fault proneness into prioritization techniques improve their effectiveness? To address these questions, we have performed several new studies in which we empirically compared prioritization techniques using both controlled experiments and case studies.

The role of the thermohaline circulation in abrupt climate change

Abstract: The possibility of a reduced Atlantic thermohaline circulation in response to increases in greenhouse-gas concentrations has been demonstrated in a number of simulations with general circulation models of the coupled ocean-atmosphere system. But it remains difficult to assess the likelihood of future changes in the thermohaline circulation, mainly owing to poorly constrained model parameterizations and uncertainties in the response of the climate system to greenhouse warming. Analyses of past abrupt climate changes help to solve these problems. Data and models both suggest that abrupt climate change during the last glaciation originated through changes in the Atlantic thermohaline circulation in response to small changes in the hydrological cycle. Atmospheric and oceanic responses to these changes were then transmitted globally through a number of feedbacks. The palaeoclimate data and the model results also indicate that the stability of the thermohaline circulation depends on the mean climate state.

High-Throughput Methods for Culturing Microorganisms in Very-Low-Nutrient Media Yield Diverse New Marine Isolates

Abstract: Microbial diversity studies based on the cloning and sequencing of DNA from nature support the conclusion that only a fraction of the microbial diversity is currently represented in culture collections. Out of over 40 known prokaryotic phyla, only half have cultured representatives. In an effort to culture the uncultured phylotypes from oligotrophic marine ecosystems, we developed high-throughput culturing procedures that utilize the concept of extinction culturing to isolate cultures in small volumes of low-nutrient media. In these experiments, marine bacteria were isolated and cultivated at in situ substrate concentrations—typically 3 orders of magnitude less than common laboratory media. Microtiter plates and a newly developed procedure for making cell arrays were employed to raise the throughput rate and lower detection sensitivity, permitting cell enumeration from 200-μl aliquots of cultures with densities as low as 103 cells/ml. Approximately 2,500 extinction cultures from 11 separate samplings of marine bacterioplankton were screened over the course of 3 years. Up to 14% of the cells collected from coastal seawater were cultured by this method, which was 14- to 1,400-fold higher than the numbers obtained by traditional microbiological culturing techniques. Among the microorganisms cultured were four unique cell lineages that belong to previously uncultured or undescribed marine Proteobacteria clades known from environmental gene cloning studies. These cultures are related to the clades SAR11 (α subclass), OM43 (β subclass), SAR92 (γ subclass), and OM60/OM241 (γ subclass). This method proved successful for the cultivation of previously uncultured marine bacterioplankton that have consistently been found in marine clone libraries.

Significance of predation by protists in aquatic microbial food webs.

Abstract: Predation in aquatic microbial food webs is dominated by phagotrophic protists, yet these microorganisms are still understudied compared to bacteria and phytoplankton. In pelagic ecosystems, predaceous protists are ubiquitous, range in size from 2 µm flagellates to >100 µm ciliates and dinoflagellates, and exhibit a wide array of feeding strategies. Their trophic states run the gamut from strictly phagotrophic, to mixotrophic: partly autotrophic and partly phagotrophic, to primarily autotrophic but capable of phagotrophy. Protists are a major source of mortality for both heterotrophic and autotrophic bacteria. They compete with herbivorous meso- and macro-zooplankton for all size classes of phytoplankton. Protist grazing may affect the rate of organic sinking flux from the euphotic zone. Protist excretions are an important source of remineralized nutrients, and of colloidal and dissolved trace metals such as iron, in aquatic systems. Work on predation by protists is being facilitated by methodological advances, e.g., molecular genetic analysis of protistan diversity and application of flow cytometry to study population growth and feeding rates. Examples of new research areas are studies of impact of protistan predation on the community structure of prey assemblages and of chemical communication between predator and prey in microbial food webs.

Dinitrogen fixation in the world's oceans

Abstract: The surface water of the marine environment has traditionally been viewed as a nitrogen (N) limited habitat, and this has guided the development of conceptual biogeochemical models focusing largely on the reservoir of nitrate as the critical source of N to sustain primary productivity. However, selected groups of Bacteria, including cyanobacteria, and Archaea can utilize dinitrogen (N2) as an alternative N source. In the marine environment, these microorganisms can have profound effects on net community production processes and can impact the coupling of C-N-P cycles as well as the net oceanic sequestration of atmospheric carbon dioxide. As one component of an integrated ‘Nitrogen Transport and Transformations’ project, we have begun to re-assess our understanding of (1) the biotic sources and rates of N2 fixation in the world’s oceans, (2) the major controls on rates of oceanic N2 fixation, (3) the significance of this N2 fixation for the global carbon cycle and (4) the role of human activities in the alteration of oceanic N2 fixation. Preliminary results indicate that rates of N2 fixation, especially in subtropical and tropical open ocean habitats, have a major role in the global marine N budget. Iron (Fe) bioavailability appears to be an important control and is, therefore, critical in extrapolation to global rates of N2 fixation. Anthropogenic perturbations may alter N2 fixation in coastal environments through habitat destruction and eutrophication, and open ocean N2 fixation may be enhanced by warming and increased stratification of the upper water column. Global anthropogenic and climatic changes may also affect N2 fixation rates, for example by altering dust inputs (i.e. Fe) or by expansion of subtropical boundaries. Some recent estimates of global ocean N2 fixation are in the range of 100−200 Tg N (1−2 × 1014 g N) yr −1, but have large uncertainties. These estimates are nearly an order of magnitude greater than historical, pre-1980 estimates, but approach modern estimates of oceanic denitrification.

Machine Learning for Sequential Data: A Review

Abstract: Statistical learning problems in many fields involve sequential data. This paper formalizes the principal learning tasks and describes the methods that have been developed within the machine learning research community for addressing these problems. These methods include sliding window methods, recurrent sliding windows, hidden Markov models, conditional random fields, and graph transformer networks. The paper also discusses some open research issues.

Harnessing microbially generated power on the seafloor

Abstract: In many marine environments, a voltage gradient exists across the water‐sediment interface resulting from sedimentary microbial activity. Here we show that a fuel cell consisting of an anode embedded in marine sediment and a cathode in overlying seawater can use this voltage gradient to generate electrical power in situ. Fuel cells of this design generated sustained power in a boat basin carved into a salt marsh near Tuckerton, New Jersey, and in the Yaquina Bay Estuary near Newport, Oregon. Retrieval and analysis of the Tuckerton fuel cell indicates that power generation results from at least two anode reactions: oxidation of sediment sulfide (a by-product of microbial oxidation of sedimentary organic carbon) and oxidation of sedimentary organic carbon catalyzed by microorganisms colonizing the anode. These results demonstrate in real marine environments a new form of power generation that uses an immense, renewable energy reservoir (sedimentary organic carbon) and has near-immediate application.

An Empirical Analysis of Design Choices in Neighborhood-Based Collaborative Filtering Algorithms

Abstract: Collaborative filtering systems predict a user's interest in new items based on the recommendations of other people with similar interests. Instead of performing content indexing or content analysis, collaborative filtering systems rely entirely on interest ratings from members of a participating community. Since predictions are based on human ratings, collaborative filtering systems have the potential to provide filtering based on complex attributes, such as quality, taste, or aesthetics. Many implementations of collaborative filtering apply some variation of the neighborhood-based prediction algorithm. Many variations of similarity metrics, weighting approaches, combination measures, and rating normalization have appeared in each implementation. For these parameters and others, there is no consensus as to which choice of technique is most appropriate for what situations, nor how significant an effect on accuracy each parameter has. Consequently, every person implementing a collaborative filtering system must make hard design choices with little guidance. This article provides a set of recommendations to guide design of neighborhood-based prediction systems, based on the results of an empirical study. We apply an analysis framework that divides the neighborhood-based prediction approach into three components and then examines variants of the key parameters in each component. The three components identified are similarity computation, neighbor selection, and rating combination.

Noble Gas Isotope Geochemistry of Mid-Ocean Ridge and Ocean Island Basalts: Characterization of Mantle Source Reservoirs

Abstract: The study of noble gases in oceanic basalts is central to understanding chemical heterogeneity of the Earth’s mantle and origin of the atmosphere. In the terrestrial environment the abundances of noble gases are quite low because they were excluded from solid materials during planetary formation in the inner solar system. This low background inventory helps to make the noble gases excellent tracers of mantle reservoirs. In this context, mid-ocean ridge and ocean island basalts provide valuable windows into the Earth’s mantle. These oceanic basalts are not prone to the degree of contamination often observed in continental lavas that results from their passage through thick continental lithosphere and crust. Mid-ocean ridge basalts (MORBs) form by partial melting as the ascending mantle beneath spreading ridges reaches its solidus temperature, and MORBs are generally accepted to represent a broad sampling of the convecting upper mantle. Ocean island basalts (OIBs) represent melting ‘anomalies’ that are generally related to mantle upwelling. The extent to which ocean islands are derived from a thermal boundary layer in the deep mantle (e.g., as a mantle plume) or from chemical heterogeneities embedded within the mantle convective flow (e.g., as a mantle ‘blob’) has been debated for decades, and is not currently resolved. The isotope compositions of noble gases in oceanic basalts bear significantly on such debates over the chemical structure of the mantle. When oceanic basalts erupt as submarine lavas, their quenched rims of glass may contain high volatile abundances (especially when they are deeply erupted under elevated hydrostatic pressure), providing the best available opportunity for precisely characterizing the noble gas composition of the Earth’s mantle. In favorable cases, inclusions of melt or fluids trapped within magmatic phenocrysts and mantle xenoliths can also be precisely analyzed for noble gas composition. Measurable changes in the isotope compositions of noble gases …

Climate Change and Latitudinal Patterns of Intertidal Thermal Stress

Abstract: The interaction of climate and the timing of low tides along the West Coast of the United States creates a complex mosaic of thermal environments, in which northern sites can be more thermally stressful than southern sites. Thus, climate change may not lead to a poleward shift in the distribution of intertidal organisms, as has been proposed, but instead will likely cause localized extinctions at a series of "hot spots." Patterns of exposure to extreme climatic conditions are temporally variable, and tidal predictions suggest that in the next 3 to 5 years "hot spots" are likely to appear at several northern sites.

Complexity in conservation: lessons from the global decline of amphibian populations

Abstract: As part of an overall ‘‘biodiversity crisis’’ many amphibian populations are in decline throughout the world. Numerous causes have been invoked to explain these declines. These include habitat destruction, climate change, increasing levels of ultraviolet radiation, environmental contamination, disease, and the introduction of non-native species. In this paper, we argue that amphibian population declines are caused by different abiotic and biotic factors acting together in a context-dependent fashion. Moreover, different species and different populations of the same species may react in different ways to the same environmental insult. Thus, the causes of amphibian population declines will vary spatially and temporally. Although some generalizations (e.g. those concerning environmental stress and disease outbreaks) can be made about amphibian population declines, we suggest that these generalizations take into account the context-dependent dynamics of ecological systems.

Use of multiline cultivars and cultivar mixtures for disease management

Abstract: The usefulness of mixtures (multiline cultivars and cultivar mixtures) for disease management has been well demonstrated for rusts and powdery mildews of small grain crops. Such mixtures are more useful under some epidemiological conditions than under others, and experimental methodology, especially problems of scale, may be crucial in evaluating the potential efficacy of mixtures on disease. There are now examples of mixtures providing both low and high degrees of disease control for a wide range of pathosystems, including crops with large plants, and pathogens that demonstrate low host specificity, or are splash dispersed, soilborne, or insect vectored. Though most analyses of pathogen evolution in mixtures consider static costs of virulence to be the main mechanism countering selection for pathogen complexity, many other potential mechanisms need to be investigated. Agronomic and marketing considerations must be carefully evaluated when implementing mixture approaches to crop management. Practical difficulties associated with mixtures have often been overestimated, however, and mixtures will likely play an increasingly important role as we develop more sustainable agricultural systems.

On the dialog between experimentalist and modeler in catchment hydrology: Use of soft data for multicriteria model calibration

Abstract: [1] The dialog between experimentalist and modeler in catchment hydrology has been minimal to date. The experimentalist often has a highly detailed yet highly qualitative understanding of dominant runoff processes; thus there is often much more information content on the catchment than we use for calibration of a model. While modelers often appreciate the need for “hard data” for the model calibration process, there has been little thought given to how modelers might access this “soft” or process knowledge. We present a new method where soft data (i.e., qualitative knowledge from the experimentalist that cannot be used directly as exact numbers) are made useful through fuzzy measures of model simulation and parameter value acceptability. We developed a three-box lumped conceptual model for the Maimai catchment in New Zealand, a particularly well-studied process-hydrological research catchment. The boxes represent the key hydrological reservoirs that are known to have distinct groundwater dynamics, isotopic composition, and solute chemistry. The model was calibrated against hard data (runoff and groundwater levels) as well as a number of criteria derived from the soft data (e.g., percent new water, reservoir volume, etc.). We achieved very good fits for the three-box model when optimizing the parameter values with only runoff (Reff = 0.93). However, parameter sets obtained in this way showed in general a poor goodness of fit for other criteria such as the simulated new water contributions to peak runoff. Inclusion of soft data criteria in the model calibration process resulted in lower Reff values (around 0.84 when including all criteria) but led to better overall performance, as interpreted by the experimentalist's view of catchment runoff dynamics. The model performance with respect to soft data (like, for instance, the new water ratio) increased significantly, and parameter uncertainty was reduced by 60% on average with the introduction of the soft data multicriteria calibration. We argue that accepting lower model efficiencies for runoff is “worth it” if one can develop a more “real” model of catchment behavior. The use of soft data is an approach to formalize this exchange between experimentalist and modeler and to more fully utilize the information content from experimental catchments.