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Corvallis, OR, United States

Oregon State University is a coeducational, public research university in Corvallis, Oregon, United States. The university offers more than 200 undergraduate, graduate, and doctoral degree programs and has the largest total enrollment in Oregon. More than 160,000 people have attended OSU since its founding. The Carnegie Foundation classifies the Oregon State University as a research university with very high research activity. In addition, it is designated by Carnigie Foundation with 'Community Engagement' classification.OSU is one of 73 land-grant universities in the United States. The school is also a sea-grant, space-grant, and sun-grant institution, making it one of only two US institutions to obtain all four designations and the only public university to do so . OSU received almost $285 million in research grants and contracts for the 2014 fiscal year, which is more research funding than all other public universities in Oregon combined. Wikipedia.

Murtaugh P.A.,Oregon State University
Ecology | Year: 2014

Statistical hypothesis testing has been widely criticized by ecologists in recent years. I review some of the more persistent criticisms of P values and argue that most stem from misunderstandings or incorrect interpretations, rather than from intrinsic shortcomings of the P value. I show that P values are intimately linked to confidence intervals and to differences in Akaike's information criterion (ΔAIC), two metrics that have been advocated as replacements for the P value. The choice of a threshold value of ΔAIC that breaks ties among competing models is as arbitrary as the choice of the probability of a Type I error in hypothesis testing, and several other criticisms of the P value apply equally to ΔAIC. Since P values, confidence intervals, and ΔAIC are based on the same statistical information, all have their places in modern statistical practice. The choice of which to use should be stylistic, dictated by details of the application rather than by dogmatic, a priori considerations. © 2014 by the Ecological Society of America.

Samelson R.M.,Oregon State University
Annual Review of Marine Science | Year: 2013

Lagrangian motion in geophysical fluids may be strongly influenced by coherent structures that support distinct regimes in a given flow. The problems of identifying and demarcating Lagrangian regime boundaries associated with dynamical coherent structures in a given velocity field can be studied using approaches originally developed in the context of the abstract geometric theory of ordinary differential equations. An essential insight is that when coherent structures exist in a flow, Lagrangian regime boundaries may often be indicated as material curves on which the Lagrangian-mean principal-axis strain is large. This insight is the foundation of many numerical techniques for identifying such features in complex observed or numerically simulated ocean flows. The basic theoretical ideas are illustrated with a simple, kinematic traveling-wave model. The corresponding numerical algorithms for identifying candidate Lagrangian regime boundaries and lines of principal Lagrangian strain (also called Lagrangian coherent structures) are divided into parcel and bundle schemes; the latter include the finite-time and finite-size Lyapunov exponent/Lagrangian strain (FTLE/FTLS and FSLE/FSLS) metrics. Some aspects and results of oceanographic studies based on these approaches are reviewed, and the results are discussed in the context of oceanographic observations of dynamical coherent structures. © 2013 by Annual Reviews. All rights reserved.

Behrenfeld M.J.,Oregon State University
Ecology | Year: 2010

The Critical Depth Hypothesis formalized by Sverdrup in 1953 posits that vernal phytoplankton blooms occur when surface mixing shoals to a depth shallower than a critical depth horizon defining the point where phytoplankton growth exceeds losses. This hypothesis has since served as a cornerstone in plankton ecology and reflects the very common assumption that blooms are caused by enhanced growth rates in response to improved light, temperature, and stratification conditions, not simply correlated with them. Here, a nine-year satellite record of phytoplankton biomass in the subarctic Atlantic is used to reevaluate seasonal plankton dynamics. Results show that (1) bloom initiation occurs in the winter when mixed layer depths are maximum, not in the spring, (2) coupling between phytoplankton growth (μ) and losses increases during spring stratification, rather than decreases, (3) maxima in net population growth rates (r) are as likely to occur in midwinter as in spring, and (4) r is generally inversely related to μ, These results are incompatible with the Critical Depth Hypothesis as a functional framework for understanding bloom dynamics. In its place, a "Dilution-Recoupling Hypothesis" is described that focuses on the balance between phytoplankton growth and grazing, and the seasonally varying physical processes influencing this balance. This revised view derives from fundamental concepts applied during field dilution experiments, builds upon earlier modeling results, and is compatible with observed phytoplankton blooms in the absence of spring mixed layer shoaling. © 2010 by the Ecological Society of America.

Ezenwa V.O.,University of Georgia | Jolles A.E.,Oregon State University
Science | Year: 2015

Parasitic worms modulate host immune responses in ways that affect microbial co-infections. For this reason, anthelmintic therapy may be a potent tool for indirectly controlling microbial pathogens. However, the population-level consequences of this type of intervention on co-infecting microbes are unknown. We evaluated the effects of anthelmintic treatment on bovine tuberculosis (BTB) acquisition, mortality after infection, and pathogen fitness in free-ranging African buffalo. We found that treatment had no effect on the probability of BTB infection, but buffalo survival after infection was ninefold higher among treated individuals. These contrasting effects translated into an approximately eightfold increase in the reproductive number of BTB for anthelmintic-treated compared with untreated buffalo. Our results indicate that anthelmintic treatment can enhance the spread of microbial pathogens in some real-world situations. © 2015, American Association for the Advancement of Science. All rights reserved.

Diederichs K.,University of Konstanz | Karplus P.A.,Oregon State University
Acta Crystallographica Section D: Biological Crystallography | Year: 2013

In macromolecular X-ray crystallography, typical data sets have substantial multiplicity. This can be used to calculate the consistency of repeated measurements and thereby assess data quality. Recently, the properties of a correlation coefficient, CC1/2, that can be used for this purpose were characterized and it was shown that CC1/2 has superior properties compared with 'merging' R values. A derived quantity, CC*, links data and model quality. Using experimental data sets, the behaviour of CC1/2 and the more conventional indicators were compared in two situations of practical importance: merging data sets from different crystals and selectively rejecting weak observations or (merged) unique reflections from a data set. In these situations controlled 'paired-refinement' tests show that even though discarding the weaker data leads to improvements in the merging R values, the refined models based on these data are of lower quality. These results show the folly of such data-filtering practices aimed at improving the merging R values. Interestingly, in all of these tests CC1/2 is the one data-quality indicator for which the behaviour accurately reflects which of the alternative data-handling strategies results in the best-quality refined model. Its properties in the presence of systematic error are documented and discussed.

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