In the late 1990s and early 2000s, large declines in numbers of chum salmon Oncorhynchus keta and Chinook salmon O. tshawytscha returning to the Arctic-YukonKuskokwim (AYK) region (Alaska, USA) illuminated the need for an improved understanding of the variables controlling salmon abundance at all life stages. In addressing questions about salmon abundance, large gaps in our knowledge of basic salmon life history and the critical early marine life stage were revealed. In this paper, results from studies conducted on the estuarine ecology of juvenile salmon in western Alaska are summarized and compared, emphasizing timing and distribution during outmigration, environmental conditions, age and growth, feeding, and energy content of salmon smolts. In western Alaska, water temperature dramatically changes with season, ranging from 0°C after ice melt in late spring/early summer to 19°C in July. Juvenile salmon were found in AYK estuaries from early May until August or September, but to date no information is available on their residence duration or survival probability. Chum salmon were the most abundant juvenile salmon reported, ranging in percent catch from <0.1% to 4.7% and most research effort has focused on this species. Abundances of Chinook salmon, sockeye salmon O. nerka, and pink salmon O. gorbuscha varied among estuaries, while coho salmon O. kisutch juveniles were consistently rare, never amounting to more than 0.8% of the catch. Dietary composition of juvenile salmon was highly variable and a shift was commonly reported from epibenthic and neustonic prey in lower salinity water to pelagic prey in higher salinity water. Gaps in the knowledge of AYK salmon estuarine ecology are still evident. For example, data on outmigration patterns and residence timing and duration, rearing conditions and their effect on diet, growth, and survival are often completely lacking or available only for few selected years and sites. Filling gaps in knowledge concerning salmon use and survival in estuarine and near-shore habitats within the AYK region will aid in assessing the relative roles of all habitats (freshwater to marine) in controlling salmon abundance.
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The endocrine control of performance should be especially pronounced in animals that undergo a developmental shift in niche, such as occurs in migratory species. By way of example, I review the developmental and environmental control of the preparatory changes for seawater entry of juvenile salmon (known as smolting) and its hormonal regulation. There is a size threshold for smolt development in juvenile Atlantic salmon that results in greater sensitivity of the growth hormone and cortisol axes to changes in daylength. These hormones, in turn, have broad effects on survival, ion homeostasis, growth and swimming performance during entry into seawater. Migratory niche shifts and metamorphic events are extreme examples of the role of hormones in animal performance and represent one end of a continuum. A framework for predicting when hormones will be involved in performance of animals is presented. Endocrine involvement in performance will be more substantial when (1) selection differentials on traits underlying performance are high and temporally discontinuous over an animal's lifetime, (2) the energetic and fitness costs of maintaining performance plasticity are less than those of constant performance, (3) cues for altering performance are reliable indicators of critical environmental conditions, require neurosensory input, and minimize effects of lag, and (4) the need for coordination of organs, tissues and cells to achieve increased performance is greater. 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From 2005 to 2008, we studied loons in northern Wisconsin and used night lighting to capture loons on nests and also designed a lift net for capturing loons prior to nesting. At night, incubating loons were approached by boat and, when within about 30-60 m, we focused a spotlight on the loon and, once at the nest, captured loons using a landing net. Using this technique, we captured 23 loons in 29 attempts (79%). In addition, taped calls and loon decoys were used to entice prenesting, territorial loons into a shoreline-based, lift-net trap at a capture efficiency of 67% (10 captures in 15 attempts) during the second year of use. Our diurnal lift-net trap and night-light nest-capture techniques allowed us to capture adult Common Loons during periods of the breeding season when previous investigators have found loons difficult to catch. These techniques may also be useful for capturing other species of territorial waterbirds, especially other species of loons. ?? 2009 Association of Field Ornithologists. 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Model variables, probabilities, functions, and parameters were derived from the analysis of two comprehensive field surveys conducted in this floodplain. This modeling approach describes the establishment, growth, competition, and death of individual trees for modeled species on a 10,000-ha landscape with spatial resolution of 1 ha. The succession characteristics of each Monte Carlo simulation are summed up to describe forest development and dynamics on a landscape level. FORSUM simulated the impacts of flood intensity and frequency on species composition and dynamics in the Upper Mississippi River floodplain ecosystem. The model provides a useful tool for testing hypotheses about forest succession and enables ecologists and managers to evaluate the impacts of flood disturbances and ecosystem restoration on forest succession. 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However, the Moon Mineralogy Mapper (M 3) on Chandrayaan-1 has recently detected absorption features near 2.8 to 3.0 micrometers on the surface of the Moon. For silicate bodies, such features are typically attributed to hydroxyl- and/or water-bearing materials. On the Moon, the feature is seen as a widely distributed absorption that appears strongest at cooler high latitudes and at several fresh feldspathic craters. The general lack of correlation of this feature in sunlit M3 data with neutron spectrometer hydrogen abundance data suggests that the formation and retention of hydroxyl and water are ongoing surficial processes. Hydroxyl/water production processes may feed polar cold traps and make the lunar regolith a candidate source of volatiles for human exploration.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Science","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1126/science.1178658","issn":"00368075","usgsCitation":"Pieters, C., Goswami, J., Clark, R.N., Annadurai, M., Boardman, J., Buratti, B., Combe, J.#., Dyar, M., Green, R., Head, J., Hibbitts, C., Hicks, M., Isaacson, P., Klima, R., Kramer, G., Kumar, S., Livo, E., Lundeen, S., Malaret, E., McCord, T., Mustard, J., Nettles, J., Petro, N., Runyon, C., Staid, M., Sunshine, J., Taylor, L., Tompkins, S., and Varanasi, P., 2009, Character and spatial distribution of OH/H2O on the surface of the moon seen by M3 on chandrayaan-1: Science, v. 326, no. 5952, p. 568-572, https://doi.org/10.1126/science.1178658.","startPage":"568","endPage":"572","numberOfPages":"5","costCenters":[],"links":[{"id":245239,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":217304,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1126/science.1178658"}],"volume":"326","issue":"5952","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059f488e4b0c8380cd4bd82","contributors":{"authors":[{"text":"Pieters, C.M.","contributorId":48733,"corporation":false,"usgs":true,"family":"Pieters","given":"C.M.","email":"","affiliations":[{"id":16929,"text":"Brown University","active":true,"usgs":false}],"preferred":false,"id":459221,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Goswami, J.N.","contributorId":41677,"corporation":false,"usgs":true,"family":"Goswami","given":"J.N.","email":"","affiliations":[],"preferred":false,"id":459219,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Clark, R. 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wastewater","interactions":[],"lastModifiedDate":"2012-03-12T17:22:09","indexId":"70037070","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3716,"text":"Water Research","onlineIssn":"1879-2448","printIssn":"0043-1354","active":true,"publicationSubtype":{"id":10}},"title":"Comparison of immunomagnetic separation/adenosine triphosphate rapid method to traditional culture-based method for E. coli and enterococci enumeration in wastewater","docAbstract":"Untreated wastewater samples from California, North Carolina, and Ohio were analyzed by the immunomagnetic separation/adenosine triphosphate (IMS/ATP) method and the traditional culture-based method for E. coli and enterococci concentrations. The IMS/ATP method concentrates target bacteria by immunomagnetic separation and then quantifies captured bacteria by measuring bioluminescence induced by release of ATP from the bacterial cells. Results from this method are available within 1 h from the start of sample processing. Significant linear correlations were found between the IMS/ATP results and results from traditional culture-based methods for E. coli and enterococci enumeration for one location in California, two locations in North Carolina, and one location in Ohio (r??values ranged from 0.87 to 0.97). No significant linear relation was found for a second location in California that treats a complex mixture of residential and industrial wastewater. With the exception of one location, IMS/ATP showed promise as a rapid method for the quantification of faecal-indicator organisms in wastewater.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Water Research","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1016/j.watres.2009.06.047","issn":"00431354","usgsCitation":"Bushon, R., Likirdopulos, C., and Brady, A., 2009, Comparison of immunomagnetic separation/adenosine triphosphate rapid method to traditional culture-based method for E. coli and enterococci enumeration in wastewater: Water Research, v. 43, no. 19, p. 4940-4946, https://doi.org/10.1016/j.watres.2009.06.047.","startPage":"4940","endPage":"4946","numberOfPages":"7","costCenters":[],"links":[{"id":217360,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1016/j.watres.2009.06.047"},{"id":245304,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"43","issue":"19","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059f86be4b0c8380cd4d0bc","contributors":{"authors":[{"text":"Bushon, R.N.","contributorId":68086,"corporation":false,"usgs":true,"family":"Bushon","given":"R.N.","affiliations":[],"preferred":false,"id":459248,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Likirdopulos, C.A.","contributorId":6265,"corporation":false,"usgs":true,"family":"Likirdopulos","given":"C.A.","affiliations":[],"preferred":false,"id":459246,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Brady, A.M.G.","contributorId":9834,"corporation":false,"usgs":true,"family":"Brady","given":"A.M.G.","email":"","affiliations":[],"preferred":false,"id":459247,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70037066,"text":"70037066 - 2009 - Detection of adsorbed water and hydroxyl on the moon","interactions":[],"lastModifiedDate":"2012-03-12T17:22:10","indexId":"70037066","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3338,"text":"Science","active":true,"publicationSubtype":{"id":10}},"title":"Detection of adsorbed water and hydroxyl on the moon","docAbstract":"Data from the Visual and Infrared Mapping Spectrometer (VIAAS) on Cassini during its flyby of the AAoon in 1999 show a broad absorption at 3 micrometers due to adsorbed water and near 2.8 micrometers attributed to hydroxyl in the sunlit surface on the AAoon. The amounts of water indicated in the spectra depend on the type of mixing and the grain sizes in the rocks and soils but could be 10 to 1000 parts per million and locally higher. Water in the polar regions may be water that has migrated to the colder environments there. Trace hydroxyl is observed in the anorthositic highlands at lower latitudes.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Science","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1126/science.1178105","issn":"00368075","usgsCitation":"Clark, R.N., 2009, Detection of adsorbed water and hydroxyl on the moon: Science, v. 326, no. 5952, p. 562-564, https://doi.org/10.1126/science.1178105.","startPage":"562","endPage":"564","numberOfPages":"3","costCenters":[],"links":[{"id":476414,"rank":10000,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1126/science.1178105","text":"Publisher Index Page"},{"id":245240,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":217305,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1126/science.1178105"}],"volume":"326","issue":"5952","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059ff6ee4b0c8380cd4f1a5","contributors":{"authors":[{"text":"Clark, R. N.","contributorId":6568,"corporation":false,"usgs":true,"family":"Clark","given":"R.","email":"","middleInitial":"N.","affiliations":[],"preferred":false,"id":459236,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":70037067,"text":"70037067 - 2009 - A spatial model of white sturgeon rearing habitat in the lower Columbia River, USA","interactions":[],"lastModifiedDate":"2012-03-12T17:22:10","indexId":"70037067","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1458,"text":"Ecological Modelling","active":true,"publicationSubtype":{"id":10}},"title":"A spatial model of white sturgeon rearing habitat in the lower Columbia River, USA","docAbstract":"Concerns over the potential effects of in-water placement of dredged materials prompted us to develop a GIS-based model that characterizes in a spatially explicit manner white sturgeon Acipenser transmontanus rearing habitat in the lower Columbia River, USA. The spatial model was developed using water depth, riverbed slope and roughness, fish positions collected in 2002, and Mahalanobis distance (D2). We created a habitat suitability map by identifying a Mahalanobis distance under which >50% of white sturgeon locations occurred in 2002 (i.e., high-probability habitat). White sturgeon preferred relatively moderate to high water depths, and low to moderate riverbed slope and roughness values. The eigenvectors indicated that riverbed slope and roughness were slightly more important than water depth, but all three variables were important. We estimated the impacts that fill might have on sturgeon habitat by simulating the addition of fill to the thalweg, in 3-m increments, and recomputing Mahalanobis distances. Channel filling simulations revealed that up to 9 m of fill would have little impact on high-probability habitat, but 12 and 15 m of fill resulted in habitat declines of ???12% and ???45%, respectively. This is the first spatially explicit predictive model of white sturgeon rearing habitat in the lower Columbia River, and the first to quantitatively predict the impacts of dredging operations on sturgeon habitat. Future research should consider whether water velocity improves the accuracy and specificity of the model, and to assess its applicability to other areas in the Columbia River.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Ecological Modelling","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1016/j.ecolmodel.2009.03.006","issn":"03043800","usgsCitation":"Hatten, J., and Parsley, M., 2009, A spatial model of white sturgeon rearing habitat in the lower Columbia River, USA: Ecological Modelling, v. 220, no. 24, p. 3638-3646, https://doi.org/10.1016/j.ecolmodel.2009.03.006.","startPage":"3638","endPage":"3646","numberOfPages":"9","costCenters":[],"links":[{"id":245241,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":217306,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1016/j.ecolmodel.2009.03.006"}],"volume":"220","issue":"24","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059e5a1e4b0c8380cd46ea4","contributors":{"authors":[{"text":"Hatten, J.R.","contributorId":39564,"corporation":false,"usgs":true,"family":"Hatten","given":"J.R.","email":"","affiliations":[],"preferred":false,"id":459237,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Parsley, M.J.","contributorId":59542,"corporation":false,"usgs":true,"family":"Parsley","given":"M.J.","email":"","affiliations":[],"preferred":false,"id":459238,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70035739,"text":"70035739 - 2009 - Delayed conifer mortality after fuel reduction treatments: Interactive effects of fuel, fire intensity, and bark beetles","interactions":[],"lastModifiedDate":"2019-03-26T10:12:55","indexId":"70035739","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1450,"text":"Ecological Applications","active":true,"publicationSubtype":{"id":10}},"title":"Delayed conifer mortality after fuel reduction treatments: Interactive effects of fuel, fire intensity, and bark beetles","docAbstract":"Many low‐elevation dry forests of the western United States contain more small trees and fewer large trees, more down woody debris, and less diverse and vigorous understory plant communities compared to conditions under historical fire regimes. These altered structural conditions may contribute to increased probability of unnaturally severe wildfires, susceptibility to uncharacteristic insect outbreaks, and drought‐related mortality. Broad‐scale fuel reduction and restoration treatments are proposed to promote stand development on trajectories toward more sustainable structures. Little research to date, however, has quantified the effects of these treatments on the ecosystem, especially delayed and latent tree mortality resulting directly or indirectly from treatments. In this paper, we explore complex hypotheses relating to the cascade of effects that influence ponderosa pine (Pinus ponderosa) and Douglas‐fir (Pseudotsuga menziesii) mortality using structural equation modeling (SEM). We used annual census and plot data through six growing seasons after thinning and four growing seasons after burning from a replicated, operational‐scale, completely randomized experiment conducted in northeastern Oregon, USA, as part of the national Fire and Fire Surrogate study. Treatments included thin, burn, thin followed by burn (thin + burn), and control. Burn and thin + burn treatments increased the proportion of dead trees while the proportion of dead trees declined or remained constant in thin and control units, although the density of dead trees was essentially unchanged with treatment. Most of the new mortality (96%) occurred within two years of treatment and was attributed to bark beetles. Bark beetle‐caused tree mortality, while low overall, was greatest in thin + burn treatments. SEM results indicate that the probability of mortality of large‐diameter ponderosa pine from bark beetles and wood borers was directly related to surface fire severity and bole charring, which in turn depended on fire intensity, which was greater in units where thinning increased large woody fuels. These results have implications when deciding among management options for restoring ecosystem health in similar ponderosa pine and Douglas‐fir forests.
","language":"English","publisher":"Ecological Society of America","doi":"10.1890/07-1751.1","issn":"10510761","usgsCitation":"Youngblood, A., Grace, J., and Mciver, J., 2009, Delayed conifer mortality after fuel reduction treatments: Interactive effects of fuel, fire intensity, and bark beetles: Ecological Applications, v. 19, no. 2, p. 321-337, https://doi.org/10.1890/07-1751.1.","productDescription":"17 p.","startPage":"321","endPage":"337","numberOfPages":"17","costCenters":[],"links":[{"id":487807,"rank":10000,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1890/07-1751.1","text":"Publisher Index Page"},{"id":244240,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":216376,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1890/07-1751.1"}],"volume":"19","issue":"2","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059fe5de4b0c8380cd4ecd1","contributors":{"authors":[{"text":"Youngblood, A.","contributorId":66085,"corporation":false,"usgs":true,"family":"Youngblood","given":"A.","affiliations":[],"preferred":false,"id":452141,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Grace, J.B. 0000-0001-6374-4726","orcid":"https://orcid.org/0000-0001-6374-4726","contributorId":38938,"corporation":false,"usgs":true,"family":"Grace","given":"J.B.","affiliations":[],"preferred":false,"id":452140,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Mciver, J.D.","contributorId":71665,"corporation":false,"usgs":true,"family":"Mciver","given":"J.D.","email":"","affiliations":[],"preferred":false,"id":452142,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70035887,"text":"70035887 - 2009 - Complete and draft genome sequences of six members of the aquificales","interactions":[],"lastModifiedDate":"2018-10-03T11:13:41","indexId":"70035887","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2192,"text":"Journal of Bacteriology","active":true,"publicationSubtype":{"id":10}},"title":"Complete and draft genome sequences of six members of the aquificales","docAbstract":"The Aquificales are widespread in marine and terrestrial hydrothermal environments. Here, we report the complete and draft genome sequences of six new members of the Aquificales: two marine species, Persephonella marina strain EX-H1 and Hydrogenivirga strain 128-5-R1 (from the East Pacific Rise, 9°50.3′N, 104°17.5′W, and the Eastern Lau Spreading Center, 176°11.5′W, 20°45.8′S, respectively), and four terrestrial isolates, Sulfurihydrogenibium azorense strain Az-Fu1, Sulfurihydrogenibium yellowstonense strain SS-5, and Sulfurihydrogenibium strain Y03AOP1 (from Furnas, Azores, Portugal, and Calcite Springs and Obsidian Pool in Yellowstone National Park, United States, respectively), and the only thermoacidophilic isolate, Hydrogenobaculum strain Y04AAS1 (from a stream adjacent to Obsidian Pool). Significant differences among the different species exist that include nitrogen metabolism, hydrogen utilization, chemotaxis, and signal transduction, providing insights into their ecological niche adaptations.
","language":"English","publisher":"American Society for Microbiology","doi":"10.1128/JB.01645-08","issn":"00219193","usgsCitation":"Reysenbach, A., Hamamura, N., Podar, M., Griffiths, E., Ferreira, S., Hochstein, R., Heidelberg, J., Johnson, J., Mead, D., Pohorille, A., Sarmiento, M., Sehweighofer, K., Seshadri, R., and Voytek, M., 2009, Complete and draft genome sequences of six members of the aquificales: Journal of Bacteriology, v. 191, no. 6, p. 1992-1993, https://doi.org/10.1128/JB.01645-08.","productDescription":"2 p.","startPage":"1992","endPage":"1993","costCenters":[{"id":589,"text":"Toxic Substances Hydrology Program","active":true,"usgs":true}],"links":[{"id":476386,"rank":10000,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2648382","text":"External Repository"},{"id":244055,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":216201,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1128/JB.01645-08"}],"volume":"191","issue":"6","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059f908e4b0c8380cd4d3b8","contributors":{"authors":[{"text":"Reysenbach, A.-L.","contributorId":8660,"corporation":false,"usgs":true,"family":"Reysenbach","given":"A.-L.","affiliations":[],"preferred":false,"id":452905,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Hamamura, N.","contributorId":85791,"corporation":false,"usgs":true,"family":"Hamamura","given":"N.","email":"","affiliations":[],"preferred":false,"id":452917,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Podar, M.","contributorId":7107,"corporation":false,"usgs":true,"family":"Podar","given":"M.","affiliations":[],"preferred":false,"id":452904,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Griffiths, E.","contributorId":52009,"corporation":false,"usgs":true,"family":"Griffiths","given":"E.","email":"","affiliations":[],"preferred":false,"id":452912,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Ferreira, S.","contributorId":22989,"corporation":false,"usgs":true,"family":"Ferreira","given":"S.","email":"","affiliations":[],"preferred":false,"id":452907,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Hochstein, R.","contributorId":57291,"corporation":false,"usgs":true,"family":"Hochstein","given":"R.","email":"","affiliations":[],"preferred":false,"id":452913,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Heidelberg, J.","contributorId":68988,"corporation":false,"usgs":true,"family":"Heidelberg","given":"J.","email":"","affiliations":[],"preferred":false,"id":452914,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Johnson, J.","contributorId":31719,"corporation":false,"usgs":true,"family":"Johnson","given":"J.","email":"","affiliations":[],"preferred":false,"id":452909,"contributorType":{"id":1,"text":"Authors"},"rank":8},{"text":"Mead, D.","contributorId":80926,"corporation":false,"usgs":true,"family":"Mead","given":"D.","email":"","affiliations":[],"preferred":false,"id":452916,"contributorType":{"id":1,"text":"Authors"},"rank":9},{"text":"Pohorille, A.","contributorId":13832,"corporation":false,"usgs":true,"family":"Pohorille","given":"A.","email":"","affiliations":[],"preferred":false,"id":452906,"contributorType":{"id":1,"text":"Authors"},"rank":10},{"text":"Sarmiento, M.","contributorId":71793,"corporation":false,"usgs":true,"family":"Sarmiento","given":"M.","email":"","affiliations":[],"preferred":false,"id":452915,"contributorType":{"id":1,"text":"Authors"},"rank":11},{"text":"Sehweighofer, K.","contributorId":30477,"corporation":false,"usgs":true,"family":"Sehweighofer","given":"K.","email":"","affiliations":[],"preferred":false,"id":452908,"contributorType":{"id":1,"text":"Authors"},"rank":12},{"text":"Seshadri, R.","contributorId":34354,"corporation":false,"usgs":true,"family":"Seshadri","given":"R.","email":"","affiliations":[],"preferred":false,"id":452910,"contributorType":{"id":1,"text":"Authors"},"rank":13},{"text":"Voytek, M.A.","contributorId":44272,"corporation":false,"usgs":true,"family":"Voytek","given":"M.A.","email":"","affiliations":[],"preferred":false,"id":452911,"contributorType":{"id":1,"text":"Authors"},"rank":14}]}} ,{"id":70035884,"text":"70035884 - 2009 - Atlantic salmon (Salmo salar) smolt production: the relative importance of survival and body growth","interactions":[],"lastModifiedDate":"2012-03-12T17:21:49","indexId":"70035884","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1169,"text":"Canadian Journal of Fisheries and Aquatic Sciences","active":true,"publicationSubtype":{"id":10}},"title":"Atlantic salmon (Salmo salar) smolt production: the relative importance of survival and body growth","docAbstract":"The complex life history of Atlantic salmon (Salmo salar) coupled with interacting abiotic and biotic factors leads to extreme demographic variability across the species' range. Our goal was to evaluate the relative importance of survival and body growth in determining smolt production across space and time. We used passive integrated transponder tags and capture-mark-recapture analyses to estimate survival, emigration, and growth for six cohorts of presmolt Atlantic salmon in two streams (three cohorts per stream) in New England, USA. We observed remarkable among-cohort consistency in mean monthly survival during a 17-month period from age-0+ autumn to age-2+ spring yet high variability in monthly survival over shorter time intervals (seasons). Despite this latter variability, survival did not translate into amongcohort differences in proportions of age-2+ versus age-3+ smolts. Alternatively, the high variability across seasons and cohorts in mean individual growth rate did lead to differences in within-cohort proportions of age-2+ versus age-3+ smolts (regardless of stream). We conclude that in our two small study streams, variability in growth and size impacted smolt age and, ultimately, smolt production. Density-dependent effects on growth at the scale of the entire study site represent a possible mechanism underlying our observations.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Canadian Journal of Fisheries and Aquatic Sciences","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1139/F09-005","issn":"0706652X","usgsCitation":"Horton, G., Letcher, B., Bailey, M., and Kinnison, M., 2009, Atlantic salmon (Salmo salar) smolt production: the relative importance of survival and body growth: Canadian Journal of Fisheries and Aquatic Sciences, v. 66, no. 3, p. 471-483, https://doi.org/10.1139/F09-005.","startPage":"471","endPage":"483","numberOfPages":"13","costCenters":[],"links":[{"id":216145,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1139/F09-005"},{"id":243993,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"66","issue":"3","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059eeabe4b0c8380cd49ebe","contributors":{"authors":[{"text":"Horton, G.E.","contributorId":8594,"corporation":false,"usgs":true,"family":"Horton","given":"G.E.","email":"","affiliations":[],"preferred":false,"id":452899,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Letcher, B. H. 0000-0003-0191-5678","orcid":"https://orcid.org/0000-0003-0191-5678","contributorId":48132,"corporation":false,"usgs":true,"family":"Letcher","given":"B.","middleInitial":"H.","affiliations":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":false,"id":452900,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Bailey, M.M.","contributorId":7494,"corporation":false,"usgs":true,"family":"Bailey","given":"M.M.","email":"","affiliations":[],"preferred":false,"id":452898,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Kinnison, M.T.","contributorId":85410,"corporation":false,"usgs":true,"family":"Kinnison","given":"M.T.","email":"","affiliations":[],"preferred":false,"id":452901,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70035882,"text":"70035882 - 2009 - Measurement of total Zn and Zn isotope ratios by quadrupole ICP-MS for evaluation of Zn uptake in gills of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss)","interactions":[],"lastModifiedDate":"2012-03-12T17:21:49","indexId":"70035882","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3517,"text":"Talanta","active":true,"publicationSubtype":{"id":10}},"title":"Measurement of total Zn and Zn isotope ratios by quadrupole ICP-MS for evaluation of Zn uptake in gills of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss)","docAbstract":"This study evaluates the potential use of stable zinc isotopes in toxicity studies measuring zinc uptake by the gills of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss). The use of stable isotopes in such studies has several advantages over the use of radioisotopes, including cost, ease of handling, elimination of permit requirements, and waste disposal. A pilot study using brown trout was performed to evaluate sample preparation methods and the ability of a quadrupole inductively coupled plasma mass spectrometer (ICP-MS) system to successfully measure changes in the 67Zn/66Zn ratios for planned exposure levels and duration. After completion of the pilot study, a full-scale zinc exposure study using rainbow trout was performed. The results of these studies indicate that there are several factors that affect the precision of the measured 67Zn/66Zn ratios in the sample digests, including variations in sample size, endogenous zinc levels, and zinc uptake rates by individual fish. However, since these factors were incorporated in the calculation of the total zinc accumulated by the gills during the exposures, the data obtained were adequate for their intended use in calculating zinc binding and evaluating the influences of differences in water quality parameters.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Talanta","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1016/j.talanta.2009.07.048","issn":"00399140","usgsCitation":"Wolf, R., Todd, A., Brinkman, S., Lamothe, P.J., Smith, K., and Ranville, J., 2009, Measurement of total Zn and Zn isotope ratios by quadrupole ICP-MS for evaluation of Zn uptake in gills of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss): Talanta, v. 80, no. 2, p. 676-684, https://doi.org/10.1016/j.talanta.2009.07.048.","startPage":"676","endPage":"684","numberOfPages":"9","costCenters":[],"links":[{"id":216114,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1016/j.talanta.2009.07.048"},{"id":243960,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"80","issue":"2","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505a5320e4b0c8380cd6c8bc","contributors":{"authors":[{"text":"Wolf, R.E.","contributorId":11827,"corporation":false,"usgs":true,"family":"Wolf","given":"R.E.","email":"","affiliations":[],"preferred":false,"id":452888,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Todd, A.S.","contributorId":53622,"corporation":false,"usgs":true,"family":"Todd","given":"A.S.","email":"","affiliations":[],"preferred":false,"id":452891,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Brinkman, S.","contributorId":75781,"corporation":false,"usgs":true,"family":"Brinkman","given":"S.","email":"","affiliations":[],"preferred":false,"id":452893,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Lamothe, P. J.","contributorId":45672,"corporation":false,"usgs":true,"family":"Lamothe","given":"P.","email":"","middleInitial":"J.","affiliations":[],"preferred":false,"id":452889,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Smith, K. S. 0000-0001-8547-9804","orcid":"https://orcid.org/0000-0001-8547-9804","contributorId":47779,"corporation":false,"usgs":true,"family":"Smith","given":"K. S.","affiliations":[],"preferred":false,"id":452890,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Ranville, J. F.","contributorId":54245,"corporation":false,"usgs":true,"family":"Ranville","given":"J. F.","affiliations":[],"preferred":false,"id":452892,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70035878,"text":"70035878 - 2009 - Food habits of American black bears as a metric for direct management of humanbear conflict in Yosemite Valley, Yosemite National Park, California","interactions":[],"lastModifiedDate":"2012-03-12T17:21:50","indexId":"70035878","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3671,"text":"Ursus","active":true,"publicationSubtype":{"id":10}},"title":"Food habits of American black bears as a metric for direct management of humanbear conflict in Yosemite Valley, Yosemite National Park, California","docAbstract":"The management of human-American black bear (Ursus americanus) conflict has been of significant concern for Yosemite National Park (YNP) personnel since the 1920s. Park managers implemented the YNP Human-Bear Management Plan in 1975 in an effort to reduce human-bear conflicts, especially in the extensively developed Yosemite Valley (YV). We used scat analysis to estimate annual and seasonal food habits of black bears in YV during 2001-02. We assessed the success of efforts to reduce the availability of anthropogenic foods, including garbage, by examining changes in the diet compared to a study from 1974-78 (Graber 1981). We also quantified consumption of non-native fruit to address its possible contribution to human-bear conflicts. The annual percent volume of human-provided food and garbage in black bear scats in YV decreased from 21% to 6% between 1978 and 2002, indicating YNP efforts have been effective. We found high use of non-native apples by bears throughout YV. Non-native food sources could be contributing to habituation and food conditioning, given their proximity to developed areas of YV. We recommend that YNP managers continue to (1) adapt and improve their management tools to address changing circumstances, (2) quantify the success of new management tools, and (3) reduce the availability of non-native food sources. ?? 2009 International Association for Bear Research and Management.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Ursus","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.2192/08GR027.1","issn":"15376176","usgsCitation":"Greenleaf, S., Matthews, S., Wright, R., Beecham, J., and Leithead, H., 2009, Food habits of American black bears as a metric for direct management of humanbear conflict in Yosemite Valley, Yosemite National Park, California: Ursus, v. 20, no. 2, p. 94-101, https://doi.org/10.2192/08GR027.1.","startPage":"94","endPage":"101","numberOfPages":"8","costCenters":[],"links":[{"id":216057,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.2192/08GR027.1"},{"id":243898,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"20","issue":"2","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505a12bae4b0c8380cd543f2","contributors":{"authors":[{"text":"Greenleaf, S.S.","contributorId":14664,"corporation":false,"usgs":true,"family":"Greenleaf","given":"S.S.","affiliations":[],"preferred":false,"id":452874,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Matthews, S.M.","contributorId":46791,"corporation":false,"usgs":true,"family":"Matthews","given":"S.M.","email":"","affiliations":[],"preferred":false,"id":452875,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Wright, R.G.","contributorId":9622,"corporation":false,"usgs":true,"family":"Wright","given":"R.G.","email":"","affiliations":[],"preferred":false,"id":452873,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Beecham, J.J.","contributorId":80101,"corporation":false,"usgs":true,"family":"Beecham","given":"J.J.","email":"","affiliations":[],"preferred":false,"id":452876,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Leithead, H.M.","contributorId":83759,"corporation":false,"usgs":true,"family":"Leithead","given":"H.M.","email":"","affiliations":[],"preferred":false,"id":452877,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70035876,"text":"70035876 - 2009 - Extremophile extracts and enhancement techniques show promise for the development of a live vaccine against Flavobacterium columnare","interactions":[],"lastModifiedDate":"2012-03-12T17:21:52","indexId":"70035876","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1349,"text":"Cryobiology","active":true,"publicationSubtype":{"id":10}},"title":"Extremophile extracts and enhancement techniques show promise for the development of a live vaccine against Flavobacterium columnare","docAbstract":"The effects of temperature, ionic strength, and new cryopreservatives derived from polar ice bacteria were investigated to help accelerate the development of economical, live attenuated vaccines for aquaculture. Extracts of the extremophile Gelidibacter algens functioned very well as part of a lyophilization cryoprotectant formulation in a 15-week storage trial. The bacterial extract and trehalose additives resulted in significantly higher colony counts of columnaris bacteria (Flavobacterium columnare) compared to nonfat milk or physiological saline at all time points measured. The bacterial extract combined with trehalose appeared to enhance the relative efficiency of recovery and growth potential of columnaris in flask culture compared to saline, nonfat milk, or trehalose-only controls. Pre-lyophilization temperature treatments significantly affected F. columnare survival following rehydration. A 30-min exposure at 0 ??C resulted in a 10-fold increase in bacterial survival following rehydration compared to mid-range temperature treatments. The brief 30 and 35 ??C pre-lyophilization exposures appeared to be detrimental to the rehydration survival of the bacteria. The survival of F. columnare through the lyophilization process was also strongly affected by changes in ionic strength of the bacterial suspension. Changes in rehydration constituents were also found to be important in promoting increased survival and growth. As the sodium chloride concentration increased, the viability of rehydrated F. columnare decreased. ?? 2009 Elsevier Inc.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Cryobiology","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1016/j.cryobiol.2009.06.006","issn":"00112240","usgsCitation":"Powell, D., Palm, R., MacKenzie, A., and Winton, J., 2009, Extremophile extracts and enhancement techniques show promise for the development of a live vaccine against Flavobacterium columnare: Cryobiology, v. 59, no. 2, p. 158-163, https://doi.org/10.1016/j.cryobiol.2009.06.006.","startPage":"158","endPage":"163","numberOfPages":"6","costCenters":[],"links":[{"id":216497,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1016/j.cryobiol.2009.06.006"},{"id":244371,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"59","issue":"2","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505a0e6ae4b0c8380cd53446","contributors":{"authors":[{"text":"Powell, D.B.","contributorId":63646,"corporation":false,"usgs":true,"family":"Powell","given":"D.B.","email":"","affiliations":[],"preferred":false,"id":452866,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Palm, R.C. Jr.","contributorId":94132,"corporation":false,"usgs":true,"family":"Palm","given":"R.C.","suffix":"Jr.","email":"","affiliations":[],"preferred":false,"id":452869,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"MacKenzie, A.P.","contributorId":77768,"corporation":false,"usgs":true,"family":"MacKenzie","given":"A.P.","email":"","affiliations":[],"preferred":false,"id":452867,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Winton, J. R. 0000-0002-3505-5509","orcid":"https://orcid.org/0000-0002-3505-5509","contributorId":82441,"corporation":false,"usgs":true,"family":"Winton","given":"J. R.","affiliations":[],"preferred":false,"id":452868,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70035829,"text":"70035829 - 2009 - Human-provided waters for desert wildlife: What is the problem?","interactions":[],"lastModifiedDate":"2012-03-12T17:21:48","indexId":"70035829","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3098,"text":"Policy Sciences","active":true,"publicationSubtype":{"id":10}},"title":"Human-provided waters for desert wildlife: What is the problem?","docAbstract":"Conflict persists in southwestern deserts of the United States over management of human-constructed devices to provide wildlife with water. We appraised decision processes in this case relative to the goal of human dignity and by the standards of civility and common interest outcomes. Our analysis suggested that conflict was scientized, rooted in worldviews, and aggravated by use of inflammatory symbols such as \"wilderness\" and \"bighorn sheep.\" Contested problem definitions, framed as matters of science, advanced factional interests largely by allocating the burden of proof and failing to disclose private concerns about well-being, affection, respect, skill and power. Decision processes were shaped by precepts of scientific management, and thus largely failed to foster civility, common ground, and a focus on common interests, and instead tended to exacerbate deprivations of dignity and respect. If the status quo continues, we foresee further erosion of human dignity because there are likely to be increases in system stressors, such as climate change and human population growth. The prognosis would be more hopeful if alternatives were adopted that entailed authoritative, equitable, and collaborative public decision-making processes that took into consideration national-level common interests such as the U.S. Endangered Species Act. ?? Springer Science+Business Media, LLC. 2008.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Policy Sciences","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1007/s11077-008-9073-z","issn":"00322687","usgsCitation":"Mattson, D., and Chambers, N., 2009, Human-provided waters for desert wildlife: What is the problem?: Policy Sciences, v. 42, no. 2, p. 113-135, https://doi.org/10.1007/s11077-008-9073-z.","startPage":"113","endPage":"135","numberOfPages":"23","costCenters":[],"links":[{"id":216287,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1007/s11077-008-9073-z"},{"id":244150,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"42","issue":"2","noUsgsAuthors":false,"publicationDate":"2008-12-02","publicationStatus":"PW","scienceBaseUri":"505a3287e4b0c8380cd5e89a","contributors":{"authors":[{"text":"Mattson, D.J.","contributorId":57022,"corporation":false,"usgs":true,"family":"Mattson","given":"D.J.","email":"","affiliations":[],"preferred":false,"id":452641,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Chambers, N.","contributorId":12291,"corporation":false,"usgs":true,"family":"Chambers","given":"N.","email":"","affiliations":[],"preferred":false,"id":452640,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70035824,"text":"70035824 - 2009 - Spectral distance decay","interactions":[],"lastModifiedDate":"2021-03-09T15:25:14.763781","indexId":"70035824","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3052,"text":"Photogrammetric Engineering and Remote Sensing","active":true,"publicationSubtype":{"id":10}},"title":"Spectral distance decay","docAbstract":"Remotely sensed data represents key information for character-izing and estimating biodiversity. Spectral distance among sites has proven to be a powerful approach for detecting species composition variability. Regression analysis of species similarity versus spectral distance may allow us to quantitatively estimate how beta-diversity in species changes with respect to spectral and ecological variability. In classical regression analysis, the residual sum of squares is minimized for the mean of the dependent variable distribution. However, many ecological datasets are characterized by a high number of zeroes that can add noise to the regression model. Quantile regression can be used to evaluate trend in the upper quantiles rather than a mean trend across the whole distribution of the dependent variable. In this paper, we used ordinary least square (OLS) and quantile regression to estimate the decay of species similarity versus spectral distance. The achieved decay rates were statistically nonzero (p < 0.05) considering both OLS and quantile regression. Nonetheless, OLS regression estimate of mean decay rate was only half the decay rate indicated by the upper quantiles. Moreover, the intercept value, representing the similarity reached when spectral distance approaches zero, was very low compared with the intercepts of upper quantiles, which detected high species similarity when habitats are more similar. In this paper we demonstrated the power of using quantile regressions applied to spectral distance decay in order to reveal species diversity patterns otherwise lost or underestimated by ordinary least square regression.
","language":"English","publisher":"American Society for Photogrammetry and Remote Sensing","doi":"10.14358/pers.75.10.1225","issn":"00991112","usgsCitation":"Rocchinl, D., Nagendra, H., Ghate, R., and Cade, B., 2009, Spectral distance decay: Photogrammetric Engineering and Remote Sensing, v. 75, no. 10, p. 1225-1230, https://doi.org/10.14358/pers.75.10.1225.","productDescription":"6 p.","startPage":"1225","endPage":"1230","numberOfPages":"6","costCenters":[],"links":[{"id":476313,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.14358/pers.75.10.1225","text":"Publisher Index Page"},{"id":384247,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"75","issue":"10","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505b953ce4b08c986b31ae01","contributors":{"authors":[{"text":"Rocchinl, D.","contributorId":40825,"corporation":false,"usgs":true,"family":"Rocchinl","given":"D.","email":"","affiliations":[],"preferred":false,"id":452590,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Nagendra, H.","contributorId":69809,"corporation":false,"usgs":true,"family":"Nagendra","given":"H.","email":"","affiliations":[],"preferred":false,"id":452592,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Ghate, R.","contributorId":12289,"corporation":false,"usgs":true,"family":"Ghate","given":"R.","email":"","affiliations":[],"preferred":false,"id":452589,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Cade, B.S.","contributorId":47315,"corporation":false,"usgs":true,"family":"Cade","given":"B.S.","affiliations":[],"preferred":false,"id":452591,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70035822,"text":"70035822 - 2009 - Nitrogen losses from dairy manure estimated through nitrogen mass balance and chemical markers","interactions":[],"lastModifiedDate":"2012-03-12T17:21:49","indexId":"70035822","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2262,"text":"Journal of Environmental Quality","active":true,"publicationSubtype":{"id":10}},"title":"Nitrogen losses from dairy manure estimated through nitrogen mass balance and chemical markers","docAbstract":"Ammonia is an important air and water pollutant, but the spatial variation in its concentrations presents technical difficulties in accurate determination of ammonia emissions from animal feeding operations. The objectives of this study were to investigate the relationship between ammonia volatilization and ??15N of dairy manure and the feasibility of estimating ammonia losses from a dairy facility using chemical markers. In Exp. 1, the N/P ratio in manure decreased by 30% in 14 d as cumulative ammonia losses increased exponentially. Delta 15N of manure increased throughout the course of the experiment and ??15N of emitted ammonia increased (p < 0.001) quadratically from -31??? to -15 ???. The relationship between cumulative ammonia losses and ??15N of manure was highly significant (p < 0.001; r2 = 0.76). In Exp. 2, using a mass balance approach, approximately half of the N excreted by dairy cows (Bos taurus) could not be accounted for in 24 h. Using N/P and N/K ratios in fresh and 24-h manure, an estimated 0.55 and 0.34 (respectively) of the N excreted with feces and urine could not be accounted for. This study demonstrated that chemical markers (P, K) can be successfully used to estimate ammonia losses from cattle manure. The relationship between manure ??15N and cumulative ammonia loss may also be useful for estimating ammonia losses. Although promising, the latter approach needs to be further studied and verified in various experimental conditions and in the field. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Journal of Environmental Quality","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.2134/jeq2009.0057","issn":"00472425","usgsCitation":"Hristov, A.N., Zaman, S., Vander Pol, M., Ndegwa, P., Campbell, L., and Silva, S., 2009, Nitrogen losses from dairy manure estimated through nitrogen mass balance and chemical markers: Journal of Environmental Quality, v. 38, no. 6, p. 2438-2448, https://doi.org/10.2134/jeq2009.0057.","startPage":"2438","endPage":"2448","numberOfPages":"11","costCenters":[],"links":[{"id":216140,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.2134/jeq2009.0057"},{"id":243988,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"38","issue":"6","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505a66ebe4b0c8380cd73086","contributors":{"authors":[{"text":"Hristov, Alexander N.","contributorId":81334,"corporation":false,"usgs":false,"family":"Hristov","given":"Alexander","email":"","middleInitial":"N.","affiliations":[],"preferred":false,"id":452581,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Zaman, S.","contributorId":47195,"corporation":false,"usgs":true,"family":"Zaman","given":"S.","email":"","affiliations":[],"preferred":false,"id":452578,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Vander Pol, M.","contributorId":91328,"corporation":false,"usgs":true,"family":"Vander Pol","given":"M.","email":"","affiliations":[],"preferred":false,"id":452582,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Ndegwa, P.","contributorId":105554,"corporation":false,"usgs":true,"family":"Ndegwa","given":"P.","email":"","affiliations":[],"preferred":false,"id":452583,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Campbell, L.","contributorId":76914,"corporation":false,"usgs":true,"family":"Campbell","given":"L.","email":"","affiliations":[],"preferred":false,"id":452580,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Silva, S.","contributorId":68518,"corporation":false,"usgs":true,"family":"Silva","given":"S.","affiliations":[],"preferred":false,"id":452579,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70035821,"text":"70035821 - 2009 - Sources of land-derived runoff to a coral reef-fringed embayment identified using geochemical tracers in nearshore sediment traps","interactions":[],"lastModifiedDate":"2017-11-05T09:13:21","indexId":"70035821","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1587,"text":"Estuarine, Coastal and Shelf Science","active":true,"publicationSubtype":{"id":10}},"title":"Sources of land-derived runoff to a coral reef-fringed embayment identified using geochemical tracers in nearshore sediment traps","docAbstract":"Geochemical tracers, including Ba, Co, Th, 7Be, 137Cs and 210Pb, and magnetic properties were used to characterize terrestrial runoff collected in nearshore time-series sediment traps in Hanalei Bay, Kauai, during flood and dry conditions in summer 2006, and to fingerprint possible runoff sources in the lower watershed. In combination, the tracers indicate that runoff during a flood in August could have come from cultivated taro fields bordering the lower reach of the river. Land-based runoff associated with summer floods may have a greater impact on coral reef communities in Hanalei Bay than in winter because sediment persists for several months. During dry periods, sediment carried by the Hanalei River appears to have been mobilized primarily by undercutting of low 7Be, low 137Cs riverbanks composed of soil weathered from tholeiitic basalt with low Ba and Co concentrations. Following a moderate rainfall event in September, high 7Be sediment carried by the Hanalei River was probably mobilized by overland flow in the upper watershed. Ba-desorption in low-salinity coastal water limited its use to a qualitative runoff tracer in nearshore sediment. 210Pb had limited usefulness as a terrestrial tracer in the nearshore due to a large dissolved oceanic source and scavenging onto resuspended bottom sediment. 210Pb-scavenging does, however, illustrate the role resuspension could play in the accumulation of particle-reactive contaminants in nearshore sediment. Co and 137Cs were not affected by desorption or geochemical scavenging and showed the greatest potential as quantitative sediment provenance indicators in material collected in nearshore sediment traps.","language":"English","publisher":"Elsevier","doi":"10.1016/j.ecss.2009.09.014","issn":"02727714","usgsCitation":"Takesue, R.K., Bothner, M., and Reynolds, R.L., 2009, Sources of land-derived runoff to a coral reef-fringed embayment identified using geochemical tracers in nearshore sediment traps: Estuarine, Coastal and Shelf Science, v. 85, no. 3, p. 459-471, https://doi.org/10.1016/j.ecss.2009.09.014.","startPage":"459","endPage":"471","numberOfPages":"13","costCenters":[],"links":[{"id":476247,"rank":1,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"https://hdl.handle.net/1912/3091","text":"External Repository"},{"id":243956,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"85","issue":"3","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505b937ee4b08c986b31a4fe","contributors":{"authors":[{"text":"Takesue, Renee K. 0000-0003-1205-0825 rtakesue@usgs.gov","orcid":"https://orcid.org/0000-0003-1205-0825","contributorId":2159,"corporation":false,"usgs":true,"family":"Takesue","given":"Renee","email":"rtakesue@usgs.gov","middleInitial":"K.","affiliations":[{"id":520,"text":"Pacific Coastal and Marine Science Center","active":true,"usgs":true}],"preferred":true,"id":452575,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Bothner, Michael H. mbothner@usgs.gov","contributorId":139855,"corporation":false,"usgs":true,"family":"Bothner","given":"Michael H.","email":"mbothner@usgs.gov","affiliations":[{"id":678,"text":"Woods Hole Coastal and Marine Science Center","active":true,"usgs":true}],"preferred":false,"id":452576,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Reynolds, Richard L. 0000-0002-4572-2942 rreynolds@usgs.gov","orcid":"https://orcid.org/0000-0002-4572-2942","contributorId":441,"corporation":false,"usgs":true,"family":"Reynolds","given":"Richard","email":"rreynolds@usgs.gov","middleInitial":"L.","affiliations":[{"id":271,"text":"Federal Center","active":false,"usgs":true}],"preferred":true,"id":452577,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70035820,"text":"70035820 - 2009 - A one-dimensional heat-transport model for conduit flow in karst aquifers","interactions":[],"lastModifiedDate":"2012-03-12T17:21:49","indexId":"70035820","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2342,"text":"Journal of Hydrology","active":true,"publicationSubtype":{"id":10}},"title":"A one-dimensional heat-transport model for conduit flow in karst aquifers","docAbstract":"A one-dimensional heat-transport model for conduit flow in karst aquifers is presented as an alternative to two or three-dimensional distributed-parameter models, which are data intensive and require knowledge of conduit locations. This model can be applied for cases where water temperature in a well or spring receives all or part of its water from a phreatic conduit. Heat transport in the conduit is simulated by using a physically-based heat-transport equation that accounts for inflow of diffuse flow from smaller openings and fissures in the surrounding aquifer during periods of low recharge. Additional diffuse flow that is within the zone of influence of the well or spring but has not interacted with the conduit is accounted for with a binary mixing equation to proportion these different water sources. The estimation of this proportion through inverse modeling is useful for the assessment of contaminant vulnerability and well-head or spring protection. The model was applied to 7 months of continuous temperature data for a sinking stream that recharges a conduit and a pumped well open to the Madison aquifer in western South Dakota. The simulated conduit-flow fraction to the well ranged from 2% to 31% of total flow, and simulated conduit velocity ranged from 44 to 353 m/d.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Journal of Hydrology","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1016/j.jhydrol.2009.09.024","issn":"00221694","usgsCitation":"Long, A., and Gilcrease, P., 2009, A one-dimensional heat-transport model for conduit flow in karst aquifers: Journal of Hydrology, v. 378, no. 3-4, p. 230-239, https://doi.org/10.1016/j.jhydrol.2009.09.024.","startPage":"230","endPage":"239","numberOfPages":"10","costCenters":[],"links":[{"id":243955,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":216109,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1016/j.jhydrol.2009.09.024"}],"volume":"378","issue":"3-4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059e4cae4b0c8380cd4692b","contributors":{"authors":[{"text":"Long, Andrew J.","contributorId":80023,"corporation":false,"usgs":false,"family":"Long","given":"Andrew J.","affiliations":[],"preferred":false,"id":452574,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Gilcrease, P.C.","contributorId":58116,"corporation":false,"usgs":true,"family":"Gilcrease","given":"P.C.","email":"","affiliations":[],"preferred":false,"id":452573,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70035818,"text":"70035818 - 2009 - Differential virulence mechanisms of infectious hematopoietic necrosis virus in rainbow trout (Oncorhynchus mykiss) include host entry and virus replication kinetics","interactions":[],"lastModifiedDate":"2016-12-28T17:43:47","indexId":"70035818","displayToPublicDate":"2009-01-01T00:00:00","publicationYear":"2009","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2301,"text":"Journal of General Virology","active":true,"publicationSubtype":{"id":10}},"title":"Differential virulence mechanisms of infectious hematopoietic necrosis virus in rainbow trout (Oncorhynchus mykiss) include host entry and virus replication kinetics","docAbstract":"Host specificity is a phenomenon exhibited by all viruses. For the fish rhabdovirus infectious hematopoietic necrosis virus (IHNV), differential specificity of virus strains from the U and M genogroups has been established both in the field and in experimental challenges. In rainbow trout (Oncorhynchus mykiss), M IHNV strains are consistently more prevalent and more virulent than U IHNV. The basis of the differential ability of these two IHNV genogroups to cause disease in rainbow trout was investigated in live infection challenges with representative U and M IHNV strains. When IHNV was delivered by intraperitoneal injection, the mortality caused by U IHNV increased, indicating that the low virulence of U IHNV is partly due to inefficiency in entering the trout host. Analyses of in vivo replication showed that U IHNV consistently had lower prevalence and lower viral load than M IHNV during the course of infection. In analyses of the host immune response, M IHNV-infected fish consistently had higher and longer expression of innate immune-related genes such as Mx-1. This suggests that the higher virulence of M IHNV is not due to suppression of the immune response in rainbow trout. Taken together, the results support a kinetics hypothesis wherein faster replication enables M IHNV to rapidly achieve a threshold level of virus necessary to override the strong host innate immune response. ?? 2009 SGM.","language":"English","publisher":"Microbiology Society ","doi":"10.1099/vir.0.012286-0","issn":"00221317","usgsCitation":"Penaranda, M., Purcell, M.K., and Kurath, G., 2009, Differential virulence mechanisms of infectious hematopoietic necrosis virus in rainbow trout (Oncorhynchus mykiss) include host entry and virus replication kinetics: Journal of General Virology, v. 90, no. 9, p. 2172-2182, https://doi.org/10.1099/vir.0.012286-0.","productDescription":"11 p.","startPage":"2172","endPage":"2182","costCenters":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"links":[{"id":476341,"rank":10000,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1099/vir.0.012286-0","text":"Publisher Index Page"},{"id":243922,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":216080,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1099/vir.0.012286-0"}],"volume":"90","issue":"9","noUsgsAuthors":false,"publicationDate":"2009-05-27","publicationStatus":"PW","scienceBaseUri":"505a0104e4b0c8380cd4fa4b","contributors":{"authors":[{"text":"Penaranda, M.M.D.","contributorId":17845,"corporation":false,"usgs":true,"family":"Penaranda","given":"M.M.D.","email":"","affiliations":[],"preferred":false,"id":452567,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Purcell, M. K.","contributorId":78464,"corporation":false,"usgs":true,"family":"Purcell","given":"M.","email":"","middleInitial":"K.","affiliations":[],"preferred":false,"id":452568,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Kurath, Gael 0000-0003-3294-560X gkurath@usgs.gov","orcid":"https://orcid.org/0000-0003-3294-560X","contributorId":100522,"corporation":false,"usgs":true,"family":"Kurath","given":"Gael","email":"gkurath@usgs.gov","affiliations":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"preferred":true,"id":452569,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ]}