The overarching goal of this research was to develop and demonstrate an automated Cropland Classification Algorithm (ACCA) that will rapidly, routinely, and accurately classify agricultural cropland extent, areas, and characteristics (e.g., irrigated vs. rainfed) over large areas such as a country or a region through combination of multi-sensor remote sensing and secondary data. In this research, a rule-based ACCA was conceptualized, developed, and demonstrated for the country of Tajikistan using mega file data cubes (MFDCs) involving data from Landsat Global Land Survey (GLS), Landsat Enhanced Thematic Mapper Plus (ETM+) 30 m, Moderate Resolution Imaging Spectroradiometer (MODIS) 250 m time-series, a suite of secondary data (e.g., elevation, slope, precipitation, temperature), and in situ data. First, the process involved producing an accurate reference (or truth) cropland layer (TCL), consisting of cropland extent, areas, and irrigated vs. rainfed cropland areas, for the entire country of Tajikistan based on MFDC of year 2005 (MFDC2005). The methods involved in producing TCL included using ISOCLASS clustering, Tasseled Cap bi-spectral plots, spectro-temporal characteristics from MODIS 250 m monthly normalized difference vegetation index (NDVI) maximum value composites (MVC) time-series, and textural characteristics of higher resolution imagery. The TCL statistics accurately matched with the national statistics of Tajikistan for irrigated and rainfed croplands, where about 70% of croplands were irrigated and the rest rainfed. Second, a rule-based ACCA was developed to replicate the TCL accurately (∼80% producer’s and user’s accuracies or within 20% quantity disagreement involving about 10 million Landsat 30 m sized cropland pixels of Tajikistan). Development of ACCA was an iterative process involving series of rules that are coded, refined, tweaked, and re-coded till ACCA derived croplands (ACLs) match accurately with TCLs. Third, the ACCA derived cropland layers of Tajikistan were produced for year 2005 (ACL2005), same year as the year used for developing ACCA, using MFDC2005. Fourth, TCL for year 2010 (TCL2010), an independent year, was produced using MFDC2010 using the same methods and approaches as the one used to produce TCL2005. Fifth, the ACCA was applied on MFDC2010 to derive ACL2010. The ACLs were then compared with TCLs (ACL2005 vs. TCL2005 and ACL2010 vs. TCL2010). The resulting accuracies and errors from error matrices involving about 152 million Landsat (30 m) pixels of the country of Tajikistan (of which about 10 million Landsat size, 30 m, cropland pixels) showed an overall accuracy of 99.6% (khat = 0.97) for ACL2005 vs. TCL2005. For the 3 classes (irrigated, rainfed, and others) mapped in ACL2005, the producer’s accuracy was >86.4% and users accuracy was >93.6%. For ACL2010 vs. TCL2010, the error matrix showed an overall accuracy on 96.2% (khat = 0.96). For the 3 classes (irrigated, rainfed, and others) mapped in ACL2010, the producer’s and user’s accuracies for the irrigated areas were ≥82.9%. Any intermixing was overwhelmingly between irrigated and rainfed croplands, indicating that croplands (irrigated plus rainfed areas) as well as irrigated areas were mapped with high levels of accuracies (∼90% or higher) even for the independent year. The ACL2005 and ACL2010, each, were produced using ACCA algorithm in ∼30 min using a Dell Precision desktop T7400 computer for the entire country of Tajikistan once the MFDCs for the years were ready. The ACCA algorithm for Tajikistan is made available through US Geological Survey’s ScienceBase: http://www.sciencebase.gov/catalog/folder/4f79f1b7e4b0009bd827f548 or at: https://powellcenter.usgs.gov/globalcroplandwater/content/models-algorithms. The research contributes to the efforts of global food security through research on global croplands and their water use (e.g., https://powellcenter.usgs.gov/globalcroplandwater/). The above results clearly demonstrated the ability of a rule-based ACCA to rapidly and accurately produce cropland data layer year after year (hindcast, nowcast, forecast) for the country it was developed using MFDCs that consist of combining multiple sensor data and secondary data. It needs to be noted that the ACCA is applicable to the area (e.g., country, region) for which it is developed. In this case, ACCA is applicable for the Country of Tajikistan to hindcast, nowcast, and forecast agricultural cropland extent, areas, and irrigated vs. rainfed. The same fundamental concept of ACCA applies to other areas of the World where ACCA codes need to be modified to suite the area/region of interest. ACCA can also be expanded to compute other crop characteristics such as crop types, cropping intensities, and phenologies.
","language":"English","publisher":"MDPI","doi":"10.3390/rs4102890","usgsCitation":"Thenkabail, P.S., and Wu, Z., 2012, An Automated Cropland Classification Algorithm (ACCA) for Tajikistan by combining Landsat, MODIS, and secondary data: Remote Sensing, v. 4, no. 10, p. 2890-2918, https://doi.org/10.3390/rs4102890.","productDescription":"29 p.","startPage":"2890","endPage":"2918","ipdsId":"IP-035313","costCenters":[{"id":273,"text":"Flagstaff Science Center","active":false,"usgs":true}],"links":[{"id":474346,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.3390/rs4102890","text":"Publisher Index Page"},{"id":430841,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Tajikistan","geographicExtents":"{\"type\":\"FeatureCollection\",\"features\":[{\"type\":\"Feature\",\"geometry\":{\"type\":\"Polygon\",\"coordinates\":[[[71.0142,40.24437],[70.64802,39.93575],[69.55961,40.10321],[69.46489,39.52668],[70.54916,39.6042],[71.78469,39.27946],[73.67538,39.43124],[73.92885,38.50582],[74.25751,38.60651],[74.86482,38.37885],[74.82999,37.99001],[74.98,37.41999],[73.9487,37.42157],[73.26006,37.49526],[72.63689,37.04756],[72.19304,36.94829],[71.84464,36.73817],[71.44869,37.06564],[71.54192,37.90577],[71.2394,37.95327],[71.34813,38.25891],[70.80682,38.48628],[70.3763,38.1384],[70.27057,37.73516],[70.11658,37.58822],[69.51879,37.609],[69.19627,37.15114],[68.85945,37.34434],[68.13556,37.02312],[67.83,37.14499],[68.39203,38.15703],[68.17603,38.90155],[67.44222,39.14014],[67.70143,39.58048],[68.53642,39.53345],[69.01163,40.08616],[69.32949,40.72782],[70.66662,40.96021],[70.45816,40.49649],[70.60141,40.21853],[71.0142,40.24437]]]},\"properties\":{\"name\":\"Tajikistan\"}}]}","volume":"4","issue":"10","noUsgsAuthors":false,"publicationDate":"2012-09-25","publicationStatus":"PW","contributors":{"authors":[{"text":"Thenkabail, Prasad S. 0000-0002-2182-8822 pthenkabail@usgs.gov","orcid":"https://orcid.org/0000-0002-2182-8822","contributorId":570,"corporation":false,"usgs":true,"family":"Thenkabail","given":"Prasad","email":"pthenkabail@usgs.gov","middleInitial":"S.","affiliations":[{"id":657,"text":"Western Geographic Science Center","active":true,"usgs":true}],"preferred":true,"id":905870,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Wu, Zhuoting 0000-0001-7393-1832 zwu@usgs.gov","orcid":"https://orcid.org/0000-0001-7393-1832","contributorId":4953,"corporation":false,"usgs":true,"family":"Wu","given":"Zhuoting","email":"zwu@usgs.gov","affiliations":[{"id":498,"text":"Office of Land Remote Sensing (Geography)","active":true,"usgs":true},{"id":657,"text":"Western Geographic Science Center","active":true,"usgs":true}],"preferred":true,"id":905871,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70040007,"text":"70040007 - 2012 - Subsurface gas hydrates in the northern Gulf of Mexico","interactions":[],"lastModifiedDate":"2012-09-25T17:16:32","indexId":"70040007","displayToPublicDate":"2012-09-25T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2682,"text":"Marine and Petroleum Geology","active":true,"publicationSubtype":{"id":10}},"title":"Subsurface gas hydrates in the northern Gulf of Mexico","docAbstract":"The northernGulf of Mexico (GoM) has long been a focus area for the study of gashydrates. Throughout the 1980s and 1990s, work focused on massive gashydrates deposits that were found to form at and near the seafloor in association with hydrocarbon seeps. However, as global scientific and industrial interest in assessment of the drilling hazards and resource implications of gashydrate accelerated, focus shifted to understanding the nature and abundance of \"buried\" gashydrates. Through 2005, despite the drilling of more than 1200 oil and gas industry wells through the gashydrate stability zone, published evidence of significant sub-seafloor gashydrate in the GoM was lacking. A 2005 drilling program by the GoM GasHydrate Joint Industry Project (the JIP) provided an initial confirmation of the occurrence of gashydrates below the GoM seafloor. In 2006, release of data from a 2003 industry well in Alaminos Canyon 818 provided initial documentation of gashydrate occurrence at high concentrations in sand reservoirs in the GoM. From 2006 to 2008, the JIP facilitated the integration of geophysical and geological data to identify sites prospective for gashydrate-bearing sands, culminating in the recommendation of numerous drilling targets within four sites spanning a range of typical deepwater settings. Concurrent with, but independent of, the JIP prospecting effort, the Bureau of Ocean Energy Management (BOEM) conducted a preliminary assessment of the GoM gashydratepetroleum system, resulting in an estimate of 607 trillion cubic meters (21,444 trillion cubic feet) gas-in-place of which roughly one-third occurs at expected high concentrations in sand reservoirs. In 2009, the JIP drilled seven wells at three sites, discovering gashydrate at high saturation in sand reservoirs in four wells and suspected gashydrate at low to moderate saturations in two other wells. These results provide an initial confirmation of the complex nature and occurrence of gashydrate-bearing sands in the GoM, the efficacy of the integrated geological/geophysical prospecting approach used to identify the JIP drilling sites, and the relevance of the 2008 BOEM assessment.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Marine and Petroleum Geology","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","publisher":"Elsevier","publisherLocation":"Amsterdam, Netherlands","doi":"10.1016/j.marpetgeo.2011.10.003","usgsCitation":"Boswell, R., Collett, T.S., Frye, M., Shedd, W., McConnell, D.R., and Shelander, D., 2012, Subsurface gas hydrates in the northern Gulf of Mexico: Marine and Petroleum Geology, v. 34, no. 1, p. 4-30, https://doi.org/10.1016/j.marpetgeo.2011.10.003.","productDescription":"27 p.","startPage":"4","endPage":"30","numberOfPages":"26","costCenters":[{"id":164,"text":"Central Energy Resources Science Center","active":true,"usgs":true}],"links":[{"id":262046,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":262043,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1016/j.marpetgeo.2011.10.003","linkFileType":{"id":5,"text":"html"}}],"country":"United States","otherGeospatial":"Gulf Of Mexico","geographicExtents":"{ \"type\": \"FeatureCollection\", \"features\": [ { \"type\": \"Feature\", \"properties\": {}, \"geometry\": { \"type\": \"Polygon\", \"coordinates\": [ [ [ -97.85,18.166666666666668 ], [ -97.85,30.383333333333333 ], [ -81.03333333333333,30.383333333333333 ], [ -81.03333333333333,18.166666666666668 ], [ -97.85,18.166666666666668 ] ] ] } } ] }","volume":"34","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"50e4dfa4e4b0e8fec6ce49b7","contributors":{"authors":[{"text":"Boswell, Ray","contributorId":12307,"corporation":false,"usgs":true,"family":"Boswell","given":"Ray","affiliations":[],"preferred":false,"id":467435,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Collett, Timothy S. 0000-0002-7598-4708 tcollett@usgs.gov","orcid":"https://orcid.org/0000-0002-7598-4708","contributorId":1698,"corporation":false,"usgs":true,"family":"Collett","given":"Timothy","email":"tcollett@usgs.gov","middleInitial":"S.","affiliations":[{"id":255,"text":"Energy Resources Program","active":true,"usgs":true},{"id":678,"text":"Woods Hole Coastal and Marine Science Center","active":true,"usgs":true},{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true},{"id":164,"text":"Central Energy Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":467434,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Frye, Matthew","contributorId":48428,"corporation":false,"usgs":true,"family":"Frye","given":"Matthew","affiliations":[],"preferred":false,"id":467439,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Shedd, William","contributorId":13851,"corporation":false,"usgs":true,"family":"Shedd","given":"William","affiliations":[],"preferred":false,"id":467436,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"McConnell, Daniel R.","contributorId":47628,"corporation":false,"usgs":true,"family":"McConnell","given":"Daniel","email":"","middleInitial":"R.","affiliations":[],"preferred":false,"id":467438,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Shelander, Dianna","contributorId":40463,"corporation":false,"usgs":true,"family":"Shelander","given":"Dianna","email":"","affiliations":[],"preferred":false,"id":467437,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70039994,"text":"70039994 - 2012 - Coupled atmosphere-ocean-wave simulations of a storm event over the Gulf of Lion and Balearic Sea","interactions":[],"lastModifiedDate":"2012-10-01T17:02:55","indexId":"70039994","displayToPublicDate":"2012-09-21T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2312,"text":"Journal of Geophysical Research","active":true,"publicationSubtype":{"id":10}},"title":"Coupled atmosphere-ocean-wave simulations of a storm event over the Gulf of Lion and Balearic Sea","docAbstract":"The coastal areas of the North-Western Mediterranean Sea are one of the most challenging places for ocean forecasting. This region is exposed to severe storms events that are of short duration. During these events, significant air-sea interactions, strong winds and large sea-state can have catastrophic consequences in the coastal areas. To investigate these air-sea interactions and the oceanic response to such events, we implemented the Coupled Ocean-Atmosphere-Wave-Sediment Transport Modeling System simulating a severe storm in the Mediterranean Sea that occurred in May 2010. During this event, wind speed reached up to 25 m.s-1 inducing significant sea surface cooling (up to 2°C) over the Gulf of Lion (GoL) and along the storm track, and generating surface waves with a significant height of 6 m. It is shown that the event, associated with a cyclogenesis between the Balearic Islands and the GoL, is relatively well reproduced by the coupled system. A surface heat budget analysis showed that ocean vertical mixing was a major contributor to the cooling tendency along the storm track and in the GoL where turbulent heat fluxes also played an important role. Sensitivity experiments on the ocean-atmosphere coupling suggested that the coupled system is sensitive to the momentum flux parameterization as well as air-sea and air-wave coupling. Comparisons with available atmospheric and oceanic observations showed that the use of the fully coupled system provides the most skillful simulation, illustrating the benefit of using a fully coupled ocean-atmosphere-wave model for the assessment of these storm events.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Journal of Geophysical Research","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","publisher":"American Geophysical Union","publisherLocation":"Washington, D.C.","doi":"10.1029/2012JC007924","usgsCitation":"Renault, L., Chiggiato, J., Warner, J., Gomez, M., Vizoso, G., and Tintore, J., 2012, Coupled atmosphere-ocean-wave simulations of a storm event over the Gulf of Lion and Balearic Sea: Journal of Geophysical Research, v. 117, 25 p.; C09019, https://doi.org/10.1029/2012JC007924.","productDescription":"25 p.; C09019","numberOfPages":"25","costCenters":[{"id":678,"text":"Woods Hole Coastal and Marine Science Center","active":true,"usgs":true}],"links":[{"id":474352,"rank":10000,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1029/2012jc007924","text":"Publisher Index Page"},{"id":262013,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":262004,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1029/2012JC007924","linkFileType":{"id":5,"text":"html"}}],"otherGeospatial":"Gulf Of Lion;Balearic Sea","volume":"117","noUsgsAuthors":false,"publicationDate":"2012-09-15","publicationStatus":"PW","scienceBaseUri":"505d7e67e4b0ea5c818244e3","contributors":{"authors":[{"text":"Renault, Lionel","contributorId":63255,"corporation":false,"usgs":true,"family":"Renault","given":"Lionel","email":"","affiliations":[],"preferred":false,"id":467402,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Chiggiato, Jacopo","contributorId":13081,"corporation":false,"usgs":true,"family":"Chiggiato","given":"Jacopo","email":"","affiliations":[],"preferred":false,"id":467398,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Warner, John C. 0000-0002-3734-8903 jcwarner@usgs.gov","orcid":"https://orcid.org/0000-0002-3734-8903","contributorId":2681,"corporation":false,"usgs":true,"family":"Warner","given":"John C.","email":"jcwarner@usgs.gov","affiliations":[{"id":678,"text":"Woods Hole Coastal and Marine Science Center","active":true,"usgs":true}],"preferred":true,"id":467397,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Gomez, Marta","contributorId":17461,"corporation":false,"usgs":true,"family":"Gomez","given":"Marta","email":"","affiliations":[],"preferred":false,"id":467399,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Vizoso, Guillermo","contributorId":34761,"corporation":false,"usgs":true,"family":"Vizoso","given":"Guillermo","email":"","affiliations":[],"preferred":false,"id":467401,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Tintore, Joaquin","contributorId":17462,"corporation":false,"usgs":true,"family":"Tintore","given":"Joaquin","email":"","affiliations":[],"preferred":false,"id":467400,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70039976,"text":"fs20123087 - 2012 - Sylvatic plague vaccine and management of prairie dogs","interactions":[],"lastModifiedDate":"2015-06-25T14:24:20","indexId":"fs20123087","displayToPublicDate":"2012-09-19T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":313,"text":"Fact Sheet","code":"FS","onlineIssn":"2327-6932","printIssn":"2327-6916","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"2012-3087","title":"Sylvatic plague vaccine and management of prairie dogs","docAbstract":"Scientists at the USGS National Wildlife Health Center (NWHC), in collaboration with colleagues at the University of Wisconsin (UW), have developed a sylvatic plague vaccine that shows great promise in protecting prairie dogs against plague (Mencher and others, 2004; Rocke and others, 2010). Four species of prairie dogs reside in the United States and Canada, and all are highly susceptible to plague and regularly experience outbreaks with devastating losses. Along with habitat loss and poisoning, plague has contributed to a significant historical decline in prairie dog populations. By some estimates, prairie dogs now occupy only 1 to 2 percent of their former range (Proctor and others, 2006), with prairie dog colonies being now much smaller and fragmented than they were historically, making individual colonies more vulnerable to elimination by plague (Antolin and others, 2002). At least one species, the Utah prairie dog (Cynomys parvidens) is listed by the U.S. Fish and Wildlife Service (FWS) as \"threatened.\" Controlling plague is a vital concern for ongoing management and conservation efforts for prairie dogs. Current efforts to halt the spread of plague in prairie dog colonies typically rely on dusting individual prairie dog burrows with pesticides to kill plague-infected fleas. Although flea-control insecticides, such as deltamethrin, are useful in stopping plague outbreaks in these prairie dog colonies, dusting of burrows is labor intensive and time consuming and may affect other insects and arthropods. As an alternative approach, NWHC and UW scientists developed a sylvatic plague vaccine (SPV) for prairie dogs that can be delivered via oral bait. Laboratory studies have shown that consumption of this vaccine-laden bait by different prairie dog species results in significant protection against plague infection that can last for at least 9 months (Rocke and others, 2010; Rocke, unpublished). Work has now shifted to optimizing baits and distribution methods for field delivery of the vaccine. Ultimately, the bait will be formulated in a size and shape that facilitates distribution by plane or overland vehicle. Field studies to assess the safety and efficacy of SPV are being planned. These studies will require involvement from numerous partners, including state and federal land management agencies, tribal organizations, private landowners and non-government agencies.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/fs20123087","usgsCitation":"Rocke, T.E., 2012, Sylvatic plague vaccine and management of prairie dogs: U.S. Geological Survey Fact Sheet 2012-3087, 2 p., https://doi.org/10.3133/fs20123087.","productDescription":"2 p.","onlineOnly":"N","additionalOnlineFiles":"N","costCenters":[{"id":456,"text":"National Wildlife Health Center","active":true,"usgs":true}],"links":[{"id":261978,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/fs_2012_3087.jpg"},{"id":261971,"rank":100,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/fs/2012/3087/","linkFileType":{"id":5,"text":"html"}},{"id":261972,"rank":300,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/fs/2012/3087/pdf/FS2012_3087_web-lr_th.pdf","linkFileType":{"id":1,"text":"pdf"}}],"country":"Canada;United States","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505ba335e4b08c986b31fbfb","contributors":{"authors":[{"text":"Rocke, Tonie E. 0000-0003-3933-1563 trocke@usgs.gov","orcid":"https://orcid.org/0000-0003-3933-1563","contributorId":2665,"corporation":false,"usgs":true,"family":"Rocke","given":"Tonie","email":"trocke@usgs.gov","middleInitial":"E.","affiliations":[{"id":456,"text":"National Wildlife Health Center","active":true,"usgs":true}],"preferred":true,"id":467360,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":70039945,"text":"70039945 - 2012 - Matrix population models from 20 studies of perennial plant populations","interactions":[],"lastModifiedDate":"2012-09-18T17:16:41","indexId":"70039945","displayToPublicDate":"2012-09-18T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1465,"text":"Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Matrix population models from 20 studies of perennial plant populations","docAbstract":"Demographic transition matrices are one of the most commonly applied population models for both basic and applied ecological research. The relatively simple framework of these models and simple, easily interpretable summary statistics they produce have prompted the wide use of these models across an exceptionally broad range of taxa. Here, we provide annual transition matrices and observed stage structures/population sizes for 20 perennial plant species which have been the focal species for long-term demographic monitoring. These data were assembled as part of the \"Testing Matrix Models\" working group through the National Center for Ecological Analysis and Synthesis (NCEAS). In sum, these data represent 82 populations with >460 total population-years of data. It is our hope that making these data available will help promote and improve our ability to monitor and understand plant population dynamics.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Ecology","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","publisher":"ESA","publisherLocation":"Ithaca, NY","doi":"10.1890/11-1052.1","usgsCitation":"Ellis, M.M., Williams, J.L., Lesica, P., Bell, T.J., Bierzychudek, P., Bowles, M., Crone, E.E., Doak, D.F., Ehrlen, J., Ellis-Adam, A., McEachern, K., Ganesan, R., Latham, P., Luijten, S., Kaye, T.N., Knight, T.M., Menges, E.S., Morris, W.F., den Nijs, H., Oostermeijer, G., Quintana-Ascencio, P.F., Shelly, J.S., Stanley, A., Thorpe, A., Tamara, T., Valverde, T., and Weekley, C.W., 2012, Matrix population models from 20 studies of perennial plant populations: Ecology, v. 93, no. 4, p. 951-951, https://doi.org/10.1890/11-1052.1.","productDescription":"1 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Other such types include habitat modification, predator interference and facilitation. However, ecological network research has been typically limited to either pure food webs or to networks of only a few (<3) interaction types. The great diversity of non-trophic interactions observed in nature has been poorly addressed by ecologists and largely excluded from network theory. Herein, we propose a conceptual framework that organises this diversity into three main functional classes defined by how they modify specific parameters in a dynamic food web model. This approach provides a path forward for incorporating non-trophic interactions in traditional food web models and offers a new perspective on tackling ecological complexity that should stimulate both theoretical and empirical approaches to understanding the patterns and dynamics of diverse species interactions in nature.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Ecology Letters","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","publisher":"Blackwell Publishing","doi":"10.1111/j.1461-0248.2011.01732.x","usgsCitation":"Kéfi, S., Berlow, E.L., Wieters, E.A., Navarrete, S.A., Petchey, O.L., Wood, S.A., Boit, A., Joppa, L.N., Lafferty, K.D., Williams, R.J., Martinez, N.D., Menge, B.A., Blanchette, C.A., Iles, A.C., and Brose, U., 2012, More than a meal: integrating non-feeding interactions into food webs: Ecology Letters, v. 15, no. 4, p. 291-300, https://doi.org/10.1111/j.1461-0248.2011.01732.x.","productDescription":"10 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2012 - Mapping wintering waterfowl distributions using weather surveillance radar","interactions":[],"lastModifiedDate":"2012-09-12T17:16:23","indexId":"70039880","displayToPublicDate":"2012-09-12T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2980,"text":"PLoS ONE","active":true,"publicationSubtype":{"id":10}},"title":"Mapping wintering waterfowl distributions using weather surveillance radar","docAbstract":"The current network of weather surveillance radars within the United States readily detects flying birds and has proven to be a useful remote-sensing tool for ornithological study. Radar reflectivity measures serve as an index to bird density and have been used to quantitatively map landbird distributions during migratory stopover by sampling birds aloft at the onset of nocturnal migratory flights. Our objective was to further develop and validate a similar approach for mapping wintering waterfowl distributions using weather surveillance radar observations at the onset of evening flights. We evaluated data from the Sacramento, CA radar (KDAX) during winters 1998–1999 and 1999–2000. We determined an optimal sampling time by evaluating the accuracy and precision of radar observations at different times during the onset of evening flight relative to observed diurnal distributions of radio-marked birds on the ground. The mean time of evening flight initiation occurred 23 min after sunset with the strongest correlations between reflectivity and waterfowl density on the ground occurring almost immediately after flight initiation. Radar measures became more spatially homogeneous as evening flight progressed because birds dispersed from their departure locations. Radars effectively detected birds to a mean maximum range of 83 km during the first 20 min of evening flight. Using a sun elevation angle of -5° (28 min after sunset) as our optimal sampling time, we validated our approach using KDAX data and additional data from the Beale Air Force Base, CA (KBBX) radar during winter 1998–1999. Bias-adjusted radar reflectivity of waterfowl aloft was positively related to the observed diurnal density of radio-marked waterfowl locations on the ground. Thus, weather radars provide accurate measures of relative wintering waterfowl density that can be used to comprehensively map their distributions over large spatial extents.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"PLoS ONE","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","publisher":"Public Library of Science","publisherLocation":"San Francisco, CA","doi":"10.1371/journal.pone.0041571","usgsCitation":"Buler, J., Randall, L.A., Fleskes, J.P., Barrow, W., Bogart, T., and Kluver, D., 2012, Mapping wintering waterfowl distributions using weather surveillance radar: PLoS ONE, v. 7, no. 7, 9 p.; e41571, https://doi.org/10.1371/journal.pone.0041571.","productDescription":"9 p.; e41571","costCenters":[{"id":455,"text":"National Wetlands Research Center","active":true,"usgs":true}],"links":[{"id":474363,"rank":10000,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1371/journal.pone.0041571","text":"Publisher Index Page"},{"id":261856,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":261838,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1371/journal.pone.0041571","linkFileType":{"id":5,"text":"html"}}],"country":"United States","volume":"7","issue":"7","noUsgsAuthors":false,"publicationDate":"2012-07-23","publicationStatus":"PW","scienceBaseUri":"505a5093e4b0c8380cd6b7ae","contributors":{"authors":[{"text":"Buler, Jeffrey J.","contributorId":78431,"corporation":false,"usgs":true,"family":"Buler","given":"Jeffrey J.","affiliations":[],"preferred":false,"id":467141,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Randall, Lori A. 0000-0003-0100-994X randalll@usgs.gov","orcid":"https://orcid.org/0000-0003-0100-994X","contributorId":2678,"corporation":false,"usgs":true,"family":"Randall","given":"Lori","email":"randalll@usgs.gov","middleInitial":"A.","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true},{"id":455,"text":"National Wetlands Research Center","active":true,"usgs":true}],"preferred":true,"id":467138,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Fleskes, Joseph P. 0000-0001-5388-6675 joe_fleskes@usgs.gov","orcid":"https://orcid.org/0000-0001-5388-6675","contributorId":1889,"corporation":false,"usgs":true,"family":"Fleskes","given":"Joseph","email":"joe_fleskes@usgs.gov","middleInitial":"P.","affiliations":[{"id":651,"text":"Western Ecological Research Center","active":true,"usgs":true}],"preferred":false,"id":467136,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Barrow, Wylie C. 0000-0003-4671-2823 barroww@usgs.gov","orcid":"https://orcid.org/0000-0003-4671-2823","contributorId":1988,"corporation":false,"usgs":true,"family":"Barrow","given":"Wylie C.","email":"barroww@usgs.gov","affiliations":[{"id":455,"text":"National Wetlands Research Center","active":true,"usgs":true}],"preferred":false,"id":467137,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Bogart, Tianna","contributorId":73868,"corporation":false,"usgs":true,"family":"Bogart","given":"Tianna","email":"","affiliations":[],"preferred":false,"id":467140,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Kluver, Daria","contributorId":9906,"corporation":false,"usgs":true,"family":"Kluver","given":"Daria","email":"","affiliations":[],"preferred":false,"id":467139,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70039864,"text":"70039864 - 2012 - Frequency of nest use by golden eagles in southwestern Idaho","interactions":[],"lastModifiedDate":"2012-09-12T17:16:23","indexId":"70039864","displayToPublicDate":"2012-09-12T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2442,"text":"Journal of Raptor Research","active":true,"publicationSubtype":{"id":10}},"title":"Frequency of nest use by golden eagles in southwestern Idaho","docAbstract":"We studied nest use by Golden Eagles (Aquila chrysaetos) from 1966 to 2011 to assess nest reuse within territories, ascertain the length of time that elapses between uses of nests, and test the hypotheses that reproductive success and adult turnover influence nest switching. Golden Eagles used 454 nests in 66 territories and used individual nests 1 to 26 times during 45 continuous years of observation. Time between reuse ranged from 1 to 39 yr. Distances between nearest adjacent alternative nests within territories ranged between <1 and 1822 m, and distances between 90% of adjacent nests were <500 m. Of all nests used, 21% fell or disintegrated, and 31% were newly constructed during the study. Nest switching was not associated with the previous year's nesting success, but eagles tended to change nests after turnover of at least one member of the pair. Five of 42 nests used in 1971 and monitored continuously through 2011 were used only once and 21 were used >5 times. Two nests were unused for 21 and 27 yr after 1971 before being used every 1 to 3 yr thereafter. Eagles used 43% of the nests in series of consecutive years (range 3 to 20 consecutive nestings). Protecting unused nests for a proposed 10 yr after the last known use would not have protected 34% of all 300 nests that were reused during the study and 49% of 37 reused nests monitored consistently for 41 yr. The 102 nests that would not have received protection were in 56 of the 66 territories.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Journal of Raptor Research","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","publisher":"The Raptor Research Foundation","publisherLocation":"http://www.raptorresearchfoundation.org/","doi":"10.3356/JRR-12-00001.1","usgsCitation":"Kochert, M.N., and Steenhof, K., 2012, Frequency of nest use by golden eagles in southwestern Idaho: Journal of Raptor Research, v. 46, no. 3, p. 239-247, https://doi.org/10.3356/JRR-12-00001.1.","productDescription":"9 p.","startPage":"239","endPage":"247","numberOfPages":"9","costCenters":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"links":[{"id":474494,"rank":10000,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.3356/jrr-12-00001.1","text":"Publisher Index Page"},{"id":261860,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":261848,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.3356/JRR-12-00001.1","linkFileType":{"id":5,"text":"html"}}],"country":"United States","state":"Idaho","volume":"46","issue":"3","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505a13d1e4b0c8380cd547b9","contributors":{"authors":[{"text":"Kochert, Michael N. 0000-0002-4380-3298 mkochert@usgs.gov","orcid":"https://orcid.org/0000-0002-4380-3298","contributorId":3037,"corporation":false,"usgs":true,"family":"Kochert","given":"Michael","email":"mkochert@usgs.gov","middleInitial":"N.","affiliations":[{"id":289,"text":"Forest and Rangeland Ecosys Science Center","active":true,"usgs":true},{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":467091,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Steenhof, Karen karen_steenhof@usgs.gov","contributorId":30585,"corporation":false,"usgs":true,"family":"Steenhof","given":"Karen","email":"karen_steenhof@usgs.gov","affiliations":[{"id":289,"text":"Forest and Rangeland Ecosys Science Center","active":true,"usgs":true}],"preferred":false,"id":467092,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70044051,"text":"70044051 - 2012 - Trimming the UCERF2 hazard logic tree","interactions":[],"lastModifiedDate":"2020-09-11T18:32:20.672253","indexId":"70044051","displayToPublicDate":"2012-09-12T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3372,"text":"Seismological Research Letters","onlineIssn":"1938-2057","printIssn":"0895-0695","active":true,"publicationSubtype":{"id":10}},"title":"Trimming the UCERF2 hazard logic tree","docAbstract":"The Uniform California Earthquake Rupture Forecast 2 (UCERF2) is a fully time‐dependent earthquake rupture forecast developed with sponsorship of the California Earthquake Authority (Working Group on California Earthquake Probabilities [WGCEP], 2007; Field et al., 2009). UCERF2 contains 480 logic‐tree branches reflecting choices among nine modeling uncertainties in the earthquake rate model shown in Figure 1. For seismic hazard analysis, it is also necessary to choose a ground‐motion‐prediction equation (GMPE) and set its parameters. Choosing among four next‐generation attenuation (NGA) relationships results in a total of 1920 hazard calculations per site. The present work is motivated by a desire to reduce the computational effort involved in a hazard analysis without understating uncertainty. We set out to assess which branching points of the UCERF2 logic tree contribute most to overall uncertainty, and which might be safely ignored (set to only one branch) without significantly biasing results or affecting some useful measure of uncertainty. The trimmed logic tree will have all of the original choices from the branching points that contribute significantly to uncertainty, but only one arbitrarily selected choice from the branching points that do not.","language":"English","doi":"10.1785/0220120012","usgsCitation":"Porter, K.A., Field, E.H., and Milner, K., 2012, Trimming the UCERF2 hazard logic tree: Seismological Research Letters, v. 83, no. 5, p. 815-828, https://doi.org/10.1785/0220120012.","productDescription":"14 p.","startPage":"815","endPage":"828","numberOfPages":"14","ipdsId":"IP-039084","costCenters":[{"id":300,"text":"Geologic Hazards Science Center","active":true,"usgs":true}],"links":[{"id":272227,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"83","issue":"5","noUsgsAuthors":false,"publicationDate":"2012-09-06","publicationStatus":"PW","scienceBaseUri":"53cd79afe4b0b2908510cfec","contributors":{"authors":[{"text":"Porter, Keith A.","contributorId":28883,"corporation":false,"usgs":true,"family":"Porter","given":"Keith","email":"","middleInitial":"A.","affiliations":[],"preferred":false,"id":474708,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Field, Edward H. 0000-0001-8172-7882 field@usgs.gov","orcid":"https://orcid.org/0000-0001-8172-7882","contributorId":52242,"corporation":false,"usgs":true,"family":"Field","given":"Edward","email":"field@usgs.gov","middleInitial":"H.","affiliations":[{"id":300,"text":"Geologic Hazards Science Center","active":true,"usgs":true}],"preferred":true,"id":474710,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Milner, Kevin","contributorId":28886,"corporation":false,"usgs":true,"family":"Milner","given":"Kevin","affiliations":[],"preferred":false,"id":474709,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70038114,"text":"70038114 - 2012 - Response to \"Comments on 'Theory for source-responsive and free-surface film modeling of unsaturated flow'\"","interactions":[],"lastModifiedDate":"2018-01-12T17:41:16","indexId":"70038114","displayToPublicDate":"2012-09-07T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3674,"text":"Vadose Zone Journal","active":true,"publicationSubtype":{"id":10}},"title":"Response to \"Comments on 'Theory for source-responsive and free-surface film modeling of unsaturated flow'\"","docAbstract":"I am grateful to Masciopinto (2012) for raising several issues from my study (Nimmo, 2010) that deserve elaboration or clarification. In this reply, I address these in what I judge to be the order of importance, the main ones being (i) the discrepancy of scales between the two domains that treat preferential and diffuse unsaturated flow, and (ii) the properties that must be evaluated to characterize the medium.
","language":"English","publisher":"Soil Science Society of America","publisherLocation":"Madison, WI","doi":"10.2136/vzj2012.0044","usgsCitation":"Nimmo, J.R., 2012, Response to \"Comments on 'Theory for source-responsive and free-surface film modeling of unsaturated flow'\": Vadose Zone Journal, v. 11, no. 4, https://doi.org/10.2136/vzj2012.0044.","costCenters":[{"id":148,"text":"Branch of Regional Research-Western Region","active":false,"usgs":true}],"links":[{"id":261772,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"11","issue":"4","noUsgsAuthors":false,"publicationDate":"2012-11-28","publicationStatus":"PW","scienceBaseUri":"505aaa88e4b0c8380cd863ad","contributors":{"authors":[{"text":"Nimmo, John R. 0000-0001-8191-1727 jrnimmo@usgs.gov","orcid":"https://orcid.org/0000-0001-8191-1727","contributorId":757,"corporation":false,"usgs":true,"family":"Nimmo","given":"John","email":"jrnimmo@usgs.gov","middleInitial":"R.","affiliations":[{"id":37277,"text":"WMA - Earth System Processes Division","active":true,"usgs":true},{"id":438,"text":"National Research Program - Western Branch","active":true,"usgs":true}],"preferred":true,"id":463462,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":70037884,"text":"70037884 - 2012 - Book review: Earthquakes and water","interactions":[],"lastModifiedDate":"2015-12-11T12:16:13","indexId":"70037884","displayToPublicDate":"2012-09-05T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1765,"text":"Geofluids","active":true,"publicationSubtype":{"id":10}},"title":"Book review: Earthquakes and water","docAbstract":"It is really nice to see assembled in one place a discussion of the documented and hypothesized hydrologic effects of earthquakes. The book is divided into chapters focusing on particular hydrologic phenomena including liquefaction, mud volcanism, stream discharge increases, groundwater level, temperature and chemical changes, and geyser period changes. These hydrologic effects are inherently fascinating, and the large number of relevant publications in the past decade makes this summary a useful milepost. The book also covers hydrologic precursors and earthquake triggering by pore pressure. A natural need to limit the topics covered resulted in the omission of tsunamis and the vast literature on the role of fluids and pore pressure in frictional strength of faults. Regardless of whether research on earthquake-triggered hydrologic effects ultimately provides insight into the physics of earthquakes, the text provides welcome common ground for interdisciplinary collaborations between hydrologists and seismologists. Such collaborations continue to be crucial for investigating hypotheses about the role of fluids in earthquakes and slow slip.
\nReview info: Earthquakes and Water. By Wang, C.-Y. and Manga, M., 2010. ISBN: 9783642008092, 218 pp.
\nTo assess how elements leach from several types of coal combustion products (CCPs) and to better understand possible risks from CCP use or disposal, coal ashes were sampled from two bituminous-coal-fired power plants. One plant located in Ohio burns high-sulfur (about 3.9%) Upper Pennsylvanian Pittsburgh coal from the Monongahela Group of the Central Appalachian Basin; the other in New Mexico burns low-sulfur (about 0.76%) Upper Cretaceous Fruitland Formation coal from the San Juan Basin, Colorado Plateau. The sampled CCPs from the Ohio plant were bottom ash (BA), economizer fly ash (EFA), and fly ash (FA); the sampled CCPs from the New Mexico plant were BA, mixed FA/EFA, FA, and cyclone-separated coarse and fine fractions of a FA/EFA and FA blend. Subsamples of each ash were leached using the long-term leaching (60-day duration) component of the synthetic groundwater leaching procedure (SGLP) or the toxicity characteristic leaching procedure (TCLP, 18-hour duration). These ashes were all alkaline. Leachate concentrations and leachabilities of the elements from the CCPs were similar between corresponding CCP types (BA, EFA, and FA) from each plant. The leachabilities of most elements were lowest in BA (least leachable) and increased from EFA to FA (most leachable). Ca and Sr were leached more from EFA than from either BA or FA. Leachability of most elements also increased as FA particle size decreased, possibly due in part to increasing specific surface areas. Several oxyanion-forming elements (As, Mo, Se, U, and V) leached more under SGLP than under TCLP; the opposite was true for most other elements analyzed.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.coal.2011.10.007","usgsCitation":"Jones, K.B., Ruppert, L.F., and Swanson, S.M., 2012, Leaching of elements from bottom ash, economizer fly ash, and fly ash from two coal-fired power plants: International Journal of Coal Geology, v. 94, p. 337-348, https://doi.org/10.1016/j.coal.2011.10.007.","productDescription":"12 p.","startPage":"337","endPage":"348","ipdsId":"IP-030166","costCenters":[{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true}],"links":[{"id":357867,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"94","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5c10bd73e4b034bf6a7efe17","contributors":{"authors":[{"text":"Jones, Kevin B. 0000-0002-6386-2623 kevinjones@usgs.gov","orcid":"https://orcid.org/0000-0002-6386-2623","contributorId":565,"corporation":false,"usgs":true,"family":"Jones","given":"Kevin","email":"kevinjones@usgs.gov","middleInitial":"B.","affiliations":[{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":746578,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Ruppert, Leslie F. 0000-0002-7453-1061 lruppert@usgs.gov","orcid":"https://orcid.org/0000-0002-7453-1061","contributorId":660,"corporation":false,"usgs":true,"family":"Ruppert","given":"Leslie","email":"lruppert@usgs.gov","middleInitial":"F.","affiliations":[{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true},{"id":245,"text":"Eastern Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":746579,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Swanson, Sharon M. 0000-0002-4235-1736 smswanson@usgs.gov","orcid":"https://orcid.org/0000-0002-4235-1736","contributorId":590,"corporation":false,"usgs":true,"family":"Swanson","given":"Sharon","email":"smswanson@usgs.gov","middleInitial":"M.","affiliations":[{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":746580,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70133432,"text":"70133432 - 2012 - Ontogenetic and among-individual variation in foraging strategies of northeast Pacific white sharks based on stable isotope analysis","interactions":[],"lastModifiedDate":"2021-01-05T17:46:49.701126","indexId":"70133432","displayToPublicDate":"2012-09-01T10:45:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2980,"text":"PLoS ONE","active":true,"publicationSubtype":{"id":10}},"title":"Ontogenetic and among-individual variation in foraging strategies of northeast Pacific white sharks based on stable isotope analysis","docAbstract":"There is growing evidence for individuality in dietary preferences and foraging behaviors within populations of various species. This is especially important for apex predators, since they can potentially have wide dietary niches and a large impact on trophic dynamics within ecosystems. We evaluate the diet of an apex predator, the white shark (Carcharodon carcharias), by measuring the stable carbon and nitrogen isotope composition of vertebral growth bands to create lifetime records for 15 individuals from California. Isotopic variations in white shark diets can reflect within-region differences among prey (most importantly related to trophic level), as well as differences in baseline values among the regions in which sharks forage, and both prey and habitat preferences may shift with age. The magnitude of isotopic variation among sharks in our study (>5‰ for both elements) is too great to be explained solely by geographic differences, and so must reflect differences in prey choice that may vary with sex, size, age and location. Ontogenetic patterns in δ15N values vary considerably among individuals, and one third of the population fit each of these descriptions: 1) δ15N values increased throughout life, 2) δ15N values increased to a plateau at ~5 years of age, and 3) δ15N values remained roughly constant values throughout life. Isotopic data for the population span more than one trophic level, and we offer a qualitative evaluation of diet using shark-specific collagen discrimination factors estimated from a 3+ year captive feeding experiment (Δ13Cshark-diet and Δ15Nshark-diet equal 4.2‰ and 2.5‰, respectively). We assess the degree of individuality with a proportional similarity index that distinguishes specialists and generalists. The isotopic variance is partitioned among differences between-individual (48%), within-individuals (40%), and by calendar year of sub-adulthood (12%). Our data reveal substantial ontogenetic and individual dietary variation within a white shark population.
","language":"English","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0045068","usgsCitation":"Kim, S., Tinker, M.T., Estes, J.A., and Koch, P., 2012, Ontogenetic and among-individual variation in foraging strategies of northeast Pacific white sharks based on stable isotope analysis: PLoS ONE, v. 7, no. 9, p. 1-11, https://doi.org/10.1371/journal.pone.0045068.","productDescription":"11 p.","startPage":"1","endPage":"11","onlineOnly":"Y","additionalOnlineFiles":"N","ipdsId":"IP-029024","costCenters":[{"id":651,"text":"Western Ecological Research Center","active":true,"usgs":true}],"links":[{"id":474369,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1371/journal.pone.0045068","text":"Publisher Index Page"},{"id":381881,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"7","issue":"9","noUsgsAuthors":false,"publicationDate":"2012-09-28","publicationStatus":"PW","scienceBaseUri":"546c7623e4b0f4a3478a6176","contributors":{"authors":[{"text":"Kim, S.L.","contributorId":127452,"corporation":false,"usgs":false,"family":"Kim","given":"S.L.","email":"","affiliations":[{"id":6949,"text":"University of California, Santa Cruz","active":true,"usgs":false}],"preferred":false,"id":525199,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Tinker, M. Tim 0000-0002-3314-839X ttinker@usgs.gov","orcid":"https://orcid.org/0000-0002-3314-839X","contributorId":2796,"corporation":false,"usgs":true,"family":"Tinker","given":"M.","email":"ttinker@usgs.gov","middleInitial":"Tim","affiliations":[{"id":651,"text":"Western Ecological Research Center","active":true,"usgs":true}],"preferred":true,"id":525197,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Estes, J. A.","contributorId":53319,"corporation":false,"usgs":true,"family":"Estes","given":"J.","email":"","middleInitial":"A.","affiliations":[],"preferred":false,"id":525198,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Koch, P.L.","contributorId":101878,"corporation":false,"usgs":true,"family":"Koch","given":"P.L.","email":"","affiliations":[],"preferred":false,"id":525200,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70039799,"text":"70039799 - 2012 - Diet of the invasive Cuban treefrog (Osteopilus septentrionalis) in pine rockland and mangrove habitats in South Florida","interactions":[],"lastModifiedDate":"2019-08-27T09:49:43","indexId":"70039799","displayToPublicDate":"2012-09-01T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1185,"text":"Caribbean Journal of Science","active":true,"publicationSubtype":{"id":10}},"displayTitle":"Diet of the invasive Cuban treefrog (Osteopilus septentrionalis) in pine rockland and mangrove habitats in South Florida","title":"Diet of the invasive Cuban treefrog (Osteopilus septentrionalis) in pine rockland and mangrove habitats in South Florida","docAbstract":"Native to Cuba, the Bahamas and the Cayman Islands, the Cuban Treefrog (CTF) is an invasive species in Florida, with the ability to inflict serious ecological damage to invaded habitats. By examining the diet of the CTF, a known predator of native frogs, better predictions may be made of the impacts on native species and ecosystems. From 2002 - 2003, CTF diet was investigated in south Florida at four sites, two each within pine rockland and mangrove habitat. Within each habitat, one site exhibited a low density of CTFs and the other a high density of CTFs. CTFs were captured in PVC pipes attached to trees and stomach contents were examined after euthanasia. Beetles were the most numerous and widely consumed prey item among sites; roaches, orthopterans, spiders, ants, and caterpillars were also major dietary components. There were significant differences in the proportion of taxa consumed by CTFs between low and high density populations within each habitat, with the low density site in every instance having the higher proportion. Across habitats, ants comprised a significantly higher proportion of the diet in mangroves, whereas beetles, orthopterans, and snails comprised a significantly higher proportion of the diet in pine rocklands. Approximately 3.5% of all stomachs examined contained anuran remains. Though not significant, CTFs from low density sites consumed a higher proportion of frogs than those at high density sites. Corroborating previous research, the data show the CTF to be a generalist feeder, consuming a wide variety of invertebrate prey, with anurans playing only a minor role in the overall diet.","language":"English","publisher":"University of Puerto Rico","publisherLocation":"Rio Piedras, Puerto Rico","doi":"10.18475/cjos.v46i2.a25","usgsCitation":"Glorioso, B., Waddle, J., Crockett, M., Rice, K., and Percival, H., 2012, Diet of the invasive Cuban treefrog (Osteopilus septentrionalis) in pine rockland and mangrove habitats in South Florida: Caribbean Journal of Science, v. 46, no. 2-3, p. 346-355, https://doi.org/10.18475/cjos.v46i2.a25.","productDescription":"10 p.","startPage":"346","endPage":"355","numberOfPages":"9","costCenters":[{"id":455,"text":"National Wetlands Research Center","active":true,"usgs":true}],"links":[{"id":260124,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","otherGeospatial":"Florida","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -81.298828125,\n 25.098035823821835\n ],\n [\n -80.52978515625,\n 25.098035823821835\n ],\n [\n -80.52978515625,\n 25.695988053632746\n ],\n [\n -81.298828125,\n 25.695988053632746\n ],\n [\n -81.298828125,\n 25.098035823821835\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"46","issue":"2-3","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505a00d6e4b0c8380cd4f94a","contributors":{"authors":[{"text":"Glorioso, B.M. 0000-0002-5400-7414","orcid":"https://orcid.org/0000-0002-5400-7414","contributorId":75344,"corporation":false,"usgs":true,"family":"Glorioso","given":"B.M.","affiliations":[],"preferred":false,"id":466942,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Waddle, J.H. 0000-0003-1940-2133","orcid":"https://orcid.org/0000-0003-1940-2133","contributorId":32654,"corporation":false,"usgs":true,"family":"Waddle","given":"J.H.","email":"","affiliations":[],"preferred":false,"id":466939,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Crockett, M.E.","contributorId":45558,"corporation":false,"usgs":true,"family":"Crockett","given":"M.E.","email":"","affiliations":[],"preferred":false,"id":466941,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Rice, K.G. 0000-0001-8282-1088","orcid":"https://orcid.org/0000-0001-8282-1088","contributorId":41949,"corporation":false,"usgs":true,"family":"Rice","given":"K.G.","affiliations":[],"preferred":false,"id":466940,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Percival, H.F.","contributorId":31716,"corporation":false,"usgs":true,"family":"Percival","given":"H.F.","email":"","affiliations":[],"preferred":false,"id":466938,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70043930,"text":"70043930 - 2012 - Developing a broader scientific foundation for river restoration: Columbia River food webs","interactions":[],"lastModifiedDate":"2018-01-26T17:13:32","indexId":"70043930","displayToPublicDate":"2012-09-01T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3165,"text":"Proceedings of the National Academy of Sciences of the United States of America","active":true,"publicationSubtype":{"id":10}},"title":"Developing a broader scientific foundation for river restoration: Columbia River food webs","docAbstract":"Well-functioning food webs are fundamental for sustaining rivers as ecosystems and maintaining associated aquatic and terrestrial communities. The current emphasis on restoring habitat structure—without explicitly considering food webs—has been less successful than hoped in terms of enhancing the status of targeted species and often overlooks important constraints on ecologically effective restoration. We identify three priority food web-related issues that potentially impede successful river restoration: uncertainty about habitat carrying capacity, proliferation of chemicals and contaminants, and emergence of hybrid food webs containing a mixture of native and invasive species. Additionally, there is the need to place these food web considerations in a broad temporal and spatial framework by understanding the consequences of altered nutrient, organic matter (energy), water, and thermal sources and flows, reconnecting critical habitats and their food webs, and restoring for changing environments. As an illustration, we discuss how the Columbia River Basin, site of one of the largest aquatic/riparian restoration programs in the United States, would benefit from implementing a food web perspective. A food web perspective for the Columbia River would complement ongoing approaches and enhance the ability to meet the vision and legal obligations of the US Endangered Species Act, the Northwest Power Act (Fish and Wildlife Program), and federal treaties with Northwest Indian Tribes while meeting fundamental needs for improved river management.","language":"English","publisher":"National Academy of Sciences","publisherLocation":"Washington, D.C.","doi":"10.1073/pnas.1213408109","usgsCitation":"Naiman, R.J., Alldredge, R., Beauchamp, D.A., Bisson, P.A., Congleton, J., Henny, C.J., Huntly, N., Lamberson, R., Levings, C., Merrill, E.N., Pearcy, W.G., Rieman, B.E., Ruggerone, G.T., Scarnecchia, D., Smouse, P.E., and Wood, C., 2012, Developing a broader scientific foundation for river restoration: Columbia River food webs: Proceedings of the National Academy of Sciences of the United States of America, v. 109, no. 52, p. 21201-21207, https://doi.org/10.1073/pnas.1213408109.","productDescription":"7 p.","startPage":"21201","endPage":"21207","ipdsId":"IP-037975","costCenters":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"links":[{"id":474371,"rank":0,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"https://doi.org/10.1073/pnas.1213408109","text":"External Repository"},{"id":268014,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":268013,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1073/pnas.1213408109"}],"volume":"109","issue":"52","noUsgsAuthors":false,"publicationDate":"2012-11-28","publicationStatus":"PW","scienceBaseUri":"5129f31be4b04edf7e93f888","contributors":{"authors":[{"text":"Naiman, Robert 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Managers need practical tools for selecting among these actions and strategies to develop a tailored management approach for specific targets at a given location. We developed and present one such tool, the participatory Adaptation for Conservation Targets (ACT) framework, which considers the effects of climate change in the development of management actions for particular species, ecosystems and ecological functions. Our framework is based on the premise that effective adaptation of management to climate change can rely on local knowledge of an ecosystem and does not necessarily require detailed projections of climate change or its effects. We illustrate the ACT framework by applying it to an ecological function in the Greater Yellowstone Ecosystem (Montana, Wyoming, and Idaho, USA)—water flows in the upper Yellowstone River. We suggest that the ACT framework is a practical tool for initiating adaptation planning, and for generating and communicating specific management interventions given an increasingly altered, yet uncertain, climate.
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Here we focus on Nile tilapia (Oreochromis niloticus Linnaeus, 1758), one of the most widely cultured fish worldwide and a species that has escaped local aquaculture facilities to become established in a coastal-draining river in Mississippi (northern Gulf of Mexico). Using empirical physiological data, logistic regression models were developed to predict the probabilities of Nile tilapia survival, growth, and reproduction at different combinations of temperature (14 and 30°C) and salinity (0–60, by increments of 10). These predictive models were combined with kriged seasonal salinity data derived from multiple long-term data sets to project the species' fundamental niche in Mississippi coastal waters during normal salinity years (averaged across all years) and salinity patterns in extremely wet and dry years (which might emerge more frequently under scenarios of climate change). The derived fundamental niche projections showed that during the summer, Nile tilapia is capable of surviving throughout Mississippi's coastal waters but growth and reproduction were limited to river mouths (or upriver). Overwinter survival was also limited to river mouths. The areas where Nile tilapia could survive, grow, and reproduce increased during extremely wet years (2–368%) and decreased during extremely dry years (86–92%) in the summer with a similar pattern holding for overwinter survival. These results indicate that Nile tilapia is capable of 1) using saline waters to gain access to other watersheds throughout the region and 2) establishing populations in nearshore, low-salinity waters, particularly in the western portion of coastal Mississippi.","language":"English","publisher":"Public Library of Science","publisherLocation":"San Francisco, CA","doi":"10.1371/journal.pone.0041580","usgsCitation":"Lowe, M.R., Wu, W., Peterson, M.S., Brown-Peterson, N.J., Slack, W.T., and Schofield, P., 2012, Survival, growth and reproduction of non-native Nile tilapia II: Fundamental niche projections and invasion potential in the northern Gulf of Mexico: PLoS ONE, v. 7, no. 7, e41580, 10 p., https://doi.org/10.1371/journal.pone.0041580.","productDescription":"e41580, 10 p.","costCenters":[{"id":566,"text":"Southeast Ecological Science Center","active":true,"usgs":true}],"links":[{"id":474374,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1371/journal.pone.0041580","text":"Publisher Index Page"},{"id":260000,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Alabama, Louisiana, Mississippi","otherGeospatial":"Gulf Of Mexico","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -89.8516845703125,\n 30.021543509740027\n ],\n [\n -87.484130859375,\n 30.021543509740027\n ],\n [\n -87.484130859375,\n 30.755998458321667\n ],\n [\n -89.8516845703125,\n 30.755998458321667\n ],\n [\n -89.8516845703125,\n 30.021543509740027\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"7","issue":"7","noUsgsAuthors":false,"publicationDate":"2012-07-27","publicationStatus":"PW","scienceBaseUri":"53cd7619e4b0b2908510aaf2","contributors":{"authors":[{"text":"Lowe, Michael R. 0000-0002-4645-9429","orcid":"https://orcid.org/0000-0002-4645-9429","contributorId":10539,"corporation":false,"usgs":true,"family":"Lowe","given":"Michael","email":"","middleInitial":"R.","affiliations":[{"id":324,"text":"Great Lakes Science Center","active":true,"usgs":true}],"preferred":false,"id":466846,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Wu, Wei","contributorId":15061,"corporation":false,"usgs":true,"family":"Wu","given":"Wei","email":"","affiliations":[],"preferred":false,"id":466847,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Peterson, Mark S.","contributorId":8979,"corporation":false,"usgs":true,"family":"Peterson","given":"Mark","email":"","middleInitial":"S.","affiliations":[],"preferred":false,"id":466845,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Brown-Peterson, Nancy J.","contributorId":53937,"corporation":false,"usgs":true,"family":"Brown-Peterson","given":"Nancy","email":"","middleInitial":"J.","affiliations":[],"preferred":false,"id":466850,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Slack, William T.","contributorId":47512,"corporation":false,"usgs":true,"family":"Slack","given":"William","email":"","middleInitial":"T.","affiliations":[],"preferred":false,"id":466849,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Schofield, Pamela J. 0000-0002-8752-2797","orcid":"https://orcid.org/0000-0002-8752-2797","contributorId":30306,"corporation":false,"usgs":true,"family":"Schofield","given":"Pamela J.","affiliations":[{"id":566,"text":"Southeast Ecological Science Center","active":true,"usgs":true}],"preferred":true,"id":466848,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70039732,"text":"70039732 - 2012 - Use of alligator hole abundance and occupancy rate as indicators for restoration of a human-altered wetland","interactions":[],"lastModifiedDate":"2012-08-30T01:02:05","indexId":"70039732","displayToPublicDate":"2012-08-29T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1456,"text":"Ecological Indicators","active":true,"publicationSubtype":{"id":10}},"title":"Use of alligator hole abundance and occupancy rate as indicators for restoration of a human-altered wetland","docAbstract":"Use of indicator species as a measure of ecosystem conditions is an established science application in environmental management. Because of its role in shaping wetland systems, the American alligator (Alligator mississippiensis) is one of the ecological indicators for wetland restoration in south Florida, USA. We conducted landscape-level aerial surveys of alligator holes in two different habitats in a wetland where anthropogenic modification of surface hydrology has altered the natural system. Alligator holes were scarcer in an area where modified hydrology caused draining and frequent dry-downs compared to another area that maintains a functional wetland system. Lower abundance of alligator holes indicates lack of alligator activities, lower overall species diversity, and lack of dry-season aquatic refugia for other organisms. The occupancy rate of alligator holes was lower than the current restoration target for the Everglades, and was variable by size class with large size-class alligators predominantly occupying alligator holes. This may indicate unequal size-class distribution, different habitat selection by size classes, or possibly a lack of recruitment. Our study provides pre-restoration baseline information about one indicator species for the Everglades. Success of the restoration can be assessed via effective synthesis of information derived by collective research efforts on the entire suite of selected ecological indicators.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Ecological Indicators","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","publisher":"Elsevier","publisherLocation":"Amsterdam, Netherlands","doi":"10.1016/j.ecolind.2012.05.011","usgsCitation":"Fujisaki, I., Mazzotti, F., Hart, K.M., Rice, K.G., Ogurcak, D., Rochford, M., Jeffery, B.M., Brandt, L., and Cherkiss, M.S., 2012, Use of alligator hole abundance and occupancy rate as indicators for restoration of a human-altered wetland: Ecological Indicators, v. 23, p. 627-633, https://doi.org/10.1016/j.ecolind.2012.05.011.","productDescription":"7 p.","startPage":"627","endPage":"633","costCenters":[{"id":566,"text":"Southeast Ecological Science Center","active":true,"usgs":true}],"links":[{"id":260002,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":259991,"rank":9999,"type":{"id":10,"text":"Digital Object Identifier"},"url":"https://dx.doi.org/10.1016/j.ecolind.2012.05.011","linkFileType":{"id":5,"text":"html"}}],"country":"United States","state":"Florida","volume":"23","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505bbeafe4b08c986b329717","contributors":{"authors":[{"text":"Fujisaki, Ikuko","contributorId":31108,"corporation":false,"usgs":false,"family":"Fujisaki","given":"Ikuko","email":"","affiliations":[{"id":12557,"text":"University of Florida, FLREC","active":true,"usgs":false}],"preferred":false,"id":466842,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Mazzotti, Frank J.","contributorId":100018,"corporation":false,"usgs":false,"family":"Mazzotti","given":"Frank J.","affiliations":[{"id":12557,"text":"University of Florida, FLREC","active":true,"usgs":false}],"preferred":false,"id":466844,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Hart, Kristen M. 0000-0002-5257-7974 kristen_hart@usgs.gov","orcid":"https://orcid.org/0000-0002-5257-7974","contributorId":1966,"corporation":false,"usgs":true,"family":"Hart","given":"Kristen","email":"kristen_hart@usgs.gov","middleInitial":"M.","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"preferred":true,"id":466837,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Rice, Kenneth G. 0000-0001-8282-1088 krice@usgs.gov","orcid":"https://orcid.org/0000-0001-8282-1088","contributorId":117,"corporation":false,"usgs":true,"family":"Rice","given":"Kenneth","email":"krice@usgs.gov","middleInitial":"G.","affiliations":[{"id":566,"text":"Southeast Ecological Science Center","active":true,"usgs":true},{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true}],"preferred":true,"id":466836,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Ogurcak, Danielle","contributorId":21815,"corporation":false,"usgs":true,"family":"Ogurcak","given":"Danielle","affiliations":[],"preferred":false,"id":466841,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Rochford, Michael","contributorId":58136,"corporation":false,"usgs":true,"family":"Rochford","given":"Michael","affiliations":[],"preferred":false,"id":466843,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Jeffery, Brian M.","contributorId":16511,"corporation":false,"usgs":false,"family":"Jeffery","given":"Brian","email":"","middleInitial":"M.","affiliations":[{"id":12557,"text":"University of Florida, FLREC","active":true,"usgs":false}],"preferred":false,"id":466839,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Brandt, Laura A.","contributorId":18608,"corporation":false,"usgs":false,"family":"Brandt","given":"Laura A.","affiliations":[{"id":6987,"text":"U.S. Fish and Wildlife Sevice","active":true,"usgs":false}],"preferred":false,"id":466840,"contributorType":{"id":1,"text":"Authors"},"rank":8},{"text":"Cherkiss, Michael S. 0000-0002-7802-6791 mcherkiss@usgs.gov","orcid":"https://orcid.org/0000-0002-7802-6791","contributorId":4571,"corporation":false,"usgs":true,"family":"Cherkiss","given":"Michael","email":"mcherkiss@usgs.gov","middleInitial":"S.","affiliations":[{"id":17705,"text":"Wetland and Aquatic Research Center","active":true,"usgs":true},{"id":566,"text":"Southeast Ecological Science Center","active":true,"usgs":true}],"preferred":true,"id":466838,"contributorType":{"id":1,"text":"Authors"},"rank":9}]}} ,{"id":70039336,"text":"70039336 - 2012 - Identification of the thiamin pyrophosphokinase gene in rainbow trout: Characteristic structure and expression of seven splice variants in tissues and cell lines and during embryo development","interactions":[],"lastModifiedDate":"2016-12-02T13:58:54","indexId":"70039336","displayToPublicDate":"2012-08-08T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1293,"text":"Comparative Biochemistry and Physiology, Part B: Biochemistry and Molecular Biology","active":true,"publicationSubtype":{"id":10}},"title":"Identification of the thiamin pyrophosphokinase gene in rainbow trout: Characteristic structure and expression of seven splice variants in tissues and cell lines and during embryo development","docAbstract":"Thiamin pyrophosphokinase (TPK) converts thiamin to its active form, thiamin diphosphate. In humans, TPK expression is down-regulated in some thiamin deficiency related syndrome, and enhanced during pregnancy. Rainbow trout are also vulnerable to thiamin deficiency in wild life and are useful models for thiamin metabolism research. We identified the tpk gene transcript including seven splice variants in the rainbow trout. Almost all cell lines and tissues examined showed co-expression of several tpk splice variants including a potentially major one at both mRNA and protein levels. However, relative to other tissues, the longest variant mRNA expression was predominant in the ovary and abundant in embryos. During embryogenesis, total tpk transcripts increased abruptly in early development, and decreased to about half of the peak shortly after hatching. In rainbow trout, the tpk transcript complex is ubiquitously expressed for all tissues and cells examined, and its increase in expression could be important in the early-middle embryonic stages. Moreover, decimated tpk expression in a hepatoma cell line relative to hepatic and gonadal cell lines appears to be consistent with previously reported down-regulation of thiamin metabolism in cancer.","language":"English","publisher":"Elsevier","publisherLocation":"Amsterdam, Netherlands","doi":"10.1016/j.cbpb.2012.05.017","usgsCitation":"Yuge, S., Richter, C., Wright-Osment, M., Nicks, D., Saloka, S.K., Tillitt, D.E., and Li, W., 2012, Identification of the thiamin pyrophosphokinase gene in rainbow trout: Characteristic structure and expression of seven splice variants in tissues and cell lines and during embryo development: Comparative Biochemistry and Physiology, Part B: Biochemistry and Molecular Biology, v. 163, no. 2, p. 193-202, https://doi.org/10.1016/j.cbpb.2012.05.017.","productDescription":"10 p.","startPage":"193","endPage":"202","costCenters":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"links":[{"id":259509,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"163","issue":"2","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"505a3840e4b0c8380cd614d0","contributors":{"authors":[{"text":"Yuge, Shinya","contributorId":30496,"corporation":false,"usgs":true,"family":"Yuge","given":"Shinya","email":"","affiliations":[],"preferred":false,"id":466086,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Richter, Catherine A.","contributorId":100990,"corporation":false,"usgs":true,"family":"Richter","given":"Catherine A.","affiliations":[],"preferred":false,"id":466090,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Wright-Osment, Maureen K.","contributorId":40337,"corporation":false,"usgs":true,"family":"Wright-Osment","given":"Maureen K.","affiliations":[],"preferred":false,"id":466087,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Nicks, Diane 0000-0001-8080-2449 dnicks@usgs.gov","orcid":"https://orcid.org/0000-0001-8080-2449","contributorId":4299,"corporation":false,"usgs":true,"family":"Nicks","given":"Diane","email":"dnicks@usgs.gov","affiliations":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"preferred":true,"id":466085,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Saloka, Stephanie K.","contributorId":53644,"corporation":false,"usgs":true,"family":"Saloka","given":"Stephanie","email":"","middleInitial":"K.","affiliations":[],"preferred":false,"id":466088,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Tillitt, Donald E. 0000-0002-8278-3955 dtillitt@usgs.gov","orcid":"https://orcid.org/0000-0002-8278-3955","contributorId":1875,"corporation":false,"usgs":true,"family":"Tillitt","given":"Donald","email":"dtillitt@usgs.gov","middleInitial":"E.","affiliations":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"preferred":true,"id":466084,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Li, Weiming","contributorId":65440,"corporation":false,"usgs":true,"family":"Li","given":"Weiming","affiliations":[],"preferred":false,"id":466089,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ,{"id":70039459,"text":"sir20125066 - 2012 - Conservation Reserve Program (CRP) contributions to wildlife habitat, management issues, challenges and policy choices--an annotated bibliography","interactions":[],"lastModifiedDate":"2012-08-08T01:02:14","indexId":"sir20125066","displayToPublicDate":"2012-08-07T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":334,"text":"Scientific Investigations Report","code":"SIR","onlineIssn":"2328-0328","printIssn":"2328-031X","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"2012-5066","title":"Conservation Reserve Program (CRP) contributions to wildlife habitat, management issues, challenges and policy choices--an annotated bibliography","docAbstract":"The following bibliography presents brief summaries of documents relevant to Conservation Reserve Program relations to wildlife habitat, habitat management in agriculturally dominated landscapes, and conservation policies potentially affecting wildlife habitats in agricultural ecosystems. Because the literature summaries furnished provide only sweeping overviews, users are urged to obtain and evaluate those papers appearing useful to obtain a more complete understanding of study findings and their implications to conservation in agricultural ecosystems. The bibliography contains references to reports that reach beyond topics that directly relate to the Conservation Reserve Program. Sections addressing grassland management and landowner surveys/opinions, for example, furnish information useful for enhancing development and administration of conservation policies affecting lands beyond those enrolled in conservation programs. Some sections of the bibliography (for example, agricultural conservation policy, economics, soils) are far from inclusive of all relevant material written on the subject. Hopefully, these sections will serve as fundamental introductions to related issues. In a few instances, references may be presented in more than one section of the bibliography. For example, individual papers specifically addressing both non-game and game birds are included in respective sections of the bibliography. Duplication of citations and associated notes has, however, been kept to a minimum.","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/sir20125066","usgsCitation":"Allen, A.W., and Vandever, M., 2012, Conservation Reserve Program (CRP) contributions to wildlife habitat, management issues, challenges and policy choices--an annotated bibliography: U.S. Geological Survey Scientific Investigations Report 2012-5066, iii, 185 p., https://doi.org/10.3133/sir20125066.","productDescription":"iii, 185 p.","startPage":"i","endPage":"185","numberOfPages":"192","onlineOnly":"Y","additionalOnlineFiles":"N","costCenters":[{"id":291,"text":"Fort Collins Science Center","active":true,"usgs":true}],"links":[{"id":259456,"rank":100,"type":{"id":15,"text":"Index Page"},"url":"https://pubs.usgs.gov/sir/2012/5066/","linkFileType":{"id":5,"text":"html"}},{"id":259455,"rank":300,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/sir/2012/5066/SIR12-5066.pdf","linkFileType":{"id":1,"text":"pdf"}},{"id":259469,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/sir_2012_5066.gif"}],"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"5059f9d7e4b0c8380cd4d7f1","contributors":{"authors":[{"text":"Allen, Arthur W.","contributorId":40648,"corporation":false,"usgs":true,"family":"Allen","given":"Arthur","email":"","middleInitial":"W.","affiliations":[],"preferred":false,"id":466280,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Vandever, Mark W.","contributorId":59870,"corporation":false,"usgs":true,"family":"Vandever","given":"Mark W.","affiliations":[],"preferred":false,"id":466281,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70039354,"text":"70039354 - 2012 - Assessment of environments for Mars Science Laboratory entry, descent, and surface operations","interactions":[],"lastModifiedDate":"2017-01-11T16:51:47","indexId":"70039354","displayToPublicDate":"2012-08-01T00:00:00","publicationYear":"2012","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3454,"text":"Space Science Reviews","active":true,"publicationSubtype":{"id":10}},"title":"Assessment of environments for Mars Science Laboratory entry, descent, and surface operations","docAbstract":"The Mars Science Laboratory mission aims to land a car-sized rover on Mars' surface and operate it for at least one Mars year in order to assess whether its field area was ever capable of supporting microbial life. Here we describe the approach used to identify, characterize, and assess environmental risks to the landing and rover surface operations. Novel entry, descent, and landing approaches will be used to accurately deliver the 900-kg rover, including the ability to sense and \"fly out\" deviations from a best-estimate atmospheric state. A joint engineering and science team developed methods to estimate the range of potential atmospheric states at the time of arrival and to quantitatively assess the spacecraft's performance and risk given its particular sensitivities to atmospheric conditions. Numerical models are used to calculate the atmospheric parameters, with observations used to define model cases, tune model parameters, and validate results. This joint program has resulted in a spacecraft capable of accessing, with minimal risk, the four finalist sites chosen for their scientific merit. The capability to operate the landed rover over the latitude range of candidate landing sites, and for all seasons, was verified against an analysis of surface environmental conditions described here. These results, from orbital and model data sets, also drive engineering simulations of the rover's thermal state that are used to plan surface operations.","language":"English","publisher":"Springer","publisherLocation":"Amsterdam, Netherlands","doi":"10.1007/s11214-012-9911-3","usgsCitation":"Vasavada, A., Chen, A., Barnes, J.R., Burkhart, P.D., Cantor, B.A., Dwyer-Cianciolo, A.M., Fergason, R.L., Hinson, D.P., Justh, H.L., Kass, D.M., Lewis, S.R., Mischna, M.A., Murphy, J.R., Rafkin, S.C., Tyler, D., and Withers, P.G., 2012, Assessment of environments for Mars Science Laboratory entry, descent, and surface operations: Space Science Reviews, v. 170, no. 1, p. 793-835, https://doi.org/10.1007/s11214-012-9911-3.","productDescription":"43 p.","startPage":"793","endPage":"835","costCenters":[{"id":131,"text":"Astrogeology Science Center","active":true,"usgs":true}],"links":[{"id":259348,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"170","issue":"1","noUsgsAuthors":false,"publicationDate":"2012-06-30","publicationStatus":"PW","scienceBaseUri":"5059ee2ee4b0c8380cd49be8","contributors":{"authors":[{"text":"Vasavada, Ashwin R.","contributorId":84125,"corporation":false,"usgs":true,"family":"Vasavada","given":"Ashwin R.","affiliations":[],"preferred":false,"id":466132,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Chen, Allen","contributorId":71430,"corporation":false,"usgs":true,"family":"Chen","given":"Allen","email":"","affiliations":[],"preferred":false,"id":466131,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Barnes, Jeffrey R.","contributorId":21813,"corporation":false,"usgs":true,"family":"Barnes","given":"Jeffrey","email":"","middleInitial":"R.","affiliations":[],"preferred":false,"id":466121,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Burkhart, P. 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