Highly pathogenic avian influenza (HPAI) viruses of the H5 A/goose/Guangdong/1/96 lineage can cause severe disease in poultry and wild birds, and occasionally in humans. In recent years, H5 HPAI viruses of this lineage infecting poultry in Asia have spilled over into wild birds and spread via bird migration to countries in Europe, Africa, and North America. In 2016/2017, this spillover resulted in the largest HPAI epidemic on record in Europe and was associated with an unusually high frequency of reassortments between H5 HPAI viruses and cocirculating low-pathogenic avian influenza viruses. Here, we show that the seven main H5 reassortant viruses had various combinations of gene segments 1, 2, 3, 5, and 6. Using detailed time-resolved phylogenetic analysis, most of these gene segments likely originated from wild birds and at dates and locations that corresponded to their hosts’ migratory cycles. However, some gene segments in two reassortant viruses likely originated from domestic anseriforms, either in spring 2016 in east China or in autumn 2016 in central Europe. Our results demonstrate that, in addition to domestic anseriforms in Asia, both migratory wild birds and domestic anseriforms in Europe are relevant sources of gene segments for recent reassortant H5 HPAI viruses. The ease with which these H5 HPAI viruses reassort, in combination with repeated spillovers of H5 HPAI viruses into wild birds, increases the risk of emergence of a reassortant virus that persists in wild bird populations yet remains highly pathogenic for poultry.
","language":"English","publisher":"National Academy of Sciences","doi":"10.1073/pnas.2001813117","usgsCitation":"Lycett, S., Pohlmann, A., Staubach, C., Caliendo, V., Woolhouse, M., Beer, M., Kuiken, T., The Global Consortium for H5N8 and Related Influenza Viruses, van Borm, S., Breed, A., Briand, F., Brown, I., Dan, A., DeLiberto, T.J., von Dobschuetz, S., Fouchier, R.A., Gilbert, M., Hill, S., Hjulsager, C.K., Ip, S., Koopmans, M., Larsen, L.E., Lee, D., Naguib, M.M., Monne, I., Pybus, O., Ramey, A.M., Savic, V., Sharshov, K., Shestopalov, A., Song, C., Steensels, M., Swayne, D., Swieton, E., Wan, X., and Zohari, S., 2020, Genesis and spread of multiple reassortants during the 2016/2017 H5 avian influenza epidemic in Eurasia: PNAS, v. 117, no. 34, p. 20814-20825, https://doi.org/10.1073/pnas.2001813117.","startPage":"20814","endPage":"20825","ipdsId":"IP-113696","costCenters":[{"id":456,"text":"National Wildlife Health 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climates","interactions":[],"lastModifiedDate":"2020-09-10T20:32:48.494124","indexId":"70212486","displayToPublicDate":"2020-08-07T10:37:55","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":5718,"text":"Journal of Geophysical Research: Planets","onlineIssn":"2169-9100","active":true,"publicationSubtype":{"id":10}},"title":"Ancient Martian aeolian sand dune deposits recorded in the stratigraphy of Valles Marineris and implications for past climates","docAbstract":"Aeolian sediment transport, deposition, and erosion have been ongoing throughout Mars's history. This record of widespread aeolian processes is preserved in landforms and geologic units that retain important clues about past environmental conditions including wind patterns. In this study we describe landforms within Melas Chasma, Valles Marineris, that occur in distinct groups with linear to crescentic shapes, arranged with a characteristic wavelength; some possess slope profiles analogous to modern sand dunes yet show evidence for lithification. Based on the features' dimensions, asymmetry, and spatial patterns relative to modern equivalents, we interpret these landforms to be two classes of aeolian bedforms: decameter‐scale megaripples and sand dunes. The presence of superposed erosional features and depositional units indicates that these landforms were cemented and likely ancient. Melas paleodunes are found atop Hesperian‐aged layered deposits, but we estimate them to be younger, likely lithified in the Amazonian period. Although a range of degradation was observed, some paleodunes are >10 m tall and maintain steep lee sides (>25°), an uncommon scenario for terrestrial examples as other geologic processes lead to dune obliteration. The preserved paleobedform geometries are largely consistent with those of modern aeolian indicators, suggesting no major shifts in wind regime or contributing boundary conditions. Finally, we propose that their appearance and context require sequential periods of dune migration, stabilization following catastrophic burial, cementation, differential erosion, exposure, and burial. The presence of wholly preserved duneforms appears to be more common on Mars compared to the Earth and may signal something important about Martian landscape evolution.
","language":"English","publisher":"American Geophysical Union","doi":"10.1029/2020JE006510","usgsCitation":"Chojnacki, M., Fenton, L.K., Weintraub, A., Edgar, L.A., Jodhpurkar, M.J., and Edwards, C., 2020, Ancient Martian aeolian sand dune deposits recorded in the stratigraphy of Valles Marineris and implications for past climates: Journal of Geophysical Research: Planets, v. 125, no. 9, e2020JE006510, 24 p., https://doi.org/10.1029/2020JE006510.","productDescription":"e2020JE006510, 24 p.","ipdsId":"IP-118939","costCenters":[{"id":131,"text":"Astrogeology Science Center","active":true,"usgs":true}],"links":[{"id":488358,"rank":0,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"http://hdl.handle.net/10150/657782","text":"External Repository"},{"id":377577,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"otherGeospatial":"Mars, Valles Marineris","volume":"125","issue":"9","noUsgsAuthors":false,"publicationDate":"2020-08-31","publicationStatus":"PW","contributors":{"authors":[{"text":"Chojnacki, Matthew","contributorId":201621,"corporation":false,"usgs":false,"family":"Chojnacki","given":"Matthew","affiliations":[{"id":27205,"text":"U. 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Simple rock detention structures have been used to manage agricultural water for over a thousand years and are now being installed to restore ecohydrological functionality but with little scientific evidence of their success. The impacts, design, and construction of such structures has been debated among local restoration practitioners, management, and permitting agencies. This article presents archeological documentation, local contentions, and examples of available research assessments of rock detention structures in the Madrean Archipelago Ecoregion. A US Geological Survey study to quantify impacts of rock detention structures using remote-sensing analyses, hydrologic monitoring, vegetation surveys, and watershed modeling is discussed, and results rendered in terms of the critical restoration ecosystem services provided. This framework provides a means for comparing management actions that might directly or indirectly impact human populations and assessing tradeoffs between them.","language":"English","publisher":"Sage Journals","doi":"10.1177/1178622120946337","usgsCitation":"Norman, L., 2020, Ecosystem services of riparian restoration: A review of rock detention structures in the Madrean Archipelago Ecoregion: Air, Soil and Water Research, v. 13, 13 p., https://doi.org/10.1177/1178622120946337.","productDescription":"13 p.","ipdsId":"IP-114137","costCenters":[{"id":657,"text":"Western Geographic Science Center","active":true,"usgs":true}],"links":[{"id":455722,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1177/1178622120946337","text":"Publisher Index Page"},{"id":377603,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Mexico, United States","state":"Arizona, Chihuahua, New Mexico, Sonora","otherGeospatial":"Madrean Archipelago Ecoregion","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -111.610107421875,\n 29.372601506681402\n ],\n [\n -108.00659179687499,\n 29.372601506681402\n ],\n [\n -108.00659179687499,\n 33.486435450999885\n ],\n [\n -111.610107421875,\n 33.486435450999885\n ],\n [\n -111.610107421875,\n 29.372601506681402\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"13","noUsgsAuthors":false,"publicationDate":"2020-08-07","publicationStatus":"PW","contributors":{"authors":[{"text":"Norman, Laura M. 0000-0002-3696-8406","orcid":"https://orcid.org/0000-0002-3696-8406","contributorId":203300,"corporation":false,"usgs":true,"family":"Norman","given":"Laura M.","affiliations":[{"id":657,"text":"Western Geographic Science Center","active":true,"usgs":true}],"preferred":true,"id":796583,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":70212590,"text":"70212590 - 2020 - Focused fluid flow along the Nootka Fault Zone and continental slope, Explorer-Juan de Fuca plate boundary","interactions":[],"lastModifiedDate":"2020-08-25T13:31:23.062953","indexId":"70212590","displayToPublicDate":"2020-08-07T08:55:59","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1757,"text":"Geochemistry, Geophysics, Geosystems","active":true,"publicationSubtype":{"id":10}},"title":"Focused fluid flow along the Nootka Fault Zone and continental slope, Explorer-Juan de Fuca plate boundary","docAbstract":"Geophysical and geochemical data indicate there is abundant fluid expulsion in the Nootka fault zone (NFZ) between the Juan de Fuca and Explorer plates and the Nootka continental slope. Here we combine observations from > 20 years of investigations to\ndemonstrate the nature of fluid-flow along the NFZ, which is the seismically most active region off Vancouver Island. Seismicity reaching down to the upper mantle is linked to near-seafloor manifestation of fluid flow through a network of faults. Along the two main fault traces, seismic reflection data imaged bright spots 100 300 m below seafloor that lie above changes inbasement topography. The bright spots are conformable to sediment layering, show opposite-toseafloor reflection polarity, and are associated with frequency-reduction and velocity push-down indicating the presence of gas in the sediments. Two seafloor mounds ~15 km seaward of the Nootka slope are underlain by deep, non-conformable high amplitude reflective zones. Measurements in the water column above one mound revealed a plume of warm water, and bottom-video observations imaged hydrothermal vent system biota. Pore fluids from a core at this mound contain predominately microbial methane (C1) with a high proportion of ethane (C2) yielding C1/C2 ratios < 500 indicating a possible slight contribution from a deep source. We infer the reflective zones beneath the two mounds are basaltic intrusions that create hydrothermal circulation within the overlying sediments. Across the Nootka continental slope, gas hydrate related bottom-simulating reflectors are widespread and occur at depths indicating heat-flow values of 80 90 mW/m2.","language":"English","publisher":"American Geophysical Union","doi":"10.1029/2020GC009095","usgsCitation":"Riedel, M., Rohr, K..., Spence, G.D., Kelley, D., Delaney, J., Lapham, L., Pohlman, J., Hyndman, R., and Willoughby, E., 2020, Focused fluid flow along the Nootka Fault Zone and continental slope, Explorer-Juan de Fuca plate boundary: Geochemistry, Geophysics, Geosystems, v. 21, no. 8, e2020GC009095, 26 p., https://doi.org/10.1029/2020GC009095.","productDescription":"e2020GC009095, 26 p.","ipdsId":"IP-120436","costCenters":[{"id":678,"text":"Woods Hole Coastal and Marine Science Center","active":true,"usgs":true}],"links":[{"id":455725,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1029/2020gc009095","text":"Publisher Index Page"},{"id":377719,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Oregon, Washington","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -127.2216796875,\n 41.83682786072714\n ],\n [\n -120.36621093749999,\n 41.83682786072714\n ],\n [\n -120.36621093749999,\n 49.06666839558117\n ],\n [\n -127.2216796875,\n 49.06666839558117\n ],\n [\n -127.2216796875,\n 41.83682786072714\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"21","issue":"8","noUsgsAuthors":false,"publicationDate":"2020-08-20","publicationStatus":"PW","contributors":{"authors":[{"text":"Riedel, M.","contributorId":238948,"corporation":false,"usgs":false,"family":"Riedel","given":"M.","affiliations":[{"id":47829,"text":"GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1 – 3, 24148 Kiel, Germany","active":true,"usgs":false}],"preferred":false,"id":796931,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Rohr, K .M. 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Using the two datasets that agreed best with PhenoCam metrics and covered 1982-2016, we conducted a trend analysis to study changes to growing seasons. Trends in phenology exhibited substantial spatial heterogeneity in the direction of trend for both datasets. Variability of metrics increased over time in some areas, particularly in the Southwest. Approximately 60% of pixels had consistent trend direction (both earlier and later) for SOS, POS, and EOS. In all ecoregions except Mediterranean California EOS trended toward a later date. This study provides a comprehensive comparison of remote sensing datasets across many important phenology and productivity metrics and discusses considerations for users to make informed decisions about their data choices.
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Article"},"seriesTitle":{"id":3301,"text":"River Research and Applications","active":true,"publicationSubtype":{"id":10}},"title":"Bidirectional connectivity via fish ladders in a large Neotropical river: Response to a comment","docAbstract":"In a recent article, we described fitting electronic tags to the fish Prochilodus lineatus to document how a fishway connected aquatic habitats downstream and upstream of a major dam. Moreover, given that tagged fish remained upstream or downstream for periods extending months and years before returning to the fishway, and that observed patterns of passage were consistent with seasonal migratory cycles, and building on existing literature, we speculated that the fishway allows fish access to spawning habitats upstream and feeding habitats downstream. Our interpretation of the movement data resulted in several comments from Pelicice, Pompeu, and Agostinho (2020) and they outline various reasons by which, in their opinion, some of our conclusions may be mistaken. Their critique is threefold. First, they argue that the percentage of fish attracted into the fishway is too low to consider the fishway an effective link between the reservoir and the river downstream. We contend that without estimates of population size it is impossible to judge if 28% passage is “limited”; conceivably, the absolute number of fish passed may still be enough to maintain a viable population. Second, they assert that because receivers were located only in the fishway it is unknown if fish that used the fishway remained near the dam, or if they continued their migration. We counter with a brief literature review that documents P. lineatus migrating through reservoirs and spawning in tributaries. Third, they advocate for a broader conservation perspective and for additional research. We agree and, in the article, had already expressed this view that fishways are only a temporary fix and that we support their use only as an element of a broader environmental management package. We also agree with the need for more research but argue that procrastinating on conservation action may not be wise because we do not know if the research will be done, how long it will take, or what the cost may be of waiting.
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Because these operate over multiple spatial and temporal scales, ranging from the eddy-scale to continental-scale; coupled numerical models that represent the full transport pathway have proved elusive though individual models have been developed to describe each of these processes. Toward a more holistic tool, a numerical workflow was developed to address pathways for sediment routing from terrestrial and coastal sources, across the continental shelf and ultimately down continental slope canyons of the northern Gulf of Mexico, where offshore infrastructure is susceptible to damage by turbidity currents. Workflow components included: 1) a calibrated simulator for fluvial discharge (Water Balance Model - Sediment; WBMsed); 2) domain grids for seabed sediment textures (dbSEABED); bathymetry, and channelization; 3) a simulator for ocean dynamics and resuspension (the Regional Ocean Modeling System; ROMS); 4) A simulator (HurriSlip) of seafloor failure and flow ignition; and 5) A Reynolds-averaged Navier–Stokes (RANS) turbidity current model (TURBINS). Model simulations explored physical oceanic conditions that might generate turbidity currents, and allowed the workflow to be tested for a year that included two hurricanes. Results showed that extreme storms were especially effective at delivering sediment from coastal source areas to the deep sea, at timescales that ranged from individual wave events (~hours), to the settling lag of fine sediment (~days).
","language":"English","publisher":"MDPI","doi":"10.3390/jmse8080586","usgsCitation":"Harris, C.K., Syvitski, J., Arango, H., Meiburg, E.H., Cohen, S., Jenkins, C., Birchler, J.J., Hutton, E.W., Kniskern, T.A., Radhakrishnan, S., and Auad, G., 2020, Data-driven, multi-model workflow suggests strong influence from hurricanes on the generation of turbidity currents in the Gulf of Mexico: Journal of Marine Science and Engineering, v. 8, no. 8, 586, 28 p., https://doi.org/10.3390/jmse8080586.","productDescription":"586, 28 p.","ipdsId":"IP-109071","costCenters":[{"id":574,"text":"St. Petersburg Coastal and Marine Science Center","active":true,"usgs":true}],"links":[{"id":455731,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.3390/jmse8080586","text":"Publisher Index Page"},{"id":377178,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Alabama, Florida, Louisiana, Mississippi, Texas","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 -97.53662109375,\n 27.410785702577023\n ],\n [\n -83.56201171875,\n 27.410785702577023\n ],\n [\n -83.56201171875,\n 30.581179257386985\n ],\n [\n -97.53662109375,\n 30.581179257386985\n ],\n [\n -97.53662109375,\n 27.410785702577023\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"8","issue":"8","noUsgsAuthors":false,"publicationDate":"2020-08-06","publicationStatus":"PW","contributors":{"authors":[{"text":"Harris, Courtney K.","contributorId":19620,"corporation":false,"usgs":false,"family":"Harris","given":"Courtney","email":"","middleInitial":"K.","affiliations":[{"id":6708,"text":"Virginia Institute of Marine Science","active":true,"usgs":false}],"preferred":false,"id":795214,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Syvitski, Jaia","contributorId":237738,"corporation":false,"usgs":false,"family":"Syvitski","given":"Jaia","email":"","affiliations":[],"preferred":false,"id":795215,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Arango, H.G.","contributorId":103772,"corporation":false,"usgs":true,"family":"Arango","given":"H.G.","email":"","affiliations":[],"preferred":false,"id":795216,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Meiburg, E. 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W. H.","contributorId":20940,"corporation":false,"usgs":true,"family":"Hutton","given":"E.","email":"","middleInitial":"W. H.","affiliations":[],"preferred":false,"id":795221,"contributorType":{"id":1,"text":"Authors"},"rank":8},{"text":"Kniskern, T. A.","contributorId":42807,"corporation":false,"usgs":false,"family":"Kniskern","given":"T.","email":"","middleInitial":"A.","affiliations":[],"preferred":false,"id":795222,"contributorType":{"id":1,"text":"Authors"},"rank":9},{"text":"Radhakrishnan, S.","contributorId":237740,"corporation":false,"usgs":false,"family":"Radhakrishnan","given":"S.","email":"","affiliations":[],"preferred":false,"id":795223,"contributorType":{"id":1,"text":"Authors"},"rank":10},{"text":"Auad, Guillermo","contributorId":78120,"corporation":false,"usgs":true,"family":"Auad","given":"Guillermo","email":"","affiliations":[],"preferred":false,"id":795224,"contributorType":{"id":1,"text":"Authors"},"rank":11}]}} ,{"id":70211653,"text":"cir1465 - 2020 - U.S. Geological Survey—Northern Prairie Wildlife Research Center 2018 research activity report","interactions":[],"lastModifiedDate":"2020-08-06T17:33:03.579914","indexId":"cir1465","displayToPublicDate":"2020-08-06T12:32:46","publicationYear":"2020","noYear":false,"publicationType":{"id":18,"text":"Report"},"publicationSubtype":{"id":5,"text":"USGS Numbered Series"},"seriesTitle":{"id":307,"text":"Circular","code":"CIR","onlineIssn":"2330-5703","printIssn":"1067-084X","active":true,"publicationSubtype":{"id":5}},"seriesNumber":"1465","displayTitle":"U.S. Geological Survey—Northern Prairie Wildlife Research Center 2018 Research Activity Report","title":"U.S. Geological Survey—Northern Prairie Wildlife Research Center 2018 research activity report","docAbstract":"The mission of Northern Prairie Wildlife Research Center is to provide scientific information needed to conserve and manage the Nation’s natural capital for current and future generations, with an emphasis on migratory birds, Department of the Interior trust resources, and ecosystems of the Nation’s interior. This report provides an overview of the studies conducted at Northern Prairie during fiscal year 2018 in pursuit of this mission. Studies are organized under a framework developed by the U.S. Geological Survey Ecosystems Mission Area, identifying primary and secondary alignment with focal areas of research, and summarizing recent scientific products resulting from these studies. Partnerships with Federal, State, and non-Governmental organizations are essential to a robust program of applied ecological research, and we thank our many collaborators and colleagues whose contributions made this work possible.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/cir1465","usgsCitation":"Sherfy, M.H., ed., 2020, U.S. Geological Survey—Northern Prairie Wildlife Research Center 2018 research activity report: U.S. Geological Survey Circular 1465, 69 p., https://doi.org/10.3133/cir1465.","productDescription":"ix, 69 p.","numberOfPages":"84","onlineOnly":"Y","ipdsId":"IP-113740","costCenters":[{"id":480,"text":"Northern Prairie Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":377078,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/circ/1465/cir1465.pdf","text":"Report","size":"32.2 MB","linkFileType":{"id":1,"text":"pdf"},"description":"Circular 1465"},{"id":377077,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/circ/1465/coverthb.jpg"}],"contact":"Director, Northern Prairie Wildlife Research Center
U.S. Geological Survey
8711 37th Street Southeast
Jamestown, ND 58401
The US Environmental Protection Agency (USEPA) is reviewing the protectiveness of the national ambient water quality criteria (WQC) for nickel (Ni) and zinc (Zn) and compiling toxicity databases to update the WQC. An amphipod (Hyalella azteca) and a unionid mussel (Lampsilis siliquoidea) have shown high sensitivity to Ni and Zn in previous studies. However, there remained uncertainties regarding the influence of test duration (48 vs 96 h) and the presence and absence of food in acute exposures with the amphipod, and there were also concerns about poor control of amphipod growth and reproduction and mussel growth in chronic exposures. We conducted acute 48‐ and 96‐h water‐only toxicity tests to evaluate the influence of feeding and test durations on the toxicity of dissolved Ni and Zn to the amphipod; we also used recently refined test methods to conduct chronic Ni and Zn toxicity tests to evaluate the sensitivity of the amphipod (6‐wk exposure) and the mussel (4‐ and 12‐wk exposures). The 96‐h 50% effect concentrations (EC50s) of 916 µg Ni/L and 99 µg Zn/L from acute amphipod tests without feeding decreased from the 48‐h EC50s by 62 and 33%, respectively, whereas the 96‐h EC50s of 2732 µg Ni/L and 194 µg Zn/L from the tests with feeding decreased from the 48‐h EC50s by 10 and 26%, indicating that the presence or absence of food had apparent implications for the 96‐h EC50. Our chronic 6‐wk EC20s for the amphipod (4.5 µg Ni/L and 35 µg Zn/L) were 50 to 67% lower than the 6‐wk EC20s from previous amphipod tests, and our chronic 4‐wk EC20s for the mussel (41 µg Ni/L and 66 µg Zn/L) were similar to or up to 42% lower than the 4‐wk EC20s from previous mussel tests. The lower EC20s from the present study likely reflect more accurate estimates of inherent sensitivity to Ni and Zn due to the refined test conditions. Finally, increasing the chronic test duration from 4 to 12 wk substantially increased the toxicity of Zn to the mussel, whereas the 4‐ and 12‐wk Ni effect needs to be re‐evaluated to understand the large degree of variation in organism responses observed in the present study.
","language":"English","publisher":"Society of Environmental Toxicology and Chemistry","doi":"10.1002/etc.4841","usgsCitation":"Wang, N., Kunz, J.L., Cleveland, D.M., Steevens, J.A., Hammer, E.J., Van Genderen, E., Ryan, A.C., and Schlekat, C., 2020, Evaluation of acute and chronic toxicity of nickel and zinc to 2 sensitive freshwater benthic invertebrates using refined testing methods: Environmental Toxicology and Chemistry, v. 39, no. 11, p. 2256-2268, https://doi.org/10.1002/etc.4841.","productDescription":"13 p.","startPage":"2256","endPage":"2268","ipdsId":"IP-119074","costCenters":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"links":[{"id":436833,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P9DH1ORZ","text":"USGS data release","linkHelpText":"Chemical and biological data from acute and chronic nickel and zinc exposure bioassays to two sensitive freshwater benthic invertebrates"},{"id":379093,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"39","issue":"11","noUsgsAuthors":false,"publicationDate":"2020-08-06","publicationStatus":"PW","contributors":{"authors":[{"text":"Wang, Ning 0000-0002-2846-3352 nwang@usgs.gov","orcid":"https://orcid.org/0000-0002-2846-3352","contributorId":2818,"corporation":false,"usgs":true,"family":"Wang","given":"Ning","email":"nwang@usgs.gov","affiliations":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"preferred":true,"id":800523,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kunz, James L. 0000-0002-1027-158X jkunz@usgs.gov","orcid":"https://orcid.org/0000-0002-1027-158X","contributorId":3309,"corporation":false,"usgs":true,"family":"Kunz","given":"James","email":"jkunz@usgs.gov","middleInitial":"L.","affiliations":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"preferred":true,"id":800524,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Cleveland, Danielle M. 0000-0003-3880-4584 dcleveland@usgs.gov","orcid":"https://orcid.org/0000-0003-3880-4584","contributorId":187471,"corporation":false,"usgs":true,"family":"Cleveland","given":"Danielle","email":"dcleveland@usgs.gov","middleInitial":"M.","affiliations":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"preferred":true,"id":800525,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Steevens, Jeffery A. 0000-0003-3946-1229","orcid":"https://orcid.org/0000-0003-3946-1229","contributorId":207511,"corporation":false,"usgs":true,"family":"Steevens","given":"Jeffery","middleInitial":"A.","affiliations":[{"id":192,"text":"Columbia Environmental Research Center","active":true,"usgs":true}],"preferred":true,"id":800526,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Hammer, Edward J.","contributorId":150723,"corporation":false,"usgs":false,"family":"Hammer","given":"Edward","email":"","middleInitial":"J.","affiliations":[{"id":18077,"text":"U. S. Environmental Protection Agency, Region 5, Water Quality Branch, Chicago, Illinois","active":true,"usgs":false}],"preferred":false,"id":800527,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Van Genderen, Eric","contributorId":242622,"corporation":false,"usgs":false,"family":"Van Genderen","given":"Eric","affiliations":[{"id":48485,"text":"International Zinc Association, Durham, NC","active":true,"usgs":false}],"preferred":false,"id":800528,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Ryan, Adam C.","contributorId":175564,"corporation":false,"usgs":false,"family":"Ryan","given":"Adam","email":"","middleInitial":"C.","affiliations":[],"preferred":false,"id":800529,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Schlekat, Christian E.","contributorId":242623,"corporation":false,"usgs":false,"family":"Schlekat","given":"Christian E.","affiliations":[{"id":48488,"text":"NiPERA Inc., Durham, NC","active":true,"usgs":false}],"preferred":false,"id":800530,"contributorType":{"id":1,"text":"Authors"},"rank":8}]}} ,{"id":70211637,"text":"70211637 - 2020 - A hybrid approach for predictive soil property mapping using conventional soil survey data","interactions":[],"lastModifiedDate":"2020-09-10T20:19:02.656543","indexId":"70211637","displayToPublicDate":"2020-08-06T10:36:57","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3420,"text":"Soil Science Society of America Journal","active":true,"publicationSubtype":{"id":10}},"title":"A hybrid approach for predictive soil property mapping using conventional soil survey data","docAbstract":"Soil property maps are important for land management and earth systems modeling. A new hybrid point-disaggregation predictive soil property mapping strategy improved mapping in the Colorado River Basin, and can be applied to other areas with similar data (e.g. conterminous United States). This new approach increased sample size ~6-fold over past efforts. Random forests related environmental raster layers representing soil forming factors to samples to predict 15 soil properties (pH, texture fractions, rock, electrical conductivity, gypsum, CaCO3, sodium adsorption ratio, available water capacity, bulk density, erodibility, organic matter) at 7 depths, depth to restrictive layer, and surface rock size and cover. Cross-validations resulted in coefficient of determinations averaging 0.52, with a range of 0.20 to 0.76; and mean absolute errors ranged from 3% to 98% of training data averages with a mean of 41%. Uncertainty estimates were also developed by creating relative prediction intervals (RPIs) for the entire study area, which allow end users to evaluate uncertainty relative to original data distributions. Average error increased with higher RPI values (higher uncertainty), and areas with the highest RPI are consistently under-sampled, suggesting that additional sampling in these areas may improve prediction accuracy. Greater uncertainty was also observed in areas with shale parent materials and physiographic settings uncommon relative to the broader study area.","language":"English","publisher":"Wiley","doi":"10.1002/saj2.20080","usgsCitation":"Nauman, T.W., and Duniway, M.C., 2020, A hybrid approach for predictive soil property mapping using conventional soil survey data: Soil Science Society of America Journal, v. 84, no. 4, p. 170-1194, https://doi.org/10.1002/saj2.20080.","productDescription":"25 p.","startPage":"170","endPage":"1194","onlineOnly":"Y","ipdsId":"IP-108106","costCenters":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"links":[{"id":436834,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P9SK0DO2","text":"USGS data release","linkHelpText":"Predictive soil property maps with prediction uncertainty at 30-meter resolution for the Colorado River Basin above Lake Mead"},{"id":377090,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"New Mexico, Colorado, Wyoming, Utah, Nevada, Arizona","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -106.61132812499999,\n 35.67514743608467\n ],\n [\n -107.490234375,\n 39.50404070558415\n ],\n [\n -108.720703125,\n 42.68243539838623\n ],\n [\n -110.302734375,\n 42.5530802889558\n ],\n [\n -112.1484375,\n 41.21172151054787\n ],\n [\n -113.818359375,\n 38.06539235133249\n ],\n [\n -115.6201171875,\n 37.3002752813443\n ],\n [\n -116.3671875,\n 36.527294814546245\n ],\n [\n -112.587890625,\n 34.56085936708384\n ],\n [\n -106.61132812499999,\n 35.67514743608467\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"84","issue":"4","noUsgsAuthors":false,"publicationDate":"2020-07-21","publicationStatus":"PW","contributors":{"authors":[{"text":"Nauman, Travis W. 0000-0001-8004-0608 tnauman@usgs.gov","orcid":"https://orcid.org/0000-0001-8004-0608","contributorId":169241,"corporation":false,"usgs":true,"family":"Nauman","given":"Travis","email":"tnauman@usgs.gov","middleInitial":"W.","affiliations":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"preferred":true,"id":794892,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Duniway, Michael C. 0000-0002-9643-2785 mduniway@usgs.gov","orcid":"https://orcid.org/0000-0002-9643-2785","contributorId":4212,"corporation":false,"usgs":true,"family":"Duniway","given":"Michael","email":"mduniway@usgs.gov","middleInitial":"C.","affiliations":[{"id":568,"text":"Southwest Biological Science Center","active":true,"usgs":true}],"preferred":true,"id":794893,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":70211646,"text":"70211646 - 2020 - Evaluation of genetic structuring within GIS‐derived Brook Trout management units","interactions":[],"lastModifiedDate":"2021-01-25T15:51:59.457998","indexId":"70211646","displayToPublicDate":"2020-08-06T10:05:06","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3624,"text":"Transactions of the American Fisheries Society","active":true,"publicationSubtype":{"id":10}},"title":"Evaluation of genetic structuring within GIS‐derived Brook Trout management units","docAbstract":"Delineation of management units across broad spatial scales can help to visualize population structuring and identify conservation opportunities. Geographical information system (GIS) approaches can be useful for developing broad‐scale management units, especially when paired with field data that can validate the GIS‐based delineations. Genetic data can be useful for evaluating whether management units accurately represent population structuring. The Eastern Brook Trout Joint Venture, a regionwide collaborative group, delineated patch‐based management units for Brook Trout Salvelinus fontinalis by using GIS approaches to inform conservation strategies across the eastern United States. The objectives of this research were to (1) evaluate how well the patches predicted Brook Trout genetic structuring in Connecticut, USA; (2) modify the patches as needed to represent contemporary genetic structuring; and (3) identify catchment‐ and patch‐scale riverscape characteristics that predict genetic diversity. Patches with dams and high levels of upstream impervious surfaces (>3%) had increased intrapatch genetic structuring, which we incorporated into our revised patch delineation algorithm. Patch area and catchment area were the best predictors of genetic diversity, suggesting the importance of maintaining connectivity and incorporating patch‐scale processes into conservation actions. The modified patch layer could be used as the basis for Brook Trout management units to help predict population structuring in the absence of watershed‐scale genetic data, allowing opportunities for Brook Trout conservation to be identified.
","language":"English","publisher":"American Fisheries Society","doi":"10.1002/tafs.10260","usgsCitation":"Nathan, L., Kanno, Y., Letcher, B., Welsh, A.B., Whiteley, A.R., and Vokoun, J., 2020, Evaluation of genetic structuring within GIS‐derived Brook Trout management units: Transactions of the American Fisheries Society, v. 149, no. 6, p. 681-694, https://doi.org/10.1002/tafs.10260.","productDescription":"14 p.","startPage":"681","endPage":"694","ipdsId":"IP-117802","costCenters":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"links":[{"id":382550,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United 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\"}}]}","volume":"149","issue":"6","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Nathan, Lucas","contributorId":236997,"corporation":false,"usgs":false,"family":"Nathan","given":"Lucas","affiliations":[{"id":36986,"text":"Michigan Department of Natural Resources","active":true,"usgs":false}],"preferred":false,"id":794912,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kanno, Y.","contributorId":214290,"corporation":false,"usgs":false,"family":"Kanno","given":"Y.","email":"","affiliations":[{"id":6621,"text":"Colorado State University","active":true,"usgs":false}],"preferred":false,"id":794913,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Letcher, Benjamin 0000-0003-0191-5678 bletcher@usgs.gov","orcid":"https://orcid.org/0000-0003-0191-5678","contributorId":169305,"corporation":false,"usgs":true,"family":"Letcher","given":"Benjamin","email":"bletcher@usgs.gov","affiliations":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":true,"id":794914,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Welsh, Amy B.","contributorId":192239,"corporation":false,"usgs":false,"family":"Welsh","given":"Amy","email":"","middleInitial":"B.","affiliations":[],"preferred":false,"id":794915,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Whiteley, Andrew R.","contributorId":150155,"corporation":false,"usgs":false,"family":"Whiteley","given":"Andrew","email":"","middleInitial":"R.","affiliations":[{"id":6932,"text":"University of Massachusetts, Amherst","active":true,"usgs":false}],"preferred":false,"id":794916,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Vokoun, Jason C.","contributorId":236998,"corporation":false,"usgs":false,"family":"Vokoun","given":"Jason C.","affiliations":[{"id":47587,"text":"University of CT","active":true,"usgs":false}],"preferred":false,"id":794917,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70211693,"text":"70211693 - 2020 - The freshwater mysid Mysis diluviana (Audzijonyte and Väinölä, 2005) (Mysida: Mysidae) consumes detritus in the presence of Daphnia (Cladocera: Daphniidae)","interactions":[],"lastModifiedDate":"2020-08-07T14:11:57.748282","indexId":"70211693","displayToPublicDate":"2020-08-06T09:09:53","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2235,"text":"Journal of Crustacean Biology","active":true,"publicationSubtype":{"id":10}},"displayTitle":"The freshwater mysid Mysis diluviana (Audzijonyte and Väinölä, 2005) (Mysida: Mysidae) consumes detritus in the presence of Daphnia (Cladocera: Daphniidae)","title":"The freshwater mysid Mysis diluviana (Audzijonyte and Väinölä, 2005) (Mysida: Mysidae) consumes detritus in the presence of Daphnia (Cladocera: Daphniidae)","docAbstract":"Freshwater mysids of the Mysis relicta group are omnivorous macroinvertebrates that form an important link between fishes and lower trophic levels in many north temperate to Arctic lakes, where they exhibit diel vertical migration (DVM) to exploit subsurface food-rich layers at night. Benthic food resources have been assumed to be less important for mysid diets than pelagic zooplankton. Studies have nevertheless indicated that mysids consume benthic sedimented detritus, calling this assumption into question. We conducted a food-choice experiment to evaluate the feeding preferences of Mysis diluviana (Audzijonyte & Vainola, 2005) by presenting field-caught specimens in individual foraging arenas with multiple choices of food. Experimental food treatments included a preferred pelagic prey (Daphnia), a presumed less desirable benthic resource (detritus), and a combination of both. We hypothesized that M. diluviana 1) prefers Daphnia over detritus and consumes only Daphnia in combination treatments, and 2) would not consume detritus except when detritus was the only food source available. Contrary to our hypothesis, M. diluviana readily consumed detritus in the presence of Daphnia. M. diluviana unexpectedly consumed more individuals of Daphnia in the presence rather than in the absence of detritus. Our results demonstrate that mysids take advantage of benthic food resources even in the presence of a presumably preferred zooplankton prey, calling to question the long-held assumption that benthic resources are unimportant when considering the trophic role of freshwater mysids of the M. relicta group.","language":"English","publisher":"Oxford Academic","doi":"10.1093/jcbiol/ruaa053","usgsCitation":"Griffin, J.E., O’Malley, B., and Stockwell, J.D., 2020, The freshwater mysid Mysis diluviana (Audzijonyte and Väinölä, 2005) (Mysida: Mysidae) consumes detritus in the presence of Daphnia (Cladocera: Daphniidae): Journal of Crustacean Biology, ruaa053, 6 p., https://doi.org/10.1093/jcbiol/ruaa053.","productDescription":"ruaa053, 6 p.","ipdsId":"IP-118255","costCenters":[{"id":324,"text":"Great Lakes Science Center","active":true,"usgs":true}],"links":[{"id":455738,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1093/jcbiol/ruaa053","text":"Publisher Index Page"},{"id":377174,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"noUsgsAuthors":false,"publicationDate":"2020-08-06","publicationStatus":"PW","contributors":{"authors":[{"text":"Griffin, Jessica E.","contributorId":237059,"corporation":false,"usgs":false,"family":"Griffin","given":"Jessica","email":"","middleInitial":"E.","affiliations":[{"id":36629,"text":"University of California","active":true,"usgs":false}],"preferred":false,"id":795094,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"O’Malley, Brian 0000-0001-5035-3080 bomalley@usgs.gov","orcid":"https://orcid.org/0000-0001-5035-3080","contributorId":216560,"corporation":false,"usgs":true,"family":"O’Malley","given":"Brian","email":"bomalley@usgs.gov","affiliations":[{"id":324,"text":"Great Lakes Science Center","active":true,"usgs":true}],"preferred":true,"id":795095,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Stockwell, Jason D. 0000-0003-3393-6799","orcid":"https://orcid.org/0000-0003-3393-6799","contributorId":61004,"corporation":false,"usgs":false,"family":"Stockwell","given":"Jason","email":"","middleInitial":"D.","affiliations":[],"preferred":false,"id":795096,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70211647,"text":"70211647 - 2020 - Dynamics of lake trout production in the main basin of Lake Huron","interactions":[],"lastModifiedDate":"2020-08-06T14:10:58.01762","indexId":"70211647","displayToPublicDate":"2020-08-06T09:05:18","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1936,"text":"ICES Journal of Marine Science","active":true,"publicationSubtype":{"id":10}},"title":"Dynamics of lake trout production in the main basin of Lake Huron","docAbstract":"To inform lake trout (Salvelinus namaycush) fishery management in Lake Huron that has undergone rapid ecosystem changes, we quantified lake trout production dynamics by coupling age-structured stock assessment and fish bioenergetics models. Our approach revealed the connection between piscivore production and prey consumption, included growth compensation to reproduction losses, and allowed comparisons between long-term dynamics of fishery harvests and fish production. We found that despite the collapse of alewives, a major non-native pelagic prey fish, lake trout production appeared to be sustainable. To a certain degree, the effect of recent recruitment declines on lake trout production was offset by release of harvest pressure from subadult lake trout, and reduction of fishing and sea lamprey induced mortality on adult lake trout. Evidence for sustainability also included the finding that no changes in average ratios of annual production to beginning-of-the-year biomass. Juvenile P:B ratio remained as high as 2.1. The effect of growth declines on adult and subadult production was offset by reduction in population mortality. Body growth and condition did not continue to decline when lake trout became more and more reliant on round goby as food, and the dynamics of total consumption of prey fish continued to be recipient controlled.","language":"English","publisher":"ICES Journal of Marine Science","doi":"10.1093/icesjms/fsaa030","collaboration":"Michigan Department of Natural Resources, Michigan State University","usgsCitation":"He, J.X., Bence, J., Madenjian, C.P., and Claramunt, R.M., 2020, Dynamics of lake trout production in the main basin of Lake Huron: ICES Journal of Marine Science, v. 77, no. 3, p. 975-987, https://doi.org/10.1093/icesjms/fsaa030.","productDescription":"13 p.","startPage":"975","endPage":"987","ipdsId":"IP-111403","costCenters":[{"id":324,"text":"Great Lakes Science Center","active":true,"usgs":true}],"links":[{"id":377081,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","otherGeospatial":"Lake Huron","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -84.6990966796875,\n 46.02366774426006\n ],\n [\n -84.7320556640625,\n 45.767522962149876\n ],\n [\n -84.232177734375,\n 45.63324613981234\n ],\n [\n -84.0838623046875,\n 45.49094569262732\n ],\n [\n -83.6993408203125,\n 45.38301927899065\n ],\n [\n -83.507080078125,\n 45.32897866218559\n ],\n [\n -83.4027099609375,\n 45.236217535866025\n ],\n [\n -83.2928466796875,\n 45.01141864227728\n ],\n [\n -83.43017578125,\n 45.042478050891546\n ],\n [\n -83.29833984375,\n 44.867549659447214\n ],\n [\n -83.3148193359375,\n 44.54742015866826\n ],\n [\n -83.3807373046875,\n 44.296332880058706\n ],\n [\n -82.9522705078125,\n 44.26093725039923\n ],\n [\n -82.254638671875,\n 44.296332880058706\n ],\n [\n -81.4031982421875,\n 44.953136827528816\n ],\n [\n -81.727294921875,\n 45.24008561090264\n ],\n [\n -82.177734375,\n 45.598665689820635\n ],\n [\n -83.056640625,\n 45.832626782661535\n ],\n [\n -83.375244140625,\n 45.836454050187726\n ],\n [\n -83.9190673828125,\n 45.98932892799953\n ],\n [\n -84.6990966796875,\n 46.02366774426006\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"77","issue":"3","noUsgsAuthors":false,"publicationDate":"2020-03-10","publicationStatus":"PW","contributors":{"authors":[{"text":"He, Ji X.","contributorId":181528,"corporation":false,"usgs":false,"family":"He","given":"Ji","email":"","middleInitial":"X.","affiliations":[],"preferred":false,"id":794918,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Bence, James R.","contributorId":95026,"corporation":false,"usgs":false,"family":"Bence","given":"James R.","affiliations":[{"id":6601,"text":"Michigan State University","active":true,"usgs":false}],"preferred":false,"id":794919,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Madenjian, Charles P. 0000-0002-0326-164X cmadenjian@usgs.gov","orcid":"https://orcid.org/0000-0002-0326-164X","contributorId":2200,"corporation":false,"usgs":true,"family":"Madenjian","given":"Charles","email":"cmadenjian@usgs.gov","middleInitial":"P.","affiliations":[{"id":324,"text":"Great Lakes Science Center","active":true,"usgs":true}],"preferred":true,"id":794920,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Claramunt, Randall M.","contributorId":190497,"corporation":false,"usgs":false,"family":"Claramunt","given":"Randall","email":"","middleInitial":"M.","affiliations":[],"preferred":false,"id":794921,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70211706,"text":"70211706 - 2020 - Methods for rapid quality assessment for national-scale land surface change monitoring","interactions":[],"lastModifiedDate":"2020-08-07T13:34:27.240855","indexId":"70211706","displayToPublicDate":"2020-08-06T08:30:46","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3250,"text":"Remote Sensing","active":true,"publicationSubtype":{"id":10}},"title":"Methods for rapid quality assessment for national-scale land surface change monitoring","docAbstract":"Providing rapid access to land surface change data and information is a goal of the U.S. Geological Survey. Through the Land Change Monitoring, Assessment, and Projection (LCMAP) initiative, we have initiated a monitoring capability that involves generating a suite of ten annual land cover and land surface change datasets across the United States at a 30-m spatial resolution. During the LCMAP automated production on a tile-by-tile basis, erroneous data can occasionally be generated due to hardware or software failure. While crucial to assure the quality of the data, rapid evaluation of results at the pixel level during production is a substantial challenge because of the massive data volumes. Traditionally, product quality relies on the validation after production, which is inefficient to reproduce the whole product when an error occurs. This paper presents a method for automatically evaluating LCMAP results during the production phase based on fourteen indices to quickly find and flag erroneous tiles in the LCMAP products. The methods involved two types of comparisons: comparing LCMAP values across the temporal record to measure internal consistency and calculating agreement with multiple intervals of the National Land Cover Database (NLCD) data to measure the consistency with existing products. We developed indices on a tile-by-tile basis in order to quickly find and flag potential erroneous tiles by comparing with surrounding tiles using local outlier factor analysis. The analysis integrates all indices into a local outlier score (LOS) to detect erroneous tiles distinct from neighbor tiles. Our analysis showed that the methods were sensitive to partially erroneous tiles in the simulated data with a LOS higher than 2. The rapid quality assessment methods also successfully identified erroneous tiles during the LCMAP production, in which land surface change results were not properly saved to the products. The LOS map and indices for rapid quality assessment also point to directions for further investigations. A map of all LOS values by tile for the published LCMAP shows all LOS values are below 2. We also investigated tiles with high LOS to ensure the distinction with neighboring tiles was reasonable. An index in this study shows the overall agreement between LCMAP and NLCD on a tile basis is above 71.5% and has an average at 89.1% across the 422 tiles in the conterminous U.S. The workflow is suitable for other studies with a large volume of image products.","language":"English","publisher":"MDPI","doi":"10.3390/rs12162524","usgsCitation":"Zhou, Q., Barber, C., and Xian, G.Z., 2020, Methods for rapid quality assessment for national-scale land surface change monitoring: Remote Sensing, v. 12, no. 16, 2524, 18 p., https://doi.org/10.3390/rs12162524.","productDescription":"2524, 18 p.","ipdsId":"IP-120030","costCenters":[{"id":222,"text":"Earth Resources Observation and Science (EROS) Center","active":true,"usgs":true}],"links":[{"id":455740,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.3390/rs12162524","text":"Publisher Index 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xian@usgs.gov","orcid":"https://orcid.org/0000-0001-5674-2204","contributorId":2263,"corporation":false,"usgs":true,"family":"Xian","given":"George","email":"xian@usgs.gov","middleInitial":"Z.","affiliations":[{"id":222,"text":"Earth Resources Observation and Science (EROS) Center","active":true,"usgs":true}],"preferred":true,"id":795200,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70212923,"text":"70212923 - 2020 - Seismicity induced by massive wastewater injection near Puerto Gaitán, Colombia","interactions":[],"lastModifiedDate":"2020-09-02T13:31:05.404093","indexId":"70212923","displayToPublicDate":"2020-08-06T08:13:06","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1803,"text":"Geophysical Journal International","active":true,"publicationSubtype":{"id":10}},"title":"Seismicity induced by massive wastewater injection near Puerto Gaitán, Colombia","docAbstract":"Seven years after the beginning of a massive wastewater injection project in eastern Colombia, local earthquake activity increased significantly. The field operator and the Colombian Geological Survey immediately reinforced the monitoring of the area. Our analysis of the temporal evolution of the seismic and injection data together with our knowledge of the geological parameters of the region indicate that the surge of seismicity is being induced by the re-injection of produced water into the same three producing reservoirs. Earthquake activity began on known faults once disposal rates had reached a threshold of ∼2 × 106 m3 of water per month. The average reservoir pressure had remained constant at 7.6 MPa after several years of production, sustained by a large, active aquifer. Surface injection pressures in the seismically active areas remain below 8.3 MPa, a value large enough to activate some of the faults. Since faults are mapped throughout the region and many do not have seismicity on them, we conclude that the existence of known faults is not the only control on whether earthquakes are generated. Stress conditions of these faults are open to future studies. Earthquakes are primarily found in four clusters, located near faults mapped by the operator. The hypocentres reveal vertical planes with orientations consistent with focal mechanisms of these events. Stress inversion of the focal mechanisms gives a maximum compression in the direction ENE-WSW, which is in agreement with borehole breakout measurements. Since the focal mechanisms of the earthquakes are consistent with the tectonic stress regime, we can conclude that the seismicity is resulting from the activation of critically stressed faults. Slip was progressive and seismic activity reached a peak before declining to few events per month. The decline in seismicity suggests that most of the stress has been relieved on the main faults. The magnitude of a large majority of the recorded earthquakes was lower than 4, as the pore pressure disturbance did not reach the mapped large faults whose activation might have resulted in larger magnitude earthquakes. Our study shows that a good knowledge of the local fault network and conditions of stress is of paramount importance when planning a massive water disposal program. These earthquakes indicate that while faults provide an opportunity to dispose produced water at an economically attractive volume–pressure ratio, the possibility of induced seismicity must also be considered.
","language":"English","publisher":"Oxford University Press","doi":"10.1093/gji/ggaa326","usgsCitation":"Molina, I., Velasquez, J., Rubinstein, J., Garcia-Aristizabal, A., and Dionicio, V., 2020, Seismicity induced by massive wastewater injection near Puerto Gaitán, Colombia: Geophysical Journal International, v. 223, no. 2, p. 777-791, https://doi.org/10.1093/gji/ggaa326.","productDescription":"25 p.","startPage":"777","endPage":"791","ipdsId":"IP-094755","costCenters":[{"id":237,"text":"Earthquake Science Center","active":true,"usgs":true}],"links":[{"id":455745,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1093/gji/ggaa326","text":"Publisher Index Page"},{"id":378094,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Colombia","city":"Puerto Gaitan","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -72.2186279296875,\n 3.436658158559092\n ],\n [\n -71.1199951171875,\n 3.436658158559092\n ],\n [\n -71.1199951171875,\n 4.469641844538532\n ],\n [\n -72.2186279296875,\n 4.469641844538532\n ],\n [\n -72.2186279296875,\n 3.436658158559092\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"223","issue":"2","noUsgsAuthors":false,"publicationDate":"2020-08-06","publicationStatus":"PW","contributors":{"authors":[{"text":"Molina, I","contributorId":239740,"corporation":false,"usgs":false,"family":"Molina","given":"I","email":"","affiliations":[{"id":47998,"text":"Servicio Geologico Colombiano","active":true,"usgs":false}],"preferred":false,"id":797819,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Velasquez, J.S.","contributorId":239741,"corporation":false,"usgs":false,"family":"Velasquez","given":"J.S.","email":"","affiliations":[{"id":47998,"text":"Servicio Geologico Colombiano","active":true,"usgs":false}],"preferred":false,"id":797820,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Rubinstein, Justin 0000-0003-1274-6785","orcid":"https://orcid.org/0000-0003-1274-6785","contributorId":215341,"corporation":false,"usgs":true,"family":"Rubinstein","given":"Justin","affiliations":[{"id":237,"text":"Earthquake Science Center","active":true,"usgs":true}],"preferred":true,"id":797821,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Garcia-Aristizabal, A","contributorId":239742,"corporation":false,"usgs":false,"family":"Garcia-Aristizabal","given":"A","email":"","affiliations":[{"id":39118,"text":"Istituto Nazionale di Geofisica e Vulcanologia","active":true,"usgs":false}],"preferred":false,"id":797822,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Dionicio, V","contributorId":239744,"corporation":false,"usgs":false,"family":"Dionicio","given":"V","email":"","affiliations":[{"id":47998,"text":"Servicio Geologico Colombiano","active":true,"usgs":false}],"preferred":false,"id":797824,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70211994,"text":"70211994 - 2020 - Generalized models to estimate carbon and nitrogen stocks of organic soil horizons in Interior Alaska","interactions":[],"lastModifiedDate":"2020-08-13T12:56:44.564102","indexId":"70211994","displayToPublicDate":"2020-08-06T07:53:36","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":6009,"text":"Earth System Science Data (ESSD)","active":true,"publicationSubtype":{"id":10}},"title":"Generalized models to estimate carbon and nitrogen stocks of organic soil horizons in Interior Alaska","docAbstract":"Boreal ecosystems comprise one tenth of the world’s land surface and contain over 20 % of the global soil carbon (C) stocks. Boreal soils are unique in that its mineral soil is covered by what can be quite thick layers of organic soil. These organic soil layers, or horizons, can differ in their state of decomposition, source vegetation, and disturbance history. These differences result in varying soil properties (bulk density, C concentration, and nitrogen (N) concentration) among soil horizons. Here we summarize these soil properties, as represented by over 3000 samples from Interior Alaska, and examine how soil drainage and stand age affect these attributes. The summary values presented here can be used to gap-fill large datasets when important soil properties were not measured, provide data to initialize process-based models, and validate model results. These data are available at https://doi.org/10.5066/P960N1F9 (Manies, 2019).","language":"English","publisher":"Copernicus Publications","doi":"10.5194/essd-12-1745-2020","usgsCitation":"Manies, K.L., Waldrop, M., and Harden, J.W., 2020, Generalized models to estimate carbon and nitrogen stocks of organic soil horizons in Interior Alaska: Earth System Science Data (ESSD), v. 12, p. 1745-1757, https://doi.org/10.5194/essd-12-1745-2020.","productDescription":"13 p.","startPage":"1745","endPage":"1757","ipdsId":"IP-109891","costCenters":[{"id":312,"text":"Geology, Minerals, Energy, and Geophysics Science Center","active":true,"usgs":true},{"id":617,"text":"Volcano Science Center","active":true,"usgs":true}],"links":[{"id":455749,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.5194/essd-12-1745-2020","text":"Publisher Index Page"},{"id":377481,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Alaska","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -160.3125,\n 63.54855223203644\n ],\n [\n -142.734375,\n 63.54855223203644\n ],\n [\n -142.734375,\n 68.13885164925573\n ],\n [\n -160.3125,\n 68.13885164925573\n ],\n [\n -160.3125,\n 63.54855223203644\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"12","noUsgsAuthors":false,"publicationDate":"2020-08-06","publicationStatus":"PW","contributors":{"authors":[{"text":"Manies, Kristen L. 0000-0003-4941-9657 kmanies@usgs.gov","orcid":"https://orcid.org/0000-0003-4941-9657","contributorId":2136,"corporation":false,"usgs":true,"family":"Manies","given":"Kristen","email":"kmanies@usgs.gov","middleInitial":"L.","affiliations":[{"id":312,"text":"Geology, Minerals, Energy, and Geophysics Science Center","active":true,"usgs":true},{"id":617,"text":"Volcano Science Center","active":true,"usgs":true}],"preferred":true,"id":796140,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Waldrop, Mark 0000-0003-1829-7140","orcid":"https://orcid.org/0000-0003-1829-7140","contributorId":216758,"corporation":false,"usgs":true,"family":"Waldrop","given":"Mark","affiliations":[],"preferred":true,"id":796141,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Harden, Jennifer W. 0000-0002-6570-8259 jharden@usgs.gov","orcid":"https://orcid.org/0000-0002-6570-8259","contributorId":1971,"corporation":false,"usgs":true,"family":"Harden","given":"Jennifer","email":"jharden@usgs.gov","middleInitial":"W.","affiliations":[{"id":615,"text":"Volcano Hazards Program","active":true,"usgs":true},{"id":312,"text":"Geology, Minerals, Energy, and Geophysics Science Center","active":true,"usgs":true},{"id":617,"text":"Volcano Science Center","active":true,"usgs":true}],"preferred":true,"id":796142,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70211605,"text":"sir20205077 - 2020 - Steps taken for calculating estimated ultimate recoveries of wells in the Eagle Ford Group and associated Cenomanian–Turonian strata, U.S. Gulf Coast, Texas, 2018","interactions":[],"lastModifiedDate":"2020-08-06T19:01:37.143617","indexId":"sir20205077","displayToPublicDate":"2020-08-06T05:52:21","publicationYear":"2020","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":"2020-5077","displayTitle":"Steps Taken for Calculating Estimated Ultimate Recoveries of Wells in the Eagle Ford Group and Associated Cenomanian–Turonian Strata, U.S. Gulf Coast, Texas, 2018","title":"Steps taken for calculating estimated ultimate recoveries of wells in the Eagle Ford Group and associated Cenomanian–Turonian strata, U.S. Gulf Coast, Texas, 2018","docAbstract":"In 2018, the U.S. Geological Survey published an assessment of technically recoverable continuous oil and gas resources of the Eagle Ford Group and associated Cenomanian–Turonian strata in the U.S. Gulf Coast of Texas. Estimated ultimate recoveries (EURs) were calculated with production data from IHS MarkitTM using DeclinePlus software in the Harmony interface. These EURs were a major component of the aforementioned quantitative resource assessment fact sheet. The calculated mean EURs for each oil assessment unit (AU) ranged from 113,000 barrels of oil in the Cenomanian–Turonian Mudstone Continuous Oil AU to 223,000 barrels of oil in the Submarine Plateau-Karnes Trough Continuous Oil AU. The calculated mean EURs for each gas AU ranged from 2.261 billion cubic feet of gas in the Submarine Plateau-Karnes Trough Continuous Gas AU to 3.116 billion cubic feet of gas in the Eagle Ford Marl Continuous Gas AU.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/sir20205077","usgsCitation":"Leathers-Miller, H.M., 2020, Steps taken for calculating estimated ultimate recoveries of wells in the Eagle Ford Group and associated Cenomanian–Turonian strata, U.S. Gulf Coast, Texas, 2018: U.S. Geological Survey Scientific Investigations Report 2020–5077, 5 p., https://doi.org/10.3133/sir20205077.","productDescription":"5 p.","numberOfPages":"5","onlineOnly":"Y","ipdsId":"IP-102505","costCenters":[{"id":164,"text":"Central Energy Resources Science Center","active":true,"usgs":true}],"links":[{"id":377009,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/sir/2020/5077/sir20205077.pdf","text":"Report","size":"5.37 MB","linkFileType":{"id":1,"text":"pdf"},"description":"SIR 2020–5077"},{"id":377008,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/sir/2020/5077/coverthb.jpg"}],"country":"United States","state":"Texas","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -94.2626953125,\n 32.80574473290688\n ],\n [\n -98.85498046875,\n 30.35391637229704\n ],\n [\n -100.72265625,\n 29.22889003019423\n ],\n [\n -100.2392578125,\n 28.246327971048842\n ],\n [\n -99.51416015625,\n 27.527758206861886\n ],\n [\n -99.31640625,\n 27.078691552927534\n ],\n [\n -96.85546875,\n 28.70986084394286\n ],\n [\n -93.8232421875,\n 30.543338954230222\n ],\n [\n -92.35107421874999,\n 31.147006308556566\n ],\n [\n -94.2626953125,\n 32.80574473290688\n ]\n ]\n ]\n }\n }\n ]\n}","contact":"Director, Central Energy Resources Science Center
U.S. Geological Survey
Box 25046, Mail Stop 939
Denver, CO 80225
Hibernation is a strategy many species employ to survive periods of thermal stress or resource shortage (e.g., harsh thermal conditions, food limitations) and habitat requirements of hibernating species may differ between summer (the active season) and winter (during hibernation). Accounting for seasonal differences in habitat affinities will help ensure that management actions are more beneficial and land-use policies are more appropriate. The northern Idaho ground squirrel (Urocitellus brunneus) is a federally listed threatened species that is in decline and hibernates for approximately 8 months per year. We collared northern Idaho ground squirrels in Adams County, Idaho from 2013–2017. The majority of northern Idaho ground squirrels we collared selected hibernacula outside of the areas they used during the active season. Furthermore, habitat features of hibernacula locations differed from habitat features of active-season areas. Hibernacula locations had greater canopy closure compared to active-season locations (36.9% and 7.0% canopy closure, respectively) and hibernaculum habitat features (particularly distance to nearest log) influenced overwinter survival. Our results suggest that recovery efforts for northern Idaho ground squirrels should include protection and management for the full range of habitat conditions used throughout summer and winter. More broadly, we emphasize the need to identify and protect habitat during all seasons because habitat requirements can differ substantially during different portions of an animal's annual cycle and effective conservation will require management of year-round habitat needs.
","language":"English","publisher":"The Wildlife Society","doi":"10.1002/jwmg.21936","usgsCitation":"Goldberg, A.R., Conway, C.J., Mack, D.E., and Burak, G.S., 2020, Winter versus summer habitat selection in a threatened ground squirrel: The Wildlife Professional, v. 84, no. 8, p. 1548-1559, https://doi.org/10.1002/jwmg.21936.","productDescription":"12 p.","startPage":"1548","endPage":"1559","ipdsId":"IP-102406","costCenters":[{"id":200,"text":"Coop Res Unit Seattle","active":true,"usgs":true}],"links":[{"id":497502,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Idaho","county":"Adams County","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -117.37553141044718,\n 45.34398367526143\n ],\n [\n -117.37553141044718,\n 44.05501390269339\n ],\n [\n -116.10109120802274,\n 44.05501390269339\n ],\n [\n -116.10109120802274,\n 45.34398367526143\n ],\n [\n -117.37553141044718,\n 45.34398367526143\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"84","issue":"8","noUsgsAuthors":false,"publicationDate":"2020-08-06","publicationStatus":"PW","contributors":{"authors":[{"text":"Goldberg, Amanda R.","contributorId":363896,"corporation":false,"usgs":false,"family":"Goldberg","given":"Amanda","middleInitial":"R.","affiliations":[{"id":39599,"text":"ui","active":true,"usgs":false}],"preferred":false,"id":952092,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Conway, Courtney J. 0000-0003-0492-2953 cconway@usgs.gov","orcid":"https://orcid.org/0000-0003-0492-2953","contributorId":2951,"corporation":false,"usgs":true,"family":"Conway","given":"Courtney","email":"cconway@usgs.gov","middleInitial":"J.","affiliations":[{"id":200,"text":"Coop Res Unit Seattle","active":true,"usgs":true}],"preferred":true,"id":952095,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Mack, Diane Evans","contributorId":363902,"corporation":false,"usgs":false,"family":"Mack","given":"Diane","middleInitial":"Evans","affiliations":[{"id":56023,"text":"idfg","active":true,"usgs":false}],"preferred":false,"id":952094,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Burak, Greg S.","contributorId":363893,"corporation":false,"usgs":false,"family":"Burak","given":"Greg","middleInitial":"S.","affiliations":[{"id":6654,"text":"USFWS","active":true,"usgs":false}],"preferred":false,"id":952091,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70216993,"text":"70216993 - 2020 - Detection of SARS-CoV-2 by RNAscope® in situ hybridization and immunohistochemistry techniques","interactions":[],"lastModifiedDate":"2020-12-28T14:14:10.993732","indexId":"70216993","displayToPublicDate":"2020-08-05T11:03:17","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":892,"text":"Archives of Virology","active":true,"publicationSubtype":{"id":10}},"title":"Detection of SARS-CoV-2 by RNAscope® in situ hybridization and immunohistochemistry techniques","docAbstract":"In situ hybridization (ISH) and immunohistochemistry (IHC) are essential tools to characterize SARS-CoV-2 infection and tropism in naturally and experimentally infected animals and also for diagnostic purposes. Here, we describe three RNAscope®-based ISH assays targeting the ORF1ab, spike, and nucleocapsid genes and IHC assays targeting the spike and nucleocapsid proteins of SARS-CoV-2.
Agassiz’s desert tortoise (Gopherus agassizii), a threatened species of the southwestern United States, has severely declined to the point where 76% of populations in critical habitat (Tortoise Conservation Areas) are below viability. The potential for rapid recovery of wild populations is low because females require 12–20 years to reach reproductive maturity and produce few eggs annually. We report on a 34‐year mark‐recapture study of tortoises initiated in 1979 at the Desert Tortoise Research Natural Area in the western Mojave Desert, California, USA, and provide substantive data on challenges faced by the species. In 1980, the United States Congress designated the Research Natural Area and protected the land from recreational vehicles, livestock grazing, and mining with a wildlife‐permeable fence. The 7.77‐km2 study area, centered on interpretive facilities, included land both within the Natural Area and outside the fence. We expected greater benefits to accrue to the tortoises and habitat inside compared to outside. Our objectives were to conduct a demographic study, analyze and model changes in the tortoise population and habitat, and compare the effectiveness of fencing to protect populations and habitat inside the fence versus outside, where populations and habitat were unprotected. We conducted surveys in spring in each of 7 survey years from 1979, when the fence was under construction, through 2012. We compared populations inside to those outside the fence by survey year for changes in distribution, structure by size and relative age, sex ratios, death rates of adults, and causes of death for all sizes of tortoises. We used a Bayesian implementation of a Jolly Seber model for mark‐recapture data. We modeled detection, density, growth and transition of tortoises to larger size‐age classes, movements from inside the protective fence to outside and vice versa, and survival. After the second and subsequent survey years, we added surveys to monitor vegetation and habitat changes, conduct health assessments, and collect data on counts of predators and predator sign. At the beginning of the study, counts and densities for all sizes of tortoises were high, but densities were approximately 24% higher inside the fence than outside. By 2002, the low point in densities, densities had declined 90% inside the fence and 95% outside. Between 2002 and 2012, the population inside the fence showed signs of improving with a 54% increase in density. Outside the fence, densities remained low. At the end of the study, when we considered the initial differences in location, densities inside the fence were roughly 2.5 times higher than outside. The pattern of densities was similar for male and female adults. When evaluating survival by blocks of years, survivorship was higher in 1979–1989 than in 1989–2002 (the low point) and highest from 2002 to 2012. Recruitment and survival of adult females into the population was important for growing the population, but survival of all sizes, including juveniles, was also critical.
","language":"English","publisher":"The Wildlife Society","doi":"10.1002/wmon.1052","usgsCitation":"Berry, K.H., Yee, J.L., Shields, T.A., and Stockton, L., 2020, The catastrophic decline of tortoises at a fenced natural area: Wildlife Monographs, v. 205, no. 1, p. 1-53, https://doi.org/10.1002/wmon.1052.","productDescription":"53 p.","startPage":"1","endPage":"53","ipdsId":"IP-114548","costCenters":[{"id":651,"text":"Western Ecological Research Center","active":true,"usgs":true}],"links":[{"id":455757,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1002/wmon.1052","text":"Publisher Index Page"},{"id":436835,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P9BY0HVH","text":"USGS data release","linkHelpText":"Demography and Habitat of Desert Tortoises at the Desert Tortoise Research Natural Area, Western Mojave Desert, California (1978 - 2014)"},{"id":436836,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P9BY0HVH","text":"USGS data release","linkHelpText":"Demography and Habitat of Desert Tortoises at the Desert Tortoise Research Natural Area, Western Mojave Desert, California (1978 - 2014)"},{"id":385754,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"California","otherGeospatial":"Desert Tortoise Research Natural Area","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -118.1634521484375,\n 34.97150033361733\n ],\n [\n -117.3504638671875,\n 34.97150033361733\n ],\n [\n -117.3504638671875,\n 35.48527461007853\n ],\n [\n -118.1634521484375,\n 35.48527461007853\n ],\n [\n -118.1634521484375,\n 34.97150033361733\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"205","issue":"1","noUsgsAuthors":false,"publicationDate":"2020-08-05","publicationStatus":"PW","contributors":{"authors":[{"text":"Berry, Kristin H. 0000-0003-1591-8394 kristin_berry@usgs.gov","orcid":"https://orcid.org/0000-0003-1591-8394","contributorId":437,"corporation":false,"usgs":true,"family":"Berry","given":"Kristin","email":"kristin_berry@usgs.gov","middleInitial":"H.","affiliations":[{"id":651,"text":"Western Ecological Research Center","active":true,"usgs":true}],"preferred":true,"id":815990,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Yee, Julie L. 0000-0003-1782-157X julie_yee@usgs.gov","orcid":"https://orcid.org/0000-0003-1782-157X","contributorId":3246,"corporation":false,"usgs":true,"family":"Yee","given":"Julie","email":"julie_yee@usgs.gov","middleInitial":"L.","affiliations":[{"id":651,"text":"Western Ecological Research Center","active":true,"usgs":true}],"preferred":true,"id":815991,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Shields, Timothy A.","contributorId":190759,"corporation":false,"usgs":false,"family":"Shields","given":"Timothy","email":"","middleInitial":"A.","affiliations":[],"preferred":false,"id":815992,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Stockton, Laura","contributorId":258217,"corporation":false,"usgs":false,"family":"Stockton","given":"Laura","email":"","affiliations":[{"id":52242,"text":"Bakersfield, CA","active":true,"usgs":false}],"preferred":false,"id":815993,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70225726,"text":"70225726 - 2020 - Channel cross-section analysis for automated stream head identification","interactions":[],"lastModifiedDate":"2021-11-05T11:52:59.985895","indexId":"70225726","displayToPublicDate":"2020-08-05T06:50:40","publicationYear":"2020","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":7164,"text":"Environmental Modelling & Software","active":true,"publicationSubtype":{"id":10}},"title":"Channel cross-section analysis for automated stream head identification","docAbstract":"Headwater streams account for more than half of the streams in the United States by length. The substantial occurrence and susceptibility to change of headwater streams makes regular updating of related maps vital to the accuracy of associated analysis and display. Here we present work testing new methods of completely automated remote headwater stream identification using metrics derived from channel Digital Elevation Model (DEM) cross-sections. A jump in standard deviation of curvature (sK) is found to correlate with the presence of stream heads. Field and remotely validated stream and channel initiation points from 4 diverse study areas in North Carolina as well as a simulated surface are used to test the sK findings. The sK value within individual catchments equal to 0.5*Tukey's upper inner fence is found to be a reliable threshold for identifying the upslope extent of channels in varied landscapes.
Mount Baker is the prominent andesitic stratocone that forms the youngest volcanic center in the Mount Baker volcanic field. Its heavily glaciated cone, rising to 3,286 meters, is an international landmark, dominating the skyline of Vancouver, British Columbia, even though the volcano is located 25 kilometers south of the international border. Mount Baker caught the attention of scientists and the public alike in 1975–76 during a period of increased steaming, thermal output, and near-vent lithic tephra falls. Although a magmatic eruption did not ensue, it awoke the populace to the possibility of renewed volcanic activity in the Cascade Range (the first since the 1914–17 eruptions of Lassen Peak, Calif.)—a possibility fulfilled just five short years later with the 1980 eruption of Mount St. Helens in southwest Washington. The 1980 Mount St. Helens eruption, with its dramatic edifice collapse, extraordinary pyroclastic density current, and catastrophic lahars, invigorated the scientific community into studying these then little-known processes. It also highlighted the need to better understand eruptive histories at other Cascade Range volcanoes in order to prepare for future eruptions.
The 1975 unrest also spawned one of the earliest volcano hazard assessments in the Cascade Range, which recognized the rich history of postglacial events at Mount Baker and identified the risk posed by volcanic mudflows, or lahars. The focus of this study is to more fully describe the late-glacial to present surficial geology, to better constrain the timing of events (including 19th-century floods), and to dovetail this history with Hildreth and others’ (2003) bedrock study.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/pp1865","usgsCitation":"Scott, K.M., Tucker, D.S., Riedel, J.L., Gardner, C.A., and McGeehin, J.P., 2020, Latest Pleistocene to present geology of Mount Baker Volcano, northern Cascade Range, Washington: U.S. Geological Survey Professional Paper 1865,\n170 p., https://doi.org/10.3133/pp1865.","productDescription":"xi, 170 p.","onlineOnly":"Y","ipdsId":"IP-068471","costCenters":[{"id":617,"text":"Volcano Science Center","active":true,"usgs":true}],"links":[{"id":377020,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/pp/1865/coverthb.jpg"},{"id":377021,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/pp/1865/pp1865.pdf","text":"Report","size":"15.1 MB","linkFileType":{"id":1,"text":"pdf"},"description":"PP 1865"}],"country":"United States","state":"Washington","otherGeospatial":"Mount Baker","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -121.92214965820311,\n 48.70455661164196\n ],\n [\n -121.72233581542967,\n 48.70455661164196\n ],\n [\n -121.72233581542967,\n 48.84302835299516\n ],\n [\n -121.92214965820311,\n 48.84302835299516\n ],\n [\n -121.92214965820311,\n 48.70455661164196\n ]\n ]\n ]\n }\n }\n ]\n}","contact":"Volcano Science Center
Cascades Volcano Observatory
U.S. Geological Survey
1300 SE Cardinal Court
Vancouver, WA, 98683
The Albuquerque Basin, located in central New Mexico, is about 100 miles long and 25–40 miles wide. The basin is hydrologically defined as the extent of consolidated and unconsolidated deposits of Tertiary and Quaternary age that encompasses the structural Rio Grande Rift between San Acacia to the south and Cochiti Lake to the north. A 20-percent population increase in the basin from 1990 to 2000 and a 22-percent population increase from 2000 to 2010 resulted in an increased demand for water in areas within the basin. Drinking-water supplies throughout the basin were obtained solely from groundwater resources until December 2008, when the Albuquerque Bernalillo County Water Utility Authority (ABCWUA) began treatment and distribution of surface water from the Rio Grande through the San Juan-Chama Drinking Water Project.
An initial network of wells was established by the U.S. Geological Survey (USGS) in cooperation with the City of Albuquerque from April 1982 through September 1983 to monitor changes in groundwater levels throughout the Albuquerque Basin. In 1983, this network consisted of 6 wells with analog-to-digital recorders and 27 wells where water levels were measured monthly. As of 2019, the network consisted of 120 wells and piezometers. (A piezometer is a specialized well open to a specific depth in the aquifer, often of small diameter and nested with other piezometers screened at different depths.) The USGS, in cooperation with the ABCWUA, the New Mexico Office of the State Engineer, and Bernalillo County, measures water levels from the 120 wells and piezometers in the network; this report, prepared in cooperation with the ABCWUA, presents water-level data collected by USGS personnel at those 120 sites through water year 2019 (October 1, 2018, through September 30, 2019). Water levels that were collected from those discontinued wells in previous water years were published in previous USGS reports.
","language":"English","publisher":"U.S. Geological Survey","publisherLocation":"Reston, VA","doi":"10.3133/ds1129","collaboration":"Prepared in cooperation with the Albuquerque Bernalillo County Water Utility Authority","usgsCitation":"Beman, J.E., 2020, Water-level data for the Albuquerque Basin and adjacent areas, central New Mexico, period of record through September 30, 2019: U.S. Geological Survey Data Series 1129, 40 p., https://doi.org/10.3133/ds1129.","productDescription":"iii, 40 p.","numberOfPages":"48","onlineOnly":"Y","ipdsId":"IP-120239","costCenters":[{"id":472,"text":"New Mexico Water Science Center","active":true,"usgs":true}],"links":[{"id":377000,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/ds/1129/coverthb.jpg"},{"id":377001,"rank":2,"type":{"id":11,"text":"Document"},"url":"https://pubs.usgs.gov/ds/1129/ds1129.pdf","text":"Report","size":"5.67 MB","linkFileType":{"id":1,"text":"pdf"},"description":"DS 1129"}],"country":"United States","state":"New Mexico","city":"Albuquerque","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -107.611083984375,\n 33.797408767572485\n ],\n [\n -105.941162109375,\n 33.797408767572485\n ],\n [\n -105.941162109375,\n 36.06686213257888\n ],\n [\n -107.611083984375,\n 36.06686213257888\n ],\n [\n -107.611083984375,\n 33.797408767572485\n ]\n ]\n ]\n }\n }\n ]\n}","contact":"Director, New Mexico Water Science Center
U.S. Geological Survey
6700 Edith Blvd. NE
Albuquerque, NM 87113
Simple biometric data of fish aid fishery management tasks such as monitoring the structure of fish populations and regulating recreational harvest. While these data are foundational to fishery research and management, the collection of length and weight data through physical handling of the fish is challenging as it is time consuming for personnel and can be stressful for the fish. Recent advances in imaging technology and machine learning now offer alternatives for capturing biometric data. To investigate the potential of deep convolutional neural networks to predict biometric data, several regressors were trained and evaluated on data stemming from the FishL™ Recognition System and manual measurements of length, girth, and weight. The dataset consisted of 694 fish from 22 different species common to Laurentian Great Lakes. Even with such a diverse dataset and variety of presentations by the fish, the regressors proved to be robust and achieved competitive mean percent errors in the range of 5.5 to 7.6% for length and girth on an evaluation dataset. Potential applications of this work could increase the efficiency and accuracy of routine survey work by fishery professionals and provide a means for longer‐term automated collection of fish biometric data.
","language":"English","publisher":"Wiley","doi":"10.1002/ece3.6618","usgsCitation":"Bravata, N., Kelly, D., Eickholt, J., Bryan, J., Miehls, S.M., and Zielinski, D., 2020, Applications of deep convolutional neural networks to predict length, circumference, and weight from mostly dewatered images of fish: Ecology and Evolution, v. 10, no. 17, p. 9313-9325, https://doi.org/10.1002/ece3.6618.","productDescription":"13 p.","startPage":"9313","endPage":"9325","ipdsId":"IP-114453","costCenters":[{"id":324,"text":"Great Lakes Science Center","active":true,"usgs":true}],"links":[{"id":455761,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1002/ece3.6618","text":"Publisher Index Page"},{"id":436838,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P90BIDOL","text":"USGS data release","linkHelpText":"Image and biometric data for fish from Great Lakes tributaries collected during spring 2019"},{"id":436837,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P90BIDOL","text":"USGS data release","linkHelpText":"Image and biometric data for fish from Great Lakes tributaries collected during spring 2019"},{"id":381446,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Illinois, Michigan, Ohio","otherGeospatial":"Black Mallard River, Cheboygan River, Illinois River, Little Manistee River, Menominee River, Muskegon River, Ocqueoc River, Sandusky River, Tittabawassee River","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -88.428955078125,\n 40.588928169693745\n ],\n [\n -82.529296875,\n 40.588928169693745\n ],\n [\n -82.529296875,\n 46.210249600187225\n ],\n [\n -88.428955078125,\n 46.210249600187225\n ],\n [\n -88.428955078125,\n 40.588928169693745\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"10","issue":"17","noUsgsAuthors":false,"publicationDate":"2020-08-04","publicationStatus":"PW","contributors":{"authors":[{"text":"Bravata, Nicholas","contributorId":245794,"corporation":false,"usgs":false,"family":"Bravata","given":"Nicholas","email":"","affiliations":[{"id":13588,"text":"Central Michigan University","active":true,"usgs":false}],"preferred":false,"id":807042,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kelly, Dylan","contributorId":245795,"corporation":false,"usgs":false,"family":"Kelly","given":"Dylan","affiliations":[{"id":13588,"text":"Central Michigan University","active":true,"usgs":false}],"preferred":false,"id":807043,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Eickholt, Jesse","contributorId":245796,"corporation":false,"usgs":false,"family":"Eickholt","given":"Jesse","affiliations":[{"id":13588,"text":"Central Michigan University","active":true,"usgs":false}],"preferred":false,"id":807044,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Bryan, Janine","contributorId":245797,"corporation":false,"usgs":false,"family":"Bryan","given":"Janine","affiliations":[{"id":13588,"text":"Central Michigan University","active":true,"usgs":false}],"preferred":false,"id":807045,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Miehls, Scott M. 0000-0002-5546-1854 smiehls@usgs.gov","orcid":"https://orcid.org/0000-0002-5546-1854","contributorId":5007,"corporation":false,"usgs":true,"family":"Miehls","given":"Scott","email":"smiehls@usgs.gov","middleInitial":"M.","affiliations":[{"id":324,"text":"Great Lakes Science Center","active":true,"usgs":true}],"preferred":true,"id":807046,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Zielinski, Daniel","contributorId":245798,"corporation":false,"usgs":false,"family":"Zielinski","given":"Daniel","affiliations":[{"id":7019,"text":"Great Lakes Fishery Commission","active":true,"usgs":false}],"preferred":false,"id":807047,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ]}