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At least 19 recordsLinked to original sources
USGS2016

sbtools: A package connecting R to cloud-based data for collaborative online research

The adoption of high-quality tools for collaboration and reproducible research such as R and Github is becoming more common in many research fields. While Github and other version management systems are excellent resources, they were originally designed to handle code and scale poorly to large text-based or binary datasets. A number of scientific data repositories are coming online and are often focused on dataset archival and publication. To handle collaborative workflows using large scientific datasets, there is increasing need to connect cloud-based online data storage to R. In this article, we describe how the new R package sbtools enables direct access to the advanced online data functionality provided by ScienceBase, the U.S. Geological Survey’s online scientific data storage platform.

The R Journal↗
USGS1993

Pressure increases, the formation of chromite seams, and the development of the ultramafic series in the Stillwater Complex, Montana

This paper explores the hypothesis that chromite seams in the Stillwater Complex formed in response to periodic increases in total pressure in the chamber. Total pressure increased because of the positive δ V of nucleation of CO 2 bubbles in the melt and their subsequent rise through the magma chamber, during which the bubbles increased in volume by a factor of 4–6. By analogy with the pressure changes in the summit chambers of Kilauea and Krafla volcanoes, the maximum variation was 0⋅2–0⋅25 kbar, or 5–10% of the total pressure in the Stillwater chamber. An evaluation of the likelihood of fountaining and mixing of a new, primitive liquid that entered the chamber with the somewhat more evolved liquid already in the chamber is based upon calculations using observed and inferred velocities and flow rates of basaltic magmas moving through volcanic fissures. The calculations indicate that hot, dense magma would have oozed, rather than fountained into the chamber, and early mixing of the new and residual magmas that could have resulted in chromite crystallizing alone did not take place.

Journal of Petrology↗
USGS1987

Fall and winter foods of northern pintails in the Sacramento Valley, California

Food habits of northern pintails ( Anas acuta ) were investigated on 3 national wildlife refuges in the western portion of the Sacramento Valley, California, from August to March 1979-82. Pintails consumed >97% (aggregate % dry wt) plant food during diurnal foraging on national wildlife refuge rice, summer- irrigated, and summer-dry habitats from August through January. Invertebrate use increased to 28.9-65.6% of the diet in these habitats during February and March. Rice, swamp timothy ( Heleochloa schoenoides ), flatsedges ( Cyperus spp.), common barnyardgrass ( Echinochloa crusgalli ), southern naiad ( Najas guadalupensis ), and smartweed ( Polygonum spp.) seeds, miscellaneous vegetation, snails (Gastropoda), and midge (Diptera) and water beetle (Coleoptera) larvae were most important. These foods usually were taken proportional to or greater than availability. Rice was the most important food of pintails feeding nocturnally off the refuges in harvested rice fields from October through January (99.7%) and February and March (63%; barnyardgrass formed 31% of the diet). In August and October, some pintails consumed invertebrates or bulrush ( Scirpus spp.) seedlings in marshes soon after feeding in refuge rice (Aug) or harvested commercial rice fields (Oct), thereby increasing dietary protein. In late winter, females and males obtained similar (P > 0.05) percentages of invertebrates from refuge habitats. Important dietary seeds and invertebrates contained high protein or metabolizable energy content. Management should maintain adequate seed production in fall and mid-winter and invertebrate biomass in late winter.

California↗
USGS1989

Estimating carcass fat and protein in northern pintails during the nonbreeding season

I used northern pintails ( Anas acuta ) collected from August through March 1979-82 in the Sacramento Valley, California to derive equations to predict ether-extracted carcass fat, carcass protein, and skeletal lean dry weight. Ether-extracted carcass fat was best predicted by total fat depot weight (wet skin, abdominal fat, and intestinal fat) (r 2 = 0.94) and estimates based on carcass water content (r 2 = 0.93-0.98). Measured carcass protein was best predicted by a multiple regression including total protein depot weight (breast muscles, leg muscles, and gizzard) and tarsus length (R 2 = 0.79). I predicted skeletal lean dry weight by a multiple regression incorporating culmen, tarsus, and wing length (R 2 = 0.77). Predicted carcass fat agreed well with measured carcass fat in an independent data set of 30 pintails using total fat depot (r 2 = 0.92-0.96) and carcass water (r 2 = 0.97-0.99), but predicted carcass protein agreed less well with measured protein.

California↗
USGS2000

Rhyolite themobarometry and the shallowing of the magma reservoir, Coso volcanic field, California

The compositionally bimodal Pleistocene Coso volcanic field is located at the western margin of the Basin and Range province ∼60 km north of the Garlock fault. Thirty-nine nearly aphyric high-silica rhyolite domes were emplaced in the past million years: one at 1 Ma from a transient magma reservoir, one at ∼0·6 Ma, and the rest since ∼0·3 Ma. Over the past 0·6 My, the depth from which the rhyolites erupted has decreased and their temperatures have become slightly higher. Pre-eruptive conditions of the rhyolite magmas, calculated from phenocryst compositions using the two-oxide thermometer and the Al-in-hornblende barometer, ranged from 740°C and 270 MPa (2·7 kbar; ∼10 km depth) for the ∼0·6 Ma magma, to 770°C and 140 MPa (1·4 kbar; ∼5·5 km) for the youngest (∼0·04 Ma) magma. Results are consistent with either a single rhyolitic reservoir moving upward through the crust, or a series of successively shallower reservoirs. As the reservoir has become closer to the surface, eruptions have become both more frequent and more voluminous.

California↗
USGS1998

Effect of restrictive harvest regulations on survival and recovery rates of American black ducks

Population management of waterfowl requires an understanding of the effects of changes in hunting regulations on harvest and survival rates. Mean survival and recovery rates of American black ducks (Anas rubripes) were estimated during 3 periods of increasingly restrictive harvest regulations: 1950-66, 1967-82, and 1983-93. From the first to the second period, direct recovery rates declined for at least 1 age class in 4 of 6 reference areas, with a mean decline of 14% for adult and 7% for immature black ducks. From the second to the third period, direct recovery rates declined in all areas, declines averaging 37% for adults and 27% for immatures. Estimated mean survival rates increased from the first to the second period, consistent with a model of additivity of hunting mortality. Limited evidence existed for increases in survival rates from the second to the third period for immature males. For adults, however, survival increased less between these periods than would be expected if hunting mortality were additive and changes in recovery rates were proportional to changes in hunting mortality. Changes in survival and recovery rates of black ducks banded postseason were similar to those of adults banded preseason. Comparisons among estimates by degree blocks of latitude and longitude indicate that, at least between 1967 and 1983, estimated survival rates of immature and adult black ducks were lower in areas with high direct recovery rates. Smaller samples of banded birds and changes in banding locations in recent years may be limiting ability to evaluate consequences of recent changes in harvest rates. These correlation-based studies are limited in their ability to explain causes of observed changes in survival rates, suggesting the need for alternative approaches such as adaptive harvest management to increase understanding of the effects of hunting on black duck populations.

Journal of Wildlife Management↗
USGS1984

Sedimentary structures formed in sand by surface tension on melting hailstones

Craters form when hailstones impact sand. When a hailstone melts, wet but unsaturated sand within the crater is attracted to the hailstone surface by surface tension. Shrinkage of the melting hailstone then produces one or more rings of sand within the impact crater.--Modified journal abstract.

Journal of Sedimentary Petrology↗
USGS1991

Segmentation and the coseismic behavior of Basin and Range normal faults: examples from east-central Idaho and southwestern Montana, U.S.A.

The range-front normal faults of the Lost River and Lemhi Ranges, and the Beaverhead and Tendoy Mountains in east-central Idaho and southwestern Montana have well-preserved fault scarps on Quaternary deposits along much of their lengths. Fault-scarp morphology, the age of deposits displaced by the faults, and the morphology of the range fronts provide a basis for dividing the faults into segments that are typically 20–25 km long. The Lost River, Lemhi and Beaverhead fault zones are 141–151 km long, and each has six segments. The 60-km-long Red Rock fault (the range-front fault of the Tendoy Mountains) has two central segments that have been active in late Quaternary time; these two segments span the central 27 km of the fault. We recognize four characteristics that help to identify segment boundaries: (1) major en échelon offsets or pronounced gaps in the continuity of fault scarps; (2) distinct, persistent, along-strike changes in fault-scarp morphology that indicate different ages of faulting; (3) major salients in the range front; and (4) transverse bedrock ridges where the cumulative throw is low compared to other places along the fault zone. Only features whose size is measured on the scale of kilometers are regarded as significant enough to represent a segment boundary that could inhibit or halt a propagating rupture.

Journal of Structural Geology↗
USGS2012

Crustal subsidence and extension and Medicine Lake volcano, northern California

The pattern of historical ground deformation, seismicity, and crustal structure near Medicine Lake volcano illustrates a close relation between magmatism and tectonism near the margin of the Cascade volcanic chain and the Basin and Range tectonic province. Between leveling surveys in 1954 and 1989 the summit of Medicine Lake volcano subsided 389±43 mm with respect to a reference bench mark 40 km to the southwest (average rate = 11.1±1.2 mm/yr). A smaller survey across the summit caldera in 1988 suggests that the subsidence rate was 15–28 mm/yr during 1988–1989. Swarms of shallow earthquakes ( M ≤ 4.6) occurred in the region during August 1978, January–February 1981, and September 1988. Except for the 1988 swarm, which occurred beneath Medicine Lake caldera, most historical earthquakes were located at least 25 km from the summit. The spatial relation between subsidence and seismicity indicates (1) radially symmetric downwarping of the volcano's summit and flanks centered near the caldera and (2) downfaulting of the entire edifice along regional faults located 25–30 km from the summit. We propose that contemporary subsidence, seismicity, and faulting are caused by (1) loading of the crust by more than 600 km 3 of erupted products plus a large volume of mafic intrusives; (2) east‐west extension in the western Basin and Range province; and, to a lesser extent, (3) crystallization or withdrawal of magma beneath the volcano. Thermal weakening of the subvolcanic crust by mafic intrusions facilitates subsidence and influences the distribution of earthquakes. Subsidence occurs mainly by aseismic creep within 25 km of the summit, where the crust has been heated and weakened by intrusions, and by normal faulting during episodic earthquake swarms in surrounding, cooler terrain.

California↗
USGS2010

Modelling postfledging survival and age-specific breeding probabilities in species with delayed maturity: A case study of Roseate Terns at Falkner Island, Connecticut

We modeled postfledging survival and age-specific breeding probabilities in endangered Roseate Terns (Sterna dougallii) at Falkner Island, Connecticut, USA using capture-recapture data from 1988-1998 of birds ringed as chicks and as adults. While no individuals bred as 2-yr-olds during this period, about three-quarters of the young that survived and returned as 3-yr-olds nested, and virtually all surviving birds had begun breeding by the time they reached 5 years of age. We found no evidence of temporal variation in age of first breeding of birds from different cohorts. There was significant temporal variation in the annual survival of adults and the survival over the typical 3-yr maturation period of prebreeding birds, with extremely low values for both groups from the 1991 breeding season. The estimated overwinter survival rate (0.62) for adults from 1991-1992 was about three-quarters the usual rate of about 0.83, but the low survival of fledglings from 1991 resulted in less than 25% of the otherwise expected number of young from that cohort returning as breeding birds; this suggests that fledglings suffered a greater proportional decrease in survival than did adults. The survival estimates of young from 1989 and 1990 show that these cohorts were not negatively influenced by the events that decimated the young from 1991, and the young from 1992 and 1993 had above-average survival estimates. The apparent decrease since 1996 in development of fidelity of new recruits to this site is suspected due mainly to nocturnal disturbance and predation of chicks causing low productivity.

Connecticut↗
USGS2007

Deep-water chaunacid and lophiid anglerfishes (Pisces: Lophiiformes) off the Southeastern United States

Recent research cruises to deep (80–910 m) reef habitats off the south-eastern U.S. and in the northern Gulf of Mexico have provided new information on the diagnostic characteristics, behaviours, colour patterns in life, bottom associations, distributions and maximum sizes of species of the anglerfish genera Chaunax , Lophiodes and Sladenia . Chaunax stigmaeus occurred much further south than previously known (Blake Plateau off South Carolina), and all C. stigmaeus observed were found associated with dense beds of dead coral ( Lophelia pertusa ) rubble or on broken hard bottom. In contrast, Chaunax suttkusi was found on soft bottoms. Chaunax stigmaeus and C. suttkusi appear to be sympatric over a major portion of their ranges. Because knowledge of pigmentation in live or freshly caught Chaunax is critical to distinguish some members of the genus, changes in the colouration of C. suttkusi were noted and documented photographically immediately after death and after fixation. The yellow spots found on some, but not all specimens, temporarily disappeared completely after death, but they reappeared after fixation, slowly disappearing thereafter along with other carotenoid pigments. Lophiodes beroe and Lophiodes monodi were collected for the first time off the Atlantic coast of the U.S., being previously known only from the Gulf of Mexico, Caribbean Sea and the northern coast of South America. For both species ( L. beroe and L. monodi ), the collections included the two largest known representatives of the species (400 and 325 mm standard length, respectively). Lophiodes beroe commonly occurred on L. pertusa rubble, and seemed to prefer this habitat. Occupying such a habitat that is deep and difficult to sample probably explains how this common species escaped detection. Only a single L. monodi was collected or observed, so this species appears to be uncommon in this geographic area or at least so on coral rubble habitat. Detailed aspects of the colour patterns of both species were noted. In particular, L. beroe displayed a characteristic pattern of white patches in life that were not apparent after death. The first photographic documentation of the colour pattern in life and of the pharyngeal pigmentation of Lophiodes reticulatus is provided. The third known specimen of Sladenia shaefersi , and the first to be taken in U.S. waters was collected from coral rubble near the base of a steep 200 m scarp on the Blake Plateau.

Gulf of Mexico↗
USGS2007

Spectral element modelling of fault-plane reflections arising from fluid pressure distributions

The presence of fault-plane reflections in seismic images, besides indicating the locations of faults, offers a possible source of information on the properties of these poorly understood zones. To better understand the physical mechanism giving rise to fault-plane reflections in compacting sedimentary basins, we numerically model the full elastic wavefield via the spectral element method (SEM) for several different fault models. Using well log data from the South Eugene Island field, offshore Louisiana, we derive empirical relationships between the elastic parameters (e.g. P-wave velocity and density) and the effective-stress along both normal compaction and unloading paths. These empirical relationships guide the numerical modelling and allow the investigation of how differences in fluid pressure modify the elastic wavefield. We choose to simulate the elastic wave equation via SEM since irregular model geometries can be accommodated and slip boundary conditions at an interface, such as a fault or fracture, are implemented naturally. The method we employ for including a slip interface retains the desirable qualities of SEM in that it is explicit in time and, therefore, does not require the inversion of a large matrix. We performa complete numerical study by forward modelling seismic shot gathers over a faulted earth model using SEM followed by seismic processing of the simulated data. With this procedure, we construct post-stack time-migrated images of the kind that are routinely interpreted in the seismic exploration industry. We dip filter the seismic images to highlight the fault-plane reflections prior to making amplitude maps along the fault plane. With these amplitude maps, we compare the reflectivity from the different fault models to diagnose which physical mechanism contributes most to observed fault reflectivity. To lend physical meaning to the properties of a locally weak fault zone characterized as a slip interface, we propose an equivalent-layer model under the assumption of weak scattering. This allows us to use the empirical relationships between density, velocity and effective stress from the South Eugene Island field to relate a slip interface to an amount of excess pore-pressure in a fault zone. ?? 2007 The Authors Journal compilation ?? 2007 RAS.

Geophysical Journal International↗
USGS2011

Multimodel inference and adaptive management

Ecology is an inherently complex science coping with correlated variables, nonlinear interactions and multiple scales of pattern and process, making it difficult for experiments to result in clear, strong inference. Natural resource managers, policy makers, and stakeholders rely on science to provide timely and accurate management recommendations. However, the time necessary to untangle the complexities of interactions within ecosystems is often far greater than the time available to make management decisions. One method of coping with this problem is multimodel inference. Multimodel inference assesses uncertainty by calculating likelihoods among multiple competing hypotheses, but multimodel inference results are often equivocal. Despite this, there may be pressure for ecologists to provide management recommendations regardless of the strength of their study’s inference. We reviewed papers in the Journal of Wildlife Management (JWM) and the journal Conservation Biology (CB) to quantify the prevalence of multimodel inference approaches, the resulting inference (weak versus strong), and how authors dealt with the uncertainty. Thirty-eight percent and 14%, respectively, of articles in the JWM and CB used multimodel inference approaches. Strong inference was rarely observed, with only 7% of JWM and 20% of CB articles resulting in strong inference. We found the majority of weak inference papers in both journals (59%) gave specific management recommendations. Model selection uncertainty was ignored in most recommendations for management. We suggest that adaptive management is an ideal method to resolve uncertainty when research results in weak inference.

Journal of Environmental Management↗
USGS2020

Wetlands in agricultural landscapes—Significant findings and recent advances from CEAP-Wetlands

The Wetlands Component of the USDA's Conservation Effects Assessment Project (CEAP-Wetlands) is a multi-agency effort advancing science related to quantifying and interpreting effects and effectiveness of conservation practices and programs on ecosystem services provided by wetlands in agricultural landscapes. This special section originated from a symposium held at the 73rd Soil and Water Conservation Society's International Annual Conference in Albuquerque New Mexico, July 29 to August 1, 2018. The symposium was jointly organized by the USDA Natural Resources Conservation Service and the US Geological Survey. To facilitate CEAP-Wetlands efforts, several regional assessments were conducted across the United States. These regional assessments were designed to address science gaps hindering wetland conservation and to develop tools facilitating conservation assessments. Conservation decisions affect not just agricultural wetlands, but also the services that these complex ecosystems provide to society. Papers in this special section of the Journal of Soil and Water Conservation present key findings and recent advances from several CEAP-Wetlands regional assessments and discuss the significant contributions of each assessment to an ever-increasing understanding of wetland ecosystems and their provisioning of ecosystem services. Modeling efforts using the Agricultural Policy and Environmental eXtender (APEX) and other process-based models are an integral component of CEAP-Wetlands. Results of these modeling efforts are also presented, and conservation implications are discussed.

Journal of Soil and Water Conservation↗
USGS2011

Comment on “An unconfined groundwater model of the Death Valley Regional Flow System and a comparison to its confined predecessor” by R.W.H. Carroll, G.M. Pohll and R.L. Hershey [Journal of Hydrology 373/3–4, pp. 316–328]

Carroll et al. (2009) state that the United States Geological Survey (USGS) Death Valley Regional Flow System (DVRFS) model, which is based on MODFLOW, is “conceptually inaccurate in that it models an unconfined aquifer as a confined system and does not simulate unconfined drawdown in transient pumping simulations.” Carroll et al. (2009) claim that “more realistic estimates of water availability” can be produced by a SURFACT-based model of the DVRFS that simulates unconfined groundwater flow and limits withdrawals from wells to avoid excessive drawdown. Differences in results from the original MODFLOW-based model and the SURFACT-based model stem primarily from application by Carroll et al. (2009) of head limits that can also be applied using the existing MODLOW model and not from any substantial difference in the accuracy with which the unconfined aquifer is represented in the two models. In a hypothetical 50-year predictive simulation presented by Carroll et al. (2009), large differences between the models are shown when simulating pumping from the lower clastic confining unit, where the transmissivity is nearly two orders of magnitude less than in an alluvial aquifer. Yet even for this extreme example, drawdowns and pumping rates from the MODFLOW and SURFACT models are similar when the head-limit capabilities of the MODFLOW MNW Package are applied. These similarities persist despite possible discrepancies between assigned hydraulic properties. The resulting comparison between the MODFLOW and SURFACT models of the DVRFS suggests that approximating the unconfined system in the DVRFS as a constant-saturated-thickness system (called a “confined system” by Carroll et al., 2009) performs very well.

Death Valley↗
USGS1998

Ecology of Siberian Taimen Hucho taimen in the Lake Baikal Basin

Taimen Hucho taimen historically inhabited most tributaries and littoral areas of Lake Baikal, in south central Siberia, where they supported subsistence and commercial fisheries. Logging, pollution, and overfishing have caused dramatic population declines or local extinction of most stocks. Most of what is known about this species has been published in eastern journals and therefore is not readily available to western scientists. New data collected during the 1980s and 1990s have been combined with other reports to provide an overview of the biology and life history of this species. Taimen are long-lived fish and can reach ages of 29 years and sizes up to 60 kg. Populations can either be strictly riverine or anadromous. Adults from both life histories ascend rivers in spring to spawn and feed, and less extensive migrations occur in fall to prey on spawning omul ( Coregonus autumnalis migratorius ). Principal food items for age 1 and 2 taimen are macroinvertebrates, but young taimen quickly become piscivorous at age 2 when they consume mainly black Baikal grayling ( Thymallus arcticus baicalensis ), and sculpins ( Taracottus kneri, Cottus kesslerij ). Males reach sexual maturity at ages 7 to 8 and later for females at ages 8 to 9. Average egg production per female was about 22,000 eggs. Parasite burdens are heavy but composed of few species and mediated by prey items consumed. This fish is a highly-specialized predator and plays an indispensable role in the structure of fish communities in mountains and foothills. Taimen conservation in the Baikal region is impossible without adoption and implementation of a dedicated rehabilitation program that includes the protection of remaining populations and habitat, and possibly introduction of hatchery-reared fish in selected areas where habitat remains, but parental stocks are low.

Journal of Great Lakes Research↗