Search USGS⌕ Search

SEARCH · Search USGS

Results for “The R Journal”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources
USGS2018

Remote sensing analysis of vegetation at the San Carlos Apache Reservation, Arizona and surrounding area

Mapping of vegetation types is of great importance to the San Carlos Apache Tribe and their management of forestry and fire fuels. Various remote sensing techniques were applied to classify multitemporal Landsat 8 satellite data, vegetation index, and digital elevation model data. A multitiered unsupervised classification generated over 900 classes that were then recoded to one of the 16 generalized vegetation/land cover classes using the Southwest Regional Gap Analysis Project (SWReGAP) map as a guide. A supervised classification was also run using field data collected in the SWReGAP project and our field campaign. Field data were gathered and accuracy assessments were generated to compare outputs. Our hypothesis was that a resulting map would update and potentially improve upon the vegetation/land cover class distributions of the older SWReGAP map over the 24,000 km 2 study area. The estimated overall accuracies ranged between 43% and 75%, depending on which method and field dataset were used. The findings demonstrate the complexity of vegetation mapping, the importance of recent, high-quality-field data, and the potential for misleading results when insufficient field data are collected.

Arizona↗
USGS1996

Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria

Evolutionary relationships among strictly anaerobic dissimilatory Fe(III)-reducing bacteria obtained from a diversity of sedimentary environments were examined by phylogenetic analysis of 16S rRNA gene sequences. Members of the genera Geobacter, Desulfuromonas, Pelobacter, and Desulfuromusa formed a monophyletic group within the delta subdivision of the class Proteobacteria. On the basis of their common ancestry and the shared ability to reduce Fe(III) and/or S0, we propose that this group be considered a single family, Geobacteraceae. Bootstrap analysis, characteristic nucleotides, and higher-order secondary structures support the division of Geobacteraceae into two subgroups, designated the Geobacter and Desulfuromonas clusters. The genus Desulfuromusa and Pelobacter acidigallici make up a distinct branch within the Desulfuromonas cluster. Several members of the family Geobacteraceae, none of which reduce sulfate, were found to contain the target sequences of probes that have been previously used to define the distribution of sulfate-reducing bacteria and sulfate-reducing bacterium-like microorganisms. The recent isolations of Fe(III)-reducing microorganisms distributed throughout the domain Bacteria suggest that development of 16S rRNA probes that would specifically target all Fe(III) reducers may not be feasible. However, all of the evidence suggests that if a 16S rRNA sequence falls within the family Geobacteraceae, then the organism has the capacity for Fe(III) reduction. The suggestion, based on geological evidence, that Fe(III) reduction was the first globally significant process for oxidizing organic matter back to carbon dioxide is consistent with the finding that acetate-oxidizing Fe(III) reducers are phylogenetically diverse.

Journal of Bacteriology↗
USGS1968

Rehabilitation of lake trout in the Apostle Islands region of Lake Superior

Marked success of rehabilitation of lake trout in Lake Superior has been due principally to the control of the sea lamprey and closure of the lake trout fishery in 1962 and large-scale plantings of yearling lake trout in 1959-66. After the sea lamprey became established in the late 1940s, spawning stocks of lake trout began to decrease and were almost nonexistent by 1960-61. After control of the sea lamprey and closure of the commercial fishery for lake trout in 1962, the abundance of spawning stocks began to rise and reached the highest levels on record in 1964-66. Successful spawning in 1964 and 1965 was demonstrated by catches of age-0 lake trout in 1965 and 1966, the first evidence of natural reproduction since 1959. Plantings of hatchery-reared lake trout in Wisconsin waters of Lake Superior began in 1952. The percentage of hatchery-reared fish in catches of juvenile lake trout increased almost steadily from 1953 to 1965 (when nearly all were of hatchery origin). The abundance of juvenile fish increased from 1959 to 1962 and remained nearly constant in 1962-66. The success of lake trout plantings was highest in 1959-61 but generally declined after 1961; the success of the plantings was inversely related to the abundance of older lake trout. Annual increments of growth of hatchery-reared lake trout varied from 1.1 to 5.0 inches after planting. The average lengths of fish of identical age-groups varied according to gear of capture, depth of water, and season. More than 65% of the season's growth of age-III lake trout took place after September. The findings indicate that the present rate of stocking lake trout may be higher than necessary to maintain optimum abundance.

Journal of the Fisheries Research Board of Canada↗
USGS1971

Plotting of bathythermograph transect data on a printer

A program for plotting bathythermograph transect data on a computer (IBM 1130) printer is available from the Great Lakes Fishery Laboratory. Temperature values are printed in positions proportional to their depths and distances from shore. Contour lines are drawn manually through the plotted points.

Journal of the Fisheries Research Board of Canada↗
USGS1973

Open-jaw syndrome in chinook salmon ( Oncorhynchus tshawytscha ) at a hatchery

Nearly 0.5% of the yearling spring chinook salmon ( Oncorhynchus tshawytscha ) at a national fish hatchery were observed with mouth agape, the condition occurring in two of 16 ponds. X-radiographs and histological preparations indicated that the articular bone of the lower jaw was malformed and dislocated dorsal and posterior to its normal point of attachment. The bone appeared to be embedded in the mandibular muscle and surrounded by an extensive fibrous tissue network. Genetic aberration, environmental interaction, and teratogenic substances are discussed as possible causes of the anomaly.

Journal of the Fisheries Research Board of Canada↗
USGS1978

Evaluation of an aerial survey of Pacific walruses

An aerial survey of Pacific walruses ( Odobenus rosmarus divergens ) was evaluated to determine the reliability of estimates of population abundance. The probability of detecting groups of walruses on the pack ice remained uniform to at least 0.93 km from the flight line, whereas the probability of detection decreased significantly beyond 0.23 km for walruses in the water. Walruses were more abundant along the ice-edge zone between 162 and 165°W than in other areas of the Chukchi Sea during September 1975. Few walruses were observed in consolidated pack ice north of the ice-edge zone or in ice-free water to the south. More walrus groups and larger mean group size were observed on September 8 than on other days. We estimated abundance for each day and all days combined using methods based on sample area and numbers of strip samples. Estimates varied among days by over an order of magnitude; this variation is attributed to the combined effect of chance sampling of an aggregated population and variation in the fraction of walruses hauled out. The coefficient of variation of the estimates ranged between 0.25 and 0.99. This imprecision was due to the aggregated distribution of walruses and the large variation in group size. Using the survey data as a basis for stratification, we calculated that, due to the high variability within strata, a sample size of 40% of the total area or 56% of the total available strips would be required to obtain 95% confidence limits within 10% of the estimate of total abundance. Variation contributed by observer error in estimating group size also is relatively unimportant to the precision of abundance estimates. Studies of natural history, particularly those oriented toward activity and habitat selection, would help investigators estimate bias due to the variable fraction hauled out and design surveys based on meaningful strata. Estimates of total abundance based on limited survey efforts will provide information of little reliability.

Journal of the Fisheries Research Board of Canada↗
USGS2022

Silurian K-bentonites of the Dnestr Basin, Podolia, Ukraine

The Dnestr Basin of Podolia, Ukraine, is an epicratonic basin consisting of neritic carbonate and calcareous mudstone facies including a nearly complete Silurian sequence ranging from late Llandovery to late Pridoli in age. The Silurian section has served as a standard for regional and interregional studies as a consequence of its well-documented macro- and microfaunal assemblages. Approximately 24 mid- to Late Silurian K-bentonites are present in this succession, and their lateral persistence has aided in establishing regional correlations. The K-bentonites range from 1 to 40 cm in thickness and occur in the Bagovitsa (late Wenlock), Malinovtsy (Ludlow) and Skala (Pridoli) Formations. Discrimination diagrams based on immobile trace elements together with rare earth element data suggest the K-bentonites had a volcanic origin in a collision margin setting related to subduction. Thickness and stratigraphic distribution considerations are consistent with a source area in the Rheic Ocean.

Dnestr Basin, Podolia↗
USGS2014

A comparison of two gears for quantifying abundance of lotic-dwelling crayfish

Crayfish (saddlebacked crayfish, Orconectes medius) catch was compared using a kick seine applied two different ways with a 1-m2 quadrat sampler (with known efficiency and bias in riffles) from three small streams in the Missouri Ozarks. Triplicate samples (one of each technique) were taken from two creeks and one headwater stream (n=69 sites) over a two-year period. General linear mixed models showed the number of crayfish collected using the quadrat sampler was greater than the number collected using either of the two seine techniques. However, there was no significant interaction with gear suggesting year, stream size, and channel unit type did not relate to different catches of crayfish by gear type. Variation in catch among gears was similar, as was the proportion of young-of-year individuals across samples taken with different gears or techniques. Negative binomial linear regression provided the appropriate relation between the gears which allows correction factors to be applied, if necessary, to relate catches by the kick seine to those of the quadrat sampler. The kick seine appears to be a reasonable substitute to the quadrat sampler in these shallow streams, with the advantage of ease of use and shorter time required per sample.

Journal of Crustacean Biology↗
USGS2004

Accuracy of a pulse-coherent acoustic Doppler profiler in a wave-dominated flow

The accuracy of velocities measured by a pulse-coherent acoustic Doppler profiler (PCADP) in the bottom boundary layer of a wave-dominated inner-shelf environment is evaluated. The downward-looking PCADP measured velocities in eight 10-cm cells at 1 Hz. Velocities measured by the PCADP are compared to those measured by an acoustic Doppler velocimeter for wave orbital velocities up to 95 cm s-1 and currents up to 40 cm s-1. An algorithm for correcting ambiguity errors using the resolution velocities was developed. Instrument bias, measured as the average error in burst mean speed, is -0.4 cm s-1 (standard deviation = 0.8). The accuracy (root-mean-square error) of instantaneous velocities has a mean of 8.6 cm s-1 (standard deviation = 6.5) for eastward velocities (the predominant direction of waves), 6.5 cm s-1 (standard deviation = 4.4) for northward velocities, and 2.4 cm s-1 (standard deviation = 1.6) for vertical velocities. Both burst mean and root-mean-square errors are greater for bursts with ub ??? 50 cm s-1. Profiles of burst mean speeds from the bottom five cells were fit to logarithmic curves: 92% of bursts with mean speed ??? 5 cm s-1 have a correlation coefficient R2 > 0.96. In cells close to the transducer, instantaneous velocities are noisy, burst mean velocities are biased low, and bottom orbital velocities are biased high. With adequate blanking distances for both the profile and resolution velocities, the PCADP provides sufficient accuracy to measure velocities in the bottom boundary layer under moderately energetic inner-shelf conditions.

Journal of Atmospheric and Oceanic Technology↗
USGS1995

Large-scale atmospheric forcing of recent trends toward early snowmelt runoff in California

Since the late 1940s, snowmelt and runoff have come increasingly early in the water year in many basins in northern and central California. This subtle trend is most pronounced in moderate-altitude basins, which are sensitive to changes in mean winter temperatures. Such basins have broad areas in which winter temperatures are near enough to freezing that small increases result initially in the formation of less snow and eventually in early snowmelt. In moderate-altitude basins of California, a declining fraction of the annual runoff has come in April–June. This decline has been compensated by increased fractions of runoff at other, mostly earlier, times in the water year. Weather stations in central California, including the central Sierra Nevada, have shown trends toward warmer winters since the 1940s. A series of regression analyses indicate that runoff timing responds equally to the observed decadal-scale trends in winter temperature and interannual temperature variations of the same magnitude, suggesting that the temperature trend is sufficient to explain the runoff-timing trends. The immediate cause of the trend toward warmer winters in California is a concurrent, long-term fluctuation in winter atmospheric circulations over the North Pacific Ocean and North America that is not immediately distinguishable from natural atmospheric variability. The fluctuation began to affect California in the 1940s, when the region of strongest low-frequency variation of winter circulations shifted to a part of the central North Pacific Ocean that is teleconnected to California temperatures. Since the late 1940s, winter wind fields have been displaced progressively southward over the central North Pacific and northward over the west coast of North America. These shifts in atmospheric circulations are associated with concurrent shifts in both West Coast air temperatures and North Pacific sea surface temperatures.

California↗
USGS1996

Interannual climate variability and snowpack in the western United States

An important part of the water supply in the western United States is derived from runoff fed by mountain snowmelt Snow accumulation responds to both precipitation and temperature variations, and forms an interesting climatic index, since it integrates these influences over the entire late fall-spring period. Here, effects of cool season climate variability upon snow water equivalent (SWE) over the western part of the conterminous United States are examined. The focus is on measurements on/and 1 April, when snow accumulation is typically greatest. The primary data, from a network of mountainous snow courses, provides a good description of interannual fluctuations in snow accumulations, since many snow courses have records of five decades or more. For any given year, the spring SWE anomaly at a particular snow course is likely to be 25%–60% of its long-term average. Five separate regions of anomalous SWE variability are distinguished, using a rotated principal components analysis. Although effects vary with region and with elevation, in general, the anomalous winter precipitation has the strongest influence on spring SWE fluctuations. Anomalous temperature has a weaker effect overall, but it has great influence in lower elevations such as in the coastal Northwest, and during spring in higher elevations. The regional snow anomaly patterns are associated with precipitation and temperature anomalies in winter and early spring. Patterns of the precipitation, temperature, and snow anomalies extend over broad regional areas, much larger than individual watersheds. These surface anomalies are organized by the atmospheric circulation, with primary anomaly centers over the North Pacific Ocean as well as over western North America. For most of the regions, anomalously low SWE is associated with a winter circulation resembling the PNA pattern. With a strong low in the central North Pacific and high pressure over the Pacific Northwest, this pattern diverts North Pacific storms northward, away from the region. Both warm and cool phases of El Niño-Southern Oscillation tend to produce regional patterns with out-of-phase SWE anomalies in the Northwest and the Southwest.

Arizona, California, Colorado, Idaho, Montana, Nev↗
USGS2001

North Pacific decadal climate variability since 1661

Climate in the North Pacific and North American sectors has experienced interdecadal shifts during the twentieth century. A network of recently developed tree-ring chronologies for Southern and Baja California extends the instrumental record and reveals decadal-scale variability back to 1661. The Pacific decadal oscillation (PDO) is closely matched by the dominant mode of tree-ring variability that provides a preliminary view of multiannual climate fluctuations spanning the past four centuries. The reconstructed PDO index features a prominent bidecadal oscillation, whose amplitude weakened in the late l700s to mid-1800s. A comparison with proxy records of ENSO suggests that the greatest decadal-scale oscillations in Pacific climate between 1706 and 1977 occurred around 1750, 1905, and 1947.

Journal of Climate↗
USGS2006

GFDL's CM2 global coupled climate models. Part I: Formulation and simulation characteristics

The formulation and simulation characteristics of two new global coupled climate models developed at NOAA's Geophysical Fluid Dynamics Laboratory (GFDL) are described. The models were designed to simulate atmospheric and oceanic climate and variability from the diurnal time scale through multicentury climate change, given our computational constraints. In particular, an important goal was to use the same model for both experimental seasonal to interannual forecasting and the study of multicentury global climate change, and this goal has been achieved. Tw o versions of the coupled model are described, called CM2.0 and CM2.1. The versions differ primarily in the dynamical core used in the atmospheric component, along with the cloud tuning and some details of the land and ocean components. For both coupled models, the resolution of the land and atmospheric components is 2?? latitude ?? 2.5?? longitude; the atmospheric model has 24 vertical levels. The ocean resolution is 1?? in latitude and longitude, with meridional resolution equatorward of 30?? becoming progressively finer, such that the meridional resolution is 1/3?? at the equator. There are 50 vertical levels in the ocean, with 22 evenly spaced levels within the top 220 m. The ocean component has poles over North America and Eurasia to avoid polar filtering. Neither coupled model employs flux adjustments. The co ntrol simulations have stable, realistic climates when integrated over multiple centuries. Both models have simulations of ENSO that are substantially improved relative to previous GFDL coupled models. The CM2.0 model has been further evaluated as an ENSO forecast model and has good skill (CM2.1 has not been evaluated as an ENSO forecast model). Generally reduced temperature and salinity biases exist in CM2.1 relative to CM2.0. These reductions are associated with 1) improved simulations of surface wind stress in CM2.1 and associated changes in oceanic gyre circulations; 2) changes in cloud tuning and the land model, both of which act to increase the net surface shortwave radiation in CM2.1, thereby reducing an overall cold bias present in CM2.0; and 3) a reduction of ocean lateral viscosity in the extratropics in CM2.1, which reduces sea ice biases in the North Atlantic. Both models have be en used to conduct a suite of climate change simulations for the 2007 Intergovernmental Panel on Climate Change (IPCC) assessment report and are able to simulate the main features of the observed warming of the twentieth century. The climate sensitivities of the CM2.0 and CM2.1 models are 2.9 and 3.4 K, respectively. These sensitivities are defined by coupling the atmospheric components of CM2.0 and CM2.1 to a slab ocean model and allowing the model to come into equilibrium with a doubling of atmospheric CO2. The output from a suite of integrations conducted with these models is freely available online (see http://nomads.gfdl.noaa.gov/). ?? 2006 American Meteorological Society.

Journal of Climate↗
USGS2006

Prediction of summer maximum and minimum temperature over the central and western United States: The roles of soil moisture and sea surface temperature

A statistical model based on canonical correlation analysis (CCA) was used to explore climatic associations and predictability of June–August (JJA) maximum and minimum surface air temperatures (Tmax and Tmin) as well as the frequency of Tmax daily extremes (Tmax90) in the central and western United States (west of 90°W). Explanatory variables are monthly and seasonal Pacific Ocean SST (PSST) and the Climate Division Palmer Drought Severity Index (PDSI) during 1950–2001. Although there is a positive correlation between Tmax and Tmin, the two variables exhibit somewhat different patterns and dynamics. Both exhibit their lowest levels of variability in summer, but that of Tmax is greater than Tmin. The predictability of Tmax is mainly associated with local effects related to previous soil moisture conditions at short range (one month to one season), with PSST providing a secondary influence. Predictability of Tmin is more strongly influenced by large-scale (PSST) patterns, with PDSI acting as a short-range predictive influence. For both predictand variables (Tmax and Tmin), the PDSI influence falls off markedly at time leads beyond a few months, but a PSST influence remains for at least two seasons. The maximum predictive skill for JJA Tmin, Tmax, and Tmax90 is from May PSST and PDSI. Importantly, skills evaluated for various seasons and time leads undergo a seasonal cycle that has maximum levels in summer. At the seasonal time frame, summer Tmax prediction skills are greatest in the Midwest, northern and central California, Arizona, and Utah. Similar results were found for Tmax90. In contrast, Tmin skill is spread over most of the western region, except for clusters of low skill in the northern Midwest and southern Montana, Idaho, and northern Arizona.

Western United States↗
USGS2019

Wave-current interaction between Hurricane Matthew wave fields and the Gulf Stream

Hurricanes interact with the Gulf Stream in the South Atlantic Bight (SAB) through a wide variety of processes, which are crucial to understand for prediction of open-ocean and coastal hazards during storms. However, it remains unclear how waves are modified by large-scale ocean currents under storm conditions, when waves are aligned with the storm-driven circulation and tightly coupled to the overlying wind field. Hurricane Matthew (2016) impacted the US southeast coast, causing extensive coastal change due to large waves and elevated water levels. The hurricane traveled on the continental shelf parallel to the SAB coastline, with the right side of the hurricane directly over the Gulf Stream. Using the Coupled Ocean Atmosphere Wave Sediment Transport Modeling System, we investigate wave-current interaction between Hurricane Matthew and the Gulf Stream. The model simulates ocean currents and waves over a grid encompassing the US east coast, with varied coupling of the hydrodynamic and wave components to isolate the effect of the currents on the waves, and the effect of the Gulf Stream relative to storm-driven circulation. The Gulf Stream modifies the direction of the storm-driven currents beneath the right side of the hurricane. Waves transitioned from following currents that result in wave lengthening, through negative current gradients that result in wave steepening and dissipation. Wave-current interaction over the Gulf Stream modified maximum coastal total water levels, and changed incident wave directions at the coast by up to 20°, with strong implications for the morphodynamic response and stability of the coast to the hurricane.

East Coast, Gulf Coast↗
USGS2005

Combined use of the ASK and SHK-1 cell lines to enhance the detection of infectious salmon anemia virus

Infectious salmon anemia (ISA) is a severe disease primarily affecting commercially farmed Atlantic salmon (Salmo salar) in seawater. The disease has been reported in portions of Canada, the United Kingdom, the Faroe Islands, and the United States. Infectious salmon anemia virus (ISAV), the causative agent of ISA, has also been isolated from several asymptomatic marine and salmonid fish species. Diagnostic assays for the detection of ISAV include virus isolation in cell culture, a reverse transcriptase-PCR, an enzyme-linked immunosorbent assay, and an indirect fluorescent antibody test. Virus isolation is considered the gold standard, and 5 salmonid cell lines are known to support growth of ISAV. In this study, the relative performance of the salmon head kidney 1 (SHK-1), Atlantic salmon kidney (ASK), and CHSE-214 cell lines in detecting ISAV was evaluated using samples from both experimentally and naturally infected Atlantic salmon. Interlaboratory comparisons were conducted using a quality control-quality assurance ring test. Both the ASK and SHK-1 cell lines performed well in detecting ISAV, although the SHK-1 line was more variable in its sensitivity to infection and somewhat slower in the appearance of cytopathic effect. Relative to the SHK-1 and ASK lines, the CHSE-214 cell line performed poorly. Although the ASK line appeared to represent a good alternative to the more commonly used SHK-1 line, use of a single cell line for diagnostic assays may increase the potential for false-negative results. Thus, the SHK-1 and ASK cell lines can be used in combination to provide enhanced ability to detect ISAV.

Journal of Veterinary Diagnostic Investigation↗
USGS2025

Laboratory assessment for recovery of porcine circovirus 2 and porcine reproductive and respiratory syndrome virus using two types of commercially available hollow-fiber ultrafilters

Groundwater near swine farms is an uninvestigated reservoir for porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circoviruses (PCVs). Enteric microorganisms are often collected from groundwater via dead-end ultrafiltration, but recovery of PRRSV and PCV with this method has not been assessed. We recovered PRRSV2 and PCV2 by dead-end ultrafiltration followed by polyethylene glycol (PEG) precipitation, nucleic acid extraction, and reverse-transcription quantitative real-time PCR. We also compared 2 commercial hemodialysis ultrafilters (Asahi Kasei Rexeed-25A, Nipro Elisio-25H) and compared PRRSV2 recovery in these filters to other waterborne microorganisms. On average, 8 ± 1% of PRRSV2 was recovered by dead-end ultrafiltration and PEG precipitation, compared to 25 ± 6% for adenovirus 41. Full-process recovery of bacteria in the same filters was 5–15%; Cryptosporidium parvum recovery was 42 ± 12%. PCV2 was detected in 4 of 12 replicate filters, but low stock concentrations precluded quantitative recovery estimates. Elisio-25H ultrafilters performed similarly to Rexeed-25A filters for all organisms tested and is an effective replacement for the Rexeed-25A, which is no longer available in the United States. Our recovery of PRRSV2 and PCV2 by dead-end ultrafiltration in the laboratory suggests that PRRSV2 detection limits are as low as 3–50 genomic copies/L in sample volumes of 100–1,500 L. Based on quantitative microbial risk assessment, these concentrations are relevant to PRRSV2 infection rates in the U.S. swine herd.

Journal of Veterinary Diagnostic Investigation↗