Search USGS⌕ Search

SEARCH · Search USGS

Results for “Nature Methods”

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 37 records · Page 2Linked to original sources
USGS1982

Optimal stochastic control in natural resource management: Framework and examples

A framework is presented for the application of optimal control methods to natural resource problems. An expression of the optimal control problem appropriate for renewable natural resources is given and its application to Markovian systems is presented in some detail. Three general approaches are outlined for determining optimal control of infinite time horizon systems and three examples from the natural resource literature are used for illustration.

Ecological Modelling↗
USGS2020

Gas hydrates in sustainable chemistry

Gas hydrates have received considerable attention due to their important role in flow assurance for the oil and gas industry, their extensive natural occurrence on Earth and extraterrestrial planets, and their significant applications in sustainable technologies including but not limited to gas and energy storage, gas separation, and water desalination. Given not only their inherent structural flexibility depending on the type of guest gas molecules and formation conditions, but also the synthetic effects of a wide range of chemical additives on their properties, these variabilities could be exploited to optimise the role of gas hydrates. This includes increasing their industrial applications, understanding and utilising their role in Nature, identifying potential methods for safely extracting natural gases stored in naturally occurring hydrates within the Earth, and for developing green technologies. This review summarizes the different properties of gas hydrates as well as their formation and dissociation kinetics and then reviews the fast-growing literature reporting their role and applications in the aforementioned fields, mainly concentrating on advances during the last decade. Challenges, limitations, and future perspectives of each field are briefly discussed. The overall objective of this review is to provide readers with an extensive overview of gas hydrates that we hope will stimulate further work on this riveting field.

Chemical Society Reviews↗
USGS1999

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory-Determination of dissolved arsenic, boron, lithium, selenium, strontium, thallium, and vanadium using inductively coupled plasma-mass spectrometry

The inductively coupled plasma-mass spectrometric (ICP-MS) methods have been expanded to include the determination of dissolved arsenic, boron, lithium, selenium, strontium, thallium, and vanadium in filtered, acidified natural water. Method detection limits for these elements are now 10 to 200 times lower than by former U.S. Geological Survey (USGS) methods, thus providing lower variability at ambient concentrations. The bias and variability of the method was determined by using results from spike recoveries, standard reference materials, and validation samples. Spike recoveries at 5 to 10 times the method detection limit and 75 micrograms per liter in reagent-water, surface-water, and groundwater matrices averaged 93 percent for seven replicates, although selected elemental recoveries in a ground-water matrix with an extremely high iron sulfate concentration were negatively biased by 30 percent. Results for standard reference materials were within 1 standard deviation of the most probable value. Statistical analysis of the results from about 60 filtered, acidified natural-water samples indicated that there was no significant difference between ICP?MS and former USGS official methods of analysis.

Open-File Report↗
USGS2002

Determination of phosphate in natural waters by activation analysis of tungstophosphoric acid

Activation analysis may be used to determine quantitatively traces of phosphate in natural waters. Methods based on the reaction 31 P( n,γ ) 32 P are subject to interference by sulfur and chlorine which give rise to 32 P through n,p and n,α reactions. If the ratio of phosphorus to sulfur or chlorine is small, as it is in most natural waters, accurate analyses by these methods are difficult to achieve. In the activation analysis method, molybdate and tungstate ions are added to samples containing phosphate ion to form tungstomolybdophosphoric acid. The complex is extracted with 2,6-dimethyl-4-heptanone. After activation of an aliquot of the organic phase for 1 hour at a flux of 10 13 neutrons per cm 2 , per second, the gamma spectrum is essentially that of tungsten-187. The induced activity is proportional to the concentration of phosphate in the sample. A test of the method showed it to give accurate results at concentrations of 4 to at least 200 p.p.b. of phosphorus when an aliquot of 100 μl. was activated. By suitable reagent purification, counting for longer times, and activation of larger aliquots, the detection limit could be lowered several hundredfold.

Environmental Science & Technology↗
USGS2007

Development and evaluation of a gas chromatographic method for the determination of triazine herbicides in natural water samples

A multi-residue method is described for the determination o triazine herbicides in natural water samples. The technique uses solvent extraction followed by gas chromatographic separation and detection employing nitrogen-selective devices. Seven compounds can be determined simultaneously at a nominal detection limit of 0.1 μg/L in a 1-litre sample. Three different natural water samples were used for error analysis via evaluation of recovery efficiencies and estimation of overall method precision. As an alternative to liquid-liquid partition (solvent extraction) for removal of compounds of interest from water, solid-phase extraction (SPE) techniques employing chromatographic grade silicas with chemically modified surfaces have been examined. SPE is found to provide rapid and efficient concentration with quantitative recovery of some triazine herbicides from natural water samples. Concentration factors of 500 to 1000 times are obtained readily by the SPE technique.

International Journal of Environmental Analytical ↗
USGS2002

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory-Arsenic speciation in natural-water samples using laboratory and field methods

Analytical methods for the determination of arsenite [As(III)], arsenate [As(V)], dimethylarsinate (DMA), monomethylarsonate (MMA), and roxarsone in filtered natural-water samples are described. Various analytical methods can be used for the determination, depending on the arsenic species being determined. Arsenic concentration is determined by using inductively coupled plasma-mass spectrometry (ICP-MS) as an arsenic-specific detector for all methods. Laboratory-speciation methods are described that use an ion chromatographic column to separate the arsenic species; the column length, column packing, and mobile phase are dependent on the species of interest. Regardless of the separation technique, the arsenic species are introduced into plasma by eithe rpneumatic nebulization or arsine generation. Analysis times range from 2 to 8 minutes and method detection limits range from 0.1 to 0.6 microgram-arsenic per liter (ug-As/L), 10 to 60 picograms absolute (for a 100-microliter injection), depending on the arsenic species determined and the analytical method used. A field-generation specciation method also is described that uses a strong anion exchange cartridge to separate As(III) from As(V) in the field. As(III) in the eluate and the As(V) in the cartridge extract are determined by direct nebulization ICP-MS. Methylated arsenic species that also are retained on the cartridge will positively bias As(V) results without further laboratory separations. The method detection limit for field speciation is 0.3 ug-As/L. The distribution of arsenic species must be preserved in the field to eliminate changes caused by photochemical oxidation or metal oxyhydroxide precipitation. Preservation techniques, such as refrigeration, the addition of acides, or the additoin of ethylene-diaminetetraacetic acid (EDTA) and the effects of ambient light were tested. Of the preservatives evaluated, EDTA was found to work best with the laboratory- and field-speciation methods for all sample matrices tested. Storing the samples in opaque polytethylene bottles eliminated the effects of photochemical oxidation. The percentage change in As(III):As(V) ratios for an EDTA-preserved acid mine drainage (AMD) sample and ground-water sample during a 3-month period was -5 percent and +3 percent, respectively. The bias and variability of the methods were evaluated by comparing results for total arsenic and As(III), As(V), DMA, and MMA concentrations in ground water, AMD, and surface water. Seventy-one ground-water, 10 AMD, and 24 surface-water samples were analyzed. Concentrations in ground-water samples reached 720 ug-As/L for As(III) and 1080 ug-As/L for As(V); AMD samples reached 12800 ug-As/L for As(III) and 7050 ug-As/L for As(V); and surface-water samples reached 5 ug-As/L for As(III) and As(V). Inorganic arsenic species distribution in the samples ranged from 0 to 90 percent As(III). DMA and MMA were present only in surface-water samples from agricultural areas where the herbicide monosodium methylarsonate was applied; concentrations never exceeded 6 ug-As/L. Statistical analyses indicated that the difference between As(III) and As(V) concentrations for samples preserved with EDTA in opaque bottles and field-speciation results were analytically insignificant at the 95-percent confidence interval. There was no significant difference among the methods tested for total arsenic concentration. Percentage recovery for field samples spiked at 50 ug-As/L and analyzed by the laboratory-speciation method (n=2) ranged from 82 to 100 percent for As(III), 97 to 102 percent for As(V), 90 to 104 percent for DMA, and 81 to 96 percent for MMA; recoveries for samples spiked at 100 ug-As/L and analyzed by the field-speciation method ranged from 102 to 107 percent for As(III) and 105 to 106 percent for As(V). Laboratory-speciation results for Environment Canada reference material SLRS-2 closely matched reported concentrations. Laboratory-speciation metho

Water-Resources Investigations Report↗
USGS2014

Connecting the dots: a collaborative USGS-NPS effort to expand the utility of monitoring data

The Natural Resource Challenge (National Park Service 1999) was a call to action. It constituted a mandate for monitoring based on the twin premises that (1) natural resources in national parks require active management and stewardship if we are to protect them from gradual degradation, and (2) we cannot protect what we do not understand. The intent of the challenge was embodied in its original description: We must expand existing inventory programs and develop efficient ways to monitor the vital signs of natural systems. We must enlist others in the scientific community to help, and also facilitate their inquiry. Managers must have and apply this information to preserve our natural resources. In this article, we report on ongoing collaborative work between the National Park Service (NPS) and the US Geological Survey (USGS) that seeks to add to our scientific understanding of the ecological processes operating behind vital signs monitoring data. The ultimate goal of this work is to provide insights that can facilitate an understanding of the systems and identify potential opportunities for active stewardship by NPS managers (Bennetts et al. 2007; Mitchell et al. 2014). The bulk of the work thus far has involved Acadia and Rocky Mountain national parks, but there are plans for extending the work to additional parks. Our story stats with work designed to consider ways of assessing the status and condition of natural resources and the potential for historical or ongoing influences of human activities. In the 1990s, the concept of "biotic integrity" began to take hold as an aspiration for developing quantitative indices describing how closely the conditions at a site resemble those found at pristine, unimpacted sites. Quantitative methods for developing indices of biotic integrity (IBIs) and elaborations of that idea (e.g., ecological integrity) have received considerable attention and application of these methods to natural resources has become widespread (Karr 1991; Barbour et al. 1999; Stoddard et al. 2008). Despite widespread use, many questions remain about how metrics are combined to form effective indices and about how to interpret both. Scientists and natural resource specialists within NPS and USGS have joined forces to critique the current analysis methods, with the collaboration involving the Rocky Mountain and Northeast Temperate NPS Inventory and Monitoring (I & M) networks, along with others, and USGS scientists from the National Wetlands Research Center and Patuxent Wildlife Research Center. Funding that initiated the project was from a joint-partnership fund managed by the USGS Ecosystems Program for National Park Monitoring research and the work was focused at Acadia National Park and Rocky Mountain National Park. Here we present synopses of two major issues addressed by the group.

The George Wright Forum↗
USGS1987

Use of stable sulphur isotopes to monitor directly the behaviour of sulphur in coal during thermal desulphurization

A method has been developed using stable sulphur isotope analyses to monitor the behaviour of sulphur forms in a coal during thermal desulphurization. In this method, the natural stable isotopic composition of the pyritic and organic sulphur in coal is used as a tracer to follow their mobility during the desulphurization process. This tracer method is based on the fact that the isotopic compositions of pyritic and organic sulphur are significantly different in some coals. Isotopic results of pyrolysis experiments at temperatures ranging from 350 to 750 °C indicate that the sulphur released with the volatiles is predominantly organic sulphur. The pyritic sulphur is evolved in significant quantities only when pyrolysis temperatures exceed 500 °C. The presence of pyrite seems to have no effect on the amount of organic sulphur evolved during pyrolysis. The chemical and isotopic mass balances achieved from three different samples of the Herrin (No. 6) coal of the Illinois Basin demonstrate that this stable isotope tracer method is quantitative. The main disadvantage of this tracing technique is that not all coals contain isotopically distinct organic and pyritic sulphur.

Illinois, Indiana, Kentucky↗
USGS2002

Use of ICP/MS with ultrasonic nebulizer for routine determination of uranium activity ratios in natural water

A method is described that allows precise determination of 234 U/ 238 U activity ratios (UAR) in most natural waters using commonly available inductively coupled plasma/mass spectrometry (ICP/MS) instrumentation and accessories. The precision achieved by this technique (±0.5% RSD, 1 sigma) is intermediate between thermal ionization mass spectrometry (±0.25% RSD, 1 sigma) and alpha particle spectrometry (±5% RSD, 1 sigma). It is precise and rapid enough to allow analysis of a large number of samples in a short period of time at low cost using standard, commercially available quadrupole instrumentation with ultrasonic nebulizer and desolvator accessories. UARs have been analyzed successfully in fresh to moderately saline waters with U concentrations of from less than 1 μg/L to nearly 100 μg/L. An example of the uses of these data is shown for a study of surface-water mixing in the North Platte River in western Nebraska. This rapid and easy technique should encourage the wider use of uranium isotopes in surface-water and groundwater investigations, both for qualitative (e.g. identifying sources of water) and quantitative (e.g. determining end-member mixing ratios purposes.

Environmental Science & Technology↗
USGS2015

Assessment of environmental DNA for detecting presence of imperiled aquatic amphibian species in isolated wetlands

Environmental DNA (eDNA) is an emerging tool that allows low-impact sampling for aquatic species by isolating DNA from water samples and screening for DNA sequences specific to species of interest. However, researchers have not tested this method in naturally acidic wetlands that provide breeding habitat for a number of imperiled species, including the frosted salamander ( Ambystoma cingulatum ), reticulated flatwoods salamanders ( Ambystoma bishopi ), striped newt ( Notophthalmus perstriatus ), and gopher frog ( Lithobates capito ). Our objectives for this study were to develop and optimize eDNA survey protocols and assays to complement and enhance capture-based survey methods for these amphibian species. We collected three or more water samples, dipnetted or trapped larval and adult amphibians, and conducted visual encounter surveys for egg masses for target species at 40 sites on 12 different longleaf pine ( Pinus palustris ) tracts. We used quantitative PCRs to screen eDNA from each site for target species presence. We detected flatwoods salamanders at three sites with eDNA but did not detect them during physical surveys. Based on the sample location we assumed these eDNA detections to indicate the presence of frosted flatwoods salamanders. We did not detect reticulated flatwoods salamanders. We detected striped newts with physical and eDNA surveys at two wetlands. We detected gopher frogs at 12 sites total, three with eDNA alone, two with physical surveys alone, and seven with physical and eDNA surveys. We detected our target species with eDNA at 9 of 11 sites where they were present as indicated from traditional surveys and at six sites where they were not detected with traditional surveys. It was, however, critical to use at least three water samples per site for eDNA. Our results demonstrate eDNA surveys can be a useful complement to traditional survey methods for detecting imperiled pond-breeding amphibians. Environmental DNA may be particularly useful in situations where detection probability using traditional survey methods is low or access by trained personnel is limited.

Alabama, Florida, Georgia, South Carolina↗
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↗
USGS2024

A methodology to estimate CO2 and energy gas storage resources in depleted conventional gas reservoirs

Depleted hydrocarbon reservoirs are subsurface geological structures capable of sequestering vast quantities of carbon dioxide (CO 2 ) as well as storing other energy gases for later usage, such as natural gas, and potentially hydrogen (H 2 ). Here we outline a methodology to quantify multi-gas storage resources in depleted conventional gas reservoirs for usage in assessments by the United States Geological Survey (USGS) at the scale of sedimentary basins. The methodology consists first of quantifying accessible pore volume in a depleted reservoir for natural gas storage using up to three equations. Input data are derived from commonly reported or estimated reservoir parameters and natural gas production volumes, and equations may be combined in linear models to improve pore volume estimates. Storage estimates from these equations are tested and validated for 31 reservoirs in the Michigan Basin Province, USA that were previously converted to underground gas storage facilities and have known (federally reported) natural gas storage capacities. Secondly, natural gas storage capacities can be transformed via fluid substitution calculations to estimate the storage resources for non-native fluids, applied here for, CO 2 , H 2 , and methane-H 2 blends, accounting for molecule-specific deviations from ideal gas behavior at reservoir pressures and temperatures as well as differing storage efficiencies. Importantly, the storage of non-native fluids may not be appropriate in all depleted gas reservoir settings due to potential risks like leakage, in particular in the case of H 2 storage, requiring additional knowledge of caprock sealing capacity. Given this caveat, we demonstrate the fluid substitution method for natural gas reservoirs of the Northern Niagaran Reef and Southern Niagaran Reef USGS plays in the Michigan Basin Province, as these trends of Silurian pinnacle reefs are capped with tight-sealing evaporite facies. The deterministic equations outlined from this methodology can be incorporated into future probabilistic USGS gas storage assessments for CO 2 , H 2 , and natural gas resources in the United States.

Michigan↗
USGS2001

Use of advanced borehole geophysical techniques to delineate fractured-rock ground-water flow and fractures along water-tunnel facilities in northern Queens County, New York

Advanced borehole geophysical methods were used to assess the geohydrology of crystalline bedrock along the course of a new water tunnel for New York City. The logging methods include natural gamma, spontaneous potential, single-point resistance, mechanical and acoustic caliper, focused electromagnetic induction, electromagnetic resistivity, magnetic susceptibility, borehole-fluid temperature and conductance, differential temperature, heat-pulse flowmeter, acoustic televiewer, borehole deviation, optical televiewer, and borehole radar. Integrated interpretation of the geophysical logs from an 825-foot borehole (1) provided information on the extent, orientation, and structure (foliation and fractures) within the entire borehole, including intensely fractured intervals from which core recovery may be poor; (2) delineated transmissive fracture zones intersected by the borehole and provided estimates of their transmissivity and hydraulic head; and (3) enabled mapping of the location and orientation of structures at distances as much as 100 ft from the borehole. Analyses of the borehole-wall image and the geophysical logs from the borehole on Crescent Street, in northern Queens County, are presented here to illustrate the application of the methods. The borehole penetrates gneiss and other crystalline bedrock that has predominantly southeastward dipping foliation and nearly horizontal and southeastward-dipping fractures. The heat-pulse flowmeter logs obtained under pumping and nonpumping conditions, together with the other geophysical logs, indicate five transmissive fracture zones. More than 90 percent of the open-hole transmissivity is associated with a fracture zone 272 feet BLS (below land surface). A transmissive zone at 787 feet BLS that consists of nearly parallel fractures lies within the projected tunnel path; here the hydraulic head is 12 to 15 feet lower than that of transmissive zones above the 315-foot depth. The 60-megahertz directional borehole radar logs indicate the location and orientation of two closely spaced radar reflectors that would intersect the projection of the borehole below its drilled depth. Subsequent excavation of the tunnel past the borehole allowed comparison of the log analysis with conditions observed in the tunnel. The tunnel was found to intersect gneiss with southeastward dipping foliation; many nearly horizontal fractures; and a southeastward dipping fracture zone whose location, character, and orientation was consistent with that of the mapped radar reflectors. The fracture zone produced inflow to the tunnel at a rate of 50 to 100 gallons per minute. All conditions indicated by the logging methods were consistent with those observed within the tunnel.

New York↗
USGS2024

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

Nature Methods↗
USGS2021

Stability of inorganic and methylated arsenic species in laboratory standards, surface water and groundwater under three different preservation regimes

Geogenic arsenic (As) adversely affects drinking water quality in geologically diverse aquifers across the globe. Although the species of As significantly affects its fate, transport, toxicity, and As treatment technology efficacy, reported effectiveness of As species preservation methods varies widely with preservation methods and natural water geochemistry. Our study 1) evaluates the shelf life of As(III), As(V), dimethylarsinate (DMA), and monomethylarsonate (MMA) in standards prepared with ultrapure water; 2) establishes a hold time for these As species in low-iron (Fe) groundwater and surface water samples preserved with a concentration of EDTA that exceeded the sum of the molar concentrations of Al, Fe, Mn, Ca, Mg, and Sr (molar excess of EDTA); and 3) evaluates As(III) species stability in groundwater samples with detectable SO 4 and up to 6.5 mg/L Fe concentrations preserved in 3 ways: less than molar excess EDTA, molar excess EDTA, and Vacuette® tubes with an unknown (proprietary) amount of EDTA. Arsenic species standards prepared with 2.5 mM EDTA in ultrapure water and stored at 4 °C had a shelf life of at least 180 days. As(III) was stable for at least 15 days and DMA and MMA were stable for at least 90 days in environmental samples with Fe less than 1 mg/L that were preserved with a molar excess of EDTA and stored in opaque containers at 4 °C. As(III) species were not stable for any holding time in samples with Fe greater than 1 mg/L and detectable SO 4 when preserved with a molar excess of EDTA and stored in white high density polyethylene bottles at room temperature, or when preserved by storage in EDTA containing Vacuette® tubes at 4 °C. For geochemical or water quality studies where the distribution of As(III) and As(V) is a critical factor, an understanding of the sample chemistry, rapid As speciation analysis after sample collection, and collecting a field spike with the sample can be helpful for collecting accurate inorganic As species data.

Applied Geochemistry↗