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At least 127 records · Page 7Linked to original sources

USGS2023

Train, inform, borrow, or combine? Approaches to process-guided deep learning for groundwater-influenced stream temperature prediction

Although groundwater discharge is a critical stream temperature control process, it is not explicitly represented in many stream temperature models, an omission that may reduce predictive accuracy, hinder management of aquatic habitat, and decrease user confidence. We assessed the performance of a previously-described process-guided deep learning model of stream temperature in the Delaware River Basin (USA). We found lower accuracy (root mean square error [RMSE] of 1.71 versus 1.35°C) and stronger seasonal bias (absolute mean monthly bias of 1.06 vs. 0.68°C) for reaches primarily influenced by deep groundwater as compared to atmospheric conditions. We then tested four approaches for improving groundwater process representation: (a) a custom loss function leveraging the unique patterns of air and water temperature coupling characteristic of different temperature drivers, (b) inclusion of additional groundwater-relevant catchment attributes, (c) incorporation of additional process model outputs, and (d) a composite model. The custom loss function and the additional attributes significantly improved the predictive accuracy in groundwater-dominated reaches (RMSE of 1.37 and 1.26°C) and reduced the seasonal bias (absolute mean monthly bias of 0.44 and 0.48°C), but neither approach could identify holdout groundwater reaches. Variable importance analysis indicates the custom loss function nudges the model to use the existing inputs more efficiently, whereas with the added features the model relies on a broader suite of inputs. This analysis is a substantial step toward more accurately representing groundwater discharge processes in stream temperature models and will improve predictive accuracy and inform habitat management.

Delaware River Basin↗

USGS2010

Simulation of aerobic and anaerobic biodegradation processes at a crude oil spill site

A two-dimensional, multispecies reactive solute transport model with sequential aerobic and anaerobic degradation processes was developed and tested. The model was used to study the field-scale solute transport and degradation processes at the Bemidji, Minnesota, crude oil spill site. The simulations included the biodegradation of volatile and nonvolatile fractions of dissolved organic carbon by aerobic processes, manganese and iron reduction, and methanogenesis. Model parameter estimates were constrained by published Monod kinetic parameters, theoretical yield estimates, and field biomass measurements. Despite the considerable uncertainty in the model parameter estimates, results of simulations reproduced the general features of the observed groundwater plume and the measured bacterial concentrations. In the simulation, 46% of the total dissolved organic carbon (TDOC) introduced into the aquifer was degraded. Aerobic degradation accounted for 40% of the TDOC degraded. Anaerobic processes accounted for the remaining 60% of degradation of TDOC: 5% by Mn reduction, 19% by Fe reduction, and 36% by methanogenesis. Thus anaerobic processes account for more than half of the removal of DOC at this site.

Water Resources Research↗

USGS2011

Diel biogeochemical processes and their effect on the aqueous chemistry of streams: A review

This review summarizes biogeochemical processes that operate on diel, or 24-h, time scales in streams and the changes in aqueous chemistry that are associated with these processes. Some biogeochemical processes, such as those producing diel cycles of dissolved O 2 and pH, were the first to be studied, whereas processes producing diel concentration cycles of a broader spectrum of chemical species including dissolved gases, dissolved inorganic and organic carbon, trace elements, nutrients, stable isotopes, and suspended particles have received attention only more recently. Diel biogeochemical cycles are interrelated because the cyclical variations produced by one biogeochemical process commonly affect another. Thus, understanding biogeochemical cycling is essential not only for guiding collection and interpretation of water-quality data but also for geochemical and ecological studies of streams. Expanded knowledge of diel biogeochemical cycling will improve understanding of how natural aquatic environments function and thus lead to better predictions of how stream ecosystems might react to changing conditions of contaminant loading, eutrophication, climate change, drought, industrialization, development, and other factors.

Chemical Geology↗

USGS2014

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.

The ISME Journal↗

USGS2020

Impacts of hydrothermal plume processes on oceanic metal cycles and transport

Chemical, physical and biological processes in hydrothermal plumes control the flux of elements from hydrothermal vents to the global oceans. The timescales of these processes range from less than a second, as the hydrothermal fluid mixes with seawater at the seafloor, to decades, as the plume disperses over thousands of kilometers. Integrating hydrothermal geochemistry throughout the lifetime of the plume reveals some well constrained processes, along with many surprises. For instance, contrary to the idea that metals are removed from the hydrothermal plume via oxidation, a survey of recent datasets reveals that oxidation of iron and manganese does not consistently result in their removal from the plume, and that manganese may be lost from the water column more rapidly than iron. These observations suggest that the understanding of element transport in hydrothermal plumes is incomplete, partly due to the change in removal processes as the plume disperses from less than 1 km from the vent to more than 4,000 km. We suggest that characterizing the plume based on regions that retain some reduced components versus those that are fully oxidized, in addition to buoyancy, will illuminate the nature of the dominant processes and allow a more complete understanding of the ultimate fate of hydrothermally derived metals.

Nature Geoscience↗

USGS2016

Competitive exclusion over broad spatial extents is a slow process: Evidence and implications for species distribution modeling

There is considerable debate about the role of competition in shaping species distributions over broad spatial extents. This debate has practical implications because predicting changes in species' geographic ranges in response to ongoing environmental change would be simpler if competition could be ignored. While this debate has been the subject of many reviews, recent literature has not addressed the rates of relevant processes. This omission is surprising in that ecologists hypothesized decades ago that regional competitive exclusion is a slow process. The goal of this review is to reassess the debate under the hypothesis that competitive exclusion over broad spatial extents is a slow process. Available evidence, including simulations presented for the first time here, suggests that competitive exclusion over broad spatial extents occurs slowly over temporal extents of many decades to millennia. Ecologists arguing against an important role for competition frequently study modern patterns and/or range dynamics over periods of decades, while much of the evidence for competition shaping geographic ranges at broad spatial extents comes from paleoecological studies over time scales of centuries or longer. If competition is slow, as evidence suggests, the geographic distributions of some, perhaps many species, would continue to change over time scales of decades to millennia, even if environmental conditions did not continue to change. If the distributions of competing species are at equilibrium it is possible to predict species distributions based on observed species–environment relationships. However, disequilibrium is widespread as a result of competition and many other processes. Studies whose goal is accurate predictions over intermediate time scales (decades to centuries) should focus on factors associated with range expansion (colonization) and loss (local extinction), as opposed to current patterns. In general, understanding of modern range dynamics would be enhanced by considering the rates of relevant processes.

Ecography↗

USGS2025

Estimating spatially explicit survival and mortality risk from telemetry data with thinned point process models

Mortality risk for animals often varies spatially and can be linked to how animals use landscapes. While numerous studies collect telemetry data on animals, the focus is typically on the period when animals are alive, even though there is important information that could be gleaned about mortality risk. We introduce a thinned spatial point process (SPP) modelling framework that couples relative abundance and space use with a mortality process to formally treat the occurrence of mortality events across the landscape as a spatial process. We show how this model can be embedded in a hierarchical statistical framework and fit to telemetry data to make inferences about how spatial covariates drive both space use and mortality risk. We apply the method to two data sets to study the effects of roads and habitat on spatially explicit mortality risk: (1) VHF telemetry data collected for willow ptarmigan in Alaska, and (2) hourly GPS telemetry data collected for black bears in Colorado. These case studies demonstrate the applicability of this method for different species and data types, making it broadly useful in enabling inferences about the mechanisms influencing animal survival and spatial population processes while formally treating survival as a spatial process, especially as the development and implementation of joint analyses continue to progress.

Ecology Letters↗

USGS2019

Predicting paleoclimate from compositional data using multivariate Gaussian process inverse prediction

Multivariate compositional count data arise in many applications including ecology, microbiology, genetics and paleoclimate. A frequent question in the analysis of multivariate compositional count data is what underlying values of a covariate(s) give rise to the observed composition. Learning the relationship between covariates and the compositional count allows for inverse prediction of unobserved covariates given compositional count observations. Gaussian processes provide a flexible framework for modeling functional responses with respect to a covariate without assuming a functional form. Many scientific disciplines use Gaussian process approximations to improve prediction and make inference on latent processes and parameters. When prediction is desired on unobserved covariates given realizations of the response variable, this is called inverse prediction. Because inverse prediction is often mathematically and computationally challenging, predicting unobserved covariates often requires fitting models that are different from the hypothesized generative model. We present a novel computational framework that allows for efficient inverse prediction using a Gaussian process approximation to generative models. Our framework enables scientific learning about how the latent processes co-vary with respect to covariates while simultaneously providing predictions of missing covariates. The proposed framework is capable of efficiently exploring the high dimensional, multi-modal latent spaces that arise in the inverse problem. To demonstrate flexibility, we apply our method in a generalized linear model framework to predict latent climate states given multivariate count data. Based on cross-validation, our model has predictive skill competitive with current methods while simultaneously providing formal, statistical inference on the underlying community dynamics of the biological system previously not available.

Annals of Applied Statistics↗

USGS1992

Role of microbial processes in linking sandstone diagenesis with organic-rich clays

Numerous chemical reactions within clay sequences have been proposed to produce dissolved material for diagenesis of deeply-buried sands. However, reactions responsible for solubilizing inorganic and organic constituents in clays at intermediate depths, and their importance to sandstone diagenesis, have not been evaluated. Results from this study show that the processes of microbial organic-acid production (via fermentation) in clays and microbial organic-acid consumption (via sulfate reduction) in sands effectively link organic-rich clays to sandstone diagenesis in the Black Creek Formation of South Carolina. Diagenetic processes have resulted in the formation of 10 volume percent calcite cement, 0.1 volume percent authigenic pyrite, and 1.5 volume percent secondary porosity in Black Creek sands. However, the distribution of these diagenetic processes is not uniform, resulting in net destruction of porosity in some parts of the sand and net porosity enhancement in other parts. Mass balance-derived rates of microbial organic-acid production (10 (super -5) mmole carbon 1 (super -1) yr (super -1) ) and microbial CO 2 production (4 x 10 (super -5) mmole l (super -1) yr (super -1) ) show that microbial processes can account for all organic carbon in the calcite cements (at least 11% of carbonate carbon based on isotope-balance calculations), all observed authigenic pyrite, and all observed secondary porosity. These findings show that microbial processes can serve to link organic-rich clays with sandstone diagenesis at intermediate depths.

Journal of Sedimentary Petrology↗

USGS2025

High-pass corner frequency selection and review tool for use in ground-motion processing

Raw seismological waveform data contain noise from the instrument’s surroundings and the instrument itself that can dominate recordings at low and high frequencies. To use these data in ground‐motion modeling, the effects of noise on the signals must be reduced and the signals’ usable frequency range identified. We present automated procedures to efficiently reduce low‐frequency noise that are implemented in the software package gmprocess. These procedures check for, and as needed remove, low‐frequency artifacts in the displacement record using polynomial fits, which can be used in combination with existing signal‐to‐noise ratio (SNR)‐based corner‐frequency selection procedures. The automated selections are then efficiently verified and refined using a graphical user interface (GUI) that plots relevant ground‐motion time series and spectra and tracks modifications to signal processing parameters. We demonstrate these procedures using recordings from the 2020 M 5.1 Sparta, North Carolina, and the 2013 M 4.7 southern Ontario earthquakes. Data processed with the SNR‐only and polynomial criteria for these events contain displacement artifacts in 37% and 23% of processed traces, respectively. Records with remaining artifacts are corrected manually using the GUI. These processing steps illustrate the workflow for efficient data processing with quality control.

Seismological Research Letters↗

USGS1991

Initiation processes and flow evolution of turbidity currents: Implications for the depositional record

Interpretations of sea-level change and source-area tectonism from the character of turbidite deposits require knowledge of the sediment source, the flow-initiation process, how the turbidity current evolved during flow, and what flow phases were associated with deposition. The flow responds to shape and size characteristics of both the erosional pathway and the morphology of previous deposits; these, in turn, reflect factors such as basin size, shape, and tectonic activity. The initiation of turbidity currents generally involves either transformation from mass failures or one of a variety of fluid-flow events involving ignitive flow. The variability of these initiating processes with geologic setting is illustrated by analysis of three case studies involving 1) initiation by storm surge on a carbonate-reef slope, 2) a seismically triggered failure of a line source within midslope sediment, and 3) a bedload delta showing both hyperpycnal flow of river bedload and failure of unstable prodelta sediment. General criteria for the initiation of turbidity currents are given. Depositional and erosional features of the turbidite deposits themselves allow recognition of changes in flow processes as the turbidity currents traverse the basin. High-concentration basal flow beneath the main turbulent turbidity current will leave a distinctive depositional record from more energetic flow, particularly in proximal and channel settings. Turbidity currents of different sizes and sediment distribution interact quite differently with local fan morphology. Many large, muddy turbidity currents are much thicker than levee-channel relief; the upper parts of such flows are "stripped off" across levees and can become rechannelized farther downslope. in restricted basins, the basin margin acts like a channel wall for larger flows, thus maintaining competence over long distances. Thinner, sandier flows flush out channel systems, and a large proportion of sediment in some turbidite deposits may be derived from bed erosion. A broad range of local bedforms, especially sediment waves and scours, reflects changes in the character of turbulence and competence within quasi-steady flows. This paper emphasizes the broad range of size, sediment distribution, and depositional processes in turbidity currents that largely reflects the variety of initiation processes. This variability means that caution is needed when interpreting depositional conditions of ancient turbidite sediment with ill-defined morphologic setting.

Book chapter↗

USGS2008

Determination of dominant biogeochemical processes in a contaminated aquifer-wetland system using multivariate statistical analysis

Determining the processes governing aqueous biogeochemistry in a wetland hydrologically linked to an underlying contaminated aquifer is challenging due to the complex exchange between the systems and their distinct responses to changes in precipitation, recharge, and biological activities. To evaluate temporal and spatial processes in the wetland-aquifer system, water samples were collected using cm-scale multi-chambered passive diffusion samplers (peepers) to span the wetland-aquifer interface over a period of 3 yr. Samples were analyzed for major cations and anions, methane, and a suite of organic acids resulting in a large dataset of over 8000 points, which was evaluated using multivariate statistics. Principal component analysis (PCA) was chosen with the purpose of exploring the sources of variation in the dataset to expose related variables and provide insight into the biogeochemical processes that control the water chemistry of the system. Factor scores computed from PCA were mapped by date and depth. Patterns observed suggest that (i) fermentation is the process controlling the greatest variability in the dataset and it peaks in May; (ii) iron and sulfate reduction were the dominant terminal electron-accepting processes in the system and were associated with fermentation but had more complex seasonal variability than fermentation; (iii) methanogenesis was also important and associated with bacterial utilization of minerals as a source of electron acceptors (e.g., barite BaSO 4 ); and (iv) seasonal hydrological patterns (wet and dry periods) control the availability of electron acceptors through the reoxidation of reduced iron-sulfur species enhancing iron and sulfate reduction.

Journal of Environmental Quality↗

USGS2015

Conflict minerals from the Democratic Republic of the Congo—Tin processing plants, a critical part of the tin supply chain

Summary The U.S. Geological Survey (USGS) analyzes mineral and metal supply chains to identify and describe major components of material flows from ore extraction, through intermediate forms, to a final product. Supply chain analyses may be used (1) to identify risks to the United States associated with the supply of critical and strategic minerals and metals and (2) to provide greater supply chain transparency so that policymakers have the fact-based information needed to formulate public policy. This fact sheet focuses on the post-mining/pre-consumer-product part of the tin supply chain. The USGS National Minerals Information Center (NMIC) has been asked by governmental and non-governmental organizations to provide information about tantalum, tin, tungsten, and gold (collectively known as “3TG minerals”) processing facilities worldwide in response to U.S. legislation aimed at identifying and removing the supply chain links between the trade in these minerals and civil unrest in the Democratic Republic of the Congo (DRC) and adjacent countries. Post-beneficiation processing plants (generally called smelters and refineries) for 3TG mineral ores and concentrates were identified by company and industry association representatives as being a link in the 3TG mineral supply chain through which these minerals can be traced to their source of origin (mine). The determination of the source of origin is critical to the development of a complete and transparent conflict-free mineral supply chain. Tungsten processing plants were the subject of the first fact sheet in this series published by the USGS NMIC in August 2014. Background information about historical conditions and multinational stakeholders’ voluntary due diligence guidance for minerals from conflict-affected and high-risk areas was presented in the tungsten fact sheet. Tantalum processing plants were the subject of the second fact sheet in this series published by the USGS NMIC in December 2014. This fact sheet, the third in the series about 3TG minerals, focuses on the tin supply chain by listing selected processors that produced tin materials commercially worldwide during 2013–14. It does not provide any information regarding the sources of the material processed in these facilities.

Fact Sheet↗

USGS2000

Acoustic Doppler Current Profiler Data Processing System manual [ADCP]

This open-file report describes the data processing software currently in use by the U.S. Geological Survey (USGS), Woods Hole Coastal and Marine Science Center (WHCMSC), to process time series of acoustic Doppler current data obtained by Teledyne RD Instruments Workhorse model ADCPs. The Sediment Transport Instrumentation Group (STG) at the WHCMSC has a long-standing commitment to providing scientists high quality oceanographic data published in a timely manner. To meet this commitment, STG has created this software to aid personnel in processing and reviewing data as well as evaluating hardware for signs of instrument malfunction. The output data format for the data is network Common Data Form (netCDF), which meets USGS publication standards. Typically, ADCP data are recorded in beam coordinates. This conforms to the USGS philosophy to post-process rather than internally process data. By preserving the original data quality indicators as well as the initial data set, data can be evaluated and reprocessed for different types of analyses. Beam coordinate data are desirable for internal and surface wave experiments, for example. All the code in this software package is intended to run using the MATLAB program available from The Mathworks, Inc. As such, it is platform independent and can be adapted by the USGS and others for specialized experiments with non-standard requirements. The software is continuously being updated and revised as improvements are required. The most recent revision may be downloaded from: http://woodshole.er.usgs.gov/operations/stg/Pubs/ADCPtools/adcp_index.htm The USGS makes this software available at the user?s discretion and responsibility.

Open-File Report↗

USGS2007

Coastal processes study at Ocean Beach, San Francisco, CA: Summary of data collection 2004-2006

Ocean Beach in San Francisco, California, contains a persistent erosional section in the shadow of the San Francisco ebb tidal delta and south of Sloat Boulevard that threatens valuable public infrastructure as well as the safe recreational use of the beach. Coastal managers have been discussing potential mediation measures for over a decade, with little scientific research available to aid in decision making. The United States Geological Survey (USGS) initiated the Ocean Beach Coastal Processes Study in April 2004 to provide the scientific knowledge necessary for coastal managers to make informed management decisions. This study integrates a wide range of field data collection and numerical modeling techniques to document nearshore sediment transport processes at the mouth of San Francisco Bay, with emphasis on how these processes relate to erosion at Ocean Beach. The Ocean Beach Coastal Processes Study is the first comprehensive study of coastal processes at the mouth of San Francisco Bay.

California↗

USGS2008

TSPP - A collection of FORTRAN programs for processing and manipulating time series

This report lists a number of FORTRAN programs that I have developed over the years for processing and manipulating strong-motion accelerograms. The collection is titled TSPP, which stands for Time Series Processing Programs. I have excluded 'strong-motion accelerograms' from the title, however, as the boundary between 'strong' and 'weak' motion has become blurred with the advent of broadband sensors and high-dynamic range dataloggers, and many of the programs can be used with any evenly spaced time series, not just acceleration time series. This version of the report is relatively brief, consisting primarily of an annotated list of the programs, with two examples of processing, and a few comments on usage. I do not include a parameter-by-parameter guide to the programs. Future versions might include more examples of processing, illustrating the various parameter choices in the programs. Although these programs have been used by the U.S. Geological Survey, no warranty, expressed or implied, is made by the USGS as to the accuracy or functioning of the programs and related program material, nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith. The programs are distributed on an 'as is' basis, with no warranty of support from me. These programs were written for my use and are being publicly distributed in the hope that others might find them as useful as I have. I would, however, appreciate being informed about bugs, and I always welcome suggestions for improvements to the codes. Please note that I have made little effort to optimize the coding of the programs or to include a user-friendly interface (many of the programs in this collection have been included in the software usdp (Utility Software for Data Processing), being developed by Akkar et al. (personal communication, 2008); usdp includes a graphical user interface). Speed of execution has been sacrificed in favor of a code that is intended to be easy to understand, although on modern computers speed of execution is rarely a problem. I will be pleased if users incorporate portions of my programs into their own applications; I only ask that reference be made to this report as the source of the programs.

Open-File Report↗

USGS2009

An Excel Workbook for Identifying Redox Processes in Ground Water

The reduction/oxidation (redox) condition of ground water affects the concentration, transport, and fate of many anthropogenic and natural contaminants. The redox state of a ground-water sample is defined by the dominant type of reduction/oxidation reaction, or redox process, occurring in the sample, as inferred from water-quality data. However, because of the difficulty in defining and applying a systematic redox framework to samples from diverse hydrogeologic settings, many regional water-quality investigations do not attempt to determine the predominant redox process in ground water. Recently, McMahon and Chapelle (2008) devised a redox framework that was applied to a large number of samples from 15 principal aquifer systems in the United States to examine the effect of redox processes on water quality. This framework was expanded by Chapelle and others (in press) to use measured sulfide data to differentiate between iron(III)- and sulfate-reducing conditions. These investigations showed that a systematic approach to characterize redox conditions in ground water could be applied to datasets from diverse hydrogeologic settings using water-quality data routinely collected in regional water-quality investigations. This report describes the Microsoft Excel workbook, RedoxAssignment_McMahon&Chapelle.xls, that assigns the predominant redox process to samples using the framework created by McMahon and Chapelle (2008) and expanded by Chapelle and others (in press). Assignment of redox conditions is based on concentrations of dissolved oxygen (O2), nitrate (NO3-), manganese (Mn2+), iron (Fe2+), sulfate (SO42-), and sulfide (sum of dihydrogen sulfide [aqueous H2S], hydrogen sulfide [HS-], and sulfide [S2-]). The logical arguments for assigning the predominant redox process to each sample are performed by a program written in Microsoft Visual Basic for Applications (VBA). The program is called from buttons on the main worksheet. The number of samples that can be analyzed is only limited by the number of rows in Excel (65,536 for Excel 2003 and XP; and 1,048,576 for Excel 2007), and is therefore appropriate for large datasets.

Open-File Report↗

USGS1978

Impact of coastal processes on resource development with an example from Icy Bay, Alaska

The coastline of Alaska is dynamic and continually readjusting to changes in the many processes that operate in the coastal zone. Because of this dynamic nature, special consideration must be made in planning for development, and. caution must be exercised in site selection for facilities to be emplaced in the coastal zone. All types of coastal processes from continuously active normal processes to the low frequency-high intensity rare event must be considered. Site-specific evaluation-s considering the broad range of possible processes must precede initiation of development. An example of the relation between coastal processes and a proposed resource treatment facility is presented for Icy Bay, Alaska. Icy Bay is the only sheltered bay near many of the offshore tracts leased for petroleum exploration in the 1976 northern Gulf of Alaska OCS (Outer Continental Shelf) lease sale. Consequently, it has been selected as a primary onshore staging site for the support of offshore exploration and development. The environment of Icy Bay has many potentially hazardous features, including a submarine moraine at the bay mouth and actively calving glaciers at the bay's head which produce many icebergs. But most significant from the point of view of locating onshore facilities and pipeline corridors are the high rates of shoreline erosion and sediment deposition. If pipelines or any onshore staging facilities are to be placed in the coastal areas of Icy Bay, then the dynamic changes in shoreline position must be considered so that man-made structures will not be eroded away or be silted in before the completion of development.

Open-File Report↗