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USGS2017

Acoustic telemetry and fisheries management

This paper reviews the use of acoustic telemetry as a tool for addressing issues in fisheries management, and serves as the lead to the special Feature Issue of Ecological Applications titled “Acoustic Telemetry and Fisheries Management” . Specifically, we provide an overview of the ways in which acoustic telemetry can be used to inform issues central to the ecology, conservation, and management of exploited and/or imperiled fish species. Despite great strides in this area in recent years, there are comparatively few examples where data have been applied directly to influence fisheries management and policy. We review the literature on this issue, identify the strengths and weaknesses of work done to date, and highlight knowledge gaps and difficulties in applying empirical fish telemetry studies to fisheries policy and practice. We then highlight the key areas of management and policy addressed, as well as the challenges that needed to be overcome to do this. We conclude with a set of recommendations about how researchers can, in consultation with stock assessment scientists and managers, formulate testable scientific questions to address and design future studies to generate data that can be used in a meaningful way by fisheries management and conservation practitioners. We also urge the involvement of relevant stakeholders (managers, fishers, conservation societies, etc.) early on in the process (i.e. in the co-creation of research projects), so that all priority questions and issues can be addressed effectively.

Ecological Applications↗

USGS2013

Sediment transport in the San Francisco Bay Coastal System: An overview

The papers in this special issue feature state-of-the-art approaches to understanding the physical processes related to sediment transport and geomorphology of complex coastal-estuarine systems. Here we focus on the San Francisco Bay Coastal System, extending from the lower San Joaquin-Sacramento Delta, through the Bay, and along the adjacent outer Pacific Coast. San Francisco Bay is an urbanized estuary that is impacted by numerous anthropogenic activities common to many large estuaries, including a mining legacy, channel dredging, aggregate mining, reservoirs, freshwater diversion, watershed modifications, urban run-off, ship traffic, exotic species introductions, land reclamation, and wetland restoration. The Golden Gate strait is the sole inlet connecting the Bay to the Pacific Ocean, and serves as the conduit for a tidal flow of ~ 8 x 109 m 3 /day, in addition to the transport of mud, sand, biogenic material, nutrients, and pollutants. Despite this physical, biological and chemical connection, resource management and prior research have often treated the Delta, Bay and adjacent ocean as separate entities, compartmentalized by artificial geographic or political boundaries. The body of work herein presents a comprehensive analysis of system-wide behavior, extending a rich heritage of sediment transport research that dates back to the groundbreaking hydraulic mining-impact research of G.K. Gilbert in the early 20th century.

California↗

USGS2009

THEMIS high-resolution digital terrain: Topographic and thermophysical mapping of Gusev Crater, Mars

We discuss a new technique to generate high-resolution digital terrain models (DTMs) and to quantitatively derive and map slope-corrected thermophysical properties such as albedo, thermal inertia, and surface temperatures. This investigation is a continuation of work started by Kirk et al. (2005), who empirically deconvolved Thermal Emission Imaging System (THEMIS) visible and thermal infrared data of this area, isolating topographic information that produced an accurate DTM. Surface temperatures change as a function of many variables such as slope, albedo, thermal inertia, time, season, and atmospheric opacity. We constrain each of these variables to construct a DTM and maps of slope-corrected albedo, slope- and albedo-corrected thermal inertia, and surface temperatures across the scene for any time of day or year and at any atmospheric opacity. DTMs greatly facilitate analyses of the Martian surface, and the MOLA global data set is not finely scaled enough (128 pixels per degree, ???0.5 km per pixel near the equator) to be combined with newer data sets (e.g., High Resolution Imaging Science Experiment, Context Camera, and Compact Reconnaissance Imaging Spectrometer for Mars at ???0.25, ???6, and ???20 m per pixel, respectively), so new techniques to derive high-resolution DTMs are always being explored. This paper discusses our technique of combining a set of THEMIS visible and thermal infrared observations such that albedo and thermal inertia variations within the scene are eliminated and only topographic variations remain. This enables us to produce a high-resolution DTM via photoclinometry techniques that are largely free of albedo-induced errors. With this DTM, THEMIS observations, and a subsurface thermal diffusion model, we generate slope-corrected maps of albedo, thermal inertia, and surface temperatures. In addition to greater accuracy, these products allow thermophysical properties to be directly compared with topography.

Journal of Geophysical Research E: Planets↗

USGS1904

Analyses of rocks from the laboratory of the United States Geological Survey, 1880-1903

The present Geological Survey of the United States was organized in 1879. In 1880 a chemical laboratory was established at Denver, in connection with the Colorado work, in charge of Dr. W. F. Hillebrand, with whom were associated Mr. Antony Guyard and, later, Mr. L. G. Eakins. In 1882 Dr. W. H. Melville was placed in charge of a second laboratory at San Francisco, and in the autumn of 1883 the central laboratory was started in Washington, with myself as chief chemist. In November, 1885, Doctor Hillebrand was transferred to Washington; early in 1888 he was followed by Mr. Eakins, and the Denver laboratory was discontinued. In the spring of 1890 Doctor Melville also was transferred to Washington, and since then the chemical work of the Survey has been concentrated at headquarters. Up to January 1, 1904, over 5,300 analyses have been made in the laboratory at Washington. These represent rocks, minerals, ores, waters, sediments, coals, metals, and so on through all the range of substances with which geology has to do. There were also some hundreds of analyses made in the laboratories at Denver and San Francisco. A fair amount of research work upon mineralogical and analytical problems has also been done. In all of this work the following chemists have been employed: E. T. Allen, Charles Catlett, T. M. Chatard, F. W. Clarke, L. G. Eakins, F. A. Gooch, Antony Guyard, W. F. Hillebrand, W. H. Melville, R. B. Riggs, W. T. Schaller, E. A. Schneider, George Steiger, H. N. Stokes, E. C. Sullivan, William Valentine, and J. E. Whitfield. As many as eight of these have been at work simultaneously; at present only six are connected with the Survey. Other officers of the Survey have been occupied more or less with chemical questions; but the men named in this list were connected directly with the laboratory. Some work for the chemical division has also been done by chemists not regularly on the rolls of the Survey; but their analyses, with the exception of a single group to be noted later, do not fall within the scope of this paper.

Bulletin↗

USGS1985

THREE-COMPONENT BOREHOLE MAGNETOMETER PROBE FOR MINERAL INVESTIGATIONS AND GEOLOGIC RESEARCH.

A small-diameter three-component fluxgate magnetometer probe with gyroscopic and inclinometer orientation has been developed to meet U. S. Geological Survey design and performance specifications for measurement of the direction and intensity of the Earth's magnetic field in vertical and inclined boreholes. The orthogonal fluxgate magnetometer elements have a measurement resolution of 10 nanoteslas (nT) and a range of plus or minus 80,000 nT. The gyroscope has an effective resolution of one degree, and the orthogonal inclinometers, 0. 1 degree. The magnetometer probe has been field tested in several holes drilled through volcanic rocks in Nevada. Results indicate that reversals of polarization can be detected, and some rock units in this area appear to be characterized by unique magnetic signatures.

Conference Paper↗

USGS2010

Analysis of accuracy of approximate, simultaneous, nonlinear confidence intervals on hydraulic heads in analytical and numerical test cases

Inaccuracies in parameter values, parameterization, stresses, and boundary conditions of analytical solutions and numerical models of groundwater flow produce errors in simulated hydraulic heads. These errors can be quantified in terms of approximate, simultaneous, nonlinear confidence intervals presented in the literature. Approximate confidence intervals can be applied in both error and sensitivity analysis and can be used prior to calibration or when calibration was accomplished by trial and error. In this paper, the method is expanded for use in numerical problems, and the accuracy of the approximate intervals is evaluated using Monte Carlo runs. Four test cases are used to compare results. In two numerical test cases, the approximate, simultaneous confidence intervals are generally accurate and are calculated efficiently enough to indicate that the method is useful for real-world problems. In one of the two analytical test cases considered, the approximate intervals are too wide to be of practical interest. Improving the method used to approximate the uncertainty of the model inputs could make the confidence intervals useful in more problems.

Water Resources Research↗

USGS2015

Identifying the location and population served by domestic wells in California

Study region California, USA. Study focus Identification of groundwater use is an important step in the regional-scale assessment of groundwater quality. In California, 1990 US Census data indicate that domestic wells provide drinking-water to about 1.2 million people. However, the location of these domestic well users of groundwater is poorly identified because the census tracts can be quite large (up to 20,000 km 2 ). The purposes of this paper are to present methods used for (1) estimating the location of domestic wells, (2) estimating the location of households using domestic well water; and (3) identifying where in California groundwater is an important source of domestic drinking supply. New hydrological insights for the region Aggregating the results indicates that three hydrogeologic provinces contain nearly 80% of all domestic wells and also have the highest density of domestic well users: Central Valley (31.6%), Sierra Nevada (31.5%), and Northern Coast Ranges (16.6%). Results were also aggregated into groundwater basins and highland areas, collectively called Groundwater Units (GUs). Twenty-eight of the 938 GUs contain more than 50% of the total population served by domestic wells, 70 GUs contain more than 75%, and 150 GUs contain 90%. The 28 GUs are mostly located in the eastern and southern San Joaquin Valley (11), the Sacramento Valley (7), and the western foothills of the Sierra Nevada province (5). Using the information presented in this research along with other information about domestic-well use, the US Geological Survey has begun sampling high-use GUs for the Shallow Aquifer Assessment component of the Groundwater Ambient Assessment (GAMA) program.

California↗

USGS2022

Fundamental science and engineering questions in planetary cave exploration

Nearly half a century ago, two papers postulated the likelihood of lunar lava tube caves using mathematical models. Today, armed with an array of orbiting and fly-by satellites and survey instrumentation, we have now acquired cave data across our solar system—including the identification of potential cave entrances on the Moon, Mars, and at least six other planetary bodies. These discoveries gave rise to the study of planetary caves. To help advance this field, we leveraged the expertise of an interdisciplinary group to identify a strategy to explore caves beyond Earth. Focusing primarily on astrobiology, the cave environment, geology, robotics, instrumentation, and human exploration, our goal was to produce a framework to guide this subdiscipline through at least the next decade. To do this, we first assembled a list of 198 science and engineering questions. Then, through a series of social surveys, 114 scientists and engineers winnowed down the list to the top 53 highest priority questions. This exercise resulted in identifying emerging and crucial research areas that require robust development to ultimately support a robotic mission to a planetary cave—principally the Moon and/or Mars. With the necessary financial investment and institutional support, the research and technological development required to achieve these necessary advancements over the next decade are attainable. Subsequently, we will be positioned to robotically examine lunar caves and search for evidence of life within martian caves; in turn, this will set the stage for human exploration and potential habitation of both the lunar and martian subsurface.

JGR Planets↗

USGS2010

Estimation of accumulation parameters for urban runoff quality modeling

Many recently developed watershed models utilize accumulation and washoff equations to simulate the quality of runofffrom urban impervious areas. These models often have been calibrated by trial and error and with little understanding of model sensitivity to the various parameters. Methodologies for estimating best fit values of the washoff parameters commonly used in these models have been presented previously. In this paper, parameter identification techniques for estimating the accumulation parameters from measured runoff quality data are presented along with a sensitivity analysis of the parameters. Results from application of the techniques and the sensitivity analysis suggest a need for data quantifying the magnitude and identifying the shape of constituent accumulation curves. An exponential accumulation curve is shown to be more general than the linear accumulation curves used in most urban runoff quality models. When determining accumulation rates, attention needs to be given to the effects of residual amounts of constituents remaining after the previous period of storm runoff or street sweeping.

Water Resources Research↗

USGS1984

U. S. GEOLOGICAL SURVEY'S RESEARCH PROGRAM IN THE NEWLY PROCLAIMED EXCLUSIVE ECONOMIC ZONE.

The U. S. Geological Survey (USGS) has been developing a program which would emphasize broad-scale surveys of the continental margin and intensive studies of 'baseline corridors' in various areas of the U. S. EEZ to gather energy and mining information in this new frontier as quickly as possible. Of twelve baseline corridors identified to date along the east and west coasts and the Gulf of Mexico, the highest priority would be placed on areas off the west coast, including Juan De Fuca and Gorda Ridges and off Hawaii. Each corridor assessment will involve collection of multi-channel and high resolution geophysical data, bottom relief and sampling, and production of reports and cartographic products displaying the scientific findings of the assessments.

Conference Paper↗

USGS2013

Review of the negative influences of non-native salmonids on native fish species

Non-native salmonids are often introduced into areas containing species of concern, yet a comprehensive overview of the short- and long-term consequences of these introductions is lacking in the Great Plains. Several authors have suggested that non-native salmonids negatively inflfluence species of concern. The objective of this paper is to review known interactions between non-native salmonids and native fifishes, with a focus on native species of concern. After an extensive search of the literature, it appears that in many cases non-native salmonids do negatively inflfl uence species of concern (e.g., reduce abundance and alter behavior) via different mechanisms (e.g., predation and competition). However, there are some instances in which introduced salmonids have had no perceived negative inflfl uence on native fifi shes. Unfortunately, the majority of the literature is circumstantial, and there is a need to experimentally manipulate these interactions.

Great Plains Research↗

USGS1985

Research on Alaskan polar bears in 1979 and 1980

In 1979 the U.S. Fish and Wildlife Service continued its program of mark and recapture. From 31 March to 4 May field crews working at Point Barrow, Alaska, captured and marked a total of 15 polar bears (Table I). The small number was due to very poor ice conditions off the coast of Alaska, making tracking and capturing difficult. Four of the bears were recaptures from previous years. In addition, as part of a multi-national program (Canada, U.S., Norway) satellite transmitters were attached to 3 adult female polar bears in the hopes of tracking them to their dens the following winter. However, due to mechanical and operational difficulties, very little information was acquired in the Alaskan sector of the project.

Alaska↗

USGS2019

Integrating the sociology of space with geospatial semantics relation properties for data graphs

This research posits that socially constructed spatial relations address concepts of interactions instead of intersections, human/tool agents instead of physical processes, and broader ranges of geographical outcomes. The hypothesis is that social space can be represented by using patterns of logic relations between sets of entities. The data corpus of spatial relations was extracted from geographic term definitions. The relations were further analyzed as primitives using Case Grammar Matrix models. These findings are being related to Web Ontology Language (OWL) properties. This approach allows an extensive range of natural language terms to instantiate ontology sub-types, while supporting inferences to study their logical implications.

Conference Paper↗

USGS2001

Model coupling intraparticle diffusion/sorption, nonlinear sorption, and biodegradation processes

Diffusion, sorption and biodegradation are key processes impacting the efficiency of natural attenuation. While each process has been studied individually, limited information exists on the kinetic coupling of these processes. In this paper, a model is presented that couples nonlinear and nonequilibrium sorption (intraparticle diffusion) with biodegradation kinetics. Initially, these processes are studied independently (i.e., intraparticle diffusion, nonlinear sorption and biodegradation), with appropriate parameters determined from these independent studies. Then, the coupled processes are studied, with an initial data set used to determine biodegradation constants that were subsequently used to successfully predict the behavior of a second data set. The validated model is then used to conduct a sensitivity analysis, which reveals conditions where biodegradation becomes desorption rate-limited. If the chemical is not pre-equilibrated with the soil prior to the onset of biodegradation, then fast sorption will reduce aqueous concentrations and thus biodegradation rates. Another sensitivity analysis demonstrates the importance of including nonlinear sorption in a coupled diffusion/sorption and biodegradation model. While predictions based on linear sorption isotherms agree well with solution concentrations, for the conditions evaluated this approach overestimates the percentage of contaminant biodegraded by as much as 50%. This research demonstrates that nonlinear sorption should be coupled with diffusion/sorption and biodegradation models in order to accurately predict bioremediation and natural attenuation processes. To our knowledge this study is unique in studying nonlinear sorption coupled with intraparticle diffusion and biodegradation kinetics with natural media.

Journal of Contaminant Hydrology↗

USGS1999

Effects of sample size on kernel home range estimates

Kernel methods for estimating home range are being used increasingly in wildlife research, but the effect of sample size on their accuracy is not known. We used computer simulations of 10-200 points/home range and compared accuracy of home range estimates produced by fixed and adaptive kernels with the reference (REF) and least-squares cross-validation (LSCV) methods for determining the amount of smoothing. Simulated home ranges varied from simple to complex shapes created by mixing bivariate normal distributions. We used the size of the 95% home range area and the relative mean squared error of the surface fit to assess the accuracy of the kernel home range estimates. For both measures, the bias and variance approached an asymptote at about 50 observations/home range. The fixed kernel with smoothing selected by LSCV provided the least-biased estimates of the 95% home range area. All kernel methods produced similar surface fit for most simulations, but the fixed kernel with LSCV had the lowest frequency and magnitude of very poor estimates. We reviewed 101 papers published in The Journal of Wildlife Management (JWM) between 1980 and 1997 that estimated animal home ranges. A minority of these papers used nonparametric utilization distribution (UD) estimators, and most did not adequately report sample sizes. We recommend that home range studies using kernel estimates use LSCV to determine the amount of smoothing, obtain a minimum of 30 observations per animal (but preferably a?Y50), and report sample sizes in published results.

Journal of Wildlife Management↗

USGS2022

Subsampling large-scale digital elevation models to expedite geospatial analyses in coastal regions

Large-area, high-resolution digital elevation models (DEMs) created from light detection and ranging (LIDAR) and/or multibeam echosounder data sets are commonly used in many scientific disciplines. These DEMs can span thousands of square kilometers, typically with a spatial resolution of 1 m or finer, and can be difficult to process and analyze without specialized computers and software. Such DEMs often can be subsampled to expedite analysis with negligible impact on results for large-scale geospatial analyses. Subsampling can be achieved by creating a grid of points that specify the locations from which to extract elevation values from the DEM. This paper presents a method that can be used to accurately perform subsampling of large-scale, high-resolution DEMs using GIS software. This subsampling method was applied to two LIDAR-derived DEMs encompassing 242 km 2 of the northern Florida Reef Tract as an example application and to test subsampling accuracy. Results indicate that subsampling 1-m-resolution DEMs using a 2-m-spaced grid results in no significant difference in mean elevation or other basic statistics for analyses performed over multiple spatial scales ranging from 1 km 2 to 242 km 2 .

Journal of Coastal Research↗

USGS1985

A relational approach to vector data structure conversion

The proliferation of geographic information systems and digital data bases is creating a need for efficient methods to convert data from one spatial data structure to another. One approach is to create ad hoc interfaces, with a potential of N(N-1) interfaces for N data structures. Using an intermediate data structure, at most 2N interfaces are required. An intermediate relational data structure is therefore proposed that takes the form of a set of normalized relations stored in a relational information management system. The advantages of this approach are found in the simplicity of the relational approach, and the availability of relational operators to be used as higher level tools, to convert from and to the relational data structure. The Relational Information Management System (RIM) is used for the ongoing research. In conjunction with the relational data structure, another higher level tool has been developed to cope with linked lists, tree structures, vectors, and matrices, which are not otherwise easily reduced. This data tracking system is programmable at a higher level, in a syntax that allows a concise expression of the desired restructuring. Output from this system can be further operated on by relational operators to arrive at the desired intermediate data structure. This, and other topology verification and checking tools, are visualized as part of a core system dedicated to the conversion and collation of spatial data from diverse origins.

Conference Paper↗

USGS2020

Detecting commonality in multidimensional fish movement histories using sequence analysis

Background Acoustic telemetry, for tracking fish movement histories, is multidimensional capturing both spatial and temporal domains. Oftentimes, analyses of such data are limited to a single domain, one domain nested within the other, or ad hoc approaches that simultaneously consider both domains. Sequence analysis, on the other hand, offers a repeatable statistical framework that uses a sequence alignment algorithm to calculate pairwise dissimilarities among individual movement histories and then hierarchical agglomerative clustering to identify groups of fish with similar movement histories. The objective of this paper is to explore how acoustic telemetry data can be fit to this statistical framework and used to identify commonalities in the movement histories of acoustic-tagged sea lamprey during upstream migration through the St. Clair-Detroit River System. Results Five significant clusters were identified among individual fish. Clusters represented differences in timing of movements (short vs long duration in the Detroit R. and Lake St. Clair); extent of upstream migration (ceased migration in Lake St. Clair, lower St. Clair R., or upper St. Clair R.), and occurrence of fallback (return to Lake St. Clair after ceasing migration in the St. Clair R.). Inferences about sea lamprey distribution and behavior from these results were similar to those reached in a previous analysis using ad-hoc analysis methods. Conclusions The repeatable statistical framework outlined here can be used to group sea lamprey movement histories based on shared sequence characteristics (i.e., chronological order of “states” occupied). Further, this framework is flexible and allows researchers to define a priori the movement aspect (e.g., order, timing, duration) that is important for identifying both common or previously undetected movement histories. As such, we do not view sequence analysis as a panacea but as a useful complement to other modelling approaches (i.e., exploratory tool for informing hypothesis development) or a stand-alone semi-quantitative method for generating a simplified, temporally and spatially structured view of complex acoustic telemetry data and hypothesis testing when observed patterns warrant further investigation.

Michigan↗