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USGS2016

National protocol framework for the inventory and monitoring of bees

This national protocol framework is a standardized tool for the inventory and monitoring of the approximately 4,200 species of native and non-native bee species that may be found within the National Wildlife Refuge System (NWRS) administered by the U.S. Fish and Wildlife Service (USFWS). However, this protocol framework may also be used by other organizations and individuals to monitor bees in any given habitat or location. Our goal is to provide USFWS stations within the NWRS (NWRS stations are land units managed by the USFWS such as national wildlife refuges, national fish hatcheries, wetland management districts, conservation areas, leased lands, etc.) with techniques for developing an initial baseline inventory of what bee species are present on their lands and to provide an inexpensive, simple technique for monitoring bees continuously and for monitoring and evaluating long-term population trends and management impacts. The latter long-term monitoring technique requires a minimal time burden for the individual station, yet can provide a good statistical sample of changing populations that can be investigated at the station, regional, and national levels within the USFWS’ jurisdiction, and compared to other sites within the United States and Canada. This protocol framework was developed in cooperation with the United States Geological Survey (USGS), the USFWS, and a worldwide network of bee researchers who have investigated the techniques and methods for capturing bees and tracking population changes. The protocol framework evolved from field and lab-based investigations at the USGS Bee Inventory and Monitoring Laboratory at the Patuxent Wildlife Research Center in Beltsville, Maryland starting in 2002 and was refined by a large number of USFWS, academic, and state groups. It includes a Protocol Introduction and a set of 8 Standard Operating Procedures or SOPs and adheres to national standards of protocol content and organization. The Protocol Narrative describes the history and need for the protocol framework and summarizes the basic elements of objectives, sampling design, field methods, training, data management, analysis, and reporting. The SOPs provide more detail and specific instructions for implementing the protocol framework. A central database, for managing all the resulting data is under development. We welcome use of this protocol framework by our partners, as appropriate for their bee inventory and monitoring objectives.

Report↗

USGS1987

Stochastic simulation of spatially correlated geo-processes

In this study, developments in the theory of stochastic simulation are discussed. The unifying element is the notion of Radon projection in Euclidean spaces. This notion provides a natural way of reconstructing the real process from a corresponding process observable on a reduced dimensionality space, where analysis is theoretically easier and computationally tractable. Within this framework, the concept of space transformation is defined and several of its properties, which are of significant importance within the context of spatially correlated processes, are explored. The turning bands operator is shown to follow from this. This strengthens considerably the theoretical background of the geostatistical method of simulation, and some new results are obtained in both the space and frequency domains. The inverse problem is solved generally and the applicability of the method is extended to anisotropic as well as integrated processes. Some ill-posed problems of the inverse operator are discussed. Effects of the measurement error and impulses at origin are examined. Important features of the simulated process as described by geomechanical laws, the morphology of the deposit, etc., may be incorporated in the analysis. The simulation may become a model-dependent procedure and this, in turn, may provide numerical solutions to spatial-temporal geologic models. Because the spatial simu??lation may be technically reduced to unidimensional simulations, various techniques of generating one-dimensional realizations are reviewed. To link theory and practice, an example is computed in detail. ?? 1987 International Association for Mathematical Geology.

Mathematical Geology↗

USGS2010

Measurement of dissolved organic matter fluorescense in aquatic environments: An interlaboratory comparison

The fluorescent properties of dissolved organic matter (DOM) are often studied in order to infer DOM characteristics in aquatic environments, including source, quantity, composition, and behavior. While a potentially powerful technique, a single widely implemented standard method for correcting and presenting fluorescence measurements is lacking, leading to difficulties when comparing data collected by different research groups. This paper reports on a large-scale interlaboratory comparison in which natural samples and well-characterized fluorophores were analyzed in 20 laboratories in the U.S., Europe, and Australia. Shortcomings were evident in several areas, including data quality-assurance, the accuracy of spectral correction factors used to correct EEMs, and the treatment of optically dense samples. Data corrected by participants according to individual laboratory procedures were more variable than when corrected under a standard protocol. Wavelength dependency in measurement precision and accuracy were observed within and between instruments, even in corrected data. In an effort to reduce future occurrences of similar problems, algorithms for correcting and calibrating EEMs are described in detail, and MATLAB scripts for implementing the study's protocol are provided. Combined with the recent expansion of spectral fluorescence standards, this approach will serve to increase the intercomparability of DOM fluorescence studies.

Environmental Science & Technology↗

USGS1983

Hole-to-surface resistivity measurements

Hole-to-surface resistivity measurements over a layered volcanic tuff sequence illustrate procedures for gathering, reducing, and interpreting hole-to-surface resistivity data. The magnitude and direction of the total surface electric field resulting from a buried current source is calculated from orthogonal potential difference measurements for a grid of closely spaced stations. A contour map of these data provides a detailed map of the distribution of the electric field away from the drill hole. Resistivity anomalies can be enhanced by calculating the difference between apparent resistivities calculated from the total surface electric field and apparent resistivities for a layered earth model.Lateral discontinutities in the geoelectric section are verified by repeating the surface field measurments for current sources in several drill holes. A qualitative interpretation of the anomalous bodies within a layered earth can be made by using a three-dimensional (3-D) resistivity model in a homogeneous half-space. The general nature of resistive and conductive bodies causing anomalies away from the source drill holes is determined with the aid of data from several source holes, layered models, and 3-D models.

Geophysics↗

USGS1964

Methods of determining permeability, transmissibility and drawdown

If the Theis graphical method is used for determining the hydraulic constants of an aquifer under water-table conditions, the observed drawdowns should be corrected for the decrease in saturated thickness. This is especially true if the drawdown is a large fraction of the original saturated thickness, for then the computed coefficient of permeability is highly inaccurate if based on observed, rather than corrected, water levels. Wenzel's limiting formula, a modification of the Theis graphical method, is useful where u=r2s/4Tt is less than about 0.01. However, a shorter procedure for determination of the coefficient of transmissibility, as well as the coefficient of storage, consists of plotting the values of the corrected drawdowns against the values of the logarithm of r. Wenzel (1942) suggested that observation wells be situated on lines that extend upgradient and downgradient from the pumped well. However, a detailed analysis of aquifer-test results indicates that such a restriction is unnecessary. The gradient method for determining permeability should yield the same results as the Thies method. The former, when applied for a distance within the range of applicability of the latter, is merely a duplication of effort or, at best, a crude check. Because of the limitations of accuracy in plotting, the gradient method is much less satisfactory. That Wenzel (1942) obtained identical results from the two methods is regarded as a coincidence. Failure to take into consideration the fact that the pumped well does not tap the full thickness of the aquifer leads to an apparent coefficient of permeability that is much too low, especially if the aquifer consists of stratified sediments. The average coefficient of permeability computed from uncorrected drawdowns may be only a little more than half of the true value.

Water Supply Paper↗

USGS1973

Imaging characteristics of photogrammetric camera systems

In view of the current interest in high-altitude and space photographic systems for photogrammetric mapping, the United States Geological Survey (U.S.G.S.) undertook a comprehensive research project designed to explore the practical aspects of applying the latest image quality evaluation techniques to the analysis of such systems. The project had two direct objectives: (1) to evaluate the imaging characteristics of current U.S.G.S. photogrammetric camera systems; and (2) to develop methodologies for predicting the imaging capabilities of photogrammetric camera systems, comparing conventional systems with new or different types of systems, and analyzing the image quality of photographs. Image quality was judged in terms of a number of evaluation factors including response functions, resolving power, and the detectability and measurability of small detail. The limiting capabilities of the U.S.G.S. 6-inch and 12-inch focal length camera systems were established by analyzing laboratory and aerial photographs in terms of these evaluation factors. In the process, the contributing effects of relevant parameters such as lens aberrations, lens aperture, shutter function, image motion, film type, and target contrast procedures for analyzing image quality and predicting and comparing performance capabilities.

Photogrammetria↗

USGS2007

Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User's Guide

In order to standardize methods and facilitate rapid calculation and archival of stream-metabolism variables, the Stream Metabolism Program was developed to calculate gross primary production, net ecosystem production, respiration, and selected other variables from continuous measurements of dissolved-oxygen concentration, water temperature, and other user-supplied information. Methods for calculating metabolism from continuous measurements of dissolved-oxygen concentration and water temperature are fairly well known, but a standard set of procedures and computation software for all aspects of the calculations were not available previously. The Stream Metabolism Program addresses this deficiency with a stand-alone executable computer program written in Visual Basic.NET?, which runs in the Microsoft Windows? environment. All equations and assumptions used in the development of the software are documented in this report. Detailed guidance on application of the software is presented, along with a summary of the data required to use the software. Data from either a single station or paired (upstream, downstream) stations can be used with the software to calculate metabolism variables.

Techniques and Methods↗

USGS1970

Salmonid viruses: Double infection of RTG-2 cells with Egtved and infectious pancreatic necrosis viruses

Egtved and infectious pancreatic necrosis (IPN) viruses were applied at high multiplicity alone and in combination to RTG-2 cells in liquid medium. Procedures were used which selectively suppressed one or the other virus, and the yields were determined after 64 hours at 15°C. The viruses showed an increase of 280 to 450 times the immediate post-adsorption level. Plaques of IPN and Egtved viruses showed some differences which can be helpful in distinguishing between the two agents. Detailed methods and results are given.

Archiv Fur Die Gesamte Virusforschung↗

USGS2002

Quantitative radiochemical methods for determination of the sources of natural radioactivity

Study of the state of equilibrium of any natural radioactive source requires determination of several key nuclides or groups of nuclides to find their contribution to the total amount of radioactivity. Alpha activity measured by scintillation counting is used for determination of protactinium-231, thorium-232, thorium-230, and radium-226. The chemical procedures for the separations of the specific elements are described, as well as the measurement techniques used to determine the abundances of the individual isotopes. To correct for deviations in the ore standards, an independent means of evaluating the efficiencies of the individual separations and measurements is used. The development of these methods of radiochemical analysis facilitates detailed investigation of the major sources of natural radioactivity.

Analytical Chemistry↗

USGS2008

Procedures for collecting and processing streambed sediment and pore water for analysis of mercury as part of the National Water-Quality Assessment Program

Mercury (Hg) contamination is an issue of national concern, affecting both wildlife and human health. The U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) Program, in association with the USGS Toxic Substances Hydrology Program and the USGS National Research Program, has initiated two levels of studies to investigate Hg contamination of the Nation's streams: reconnaissance and detailed studies. Reconnaissance studies entailed one-time sampling events at 266 stream sites across the Nation. Detailed studies entailed intensive spatial and temporal sampling of a small number of streams across the Nation in an effort to develop a more complete, process-level understanding of benthic Hg geochemistry and the underlying factors controlling it. This report summarizes the sampling methods used for the collection and processing of streambed sediment and pore water in association with both of these study levels. Bed-sediment characteristics, such as organic content and grain size, strongly influence Hg geochemistry; detailed characterization of these constituents within a stream reach will allow for the extrapolation of related Hg biogeochemical constituents to the reach scale.

Open-File Report↗

USGS2001

Three-dimenstional crustal velocity structure beneath the Strait of Georgia, British Columbia

The Strait of Georgia is a topographic depression straddling the boundary between the Insular and Coast belts in southwestern British Columbia. Two shallow earthquakes located within the strait ( M = 4.6 in 1997 and M = 5.0 in 1975) and felt throughout the Vancouver area illustrate the seismic potential of this region. As part of the 1998 Seismic Hazards Investigation of Puget Sound (SHIPS) experiment, seismic instruments were placed in and around the Strait of Georgia to record shots from a marine source within the strait. We apply a tomographic inversion procedure to first-arrival traveltime data to derive a minimum-structure 3-D P -wave velocity model for the upper crust to about 13 km depth. We also present a 2-D velocity model for a profile orientated across the Strait of Georgia derived using a minimum-parameter traveltime inversion approach. This paper represents the first detailed look at crustal velocity variations within the major Cretaceous to Cenozoic Georgia Basin, which underlies the Strait of Georgia. The 3-D velocity model clearly delineates the structure of the Georgia Basin. Taking the 6 km s −1 isovelocity contour to represent the top of the underlying basement, the basin thickens from between 2 and 4 km in the northwestern half of the strait to between 8 and 9 km at the southeastern end of the study region. Basin velocities in the northeastern half are 4.5–6 km s −1 and primarily represent the Upper Cretaceous Nanaimo Group. Velocities to the south are lower (3–6 km s −1 ) because of the additional presence of the overlying Tertiary Huntingdon Formation and more recent sediments, including glacial and modern Fraser River deposits. In contrast to the relatively smoothly varying velocity structure of the basin, velocities of the basement rocks, which comprise primarily Palaeozoic to Jurassic rocks of the Wrangellia Terrane and possibly Jurassic to mid-Cretaceous granitic rocks of the Coast Belt, show significantly more structure, probably an indication of the varying basement rock lithologies. The 2-D velocity model more clearly reveals the velocity layering associated with the recent sediments, Huntingdon Formation and Nanaimo Group of the southern Georgia Basin, as well as the underlying basement. We interpret lateral variation in sub-basin velocities of the 2-D model as a transition from Wrangellian to Coast Belt basement rocks. The effect of the narrow, onshore–offshore recording geometry of the seismic experiment on model resolution was tested to allow a critical assessment of the validity of the 3-D velocity model. Lateral resolution throughout the model to a depth of 3–5 km below the top of the basement is generally 10–20 km.

British Columbia↗

USGS2005

Augmenting two-dimensional hydrodynamic simulations with measured velocity data to identify flow paths as a function of depth on Upper St. Clair River in the Great Lakes basin

Upper St. Clair River, which receives outflow from Lake Huron, is characterized by flow velocities that exceed 7 feet per second and significant channel curvature that creates complex flow patterns downstream from the Blue Water Bridge in the Port Huron, Michigan, and Sarnia, Ontario, area. Discrepancies were detected between depth-averaged velocities previously simulated by a two-dimensional (2D) hydrodynamic model and surface velocities determined from drifting buoy deployments. A detailed ADCP (acoustic Doppler current profiler) survey was done on Upper St. Clair River during July 1–3, 2003, to help resolve these discrepancies. As part of this study, a refined finite-element mesh of the hydrodynamic model used to identify source areas to public water intakes was developed for Upper St. Clair River. In addition, a numerical procedure was used to account for radial accelerations, which cause secondary flow patterns near channel bends. The refined model was recalibrated to better reproduce local velocities measured in the ADCP survey. ADCP data also were used to help resolve the remaining discrepancies between simulated and measured velocities and to describe variations in velocity with depth. Velocity data from ADCP surveys have significant local variability, and statistical processing is needed to compute reliable point estimates. In this study, velocity innovations were computed for seven depth layers posited within the river as the differences between measured and simulated velocities. For each layer, the spatial correlation of velocity innovations was characterized by use of variogram analysis. Results were used with kriging to compute expected innovations within each layer at applicable model nodes. Expected innovations were added to simulated velocities to form integrated velocities, which were used with reverse particle tracking to identify the expected flow path near a sewage outfall as a function of flow depth. Expected particle paths generated by use of the integrated velocities showed that surface velocities in the upper layers tended to originate nearer the Canadian shoreline than velocities near the channel bottom in the lower layers. Therefore, flow paths to U.S. public water intakes located on the river bottom are more likely to be in the United States than withdrawals near the water surface. Integrated velocities in the upper layers are generally consistent with the surface velocities indicated by drifting-buoy deployments. Information in the 2D hydrodynamic model and the ADCP measurements was insufficient to describe the vertical flow component. This limitation resulted in the inability to account for vertical movements on expected flow paths through Upper St. Clair River. A three dimensional hydrodynamic model would be needed to account for these effects.

Scientific Investigations Report↗

USGS2020

Standardized guide to the examination and necropsy of the horseshoe crab using Limulus polyphemus as Limulidae prototype

The Atlantic, or American, horseshoe crab (L imulus polyphemus ) has existed largely unchanged for over 100 million years. Millions of individuals are commonly observed ashore in spring and summer months during spawning events along the entire North American coastline expanding from the East to the Gulf coasts of the United States and Mexico. Other species can be found in the Indian and Pacific Ocean. The massive deposit of eggs in nearshore sand provides a critical source of food for endangered migrating birds, especially the Red Knot ( Calidruis canutus rufa ) in the Delaware Bay. Horseshoe crabs are also an important component of the sea turtle diet. In addition to the ecological importance, horseshoe crabs are used commercially for bait in eel and conch fisheries and for biomedical purposes in the production of Limulus Amebocyte Lysate (LAL) to detect bacterial toxins in injectable drugs and implantable devices. Commercial demands have led to population declines in some regions. Fisheries are regulated by state and the current International Union for Conservation of Nature (IUCN) listing for L. polyphemus is vulnerable. A small number of individuals are housed in public aquaria for educational purposes. With growing interest in animal welfare, the health and stability of populations, and potential stressors that can contribute to decline , it is important to have clear and detailed descriptions of horseshoe crab anatomy and necropsy techniques. The purpose of this guide is to illustrate the normal anatomy and the step-by-step technique for dissection of horseshoe crabs. The contents are largely excerpts of the master’s thesis of artist, Katie (Bergdale) Roorda, which was based on photographs from C. Meteyer documenting the sequence and procedure used for necropsy dissection.

Cooperator Report↗

USGS2021

Multi-period response spectra

Multi-period response spectra (MPRS) are incorporated in the development of seismic design ground motions in the 2020 edition of the NEHRP Recommended Seismic Provisions for New Buildings and Other Structures (2020 NEHRP Provisions) and are approved for adoption in the American Society of Civil Engineers (ASCE) Standard, Minimum Design Loads and Associated Criteria for Buildings and Other Structures (ASCE/SEI 7-22). MPRS are incorporated in these design regulations because it was discovered that the standard spectral shape based on two periods and one reference site class was substantially understating spectral response in moderately long period structures located on soft soil sites where ground motion hazard is dominated by large magnitude events. These are the motions that are relevant to tall buildings in the Los Angeles region and of interest to the Los Angeles Tall Buildings Seismic Design Council (LATBSDC). The MPRS incorporation updated Chapters 11, 20, 21, and 22 of the 2020 NEHRP Provisions (a.k.a. FEMA P-2082); changes are described in detail in the commentary of FEMA P-2082. The MPRS also influenced the development of the 2018 U.S. Geological Survey (USGS) National Seismic Hazard Model (NSHM) for the conterminous U.S. because valid ground motion models for all periods and site classes of interest were required. FEMA P-2082 is complemented by the FEMA P-2078 technical report that provides a procedure for approximating MPRS outside of the conterminous U.S. This paper presents a condensed version of the relevant sections of FEMA P-2082 and FEMA P-2078 that would interest the LATBSDC.

Conference Paper↗

USGS2020

The elephant in the lab (and field): Contamination in aquatic environmental DNA studies

The rapid evolution of environmental (e)DNA methods has resulted in knowledge gaps in smaller, yet critical details like proper use of negative controls to detect contamination. Detecting contamination is vital for confident use of eDNA results in decision-making. We conducted two literature reviews to summarize (a) the types of quality assurance measures taken to detect contamination of eDNA samples from aquatic environments, (b) the occurrence, frequency and attribution (i.e., putative sources) of unexpected amplification in these quality assurance samples, and (c) how results were interpreted when contamination occurred. In the first literature review, we reviewed 156 papers and found that 91% of targeted and 73% of metabarcoding eDNA studies reported inclusion of negative controls within their workflows. However, a large percentage of targeted (49%) and metabarcoding (80%) studies only reported negative controls for laboratory procedures, so results were potentially blind to field contamination. Many of the 156 studies did not provide critical methodological information and amplification results of negative controls. In our second literature review, we reviewed 695 papers and found that 30 targeted and 32 metabarcoding eDNA studies reported amplification of negative controls. This amplification occurred at similar proportions for field and lab workflow steps in targeted and metabarcoding studies. These studies most frequently used amplified negative controls to delimit a detection threshold above which is considered significant or provided rationale for why the unexpected amplifications did not affect results. In summary, we found that there has been minimal convergence over time on negative control implementation, methods, and interpretation, which suggests that increased rigor in these smaller, yet critical details remains an outstanding need. We conclude our review by highlighting several studies that have developed especially effective quality assurance, control and mitigation methods.

Frontiers in Ecology and Evolution↗

USGS1989

Bias in groundwater samples caused by wellbore flow

Design of physical installations and sampling procedures for ground-water monitoring networks, particularly for detection and analysis of possible contaminants, is a topic of great scientific and practical interest at the present time. Recent practice in the design of monitoring networks associated with known contaminant sources sometimes includes an array of monitoring wells with long well screens (up to 50 feet or more). Numerical experiments with a detailed three-dimensional ground-water flow model indicate that significant wellbore flow can occur in contaminant monitoring wells with long well screens that are embedded in homogeneous aquifers with very small vertical head differences in the aquifer. This ``short circuiting'' of flow through boreholes should exist at some level on all scales. Consideration of the general flow pattern within the borehole, the flow pattern in the aquifer adjacent to the borehole, and the process of obtaining water samples from the borehole suggests that in many situations the practice of installing long well screens in contaminant monitoring wells should be abandoned.

Journal of Hydraulic Engineering↗

USGS2007

Theory, construction and operation of simple tensiometers

The tensiometer, introduced by Richards and Gardner (1936) has been a tool often ignored in unsaturated zone investigations. Hazardous waste disposal studies that require values of unsaturated zone matric potentials will expand tensiometer use. Familiarity with operation and installation principles is necessary to ensure quality data collection. The essential elements of a tensiometer are a porous cup connected with tubing to a vacuum gauge; all are filled with water. When the porous cup is buried in unsaturated soil, the soil draws water through the cup wall, until the water tension inside the cup equals the surrounding soil-water tension. The tension is transmitted through the water filled tube to an accessible vacuum gauge (manometer or transducer) and is recorded manually or automatically. Although specialized tensiometers exist, the tensiometer presented here in detail is suited to diverse on-site applications. Constructed from readily available, inexpensive parts, it can measure as much as 0.85 bar of tension. Design features include a flushing system for removal of entrapped air or mercury, and an easily maintained modular network of nylon manometers and water-supply tubes. Good hydraulic connection between porous cup and soil and meticulous backfill procedures are necessary for accurate measurement of representative matric potentials. Proper and consistent use of tensiometers should yield reliable values of matric potentials, and lead to a better understanding of unsaturated zone processes.

Groundwater Monitoring and Remediation↗

USGS2017

Making ecological models adequate

Critical evaluation of the adequacy of ecological models is urgently needed to enhance their utility in developing theory and enabling environmental managers and policymakers to make informed decisions. Poorly supported management can have detrimental, costly or irreversible impacts on the environment and society. Here, we examine common issues in ecological modelling and suggest criteria for improving modelling frameworks. An appropriate level of process description is crucial to constructing the best possible model, given the available data and understanding of ecological structures. Model details unsupported by data typically lead to over parameterisation and poor model performance. Conversely, a lack of mechanistic details may limit a model's ability to predict ecological systems’ responses to management. Ecological studies that employ models should follow a set of model adequacy assessment protocols that include: asking a series of critical questions regarding state and control variable selection, the determinacy of data, and the sensitivity and validity of analyses. We also need to improve model elaboration, refinement and coarse graining procedures to better understand the relevancy and adequacy of our models and the role they play in advancing theory, improving hind and forecasting, and enabling problem solving and management.

Ecology Letters↗