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USGS2003

Elevation effects in volcano applications of the COSPEC

Volcano applications commonly involve sizeable departures from the reference pressure and temperature of COSPEC calibration cells. Analysis shows that COSPEC SO2 column abundances and derived mass emission rates are independent of pressure and temperature, and thus unaffected by elevation effects related to deviations from calibration cell reference state. However, path-length concentrations are pressure and temperature dependent. Since COSPEC path-length concentration data assume the reference pressure and temperature of calibration cells, they can lead to large errors when used to calculate SO2 mixing ratios of volcanic plumes. Correction factors for COSPEC path-length concentrations become significant (c.10%) at elevations of about 1 km (e.g. Kilauea volcano) and rise rapidly to c.80% at 6 km (e.g. Cotopaxi volcano). Calculating SO2 mixing ratios for volcanic plumes directly from COSPEC path-length concentrations always gives low results. Corrections can substantially increase mixing ratios; for example, corrections increase SO2 ppm concentrations reported for the Mount St Helens, Colima, and Erebus plumes by 25-50%. Several arguments suggest it would be advantageous to calibrate COSPEC measurements in column abundance units rather than path-length concentration units.

Geological Society Special Publication↗

USGS2006

New ghost-node method for linking different models with varied grid refinement

A flexible, robust method for linking grids of locally refined ground-water flow models constructed with different numerical methods is needed to address a variety of hydrologic problems. This work outlines and tests a new ghost-node model-linking method for a refined "child" model that is contained within a larger and coarser "parent" model that is based on the iterative method of Steffen W. Mehl and Mary C. Hill (2002, Advances in Water Res., 25, p. 497-511; 2004, Advances in Water Res., 27, p. 899-912). The method is applicable to steady-state solutions for ground-water flow. Tests are presented for a homogeneous two-dimensional system that has matching grids (parent cells border an integer number of child cells) or nonmatching grids. The coupled grids are simulated by using the finite-difference and finite-element models MODFLOW and FEHM, respectively. The simulations require no alteration of the MODFLOW or FEHM models and are executed using a batch file on Windows operating systems. Results indicate that when the grids are matched spatially so that nodes and child-cell boundaries are aligned, the new coupling technique has error nearly equal to that when coupling two MODFLOW models. When the grids are nonmatching, model accuracy is slightly increased compared to that for matching-grid cases. Overall, results indicate that the ghost-node technique is a viable means to couple distinct models because the overall head and flow errors relative to the analytical solution are less than if only the regional coarse-grid model was used to simulate flow in the child model's domain.

Conference Paper↗

USGS1988

Extracting topographic structure from digital elevation data for geographic information-system analysis

Software tools have been developed at the U.S. Geological Survey's EROS Data Center to extract topographic structure and to delineate watersheds and overland flow paths from digital elevation models. The tools are specialpurpose FORTRAN programs interfaced with general-purpose raster and vector spatial analysis and relational data base management packages. The first phase of analysis is a conditioning phase that generates three data sets: the original OEM with depressions filled, a data set indicating the flow direction for each cell, and a flow accumulation data set in which each cell receives a value equal to the total number of cells that drain to it. The original OEM and these three derivative data sets can then be processed in a variety of ways to optionally delineate drainage networks, overland paths, watersheds for userspecified locations, sub-watersheds for the major tributaries of a drainage network, or pour point linkages between watersheds. The computer-generated drainage lines and watershed polygons and the pour point linkage information can be transferred to vector-based geographic information systems for futher analysis. Comparisons between these computergenerated features and their manually delineated counterparts generally show close agreement, indicating that these software tools will save analyst time spent in manual interpretation and digitizing.

Photogrammetric Engineering and Remote Sensing↗

USGS1988

Phytoplankton growth rates in a light-limited environment, San Francisco Bay

Phytoplankton cells reside in a turbulent medium partitioned into an upper photic zone that sustains photosynthesis, and a lower aphotic zone that does not. In estuaries, vertical mixing rates between these 2 zones can be rapid (< 1 generation time) because of tidal stirring and because the mixing depth is generally shallow. Moreover, the photic depth is characteristically shallow in estuaries because of the high seston concentrations that typify these systems (e.g. Cloern 1987). Hence the mean light exposure of phytoplankton cells, and their rates of photosynthesis and growth in estuaries, should be related to the ratio of photic depth Z p to mixing Z m , (defined as either the water column depth, or the surface layer depth in a stratified estuary). Grobbelar (1985) has measured phytoplankton production in turbid waters and used the ratio Z p :Z m as a simple index to quantify the degree of light limitation. Harris and his colleagues have examined in detail the importance of the Z p :Z m ratio in lakes for influencing variability of phytoplankton production and photosynthetic parameters (Harris et al. 1980), and variability of species composition both temporally (Harris & Piccinin 1980) and spatially (Haffner et al. 1980). Phytoplankton growth rates have only rarely been measured in estuaries (Malone 1977, Furnas 1982, Harding et al. 1986) where cycling rates between the photic and aphotic zones can be much faster than in lakes or the open ocean. This study was motivated by the need for quantitative measures of phytoplankton population growth rate in an estuarine environment, and was designed around the presumption that growth rates can be related empirically to light exposure. We conducted the study in San Francisco Bay (California, USA), which has large horizontal gradients in light availability (Z p :Z m ) typical of many coastal plain estuaries, and nutrient concentrations that often exceed those presumed to limit phytoplankton growth (Cloern et al. 1985). We tested the hypothesis that light availability is the primary control of phytoplankton growth, and that previous estimates of growth rate based on the ratio of productivity to biomass (Cloern et al. 1985) are realistic. Specifically, we wanted to verify that growth rate varies spatially along horizontal gradients of light availability indexed as Z p :Z m , such that phytoplankton turnover rate is rapid in shallow clear areas (high Z p :Z m ) and slow in deep turbid areas (low Z p :Z m ). We used an in situ incubation technique which simulated vertical mixing, and measured both changes in cell number and carbon production as independent estimates of growth rate across a range of Z p :Z m ratios.

California↗

USGS2023

Site occupancy of focal shorebird species at Whiskey Island and Caminada Headland, Louisiana 2012–2020

Coastal restoration through island construction and augmentation is an increasingly common management method in the northern Gulf of Mexico, but evaluating the impacts to shorebird species is difficult. Shorebirds are mostly migratory and many aspects of their life history, including reproduction in some species, occur in other places. In addition, counts or observations of shorebirds made at any given time represent only a portion of the population and that proportion may change with site conditions such as time of day and weather. Dynamic occupancy models can account for imperfect detection and produce estimates of the proportion of area occupied over time as a way to track trends in bird utilization over time. In this chapter we report on occupancy trends for five focal shorebird species from Caminada Headland and Whiskey Island: American Oystercatcher ( Haematopus palliatus ), Piping Plover ( Charadrius melodus ), Red Knot ( Calidris canutus ), Snowy Plover ( Charadrius nivosus ), and Wilson’s Plover ( Charadrius wilsonia ). We examined up to nine years of surveys at the two sites to model long-term trends in occupancy rates from a period spanning before, during, and after restoration. Our objective was to determine if there was change in occupancy over time (trend) during the restoration period. Field sampling was conducted as described in Chapter 1 for the five focal species in this chapter. To create spatial units for occupancy analysis we used a grid of 53 unique cells at Caminada Headland and 26 unique cells at Whiskey Island. All observations of the species were located into spatial units using GIS and presence of each species in each cell was determined for each visit within a sampling season. Sampling seasons were defined for species as the period of time where they were most likely to be using the study area, and corresponded with wintering (August–May), breeding (April–August), or staging (March–October). We did not include covariates for initial occupancy or colonization and site survival because these were small sites with homogenous habitat. We did account for time of year within a season by treating survey date as a covariate of detection probability and allowed it to vary throughout the season. We tested for a trend in occupancy over time by determining if the estimated slope through the series of annual occupancy estimates was significantly different from 0. We conducted 153 total surveys at Caminada Headland from 11 January 2013 to 5 June 2019, and 213 total surveys at Whiskey Island from 7 August 2012 to 19 August 2020. The number of surveys per year varied by species and site and range from 6–23 per species annually at Caminada Headland and 11–28 per species annually at Whiskey Island. Occupancy trends were able to be assessed for all species at both sites, with the exception of the American Oystercatcher, which were only observed in sufficient numbers to estimate occupancy at Whiskey Island. We found a significant positive trend in occupancy from 0.325 to 0.741 for American Oystercatcher at Whiskey Island. There was no significant trend in Piping Plover occupancy at Caminada Headland where occupancy was consistently high (0.910 to 0.947). At Whiskey Island, Piping Plover occupancy estimates increased from 0.574 to 0.908 during the study period which was a significant increase. At Caminada Headland and Whiskey Island Red Knot occupancy varied from 0.482 to 0.891 and 0.350 to 0.742, respectively, but showed no significant trend over the study period. Snowy Plover occupancy at Caminada Headland increased significantly from 0.295 to 0.785 over the study period. Snowy Plover occupancy also increased significantly at Whiskey Island from 0.442 to 0.906. Wilson’s Plover occupancy declined slightly during the study period from 0.946 to 0.935 at Caminada Headland, and from 0.858 to 0.736 at Whiskey Island, but the decline was not significant at either site. We found no evidence that occupancy declined significantly for any of the species during the period prior to, during, and after restoration. We did find a significant increasing trend in occupancy for Snowy Plover at Caminada Headland and a significant increasing trend for American Oystercatcher, Piping Plover, and Snowy Plover at Whiskey Island. Our modeling results indicate that sampling such as this is sufficient for occupancy modeling and can provide a robust metric for comparison over time or among sites. In future research we plan to investigate the sample size needed to detect a trend. We are currently conducting a power analysis to determine the minimum amount of sampling necessary to have power to detect a trend based on the detection probabilities from this study.

Report↗

USGS2026

Appendix 6: Overview of iPOM 2.0: Updates to wolf abundance estimation in Montana

Montana Fish, Wildlife and Parks (MFWP) uses the integrated Patch Occupancy Model (iPOM) to estimate statewide and regional wolf abundance. During the early years of recovery, wolf abundance was tracked using minimum counts. As the population increased, limitations of this method became apparent, motivating development of a model-based approach for estimating abundance. iPOM development began in 2006, was operationalized in 2013, and has been used in its current form (iPOM 1.0) since 2021. Since its inception, iPOM has been developed and presented as an adaptive modeling framework intended to evolve as new data and analytical methods become available1. Here, we briefly present ongoing work to produce the next iteration of iPOM, hereafter iPOM 2.0, and summarize major model updates and resulting preliminary wolf abundance estimates. iPOM uses models for occupancy, territory size, and pack size, along with monitoring data collected by MFWP wolf specialists and potential wolf sightings reported by deer and elk hunters during the 5-week general rifle season each Nov-Dec. These monitoring data, wolf sightings, and covariates for habitat and survey effort are used to model occupancy of packs on a statewide grid of 600-km 2 cells. The area used by wolves is then estimated as each cell’s occupancy estimate multiplied by grid cell area. iPOM estimates pack abundance by dividing this area by predicted territory sizes, and in-pack wolf abundance by multiplying pack abundance by estimated group size. This is combined with a lone wolf rate to estimate total wolf abundance (see Sells et al. 1 for a full description of iPOM 1.0). This technical summary provides a high-level overview of the proposed iPOM updates and their implications for wolf abundance estimates. The estimates presented here represent results as of June 2026 and are provided to inform upcoming discussions surrounding harvest management and regulations (e.g., season dates, quotas, methods). Results are preliminary and remain subject to final model refinement and peer review.

Montana↗

USGS2025

Flow cytometric detection of waterborne bacteria metabolic response to anthropogenic chemical inputs to aquatic ecosystems

Typical investigations into the biological consequences of suspected xenobiotics or nutrients introduced in watersheds include analytical chemistry screens of environmental samples—such as periphyton responses or studies of fish condition—which are all costly in terms of equipment, reagents, time, and human resources. An alternative is to assess pollutant effects on waterborne bacteria. A flow cytometric method was developed to yield rapid, same-day results that could be used to proactively screen for suspected chemical inputs into watersheds using water sampling methods that are identical to those in standard use. The analytical methods are microbe cultivation-independent, for use with waterborne bacteria that are typically viable but not culturable. The procedure is quick and inexpensive, generating measures of bacterial esterase that reflect metabolic activity and are sensitive and statistically robust. After phosphate-EDTA incubation to increase cell wall permeability, staining was performed with 5(6) carboxyfluorescein diacetate (enzyme activity) and propidium iodide (cell viability) with three bacterial species in exponential phase growth having been incubated with organic wastewater compounds (atrazine, pharmaceuticals [17α-ethynylestradiol and trenbolone], and antimicrobials [tylosin and butylparaben]). This method successfully detected metabolic changes in all bacterial species, with atrazine inducing the greatest change. Additional fluorescent stains can target specific microbial structures or functions of interest in a particular watershed. This biotechnology can inform analytical chemistry and study of biota at sites of interest and has the potential to be automated.

Cells↗

USGS2016

Tomographic Rayleigh-wave group velocities in the Central Valley, California centered on the Sacramento/San Joaquin Delta

If shaking from a local or regional earthquake in the San Francisco Bay region were to rupture levees in the Sacramento/San Joaquin Delta then brackish water from San Francisco Bay would contaminate the water in the Delta: the source of fresh water for about half of California. As a prelude to a full shear-wave velocity model that can be used in computer simulations and further seismic hazard analysis, we report on the use of ambient noise tomography to build a fundamental-mode, Rayleigh-wave group velocity model for the region around the Sacramento/San Joaquin Delta in the western Central Valley, California. Recordings from the vertical component of about 31 stations were processed to compute the spatial distribution of Rayleigh wave group velocities. Complex coherency between pairs of stations were stacked over 8 months to more than a year. Dispersion curves were determined from 4 to about 18 seconds. We calculated average group velocities for each period and inverted for deviations from the average for a matrix of cells that covered the study area. Smoothing using the first difference is applied. Cells of the model were about 5.6 km in either dimension. Checkerboard tests of resolution, which is dependent on station density, suggest that the resolving ability of the array is reasonably good within the middle of the array with resolution between 0.2 and 0.4 degrees. Overall, low velocities in the middle of each image reflect the deeper sedimentary syncline in the Central Valley. In detail, the model shows several centers of low velocity that may be associated with gross geologic features such as faulting along the western margin of the Central Valley, oil and gas reservoirs, and large cross cutting features like the Stockton arch. At shorter periods around 5.5s, the model’s western boundary between low and high velocities closely follows regional fault geometry and the edge of a residual isostatic gravity low. In the eastern part of the valley, the boundaries of the low velocity zone and gravity anomaly are better aligned at longer periods (around 10.5s) suggesting that the eastern edge of the gravity low is associated with deeper structure. There is a strong correspondence between a low in gravity near the Kirby Hills fault and low velocities from the ambient noise tomography. At longer periods, higher velocities creep in from the east and narrow the overall dimension defined by the lower velocities. Overall, there is a strong correspondence between the shape and location of low velocities in the Rayleigh wave velocity images, and geological and geophysical features.

California↗

USGS2017

Potential paths for male-mediated gene flow to and from an isolated grizzly bear population

For several decades, grizzly bear populations in the Greater Yellowstone Ecosystem (GYE) and the Northern Continental Divide Ecosystem (NCDE) have increased in numbers and range extent. The GYE population remains isolated and although effective population size has increased since the early 1980s, genetic connectivity between these populations remains a long-term management goal. With only ~110 km distance separating current estimates of occupied range for these populations, the potential for gene flow is likely greater now than it has been for many decades. We sought to delineate potential paths that would provide the opportunity for male-mediated gene flow between the two populations. We first developed step-selection functions to generate conductance layers using ecological, physical, and anthropogenic landscape features associated with non-stationary GPS locations of 124 male grizzly bears (199 bear-years). We then used a randomized shortest path (RSP) algorithm to estimate the average number of net passages for all grid cells in the study region, when moving from an origin to a destination node. Given habitat characteristics that were the basis for the conductance layer, movements follow certain grid cell sequences more than others and the resulting RSP values thus provide a measure of movement potential. Repeating this process for 100 pairs of random origin and destination nodes, we identified paths for three levels of random deviation (θ) from the least-cost path. We observed broad-scale concordance between model predictions for paths originating in the NCDE and those originating in the GYE for all three levels of movement exploration. Model predictions indicated that male grizzly bear movement between the ecosystems could involve a variety of routes, and verified observations of grizzly bears outside occupied range supported this finding. Where landscape features concentrated paths into corridors (e.g., because of anthropogenic influence), they typically followed neighboring mountain ranges, of which several could serve as pivotal stepping stones. The RSP layers provide detailed, spatially explicit information for land managers and organizations working with land owners to identify and prioritize conservation measures that maintain or enhance the integrity of potential areas conducive to male grizzly bear dispersal.

Montana↗

USGS2022

Modeling spatiotemporal abundance and movement dynamics using an integrated spatial capture–recapture movement model

Animal movement is a fundamental ecological process affecting the survival and reproduction of individuals, the structure of populations, and the dynamics of communities. Methods to quantify animal movement and spatiotemporal abundances, however, are generally separate and therefore omit linkages between individual-level and population-level processes. We describe an integrated spatial capture–recapture (SCR) movement model to jointly estimate (1) the number and distribution of individuals in a defined spatial region and (2) movement of those individuals through time. We applied our model to a study of polar bears ( Ursus maritimus ) in a 28,125 km 2 survey area of the eastern Chukchi Sea, USA in 2015 that incorporated capture–recapture and telemetry data. In simulation studies, the model provided unbiased estimates of movement, abundance, and detection parameters using a bivariate normal random walk and correlated random walk movement process. Our case study provided detailed evidence of directional movement persistence for both male and female bears, where individuals regularly traversed areas larger than the survey area during the 36-day study period. Scaling from individual- to population-level inferences, we found that densities varied from <0.75 bears/625 km 2 grid cell/day in nearshore cells to 1.6–2.5 bears/grid cell/day for cells surrounded by sea ice. Daily abundance estimates ranged from 53 to 69 bears, with no trend across days. The cumulative number of unique bears that used the survey area increased through time due to movements into and out of the area, resulting in an estimated 171 individuals using the survey area during the study (95% credible interval 124–250). Abundance estimates were similar to a previous multiyear integrated population model using capture–recapture and telemetry data (2008–2016; Regehr et al., Scientific Reports 8:16780, 2018). Overall, the SCR–movement model successfully quantified both individual- and population-level space use, including the effects of landscape characteristics on movement, abundance, and detection, while linking the movement and abundance processes to directly estimate density within a prescribed spatial region and temporal period. Integrated SCR–movement models provide a generalizable approach to incorporate greater movement realism into population dynamics and link movement to emergent properties including spatiotemporal densities and abundances.

eastern Chukchi Sea↗

USGS2012

Dissolved organic matter reduces algal accumulation of methylmercury

Dissolved organic matter (DOM) significantly decreased accumulation of methylmercury (MeHg) by the diatom Cyclotella meneghiniana in laboratory experiments. Live diatom cells accumulated two to four times more MeHg than dead cells, indicating that accumulation may be partially an energy-requiring process. Methylmercury enrichment in diatoms relative to ambient water was measured by a volume concentration factor (VCF). Without added DOM, the maximum VCF was 32 x 10 4 , and the average VCF (from 10 to 72 h) over all experiments was 12.6 x 10 4 . At very low (1.5 mg/L) added DOM, VCFs dropped by approximately half. At very high (20 mg/L) added DOM, VCFs dropped 10-fold. Presumably, MeHg was bound to a variety of reduced sulfur sites on the DOM, making it unavailable for uptake. Diatoms accumulated significantly more MeHg when exposed to transphilic DOM extracts than hydrophobic ones. However, algal lysate, a labile type of DOM created by resuspending a marine diatom in freshwater, behaved similarly to a refractory DOM isolate from San Francisco Bay. Addition of 67 μM L-cysteine resulted in the largest drop in VCFs, to 0.28 x 10 4 . Although the DOM composition influenced the availability of MeHg to some extent, total DOM concentration was the most important factor in determining algal bioaccumulation of MeHg.

Environmental Toxicology and Chemistry↗

USGS2018

Hematological indices of injury to lightly oiled birds from the Deepwater Horizon oil spill

Avian mortality events are common following large‐scale oil spills. However, the sublethal effects of oil on birds exposed to light external oiling are not clearly understood. We found that American oystercatchers (area of potential impact n = 42, reference n = 21), black skimmers (area of potential impact n = 121, reference n = 88), brown pelicans (area of potential impact n = 91, reference n = 48), and great egrets (area of potential impact n = 57, reference n = 47) captured between 20 June 2010 and 23 February 2011 following the Deepwater Horizon oil spill experienced oxidative injury to erythrocytes, had decreased volume of circulating erythrocytes, and showed evidence of a regenerative hematological response in the form of increased reticulocytes compared with reference populations. Erythrocytic inclusions consistent with Heinz bodies were present almost exclusively in birds from sites impacted with oil, a finding pathognomonic for oxidative injury to erythrocytes. Average packed cell volumes were 4 to 19% lower and average reticulocyte counts were 27 to 40% higher in birds with visible external oil than birds from reference sites. These findings provide evidence that small amounts of external oil exposure are associated with hemolytic anemia. Furthermore, we found that some birds captured from the area impacted by the spill but with no visible oiling also had erythrocytic inclusion bodies, increased reticulocytes, and reduced packed cell volumes when compared with birds from reference sites. Thus, birds suffered hematologic injury despite no visible oil at the time of capture. Together, these findings suggest that adverse effects of oil spills on birds may be more widespread than estimates based on avian mortality or severe visible oiling.

Environmental Toxicology and Chemistry↗

USGS2021

Sex- and developmental stage-related differences in the hepatic transcriptome of Japanese quail (Coturnix japonica) exposed to 17β-Trenbolone

Endocrine-disrupting chemicals can cause transcriptomic changes that may disrupt biological processes associated with reproductive function including metabolism, transport, and cell growth. We investigated effects from in ovo and dietary exposure to 17β-trenbolone (at 0, 1, and 10 ppm) on the Japanese quail ( Coturnix japonica ) hepatic transcriptome. Our objectives were to identify differentially expressed hepatic genes, assess perturbations of biological pathways, and examine sex- and developmental stage–related differences. The number of significantly differentially expressed genes was higher in embryos than in adults. Male embryos exhibited greater differential gene expression than female embryos, whereas in adults, males and females exhibited similar numbers of differentially expressed genes (>2-fold). Vitellogenin and apovitellenin-1 were up-regulated in male adults exposed to 10 ppm 17β-trenbolone, and these birds also exhibited indications of immunomodulation. Functional grouping of differentially expressed genes identified processes including metabolism and transport of biomolecules, enzyme activity, and extracellular matrix interactions. Pathway enrichment analyses identified as perturbed peroxisome proliferator–activated receptor pathway, cardiac muscle contraction, gluconeogenesis, growth factor signaling, focal adhesion, and bile acid biosynthesis. One of the primary uses of 17β-trenbolone is that of a growth promoter, and these results identify effects on mechanistic pathways related to steroidogenesis, cell proliferation, differentiation, growth, and metabolism of lipids and proteins.

Environmental Toxicology and Chemistry↗

USGS1986

Adaptation of Selenastrum capricornutum (Chlorophyceae) to copper

Selenastrum capricornutum Printz, growing in a chemically defined medium, was used as a model for studying adaptation of algae to a toxic metal (copper) ion. Cells exhibited lag‐phase adaptation to 0.8 μM total Cu (10 −12 M free ion concentration) after 20 generations of Cu exposure. Selenastrum adapted to the same concentration when Cu was gradually introduced over an 8‐h period using a specially designed apparatus that provided a transient increase in exposure concentration. Cu adaptation was not attributable to media conditioning by algal exudates. Duration of lag phase was a more sensitive index of copper toxicity to Selenastrum that was growth rate or stationary‐phase cell density under the experimental conditions used. Chemical speciation of the Cu dosing solution influenced the duration of lag phase even when media formulations were identical after dosing. Selenastrum initially exposed to Cu in a CuCl 2 injection solution exhibited a lag phase of 3.9 d, but this was reduced to 1.5 d when a CuEDTA solution was used to achieve the same total Cu and EDTA concentrations. Physical and chemical processes that accelerated the rate of increase in cupric ion concentration generally increased the duration of lag phase.

Environmental Toxicology and Chemistry↗

USGS2006

Flow cytometry, morphometry and histopathology as biomarkers of benzo[a]pyrene exposure in brown bullheads (ameiurus nebulosus)

Brown bullheads were given a single intraperitoneal dose of 0, 5, 25 or 125 mg kg −1 benzo[ a ]pyrene (BaP), a carcinogenic polycyclic aromatic hydrocarbon, and evaluated over 18 months. Flow cytometric analyses of hepatocyte DNA content indicated an increase in DNA synthesis in BaP-exposed fish prior to day 14 post-exposure. Thereafter, all flow cytometric variables returned to initial levels. Histopathological evaluation of livers from fish sampled at 18 months revealed significant differences among treatments in the amount of hepatic macrophage ceroid pigmentation and basophilic staining intensity. No neoplasms or changes in blood cell DNA content were detected. Significant morphometric variations existed among fish, but differences between sexes overshadowed differences attributable to dose. Flow cytometry yielded no evidence of long-term DNA alterations from a single exposure to BaP; however, the differences detected by DNA analysis shortly after the toxic event suggest that flow cytometric cell cycle analysis may be useful for documenting continuing exposures.

Journal of Applied Toxicology↗

USGS2013

Hydrodynamics of spur and groove formations on a coral reef

Spur and groove (SAG) formations are found on the fore reefs of many coral reefs worldwide. Although these formations are primarily present in wave‐dominated environments, their effect on wave‐driven hydrodynamics is not well understood. A two‐dimensional, depth‐averaged, phase‐resolving nonlinear Boussinesq model ( funwaveC ) was used to model hydrodynamics on a simplified SAG system. The modeling results show that the SAG formations together with shoaling waves induce a nearshore Lagrangian circulation pattern of counter‐rotating circulation cells. The mechanism driving the modeled flow is an alongshore imbalance between the pressure gradient (PG) and nonlinear wave (NLW) terms in the momentum balance. Variations in model parameters suggest the strongest factors affecting circulation include spur‐normal waves, increased wave height, weak alongshore currents, increased spur height, and decreased bottom drag. The modeled circulation is consistent with a simple scaling analysis based on the dynamical balance of NLW, PG, and bottom stress terms. Model results indicate that the SAG formations efficiently drive circulation cells when the alongshore SAG wavelength allows for the effects of diffraction to create alongshore differences in wave height without changing the mean wave angle.

Journal of Geophysical Research C: Oceans↗

USGS2006

Use of the gamma distribution to represent monthly rainfall in Africa for drought monitoring applications

Evaluating a range of scenarios that accurately reflect precipitation variability is critical for water resource applications. Inputs to these applications can be provided using location- and interval-specific probability distributions. These distributions make it possible to estimate the likelihood of rainfall being within a specified range. In this paper, we demonstrate the feasibility of fitting cell-by-cell probability distributions to grids of monthly interpolated, continent-wide data. Future work will then detail applications of these grids to improved satellite-remote sensing of drought and interpretations of probabilistic climate outlook forum forecasts. The gamma distribution is well suited to these applications because it is fairly familiar to African scientists, and capable of representing a variety of distribution shapes. This study tests the goodness-of-fit using the Kolmogorov–Smirnov (KS) test, and compares these results against another distribution commonly used in rainfall events, the Weibull. The gamma distribution is suitable for roughly 98% of the locations over all months. The techniques and results presented in this study provide a foundation for use of the gamma distribution to generate drivers for various rain-related models. These models are used as decision support tools for the management of water and agricultural resources as well as food reserves by providing decision makers with ways to evaluate the likelihood of various rainfall accumulations and assess different scenarios in Africa.

International Journal of Climatology↗

USGS2008

Physiographically sensitive mapping of climatological temperature and precipitation across the conterminous United States

Spatial climate data sets of 1971–2000 mean monthly precipitation and minimum and maximum temperature were developed for the conterminous United States. These 30‐arcsec (∼800‐m) grids are the official spatial climate data sets of the U.S. Department of Agriculture. The PRISM (Parameter‐elevation Relationships on Independent Slopes Model) interpolation method was used to develop data sets that reflected, as closely as possible, the current state of knowledge of spatial climate patterns in the United States. PRISM calculates a climate–elevation regression for each digital elevation model (DEM) grid cell, and stations entering the regression are assigned weights based primarily on the physiographic similarity of the station to the grid cell. Factors considered are location, elevation, coastal proximity, topographic facet orientation, vertical atmospheric layer, topographic position, and orographic effectiveness of the terrain. Surface stations used in the analysis numbered nearly 13 000 for precipitation and 10 000 for temperature. Station data were spatially quality controlled, and short‐period‐of‐record averages adjusted to better reflect the 1971–2000 period. PRISM interpolation uncertainties were estimated with cross‐validation (C‐V) mean absolute error (MAE) and the 70% prediction interval of the climate–elevation regression function. The two measures were not well correlated at the point level, but were similar when averaged over large regions. The PRISM data set was compared with the WorldClim and Daymet spatial climate data sets. The comparison demonstrated that using a relatively dense station data set and the physiographically sensitive PRISM interpolation process resulted in substantially improved climate grids over those of WorldClim and Daymet. The improvement varied, however, depending on the complexity of the region. Mountainous and coastal areas of the western United States, characterized by sparse data coverage, large elevation gradients, rain shadows, inversions, cold air drainage, and coastal effects, showed the greatest improvement. The PRISM data set benefited from a peer review procedure that incorporated local knowledge and data into the development process.

International Journal of Climatology↗