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At least 1,045 records · Page 58Linked to original sources
USGS2001

Immunogenetics and resistance to avian malaria in Hawaiian honeycreepers (Drepanidinae)

Although a number of factors have contributed to the decline and extinction of Hawai‘i’s endemic terrestrial avifauna, introduced avian malaria ( Plasmodium relicturn ) is probably the single most important factor preventing recovery of these birds in low-elevation habitats. Continued decline in numbers, fragmentation of populations, and extinction of species that are still relatively common will likely continue without new, aggressive approaches to managing avian disease. Methods of intervention in the disease cycle such as chemotherapy and vaccine development are not feasible because of efficient immune-evasion strategies evolved by the parasite, technical difficulties associated with treating wild avian populations, and increased risk of selection for more virulent strains of the parasite. We are investigating the natural evolution of disease resistance in some low-elevation native bird populations, particularly Hawai‘i ‘Amakihi ( Hemignathus virens ), to perfect genetic methods for identifying individuals with a greater immunological capacity to survive malarial infection. We are focusing on genetic analyses of the major histocompatibility complex, due to its critical role in both humoral and cell-mediated immune responses. In the parasite, we are evaluating conserved ribosomal genes as well as variable genes encoding cell-surface molecules as a first step in developing a better understanding of the complex interactions between malarial parasites and the avian immune system. A goal is to provide population managers with new criteria for maintaining long-term population stability for threatened species through the development of methods for evaluating and maintaining genetic diversity in small populations at loci important in immunological responsiveness to pathogens.

Hawai'i↗
USGS2017

Groundwater flow model for the Little Plover River basin in Wisconsin’s Central Sands

The Little Plover River is a groundwater-fed stream in the sand plains region of central Wisconsin. In this region, sandy sediment deposited during or soon after the last glaciation forms an important unconfined sand and gravel aquifer. This aquifer supplies water for numerous high-capacity irrigation, municipal, and industrial wells that support a thriving agricultural industry. In recent years the addition of many new wells, combined with observed diminished flows in the Little Plover and other nearby rivers, has raised concerns about the impacts of the wells on groundwater levels and on water levels and flows in nearby lakes, streams, and wetlands. Diverse stakeholder groups, including well operators, Growers, environmentalists, local land owners, and regulatory and government officials have sought a better understanding of the local groundwater-surface water system and have a shared desire to balance the water needs of the he liagricultural, industrial, and urban users with the maintenance and protection of groundwater-dependent natural resources. To help address these issues, the Wisconsin Department of Natural Resources requested that the Wisconsin Geological and Natural History Survey and U.S. Geological Survey cooperatively develop a groundwater flow model that could be used to demonstrate the relationships among groundwater, surface water, and well withdrawals and also be a tool for testing and evaluating alternative water management strategies for the central sands region. Because of an abundance of previous studies, data availability, local interest, and existing regulatory constraints the model focuses on the Little Plover River watershed, but the modeling methodology developed during this study can apply to much of the larger central sands of Wisconsin. The Little Plover River groundwater flow model simulates three-dimensional groundwater movement in and around the Little Plover River basin under steady-state and transient conditions. This model explicitly includes all high-capacity wells in the model domain and simulates seasonal variations in recharge and well pumping. The model represents the Little Plover River, and other significant streams and drainage ditches in the model domain, as fully connected to the groundwater system, computes stream base flow resulting from groundwater discharge, and routes the flow along the stream channel. A separate soil-water-balance (SWB) model was used to develop groundwater recharge arrays as input for the groundwater flow model. The SWB model uses topography, soils, land use, and climatic data to estimate recharge as deep drainage from the soil zone. The SWB model explicitly includes recharge originating as irrigation water, and computes irrigation using techniques similar to those used by local irrigation operators. The groundwater flow model uses the U.S. Geological Survey’s MODFLOW modeling code which is freely available, widely accepted, and commonly used by the groundwater community. The groundwater flow model and the SWB model use identical high-resolution numerical grids having model cells 100 feet on a side, with physical properties assigned to each grid cell. This grid allows accurate geographic placement of wells, streams, and other model features. The 3-dimensional grid has three layers; layers 1 and 2 represent the sand and gravel aquifer and layer 3 represents the underlying sandstone. The distribution of material properties in the model (hydraulic conductivity, aquifer thickness, etc.) comes from previous published geologic studies of the region, updated by calibration to recent streamflow and groundwater level data. The SWB model operates on a daily time step. The groundwater flow model was calibrated to monthly stress periods with time steps ranging from 1 to 16 days. More detailed time discretization is possible. The groundwater model was calibrated to water-level and streamflow data collected during 2013 and 2014 by adjusting model parameters (primarily hydraulic conductivity, storage, and recharge) until the model produced a conditionally optimal fit between field observations and model output, subject to consistency with previously published geologic studies. Calibration was performed under both steady and transient conditions, and used a sophisticated parameter-estimation procedure (PEST) for the calibration process and to identify important model parameters. For the Little Plover River, the two most important parameters are the global recharge multiplier and the hydraulic conductivity of the stream bed. The calibrated model produces water-level and mass-balance results that are consistent with field observations and previous studies of the area. The completed model is a powerful tool for testing and demonstrating alternative water-management scenarios. Example model applications described in this report include simulating how the cumulative impacts of pumping and land-use change have affected average baseflow in the Little Plover River. Depletion-potential mapping represents a method for predicting which wells and well locations have the greatest impact on nearby surface-water resources. The completed model is publicly available, along with a companion user’s guide to assist with its operation, at http://wgnhs.org/littleplover- river-groundwater-model.

Wisconsin↗
USGS1996

Hematology and clinical chemistry of sea otters vaptured in Prince William Sound, Alaska following the Exxon Valdez Oil Spill

Hematologic and serum chemical analyses were performed on sea otter blood samples collected from 31 adult males, 63 adult females, and 42 pups captured in western Prince William Sound (oiled area), and 12 adult males, 40 adult females, and 15 pups captured in eastern Prince William Sound (unoiled area) in 1989 and 1990. Hematologic differences between eastern and western adult males were minimal. Both hematocrits and hemoglobins were higher in western than eastern otters but the biological significance of this is equivocal. Western males had higher absolute eosinophil counts, suggesting possible systemic hypersensitivity reactions. Western males had higher serum protein and serum globulin levels than eastern males, suggesting greater antigenic stimulation (more inflammatory and/or infectious conditions). There were no differences in hematologic parameters between eastern and western female otters. Some chemistry changes were present, but the degree of difference was small. Total protein and serum globulin levels were slightly higher in western females, a finding also seen in adult males. Mean levels of liver enzymes for western females were somewhat higher than for the eastern otters, suggesting the possibility of subclinical liver disease. As a group, western pup hematocrits, hemoglobins, and red cell counts were significantly lower than those of eastern pups. From a biological perspective, these reductions were minimal but supported by individual animal data. The red cell data suggest a mild anemia in western pups; however, the degree of anemia was minimal, so that biological significance was equivocal. Other hematologic and clinical chemical differences between eastern and western pups were not striking and were also of equivocal biological significance.

Alaska↗
USGS2018

2D and 3D potential field mapping and modelling at the Fallon FORGE site, Nevada, USA

Accurate geological characterization of Fallon FORGE is important for preparing the site as an EGS laboratory. As part of this effort, a 3D geologic map was constructed previously from well logs, surface geologic mapping, 2D seismic profiles, interpreted gravity & magnetic maps, and a gravity-inferred basement surface. In this study, we have conducted both 2D and 3D modelling of high-resolution gravity and magnetic data (pre-existing and new) in an effort to further refine and test this 3D geologic map at Fallon. This effort enabled a direct comparison of the 2D and 3D model results. Potential field modelling was guided by rock-property measurements of samples from drill-core and outcrop from the Fallon area. In total, five 2D potential field model profiles, up to 30 km in length, were constructed that extend across the Fallon area. The 3D gravity model volume was 8 km (N-S) x 8 km (E-W) x 4 km (thick). The majority of the 3D gravity model volume had 100 m cubic cells; but cells near the land surface were 1 m thick to adequately capture topography. Overall, the 2D & 3D geophysical modelling largely confirmed the previously constructed 3D geologic map at Fallon for three reasons: 1) lithologic boundaries in the 2D & 3D density models mostly agree with those in the 3D geologic map, 2) the rock properties used in the models lie within the range of independent measurements made on representative rock samples from the region, and 3) the match between the observed and calculated anomalies are largely within the measurement error of the observed fields. In places where the geophysical and geologic models differ, geophysical model results have revealed subsurface structural features that have helped refine geologic interpretations which, in turn, lead to adjustments to the 3D geologic map. In this paper, we present the 2D & 3D geophysical model results and discuss how they were utilized to confirm and refine our 3D geologic understanding of the Fallon FORGE site.

Geothermal Resources Council Transactions↗
USGS1969

The role of larval Chironomidae in the production of lacustrine copropel in Mud Lake, Marion County, Florida

Mud Lake is a shallow (avg 45 cm), alkaline (pH 7.7–10.2), brown‐water lake having an area of about 180 ha. A study of its organic sediment was undertaken because it appears to be a present‐day analogue of the richly organic lacustrine oozes that were the precursors of the oil shales of the Green River Formation (Eocene). The water contains about 200 ppm total dissolved solids. The soft ooze is about 1 m thick and consists of minute fecal pellets produced primarily by larvae of Chironomus ( Chironomus ) sp. Mean numbers of larvae ranged from 120 to 580 m −2 ; such a small population may reflect extensive predation by fish. The small diversity of Chironomidae at this latitude may reflect the fact that few organisms can tolerate the physical conditions produced by the shallow water. Experiments with laboratory‐reared Mud Lake midges showed that the numbers of fecal pellets produced generally increased with the concentration of algal cells available; that only when the larvae were fed blue‐green algae were the fecal pellets coherent and durable—larvae fed green algae produced pellets that disintegrated, returning the undigested algae to the food supply; and that larvae fed blue‐green algae changed from filter‐feeding to grazing on the fecal pellets when suspended algal cells became sparse. We conclude that the sediment in Mud Lake is pelletal because only blue‐green algae are available for food and that the larvae probably graze because all the blue‐greens live only on, or in, the fecal pellets. Early instars produce ovoid pellets; later instars produce longer, cylindrical pellets. The analogy between the Mud Lake pelletal ooze and the Eocene precursors of the Green River Formation oil shale is enhanced by the facts that some oil shale thin sections show minute fecal pellets and that certain beds of rich oil shale contain numerous unmineralized remains of immature chironomids.

Florida↗
USGS2022

Exploring declustering methodology for addressing geothermal exploration bias

Geothermal resources assessments use data that are unevenly distributed in space, with more data collected in areas with known thermal features. To meet the assumptions for geostatistical modeling (e.g., variography and kriging) such as having a random sample representative of the population, declustering may be needed to correct for spatial sample bias. Several declustering methods exist and to understand how best to use these methods, we apply these to real data and samples of that data. The work described herein summarizes the application of cell-based declustering to shallow temperature data (~20 cm) collected in a survey across a thermal feature in the Lower Geyser Basin, Yellowstone National Park, Wyoming. The sample dataset is a regular grid (3-m spacing) of temperatures across a 72-m square area, providing a shallow, subsurface temperature dataset collected with minimal spatial bias (a few grid locations near a hot spring could not be sampled). To test the influence of sample clustering on geothermal estimates, this dense dataset is sub-sampled irregularly to evaluate bias on temperature estimation. Three sampling strategies were tested: a simple random sample, a stratified random sample, and a stratified biased random sample. The naive mean (before declustering) values for each dataset were compared to the post-declustering mean to evaluate the effectiveness of declustering on correcting the mean for spatial bias. For the limited number of sample datasets evaluated, we found that although cell-based declustering did partially correct the mean, some bias remained (i.e., the estimate was improved, but not fully corrected). It is possible that the procedure documented herein (applied here to only a few random samples) could be applied to many random samples, so that robust conclusions might be drawn (e.g., Is there always some remaining bias in declustered estimates? Does it depend on the number of sample points?). In particular, bias could be evaluated for persistency, and uncertainty could be evaluated.

Geothermal Resources Council Transactions↗
USGS2002

The epizootiology of type C botulism in fish-eating birds at Salton Sea, California

During 1996, type C avian botulism killed over 15,000 fish-eating birds at the Salton Sea in southern California. Amont those affected were nearly 10,000 western white pelicans (Pelecanus erythrorhynchos) and over 1,200 endangered California brown pelicans (Pelecanus occidentalis californicus). Since 1996, smaller epizootics have occurred every year. Type C botulism is not typically associated with fish-eating birds. In the case of the Salton Sea, Mozambique tilapia (Oreochromis mossambicus) are the suspected source of type C toxin, although the mechanism by which the fish acquire the toxin is still unknown. The goals of this study were to: 1) Determine presence/absence of active Clostridium botulinum type C and type C botulinum toxin in tilapia in the Salton Sea. 2) Use geospatial analyses to evaluate relationships between patterns of mortality in birds and fish and presence/absence of toxin and/or toxin-producing bacteria in sediments and fish. We investigated a method of detecting C. botulinum type C cells in the intestinal contents of Mozambique tilapia. This method involved extraction of predominantly cellular DNA and uses a polymerase chain reaction assay to detect presence of type C toxin gene. We collected sick, dead and healthy fish from various sites throughout the Sea during the summers of 1999 to 2001 in order to test them for the presence of active C. botulinum type C by PCR and for the presence of type C toxin by ELISA and mouse test. The results demonstrate that the tilapia population in the Salton Sea harbors C. botulinum type C cells within their gastrointestinal tract and the prevalence of this organism varies from year to year. The total number of fish with toxin-producing bacteria was significantly greater in 2000 than in 2001. No difference in the numbers of positives was detected between sick and dead fish compared to live fish, and there were no differences noted with regard to location of fish collection. The prevalence of active type C toxin in tilapia was low and the majority of samples positive for toxin by ELISA were negative on mouse test. Further investigation is currently underway. From 1999-2001, routine surveillance was conducted July through November to detect morbidity and mortality in pelicans. Location of retrieval and total number of birds collected were documented. In all three years, the majority of botulism-affected pelicans were retrieved from the vicinities of the river deltas although the Whitewater River had the fewest birds of the three. It has yet to be determined what roles the tilapia and pelican populations play in influencing these patterns.

California↗
USGS1977

Virion RNA polymerases of two salmonid rhabdoviruses

RNA-dependent RNA polymerases were found to be associated with two salmonid rhabdoviruses: infectious hematopoietic necrosis (IHN) virus and the virus of hemorrhagic septicemia (VHS). The protein composition of these rhabdoviruses closely resembles that of rabies virus rather than that of vesicular stomatitis virus (McAllister and Wagner, 1975). The optimal temperature for in vitro transcription was found to be approximately 18 degrees C for IHN virus and approximately 15 degrees for VHS, closely approximating optimal temperatures for growth of these viruses in salmonid cells. Unlike vesicular stomatitis virus, manganese ion (1 mM) could be used as a divalent cation substitute for magnesium ion (5 mM). The in vitro transcription products of IHN and VHS viruses hybridized completely to the homologous genome but not at all to the heterologous genome.

Journal of Virology↗
USGS1996

Global distribution of plant-extractable water capacity of soil

Plant-extractable water capacity of soil is the amount of water that can be extracted from the soil to fulfill evapotranspiration demands. It is often assumed to be spatially invariant in large-scale computations of the soil-water balance. Empirical evidence, however, suggests that this assumption is incorrect. In this paper, we estimate the global distribution of the plant-extractable water capacity of soil. A representative soil profile, characterized by horizon (layer) particle size data and thickness, was created for each soil unit mapped by FAO (Food and Agriculture Organization of the United Nations)/Unesco. Soil organic matter was estimated empirically from climate data. Plant rooting depths and ground coverages were obtained from a vegetation characteristic data set. At each 0.5°×0.5° grid cell where vegetation is present, unit available water capacity (cm water per cm soil) was estimated from the sand, clay, and organic content of each profile horizon, and integrated over horizon thickness. Summation of the integrated values over the lesser of profile depth and root depth produced an estimate of the plant-extractable water capacity of soil. The global average of the estimated plant-extractable water capacities of soil is 8ċ6cm (Greenland, Antarctica and bare soil areas excluded). Estimates are less than 5, 10 and 15 cm—over approximately 30, 60, and 89 per cent of the area, respectively. Estimates reflect the combined effects of soil texture, soil organic content, and plant root depth or profile depth. The most influential and uncertain parameter is the depth over which the plant- extractable water capacity of soil is computed, which is usually limited by root depth. Soil texture exerts a lesser, but still substantial, influence. Organic content, except where concentrations are very high, has relatively little effect.

International Journal of Climatology↗
USGS2016

Evaluation of downscaled, gridded climate data for the conterminous United States

Weather and climate affect many ecological processes, making spatially continuous yet fine-resolution weather data desirable for ecological research and predictions. Numerous downscaled weather data sets exist, but little attempt has been made to evaluate them systematically. Here we address this shortcoming by focusing on four major questions: (1) How accurate are downscaled, gridded climate data sets in terms of temperature and precipitation estimates?, (2) Are there significant regional differences in accuracy among data sets?, (3) How accurate are their mean values compared with extremes?, and (4) Does their accuracy depend on spatial resolution? We compared eight widely used downscaled data sets that provide gridded daily weather data for recent decades across the United States. We found considerable differences among data sets and between downscaled and weather station data. Temperature is represented more accurately than precipitation, and climate averages are more accurate than weather extremes. The data set exhibiting the best agreement with station data varies among ecoregions. Surprisingly, the accuracy of the data sets does not depend on spatial resolution. Although some inherent differences among data sets and weather station data are to be expected, our findings highlight how much different interpolation methods affect downscaled weather data, even for local comparisons with nearby weather stations located inside a grid cell. More broadly, our results highlight the need for careful consideration among different available data sets in terms of which variables they describe best, where they perform best, and their resolution, when selecting a downscaled weather data set for a given ecological application.

Ecological Applications↗
USGS2015

Seismic source dynamics of gas-piston activity at Kı̄lauea Volcano, Hawai‘i

Since 2008, eruptive activity at the summit of Kı̄lauea Volcano, Hawai‘i has been confined to the new Overlook pit crater within the Halema‘uma‘u Crater. Among the broad range of magmatic processes observed in the new pit are recurring episodes of gas pistoning. The gas-piston activity is accompanied by seismic signals that are recorded by a broadband network deployed in the summit caldera. We use raw data recorded with this network to model the source mechanism of representative gas-piston events in a sequence that occurred on 20–25 August 2011 during a gentle inflation of the Kı̄lauea summit. To determine the source centroid location and source mechanism, we minimize the residual error between data and synthetics calculated by the finite difference method for a point source embedded in a homogeneous medium that takes topography into account. We apply a new waveform inversion method that accounts for the contributions from both translation and tilt in horizontal seismograms through the use of Green's functions representing the seismometer response to translation and tilt ground motions. This method enables a robust description of the source mechanism over the period range 1–10,000 s. Most of the seismic wavefield produced by gas-pistoning originates in a source region ∼1 km below the eastern perimeter of the Halema‘uma‘u pit crater. The observed waveforms are well explained by a simple volumetric source with geometry composed of two intersecting cracks featuring an east striking crack (dike) dipping 80°to the north, intersecting a north striking crack (another dike) dipping 65° to the east. Each gas-piston event is marked by a similar rapid inflation lasting a few minutes, trailed by a slower deflation ramp extending up to 15 min, attributed to the efficient coupling at the source centroid location of the pressure and momentum changes accompanying the growth and collapse of a layer of foam at the top of the lava column. Assuming a simple lumped parameter representation of the shallow magmatic system, the observed pressure and volume variations can be modeled with the following attributes : foam thickness (10–50 m), foam cell diameter (0.04–0.10 m), and gas-injection velocity (0.01–0.06 m s −1 ). Gas-piston activity occurs in a narrow pipe with diameter of 6 m connecting the Halema‘uma‘u pit crater to the subjacent dike system. The height of the magma column is estimated at ∼104 m at the start of the sequence based on the period of very long period (VLP) oscillations accompanying the onset of the gas-piston signal. Based on the change in the period of VLP oscillations and tilt evidence, the height of the magma column is inferred to have risen by up to ∼23 m by the end of the 5 day long sequence. A penny-shaped crack model of the dike geometry yields effective diameters of ∼1.2–2.9 km for the east dike and 0.7 km for the north dike. The shallower north dike segment is embedded in a relatively weak medium, compatible with expected mechanical properties in the hydrothermal environment of this dike.

Hawaii↗
USGS2015

A Bayesian kriging approach for blending satellite and ground precipitation observations

Drought and flood management practices require accurate estimates of precipitation. Gauge observations, however, are often sparse in regions with complicated terrain, clustered in valleys, and of poor quality. Consequently, the spatial extent of wet events is poorly represented. Satellite-derived precipitation data are an attractive alternative, though they tend to underestimate the magnitude of wet events due to their dependency on retrieval algorithms and the indirect relationship between satellite infrared observations and precipitation intensities. Here we offer a Bayesian kriging approach for blending precipitation gauge data and the Climate Hazards Group Infrared Precipitation satellite-derived precipitation estimates for Central America, Colombia, and Venezuela. First, the gauge observations are modeled as a linear function of satellite-derived estimates and any number of other variables—for this research we include elevation. Prior distributions are defined for all model parameters and the posterior distributions are obtained simultaneously via Markov chain Monte Carlo sampling. The posterior distributions of these parameters are required for spatial estimation, and thus are obtained prior to implementing the spatial kriging model. This functional framework is applied to model parameters obtained by sampling from the posterior distributions, and the residuals of the linear model are subject to a spatial kriging model. Consequently, the posterior distributions and uncertainties of the blended precipitation estimates are obtained. We demonstrate this method by applying it to pentadal and monthly total precipitation fields during 2009. The model's performance and its inherent ability to capture wet events are investigated. We show that this blending method significantly improves upon the satellite-derived estimates and is also competitive in its ability to represent wet events. This procedure also provides a means to estimate a full conditional distribution of the “true” observed precipitation value at each grid cell.

Water Resources Research↗
USGS2015

Electrical properties of methane hydrate + sediment mixtures

Knowledge of the electrical properties of multicomponent systems with gas hydrate, sediments, and pore water is needed to help relate electromagnetic (EM) measurements to specific gas hydrate concentration and distribution patterns in nature. Toward this goal, we built a pressure cell capable of measuring in situ electrical properties of multicomponent systems such that the effects of individual components and mixing relations can be assessed. We first established the temperature-dependent electrical conductivity ( σ ) of pure, single-phase methane hydrate to be ~5 orders of magnitude lower than seawater, a substantial contrast that can help differentiate hydrate deposits from significantly more conductive water-saturated sediments in EM field surveys. Here we report σ measurements of two-component systems in which methane hydrate is mixed with variable amounts of quartz sand or glass beads. Sand by itself has low σ but is found to increase the overall σ of mixtures with well-connected methane hydrate. Alternatively, the overall σ decreases when sand concentrations are high enough to cause gas hydrate to be poorly connected, indicating that hydrate grains provide the primary conduction path. Our measurements suggest that impurities from sand induce chemical interactions and/or doping effects that result in higher electrical conductivity with lower temperature dependence. These results can be used in the modeling of massive or two-phase gas-hydrate-bearing systems devoid of conductive pore water. Further experiments that include a free water phase are the necessary next steps toward developing complex models relevant to most natural systems.

Journal of Geophysical Research↗
USGS2017

A detached eddy simulation model for the study of lateral separation zones along a large canyon-bound river

Lateral flow separation occurs in rivers where banks exhibit strong curvature. In canyon-boundrivers, lateral recirculation zones are the principal storage of fine-sediment deposits. A parallelized,three-dimensional, turbulence-resolving model was developed to study the flow structures along lateralseparation zones located in two pools along the Colorado River in Marble Canyon. The model employs thedetached eddy simulation (DES) technique, which resolves turbulence structures larger than the grid spacingin the interior of the flow. The DES-3D model is validated using Acoustic Doppler Current Profiler flowmeasurements taken during the 2008 controlled flood release from Glen Canyon Dam. A point-to-pointvalidation using a number of skill metrics, often employed in hydrological research, is proposed here forfluvial modeling. The validation results show predictive capabilities of the DES model. The model reproducesthe pattern and magnitude of the velocity in the lateral recirculation zone, including the size and position ofthe primary and secondary eddy cells, and return current. The lateral recirculation zone is open, havingcontinuous import of fluid upstream of the point of reattachment and export by the recirculation returncurrent downstream of the point of separation. Differences in magnitude and direction of near-bed andnear-surface velocity vectors are found, resulting in an inward vertical spiral. Interaction between therecirculation return current and the main flow is dynamic, with large temporal changes in flow direction andmagnitude. Turbulence structures with a predominately vertical axis of vorticity are observed in the shearlayer becoming three-dimensional without preferred orientation downstream.

Arizona↗
USGS2016

Bounded fractional diffusion in geological media: Definition and Lagrangian approximation

Spatiotemporal Fractional-Derivative Models (FDMs) have been increasingly used to simulate non-Fickian diffusion, but methods have not been available to define boundary conditions for FDMs in bounded domains. This study defines boundary conditions and then develops a Lagrangian solver to approximate bounded, one-dimensional fractional diffusion. Both the zero-value and non-zero-value Dirichlet, Neumann, and mixed Robin boundary conditions are defined, where the sign of Riemann-Liouville fractional derivative (capturing non-zero-value spatial-nonlocal boundary conditions with directional super-diffusion) remains consistent with the sign of the fractional-diffusive flux term in the FDMs. New Lagrangian schemes are then proposed to track solute particles moving in bounded domains, where the solutions are checked against analytical or Eularian solutions available for simplified FDMs. Numerical experiments show that the particle-tracking algorithm for non-Fickian diffusion differs from Fickian diffusion in relocating the particle position around the reflective boundary, likely due to the non-local and non-symmetric fractional diffusion. For a non-zero-value Neumann or Robin boundary, a source cell with a reflective face can be applied to define the release rate of random-walking particles at the specified flux boundary. Mathematical definitions of physically meaningful nonlocal boundaries combined with bounded Lagrangian solvers in this study may provide the only viable techniques at present to quantify the impact of boundaries on anomalous diffusion, expanding the applicability of FDMs from infinite do mains to those with any size and boundary conditions.

Water Resources Research↗
USGS2019

Comparisons of stereological and other approaches for quantifying macrophage aggregates in piscine spleens

Macrophage aggregates (MA s) are focal accumulations of pigmented macrophages in the spleen and other tissues of fish. A central role of MA s is the clearance and destruction of degenerating cells and recycling of some cellular components. Macrophage aggregates also respond to chemical contaminants and infectious agents and may play a role in the adaptive immune response. Tissue damage or physiological stress can result in increased MA accumulation. As a result, MA s may be sensitive biomarkers of environmental stress in fish. Abundance of MA s in tissues has been reported in a variety of ways—most commonly as density, mean size, and relative area—but the utility of these estimates has not been compared. In this study, four different types of splenic MA abundance estimates (abundance score, density, relative area, and total volume) were compared in two fish populations (Striped Bass Morone saxatilis and White Perch M. americana ) with a wide range in ages. Stereological estimates of total volume indicated an increase in MA abundance with spleen volume, which generally corresponded to fish age, and with splenic infections (mycobacteria or trematode parasites). Abundance scores were generally limited in the ability to detect changes in MA abundance by these factors, whereas density estimates were greatly influenced by changes in spleen volume. In some instances, densities declined while the total volume of MA s and spleen volume increased. Experimentally induced acute stress resulted in a decrease in spleen volume and an increase in MA density, although the total volume of MA s remained unchanged. Relative area estimates accounted for the size and number of MA s but not for changes in organ volume. Total volume is an absolute measure of MA abundance irrespective of changes in organ volume or patterns of accumulation and may provide an improved means of quantifying MA s in the spleens of fish.

Maryland↗
USGS2021

Chemical and structural degradation of CH3NH3PbI3 propagate from PEDOT:PSS interface in the presence of humidity

Understanding interfacial reactions that occur between the active layer and charge-transport layers can extend the stability of perovskite solar cells. In this study, the exposure of methylammonium lead iodide (CH 3 NH 3 PbI 3 ) thin films prepared on poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS)-coated glass to 70% relative humidity (R.H.) leads to a perovskite crystal structure change from tetragonal to cubic within 2 days. Interface-sensitive photoluminescence measurements indicate that the structural change originates at the PEDOT:PSS/perovskite interface. During exposure to 30% R.H., the same structural change occurs over a much longer time scale (>200 days), and a reflection consistent with the presence of (CH 3 ) 2 NH 2 PbI 3 is detected to coexist with the cubic phase by X-ray diffraction pattern. The authors propose that chemical interactions at the PEDOT:PSS/perovskite interface, facilitated by humidity, promote the formation of dimethylammonium, (CH 3 ) 2 NH 2 + . The partial A-site substitution of CH 3 NH 3 + for (CH 3 ) 2 NH 2 + to produce a cubic (CH 3 NH 3 ) 1− x [(CH 3 ) 2 NH 2 ] x PbI 3 phase explains the structural change from tetragonal to cubic during short-term humidity exposure. When (CH 3 ) 2 NH 2 + content exceeds its solubility limit in the perovskite during longer humidity exposures, a (CH 3 ) 2 NH 2 + -rich, hexagonal phase of (CH 3 NH 3 ) 1− x [(CH 3 ) 2 NH 2 ] x PbI 3 emerges. These interfacial interactions may have consequences for device stability and performance beyond CH 3 NH 3 PbI 3 model systems and merit close attention from the perovskite research community.

Advanced Materials Interfaces↗
USGS2019

Detecting the undetectable: Characterization, optimization, and validation of an eDNA detection assay for the federally endangered dwarf wedgemussel, Alasmidonta heterodon (Bivalvia: Unionoida)

Environmental (e)DNA assays are valuable tools for monitoring presence and distribution of cryptic species. Like many freshwater mussels, the dwarf wedgemussel, Alasmidonta heterodon numbers have dwindled and its range has diminished. As of its listing in 1993, only 10 to 20 locations were known to persist of the 70 Atlantic slope locations known historically. A qPCR assay to detect the presence of A. heterodon was developed that uses two probes to accommodate a single nucleotide polymorphism (SNP) in the probe binding site within the cytochrome oxidase I (COI) gene. This SNP defines northern and southern major phylogenetic lineages. The primers match exactly the previously determined cytochrome oxidase I sequences of twenty dwarf wedgemussel individuals representing Atlantic slope populations from North Carolina, Virginia, Maryland, New York, and New Hampshire. Other than for the qPCR assay described here these primers can be used for sequencing and/or metabarcoding to further delineate dwarf wedgemussel populations phylogenetically. A simple eDNA preparation method is introduced using flocculation to concentrate free DNA in solution as well as cellular material (including shed animal cells, bacteria, virus, and dissolved DNA). In addition to the specific application described here, the methodological approaches used in this study are widely applicable to the study of conservation issues including, but not limited to general aquatic biodiversity, phylogenetic studies, and detection of pathogenic microbes.

North Carolina, Virginia, Maryland, New York, New ↗