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Results for “Methods in Cell Science”

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At least 19 recordsLinked to original sources
USGS1997

Preparation, cryopreservation, and growth of cells prepared from the green turtle (Chelonia mydas)

Techniques are described for preparing, preserving, and growing cell cultures from 30 to 40-day old green turtle embryos (2.0-3.0 cm length) including cells derived from skeletal muscle, liver, heart, kidney, eye, lung, and brain. Acceptable growth of all cells occurred in all standard cell culture media tested, with optimum growth temperature near 30??C. These cell cultures will be used in the study of sea turtle viral diseases including fibropapillomatosis, which is currently epidemic in some green turtle populations.

Methods in Cell Science↗
USGS2022

Human-in-the-Loop segmentation of earth surface imagery

Segmentation, or the classification of pixels (grid cells) in imagery, is ubiquitously applied in the natural sciences. Manual methods are often prohibitively time-consuming, especially those images consisting of small objects and/or significant spatial heterogeneity of colors or textures. Labeling complicated regions of transition that in Earth surface imagery are represented by collections of mixed-pixels, -textures, and -spectral signatures, can be especially error-prone because it is difficult to reliably unmix, identify and delineate consistently. However, the success of supervised machine learning (ML) approaches is entirely dependent on good label data. We describe a fast, semi-automated, method for interactive segmentation of N-dimensional (x, y, N) images into two-dimensional (x, y) label images. It uses human-in-the-loop ML to achieve consensus between the labeler and a model in an iterative workflow. The technique is reproducible; the sequence of decisions made by human labeler and ML algorithms can be encoded to file, so the entire process can be played back and new outputs generated with alternative decisions and/or algorithms. We illustrate the scientific potential of segmentation of imagery of diverse settings and image types using six case studies from river, estuarine, and open coast environments. These photographic and non-photographic imagery consist of 1- and 3-bands on regular and irregular grids ranging from centimeters to tens of meters. We demonstrate high levels of agreement in label images generated by several labelers on the same imagery, and make suggestions to achieve consensus and measure uncertainty, ideal for widespread application in training supervised ML for image segmentation.

Earth and Space Science↗
USGS2019

Occupancy models for citizen-science data

Large‐scale citizen‐science projects, such as atlases of species distribution, are an important source of data for macroecological research, for understanding the effects of climate change and other drivers on biodiversity, and for more applied conservation tasks, such as early‐warning systems for biodiversity loss. However, citizen‐science data are challenging to analyse because the observation process has to be taken into account. Typically, the observation process leads to heterogeneous and non‐random sampling, false absences, false detections, and spatial correlations in the data. Increasingly, occupancy models are being used to analyse atlas data. We advocate a dual approach to strengthen inference from citizen science data for the questions the programme is intended to address: (a) the survey design should be chosen with a particular set of questions and associated analysis strategy in mind and (b) the statistical methods should be tailored not only to those questions but also to the specific characteristics of the data. We review the consequences of particular survey design choices that typically need to be made in atlas‐style citizen‐science projects. These include spatial resolution of the sampling units, allocation of effort in space, and collection of information about the observation process. On the analysis side, we review extensions of the basic occupancy models that are frequently necessary with atlas data, including methods for dealing with heterogeneity, non‐independent detections, false detections, and violation of the closure assumption. New technologies, such as cell‐phone apps and fixed remote detection devices, are revolutionizing citizen‐science projects. There is an opportunity to maximize the usefulness of the resulting datasets if the protocols are rooted in robust statistical designs and data analysis issues are being considered. Our review provides guidelines for designing new projects and an overview of the current methods that can be used to analyse data from such projects.

Methods in Ecology and Evolution↗
USGS2002

Development and evaluation of a local grid refinement method for block-centered finite-difference groundwater models using shared nodes

A new method of local grid refinement for two-dimensional block-centered finite-difference meshes is presented in the context of steady-state groundwater-flow modeling. The method uses an iteration-based feedback with shared nodes to couple two separate grids. The new method is evaluated by comparison with results using a uniform fine mesh, a variably spaced mesh, and a traditional method of local grid refinement without a feedback. Results indicate: (1) The new method exhibits quadratic convergence for homogeneous systems and convergence equivalent to uniform-grid refinement for heterogeneous systems. (2) Coupling the coarse grid with the refined grid in a numerically rigorous way allowed for improvement in the coarse-grid results. (3) For heterogeneous systems, commonly used linear interpolation of heads from the large model onto the boundary of the refined model produced heads that are inconsistent with the physics of the flow field. (4) The traditional method works well in situations where the better resolution of the locally refined grid has little influence on the overall flow-system dynamics, but if this is not true, lack of a feedback mechanism produced errors in head up to 3.6% and errors in cell-to-cell flows up to 25%. ?? 2002 Elsevier Science Ltd. All rights reserved.

Advances in Water Resources↗
USGS2022

Status and trends of North American bats: Summer occupancy analysis 2010-2019

• We developed an analytical pipeline supported by web-based infrastructure for integrating continental scale bat monitoring data (stationary acoustic, mobile acoustic, and capture records) to estimate summer (May 1–Aug 31) occupancy probabilities and changes in occupancy over time for 12 North American bat species. This serves as one of multiple lines of evidence that inform the status and trends of bat populations. • We analyzed data from a total of 12 bat species (Table 1), 11 of which have tested positive for Pseudogymnoascus destructans (Pd), a fungal pathogen that causes white-nose syndrome (WNS)—a disease that has led to significant rates of mortality for subterranean hibernating bat species in North America. A twelfth species was also selected because of high rates of mortality at wind energy facilities. Additional species were considered but not selected due to data limitations. • We estimated occupancy probabilities for 2010 through 2019 for three species ( Myotis lucifugus , MYLU; Myotis septentrionalis , MYSE; and P erimyotis subflavus , PESU). For an additional nine species, we estimated occupancy probabilities for 2016 through 2019 ( Myotis evotis , MYEV; Myotis grisescens , MYGR; Myotis leibii , MYLE; Myotis thysanodes , MYTH; Myotis volans , MYVO; Myotis yumanensis , MYYU; Eptesicus fuscus , EPFU; Lasionycteris noctivagans , LANO; and Lasiurus cinereus , LACI). • For each species, we provide range-wide occupancy probability predictions (e.g., predicted summer occupancy distribution maps) each year at a spatial resolution of 100 km2 and provide regional estimates of mean occupancy probability aggregated at larger spatial scales (state/province/territory, range-wide). • For each species, we also provide trends over time (average annual change rate and total change rate) in mean occupancy probabilities at multiple spatial scales (state/province/territory, range-wide) and when possible, over multiple timescales (short, medium, long). • Results suggest that over the short-term (2016-2019), two ( Myotis lucifugus and Perimyotis subflavus ) of 12 species have experienced declines in range-wide average occupancy probability with at least 95% certainty. Seven species showed either minor increases or decreases in range-wide average occupancy probability but with less than 95% certainty in both trend indicators. Results over the longer term (eight years and 10 years of sampling) suggest that three hibernating species known to be highly affected by white-nose syndrome ( Myotis lucifugus , Myotis septentrionalis , and Perimyotis subflavus ) have experienced marked declines in range-wide average occupancy probabilities, with severity varying by species and region. Finally, the results for three species ( Eptesicus fuscus , Lasiurus cinereus , Lasionycteris noctivagans ) were inconclusive due to 1) borderline convergence issues in the model fitting procedure which suggests potentially unreliable estimates, 2) failure to reliably distinguish between false positives and true positive detections for ambiguous detections, and 3) largely uninformative covariates for occupancy and detection. • For Myotis lucifugus , Myotis septentrionalis , and Perimyotis subflavus we found meaningful associations in space and time between declining winter populations (likely a result of WNS) and summer occupancy distributions. • The representativeness of sampling data for each species’ status and trend estimates (e.g., state/province/territory) were also evaluated based on the percent of grid cells sampled each year with a goal of understanding the reliability of regional estimates and improving future monitoring efforts. • This work represents the most comprehensive effort to date to model North American bat distributions across their continental ranges. Despite current limitations highlighted in the discussion, the analytical methods and resulting status and trends estimates provide the best available science on summer bat populations across North America and will continue to improve over time as monitoring data sets and analytical methods improve. • Moving forward, our occupancy analyses will continue to improve with submission of more 1) data from currently underrepresented areas (i.e., improved geographic representation), 2) manually-vetted acoustic recordings, 3) capture records, and 4) roost location and count data (summer and winter).

Report↗
USGS2002

Evaluation of a local grid refinement method for steady-state block-centered finite-difference groundwater models

A new method of local grid refinement for two-dimensional block-centered finite difference meshes that uses an iteration-based feedback to couple two separate grids has been developed. Its convergence properties have been evaluated and comparisons with alternative methods have been completed (Mehl and Hill, in review a). This work further investigates a difficulty encountered with the traditional telescopic mesh refinement (TMR) methods that lack a feedback. Results indicate: (1) Coupling the coarse grid with the refined grid in a numerically rigorous way that allows for a feedback can improve the coarse grid results; this improvement is not possible using the TMR methods because there is no feedback. (2) The TMR methods work well in situations where the better resolution of the locally refined grid has little influence on the overall flow-system dynamics, but if this is not true, lack of a feedback mechanism produced errors in head up to 6.8% and errors in cell-to-cell fluxes up to 7.1% for the case presented. (3) For the TMR methods, coupling using flux boundary conditions produces significant inconsistencies in the head distribution at the boundary interface. TMR inaccuracies can substantially effect parameter estimation (Mehl and Hill, in review b).

Developments in Water Science↗
USGS2003

An overview on current fluid-inclusion research and applications

This paper provides an overview of some of the more important developments in fluid-inclusion research and applications in recent years, including fluid-inclusion petrography, PVTX studies, and analytical techniques. In fluid-inclusion petrography, the introduction of the concept of 'fluid-inclusion assemblage' has been a major advance. In PVTX studies, the use of synthetic fluid inclusions and hydrothermal diamond-anvil cells has greatly contributed to the characterization of the phase behaviour of geologically relevant fluid systems. Various analytical methods are being developed and refined rapidly, with the Laser-Raman and LA-ICP-MS techniques being particularly useful for volatile and solute analyses, respectively. Ore deposit research has been and will continue to be the main field of application of fluid inclusions. However, fluid inclusions have been increasingly applied to other fields of earth science, especially in petroleum geology and the study of magmatic and earth interior processes.

Acta Petrologica Sinica↗
USGS1984

Selected papers in the hydrologic sciences 1984; July 1984

The rapid, accurate measurement of the oxygen content of soil gas in the unsaturated zone or dissolved oxygen in soil water in the saturated zone can be useful in wetland vegetation studies. A method has been devised and tested in the Great Dismal Swamp, a wetland with fine silt-clay and organic soils, that appears to provide good results. A 60-milliliter sample of soil gas or water is withdrawn from permanently installed chambers at various depths in the soil profile. The oxygen concentration of air samples is measured with a specially constructed analyzer cell fitted to the polarographic oxygen electrode of a portable oxygen meter. The dissolved oxygen concentration of water samples is measured directly with the oxygen electrode while stirring the sample in a 32-milliliter glass bottle with a portable magnetic stirrer. Field tests with duplicate chamber installations showed that consistent results are obtained for soil gas and water.

Water Supply Paper↗
USGS2007

Prediction of resource volumes at untested locations using simple local prediction models

This paper shows how local spatial nonparametric prediction models can be applied to estimate volumes of recoverable gas resources at individual undrilled sites, at multiple sites on a regional scale, and to compute confidence bounds for regional volumes based on the distribution of those estimates. An approach that combines cross-validation, the jackknife, and bootstrap procedures is used to accomplish this task. Simulation experiments show that cross-validation can be applied beneficially to select an appropriate prediction model. The cross-validation procedure worked well for a wide range of different states of nature and levels of information. Jackknife procedures are used to compute individual prediction estimation errors at undrilled locations. The jackknife replicates also are used with a bootstrap resampling procedure to compute confidence bounds for the total volume. The method was applied to data (partitioned into a training set and target set) from the Devonian Antrim Shale continuous-type gas play in the Michigan Basin in Otsego County, Michigan. The analysis showed that the model estimate of total recoverable volumes at prediction sites is within 4 percent of the total observed volume. The model predictions also provide frequency distributions of the cell volumes at the production unit scale. Such distributions are the basis for subsequent economic analyses. ?? Springer Science+Business Media, LLC 2007.

Natural Resources Research↗
USGS1996

Improved method for measuring water imbibition rates on low-permeability porous media

Existing methods for measuring water imbibition rates are inadequate when imbibition rates are small (e.g., clay soils and many igneous rocks). We developed an improved laboratory method for performing imbibition measurements on soil or rock cores with a wide range of hydraulic properties. Core specimens are suspended from an electronic strain gauge (load cell) in a closed chamber while maintaining the lower end of the core in contact with a free water surface in a constant water level reservoir. The upper end of the core is open to the atmosphere. During imbibition, mass increase of the core is recorded continuously by a datalogger that converts the load cell voltage signal into mass units using a calibration curve. Computer automation allows imbibition rate measurement on as many as eight cores simultaneously and independently. Performance of each component of the imbibition apparatus was evaluated using a set of rock cores (2.5 cm in diameter and 2–5 cm in length) from a signle lithostratigraphic unit composed of non-to-moderately welded ash-flow tuff (a glass-rich pyroclastic rock partially fused by heat and pressure) with porosities ranging from 0.094 to 0.533 m 3 m -3 . Reproducibility of sample handling and testing procedures was demonstrated using replicate measurements. Precision and accuracy of load cell measurements were assessed using mass balance calculations and indicated agreement within a few tenths of a percent of total mass. Computed values of sorptivity, S , ranged from 8.83 × 10 -6 to 4.55 × 10 -4 m s -0.5 . The developed method should prove useful for measuring imbibition rates on a wide range of porous materials.

Soil Science Society of America Journal↗
USGS2022

Comparing Landsat Dynamic Surface Water Extent to alternative methods of measuring inundation in developing waterbird habitats

This study investigates the applicability of the Landsat Dynamic Surface Water Extent (DSWE) science product for waterbird habitat modeling in multiple non-canopied habitat types. We compare surface water distribution estimates derived from DSWE to two site-specific survey methods: visual surveys and digitized aerial imagery. These site-specific surveys were conducted on Poplar Island, a restoration island project in the Chesapeake Bay, USA. Visual surveys were collected bimonthly from 2006 – 2013, and digitized aerial imagery was collected annually from 2006 – 2015. As a restoration island, Poplar Island presents a unique opportunity to analyze DSWE in a rapidly changing site. We structure our analysis based on the procedural development of individual sub-island cells developed from unconsolidated dredge material into fully restored wetlands that have independent hydrologic connection to the surrounding bay. Each development status is analyzed using our three DSWE classifications: Open Water (OW), a conservative estimate; Wetland Inclusive (WI), an aggressive estimate; and Development Dependent (DD), a landcover adaptive estimate. The OW classification consistently underestimates surface water coverage especially in the more complex, fully developed cells. The WI classification is better able to capture the tidal channels in these cells, but marginally overestimates surface water coverage in more sparsely vegetated cells. The DD classification does not significantly improve upon the estimations of the WI classification. Our data indicate that DSWE can be a capable alternative to our site-specific survey methods. However, the product is limited by Landsat’s 30 m spatial resolution, especially in more structurally complex wetlands. A recommended classification method for characterizing waterbird habitats would depend on the goals and targeted scale of analysis, for which DSWE may be a viable option.

Maryland↗
USGS2016

Complementary approaches to diagnosing marine diseases: a union of the modern and the classic

Linking marine epizootics to a specific aetiology is notoriously difficult. Recent diagnostic successes show that marine disease diagnosis requires both modern, cutting-edge technology (e.g. metagenomics, quantitative real-time PCR) and more classic methods (e.g. transect surveys, histopathology and cell culture). Here, we discuss how this combination of traditional and modern approaches is necessary for rapid and accurate identification of marine diseases, and emphasize how sole reliance on any one technology or technique may lead disease investigations astray. We present diagnostic approaches at different scales, from the macro (environment, community, population and organismal scales) to the micro (tissue, organ, cell and genomic scales). We use disease case studies from a broad range of taxa to illustrate diagnostic successes from combining traditional and modern diagnostic methods. Finally, we recognize the need for increased capacity of centralized databases, networks, data repositories and contingency plans for diagnosis and management of marine disease.

Philosophical Transactions of the Royal Society B:↗
USGS1986

Selected papers in the hydrologic sciences, 1986

West Point Reservoir is a multiple-purpose project on the Chattahoochee River about 112 river kilometers downstream from Atlanta on the Alabama-Georgia border. Urbanization has placed large demands on the Chattahoochee River, and water quality below Atlanta was degraded even before impoundment. Water-quality, bottom-sediment, and fish-tissue samples were collected from the reservoir to determine whether water-quality problems have occurred subsequent to impoundment. Severe hypolimnetic oxygen deficiency occurred in the reservoir following thermal stratification in the spring of 1978 and 1979. During stratified periods, concentrations of dissolved iron and manganese in the hypolimnion at the dam pool ranged from 0 to 7,700 and 30 to 2,000 micrograms per liter, respectively. During thermally stratified periods, phytoplankton standing crops in the upper lentic section of the reservoir ranged from 39,000 to 670,000 cells per milliliter. A maximum algal growth potential value (U.S. Geological Survey method) of 48.0 milligrams per liter was obtained at the uppermost data-collection station. The primary growth-limiting nutrients were nitrogen in the Iotic section and phosphorus in the lentic section. The highest measured concentrations of volatile solids and total iron, manganese, phosphorus, and organic carbon in sediments occurred in the lentic section of the reservoir, where bottom sediments consist mainly of silt and clay. Polychlorinated biphenyls and chlordane concentrations in the bottom sediments were as high as 740 and 210 micrograms per kilogram, respectively. Concentrations of polychlorinated biphenyls and chlordane in fish tissue ranged from 19 to 3,800 and 6.0 to 280 micrograms per kilogram, respectively.

Water Supply Paper↗
USGS2007

Use of eyeballs for establishing ploidy of Asian carp

Grass carp Ctenopharyngodon idella, silver carp Hypophthalmichthys molitrix, and bighead carp H. nobilis are now established and relatively common in the Mississippi and Atchafalaya rivers. Commercial fishers of Louisiana's large rivers report recurrent catches of grass carp, and the frequency of bighead carp and silver carp catch is increasing. Twelve black carp Mylopharyngodon piceus were recently captured from the Mississippi and Atchafalaya River system, and 10 were analyzed for ploidy. By using the methods described herein, all 10 fish were determined to be diploid. Such correct identifications of ploidy of feral Asian carp species, as well as other species, would provide science-based information constructive for meeting reporting requirements, tracking fish movements, and forecasting expansion of species distribution. To investigate the postmortem period for sample collection and to lessen demands on field operations for obtaining samples, a laboratory study was performed to determine the length of time for which eyeballs from postmortem black carp could be used for ploidy determinations. Acquiring eyes rather than blood is simpler and quicker and requires no special supplies. An internal DNA reference standard with a documented genome size, including erythrocytes from diploid black carp or Nile tilapia Oreochromis niloticus, was analyzed simultaneously with cells from seven known triploid black carp to assess ploidy through 12 d after extraction. Ploidy determinations were reliable through 8 d postmortem. The field process entails excision of an eyeball, storage in a physiological buffer, and shipment within 8 d at refrigeration temperatures (4??C) to the laboratory for analysis by flow cytometry. ?? Copyright by the American Fisheries Society 2007.

North American Journal of Fisheries Management↗
USGS2015

Downscaling global land-use/land-cover projections for use in region-level state-and-transition simulation modeling

Global land-use/land-cover (LULC) change projections and historical datasets are typically available at coarse grid resolutions and are often incompatible with modeling applications at local to regional scales. The difficulty of downscaling and reapportioning global gridded LULC change projections to regional boundaries is a barrier to the use of these datasets in a state-and-transition simulation model (STSM) framework. Here we compare three downscaling techniques to transform gridded LULC transitions into spatial scales and thematic LULC classes appropriate for use in a regional STSM. For each downscaling approach, Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathway (RCP) LULC projections, at the 0.5 × 0.5 cell resolution, were downscaled to seven Level III ecoregions in the Pacific Northwest, United States. RCP transition values at each cell were downscaled based on the proportional distribution between ecoregions of (1) cell area, (2) land-cover composition derived from remotely-sensed imagery, and (3) historic LULC transition values from a LULC history database. Resulting downscaled LULC transition values were aggregated according to their bounding ecoregion and “cross-walked” to relevant LULC classes. Ecoregion-level LULC transition values were applied in a STSM projecting LULC change between 2005 and 2100. While each downscaling methods had advantages and disadvantages, downscaling using the historical land-use history dataset consistently apportioned RCP LULC transitions in agreement with historical observations. Regardless of the downscaling method, some LULC projections remain improbable and require further investigation.

AIMS Environmental Science↗
USGS2003

Using multiple logistic regression and GIS technology to predict landslide hazard in northeast Kansas, USA

Landslides in the hilly terrain along the Kansas and Missouri rivers in northeastern Kansas have caused millions of dollars in property damage during the last decade. To address this problem, a statistical method called multiple logistic regression has been used to create a landslide-hazard map for Atchison, Kansas, and surrounding areas. Data included digitized geology, slopes, and landslides, manipulated using ArcView GIS. Logistic regression relates predictor variables to the occurrence or nonoccurrence of landslides within geographic cells and uses the relationship to produce a map showing the probability of future landslides, given local slopes and geologic units. Results indicated that slope is the most important variable for estimating landslide hazard in the study area. Geologic units consisting mostly of shale, siltstone, and sandstone were most susceptible to landslides. Soil type and aspect ratio were considered but excluded from the final analysis because these variables did not significantly add to the predictive power of the logistic regression. Soil types were highly correlated with the geologic units, and no significant relationships existed between landslides and slope aspect. ?? 2003 Elsevier Science B.V. All rights reserved.

Engineering Geology↗
USGSDate not supplied

Characterizing the two-dimensional thermal conductivity distribution in a sand and gravel aquifer

Both hydrologic and thermal transport properties play a significant role in the movement of heat through permeable sedimentary material; however, the thermal conductivity is rarely characterized in detailed spatial resolution. As part of a study of the movement of thermal plumes through a sand and gravel aquifer, we have constructed a two-dimensional profile of thermal conductivity. This work consisted of: (i) measuring the thermal conductivity of the soil solids, λ s , for the main stratigraphic units using the steady-state divided-bar apparatus and estimating conductivity from mineral composition; (ii) measuring the volumetric water content and porosity using crosshole ground-penetrating radar; (iii) evaluating four models used to predict the apparent thermal conductivity, λ, of variably saturated soils and selecting the best model using the information-theoretic approach, (iv) calculating the λ field on a 0.25-m square cell grid using measured data and the selected model, and (v) simulating thermal transport within the two-dimensional domain using a finite element numerical model. The apparent thermal conductivity in the saturated aquifer ranges from 2.14 to 2.69 W m −1 K −1 with a mean of 2.42 W m −1 K −1 Numerical simulations show that the heterogeneous thermal conductivity field results in increased thermal dispersion that is most pronounced at the plume front. Our values for λ and λ s may be used for glacial soils with similar mineralogy and texture. Our methods may also be used at other sites to construct the thermal conductivity distribution.

Ontario↗