USGS Science⌕ Search

SEARCH · USGS Science

Results for “Cells”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,009 records · Page 56Linked to original sources
USGS1989

Pulmonary lesions in disseminated visceral coccidiosis of sandhill and whooping cranes

Fifty cranes, consisting of 46 sandhill (Grus canadensis) and four whooping cranes (Grus americana), were studied. Eighteen sandhill cranes and the four whooping cranes were naturally infected with disseminated visceral coccidiosis (DVC). The remaining sandhill cranes were chicks experimentally infected with oocysts of Eimeria reichenowi and/or E. gruis; five chicks served as controls. There were no clinical signs attributed to respiratory infection. Necropsy of naturally infected adult birds revealed nodules in many organs, including the lung, air sacs, trachea and nares. Artificially infected sandhill cranes and the whooping crane chicks that died from DVC had congestion and consolidated areas in the lung with frothy fluid in the airways. Grossly visible nodules were observed from 10 days postinoculation. Granulomatous pneumonia and tracheitis were observed with light microscopy. Lesions were associated with merogonic and gametogonic stages of eimerian coccidia. Granulomas and granulomatous foci contained parasitized large mononuclear cells. Merogonic stages were seen in lymphoid cells by ultrastructural examination. Oocysts were observed in the trachea and bronchial mucosa and admixed with exudate in the airways, indicating that crane eimerians can complete their life cycle at these sites. Of the few eimeriid coccidia that have extraintestinal stages of development in birds and mammals, only the species in cranes complete their life cycle in both the digestive and respiratory tracts.

Journal of Wildlife Diseases↗
USGS1999

Relating tumor score to hematology in green turtles with fibropapillomatosis in Hawaii

The relationship between hematologic status and severity of tumor affliction in green turtles (Chelonia mydas) with fibropapillomatosis (FP) was examined. During 1 wk periods in July 1997 and July 1998, we bled 108 free-ranging green turtles from Pala'au (Molokai, Hawaii, USA) where FP is endemic. Blood was analyzed for hematocrit, estimated total solids, total white blood cell (WBC) count and differential WBC count. Each turtle was assigned a subjective tumor score ranging from 0 (no visible external tumors) to 3 (heavily tumored) that indicated the severity of FP. There was a progressive increase in monocytes and a decrease in all other hematologic parameters except heterophils and total numbers of white blood cells as tumor score increased. These data indicate that tumor score can relate to physiologic status of green turtles afflicted with FP, and that tumor score is a useful field monitor of severity of FP in this species.

Hawai'i↗
USGS2000

Characterization of poxviruses from forest birds in Hawaii

Two strains of avian pox viruses were isolated from cutaneous lesions in Hawaiian crows ( Corvus hawaiiensis ) examined in 1994 and a third from a biopsy obtained in 1992 from an infected bird of the Apapane species ( Himatione sanguinea ) by inoculation of the chorioallantoic membranes (CAM) of developing chicken embryos. The resulting proliferative CAM lesions contained eosinophilic cytoplasmic inclusion bodies characteristic of pox virus infection. The pathogenicity of these three viruses in domestic chickens was mild as evidenced by the development of relatively minor lesions of short duration at the sites of inoculation. Their virulence in this host was similar to that of a fowlpox virus (FPV) vaccine strain and contrasted greatly with the ability of two field strains of FPV to produce extensive proliferative lesions. One of the Hawaiian crow pox virus isolates as well as the one originating from the Apapane species could be propagated in two secondary avian cell lines, QT-35 and LMH. A comparison of the restriction fragment length polymorphisms (RFLP) of the genomes of the two cell line-adapted viruses, generated by Eco RI digestion, revealed a limited degree of similarity. Moreover, neither profile was comparable to those of the two field isolates of FPV, which were almost indistinguishable from each other. Thus, based on the genetic distinctness of the two Hawaiian bird viruses, they appear to represent different strains of avipoxvirus.

Hawaii↗
USGS1998

A female black bear denning habitat model using a geographic information system

We used the Mahalanobis distance statistic and a raster geographic information system (GIS) to model potential black bear ( Ursus americanus ) denning habitat in the Ouachita Mountains of Arkansas. The Mahalanobis distance statistic was used to represent the standard squared distance between sample variates in the GIS database (forest cover type, elevation, slope, aspect, distance to streams, distance to roads, and forest cover richness) and variates at known bear dens. Two models were developed: a generalized model for all den locations and another specific to dens in rock cavities. Differences between habitat at den sites and habitat across the study area were represented in 2 new GIS themes as Mahalanobis distance values. Cells similar to the mean vector derived from the known dens had low Mahalanobis distance values, and dissimilar cells had high values. The reliability of the predictive model was tested by overlaying den locations collected subsequent to original model development on the resultant den habitat themes. Although the generalized model demonstrated poor reliability, the model specific to rock dens had good reliability. Bears were more likely to choose rock den locations with low Mahalanobis distance values and less likely to choose those with high values. The model can be used to plan the timing and extent of management actions (e.g., road building, prescribed fire, timber harvest) most appropriate for those sites with high or low denning potential.

Arkansas↗
USGS1999

Intestinal coccidiosis

Coccidia are a complex and diverse group of protozoan (single-celled organisms) parasites; the coccidia group contains many species, most of which do not cause clinical disease. In birds, most disease-causing or pathogenic forms of coccidia parasites belong to the genus Eimeria. Coccidia usually invade the intestinal tract, but some invade other organs, such as the liver and kidney (see Chapter 27). Clinical illness caused by infection with these parasites is referred to as coccidiosis, but their presence without disease is called coccidiasis. In most cases, a bird that is infected by coccidia will develop immunity from disease and it will recover unless it is reinfected. The occurrence of disease depends, in part, upon the number of host cells that are destroyed by the juvenile form of the parasite, and this is moderated by many factors. Severely infected birds may die very quickly. Often, tissue damage to the bird’s intestine results in interrupted feeding; disruption of digestive processes or nutrient absorption; dehydration; anemia; and increased susceptibility to other disease agents. In cranes, coccidia that normally inhabit the intestine sometimes become widely distributed throughout the body. The resulting disease, disseminated visceral coccidiosis (DVC) of cranes, is characterized by nodules, or granulomas, on the surface of organs and tissues that contain developmental stages of the parasite. Collectively, coccidia are important parasites of domestic animals, but, because each coccidia species has a preference for parasitizing a particular bird species and because of the self-limiting nature of most infections, coccidiosis in freeranging birds has not been of great concern. However, habitat losses that concentrate bird populations and the increasing numbers of captive-reared birds that are released into the wild enhance the potential for problems with coccidiosis.

Information and Technology Report↗
USGS2007

Overview of developmental, reproductive, and behavioral/ neurological effects of mercury exposures in wildlife

We review wildlife/mercury literature and our own research findings that demonstrate the relevance of wildlife toxicity data in protecting human health. Methylmercury affects wildlife through reduced adult survival and reproduction, aberrant behavior, immune system effects, and teratogenic effects. Methylmercury can readily cross the blood-brain barrier, is excreted into eggs in birds, and is transferred to young mammals across the placenta and in milk. Its principal effect on wildlife is on neurological functions. Wild mink (Mustela vison) and otter (Lutra canadensis) have died from methylmercury poisoning, with signs of poisoning including anorexia, loss of weight, incoordination, tremors, and convulsions, which are symptoms similar to those experienced by mercury-poisoned humans. Mammals also may experience tonic and clonic convulsions and an increase in fetal anomalies, again paralleling toxic problems in people. Antibody-producing cells can be suppressed by methylmercury. Microscopically, the most notable lesions are in the cerebrum. Extensive vacuolation of hepatocytes in the liver and necrosis and other changes in the appearance of the proximal convoluted tubules of the kidneys are often noted. When harp seals (Pagophilus groenlandicus) were dosed with methylmercury chloride the number of circulating erythrocytes decreased and white blood cell counts greatly increased. The poisoned seals also suffered from uremia, hyperproteinemia, hypercholesterolemia, hyperbilirubinemia, and elevations in lactic dehydrogenase and alkaline phosphatase. In birds, signs of methylmercury poisoning included emaciation and weakness in the extremities, which progressed until the birds died. Mercury poisoning in birds and mammals can be diagnosed from a combination of the signs of poisoning if the animal is still alive, the pathological effects seen in a gross necropsy, the histopathological effects seen with a microscope, and the concentrations of mercury in various tissues. Our studies with mallards (Anas platyrhynchos) suggest that the dietary concentrations of mercury that cause toxicity are lower than those set in fish consumption advisories to protect humans. Because wild mammals and birds are so sensitive to methylmercury poisoning and cannot escape dietary exposure the way humans can, guidelines set to protect wild birds and mammals may very well provide a margin of safety for human health.

Book chapter↗
USGS1987

A prospective field evaluation of an enzyme immunoassay: Detection of eastern equine encephalomyelitis virus antigen in pools of Culiseta melanura

A prospective field study was conducted to determine the sensitivity and specificity of an enzyme immunoassay (EIA) compared to virus isolation in cell culture for the detection of eastern equine encephalomyelitis (EEE) virus in naturally infected mosquitoes. A total of 10,811 adult female Culiseta melanura were collected in light traps during 1985 from four locations in Maryland. Eastern equine encephalomyelitis virus was isolated from 5 of 495 mosquito pools in African green monkey kidney and baby hamster kidney cell cultures. All five virus-infected pools were detected by the EIA, and all 490 uninfected pools were correctly scored as not containing virus. The EIA did not produce false positive or false negative results. Results support the assertion of previous researchers that the antigen detection EIA is a rapid, sensitive, specific, and simple alternative to traditional bioassays for the detection of EEE virus in mosquitoes.

Journal of the American Mosquito Control Associati↗
USGS1996

Ultrastructure of the haemocytes of Ixodes scapularis (Acari: Ixodidae)

Haemocytes of Ixodes scapularis were characterized on the basis of their ultrastructure by transmission electron microscopy of thin sections. Three types of haemocytes were identified: prohaemocytes, plasmatocytes, and granulocytes. Prohaemocytes are undifferentiated cells containing very little cytoplasm (high nucelo-cytoplasmic ratio). Plasmatocytes are rich in free ribosomes, mitochondria, rough endoplasmic reticulum, and have numerous peripheral vacuoles. Granulocytes are polymorphic cells containing granular inclusions and filopodia on the surface. Granulocytes are divided into two morphological types, type I and II, based on the structure of the granules.

Acarologia↗
USGS2009

Toxicity of polybrominated diphenyl ethers (de-71) in chicken (Gallus gallus), mallard (Anas platyrhynchos), and American kestrel (Falco sparverius) embryos and hatchlings

Embryonic survival, pipping and hatching success, and sublethal biochemical, endocrine, and histological endpoints were examined in hatchling chickens (Gallus gallus), mallards (Anas platyrhynchos), and American kestrels (Falco sparverius) following air cell administration of a pentabrominated diphenyl ether (penta-BDE; DE-71) mixture (0.01-20 mu g/g egg) or polychlorinated biphenyl (PCB) congener 126 (3,3', 4,4', 5-pentachlorobiphenyl; 0.002 mu g/g egg). The penta-BDE decreased pipping and hatching success at concentrations of 10 and 20 mu g/g egg in kestrels but had no effect on survival endpoints in chickens or mallards. Sublethal effects in hatchling chickens included ethoxyresorufin-O-dealkylase (EROD) induction and histological changes in the bursa, but these responses were not observed in other species. Polychlorinated biphenyl congener 126 (positive control) reduced survival endpoints in chicken and kestrel embryos and caused sublethal effects (EROD induction, reduced bursal mass and follicle size) in chickens. Mallards were clearly less sensitive than the other species to administered penta-BDE and PCB 126. In a second experiment, the absorption of penta-BDE (11.1 mu g/g egg, air cell administered during early development) into the contents of chicken and kestrel eggs was determined at various intervals (24 h postinjection, midincubation, and pipping). By pipping, 29% of the penta-BDE administered dose was present in the egg contents in chickens, and 18% of the administered dose was present in kestrel egg contents. Based on uptake in kestrels, the lowest-observed-effect level on pipping and hatching success may be as low as 1.8 mu g total penta-BDE/g egg, which approaches concentrations detected in eggs of free-ranging birds. Because some penta-BDE congeners are still increasing in the environment, the toxic effects observed in the present study are cause for concern in wildlife.

Environmental Toxicology and Chemistry↗
USGS2000

Field guide to malformations of frogs and toads: with radiographic interpretations

In 1995, students found numerous malformed frogs on a field trip to a Minnesota pond. Since that time, reports of malformed frogs have increased dramatically. Malformed frogs have now been reported in 44 states in 38 species of frogs, and 19 species of toads. Estimates as high as 60% of the newly metamorphosed frog populations have had malformations at some ponds (NARCAM, ’99). The wide geographic distribution of malformed frogs and the variety of malformations are a concern to resource managers, research scientists and public health officials. The potential for malformations to serve as a signal of ecosystem disruption, and the affect this potential disruption might have on other organisms that share those ecosystems, has not been resolved. Malformations represent an error that occurred early in development. The event that caused the developmental error is temporally distant from the malformation we see in the fully developed animal. Knowledge of normal developmental principles is necessary to design thoughtful investigations that will define the events involved in abnormal development in wild frog populations. Development begins at the time an egg is fertilized and progresses by chemical communication between cells and cell layers. This communication is programmed through gene expression. Malformations represent primary errors in development, errors in chemical communication or translation of genetic information. Deformations arise later in development and usually result from the influence of mechanical factors (such as amputation) that alter shape or anatomy of a structure that has developed normally. The occurrence and the type of malformations are influenced by the type of error or insult as well as the timing of the error (the developmental stage at which the error occurred). The appearance of the malformation can therefore provide clues that suggest when the error may have occurred. If the malformation is an incomplete organ, such as an incomplete limb, the factor or insult acted during a susceptible period prior to organ completion. Although defining the anatomy of the malformed metamorphosed frog can give us an idea of the approximate window during which the developmental insult was initiated, and might even suggest the type of insult that may have occurred, the morphology of the malformation does not define the cause. To define causes and mechanisms of frog malformations we need to use well designed investigations that are different from traditional tests used in acute toxicity or disease pathogenicity studies. When investigating malformations in metamorphosed frogs, we are looking at the affect of exposure to an agent that occurred early in tadpole development. Therefore investigations to determine causes of malformations need to look at agents that are present in the tadpoles or their environments at these early developmental times. Laboratory experiments need to expose embryos and tadpoles to suspect agents at appropriate developmental stages and look at acute results, such as toxicity and death, as well as following the developmental process to completion to determine the impact of the agent on the developing tadpole and the fully developed frog. This means holding animals past metamorphic climax to assure that the anatomy and physiology of the adult have developed normally. As we look at field collections of abnormal frogs, we need to keep in mind that these collections reflect survivors only. We are looking at malformations that were not fatal to tadpoles. We cannot assume that because we do not collect other malformations, they did not exist. More work needs to be done on the developing tadpole, in the field and in the laboratory, to better elucidate the range, frequency, character and causes of anuran malformations.

Biological Science Report↗
USGS1992

Contribution of 222Rn in domestic water supplies to 222Rn in indoor air in Colorado homes

The contribution of 222Rn from domestic water wells to indoor air was investigated in a study of 28 houses near Conifer, CO. Air concentrations determined by alpha-track detectors (ATDs) and continuous radon monitors were compared with the predictions of a single-cell model. In many of the houses, the water supply was shown to contribute significantly to levels of indoor 222Rn. The data from the ATD study were augmented with a continuous monitoring study of a house near Lyons, CO. The well water in that house has the highest known concentration of 222Rn in water yet reported (93 MBq m-3). The temporal pattern in the indoor 222Rn concentration corresponds to water-use records. In general, it is difficult to quantify the proportion of indoor radon attributable to water use. Several lines of evidence suggest that the single-cell model underestimates this proportion. Continuous- monitoring data, although useful, are impractical due to the cost of the equipment. We propose a protocol for 222Rn measurement based on three simultaneous integrating radon detectors that may help estimate the proportion of indoor 222Rn derived from the water supply.

Health Physics↗
USGS1998

Production of carbonate sediments by a unicellular green alga

This study investigates the ability of the unicellular green alga Natmochloris atoimis to precipitate CaCO3, quantifies mineral precipitation rates, estimates sediment production in a N. atomiis bloom, and discusses the implications of microbial calcification for carbonate sediment deposition. A series of N. atomus cultures, isolated from Lake Reeve, Australia, were incubated at various pH and calcium concentrations to determine environmental parameters for calcification. Rates of calcification were calculated from initial and postincubation alkalinity, pH, and calcium measurements. Replicate experiments and controls consisting of non-calcifying cultures, uninoculated media, and dead cell cultures were performed using environmental culture parameters determined in series cultures. Average calcification rates from replicate experiments were used to predict daily sediment production rates in a small bloom of N. atomus. N. atomus precipitates 0.138 g/L of calcite in approximately 4 h when incubated at pH 8.5, 14.24 mM calcium concentration, 33 ??C, 100 ??E/m2/s light intensity, and a cell population density of 107 cells/mL. Assuming continuous precipitation, this corresponds to a maximum estimated sediment production rate of 1.6 ?? 106 kg of CaCO3, per 12 h day in a single bloom of 3.2 ?? 109 L. Our results suggest that microbial calcification contributes significantly to the carbonate sediment budget.

American Mineralogist↗
USGS1998

Stochastic calibration of an orographic percipitation model

In this study a stochastic approach to calibration of an orographic precipitation model (Rhea, 1978) was applied in the Gunnison River Basin of south-western Colorado. The stochastic approach to model calibration was used to determine: (1) the model parameter uncertainty and sensitivity; (2) the grid-cell resolution to run the model (10 or 5 km grids); (3) the model grid rotation increment; and (4) the basin subdivision by elevation band for parameter definition. Results from the stochastic calibration are location and data dependent. Uncertainty, sensitivity and range in the final parameter sets were found to vary by grid-cell resolution and elevation. Ten km grids were found to be a more robust model configuration than 5 km grids. Grid rotation increment, tested using only 10 km grids, indicated increments of less than 10 degrees to be superior. Basin subdivision into two elevation bands was found to produce 'optimal' results for both 10 and 5 km grids.

Hydrological Processes↗
USGS2003

Goldquarryite, a new Cd-bearing phosphate mineral from the Gold Quarry mine, Eureka County, Nevada

Goldquarryite, idealized formula CuCd2Al3(PO44F2(H2O)10(H2O 2, structure-derived formula (Cu0.70???0.30??1.00(Cd1.68Ca0.32??2.00Al3 (PO44F2(H2O)10[(H2O 1.60F0.40]??2.00, is triclinic, space group P1, with unit-cell parameters derived from crystal structure: a = 6.787(1), b = 9.082(2), c = 10.113(2) A??, ?? = 101.40(1)??, ?? = 104.27(1)??, ?? = 102.51(1)??, V = 568.7(3) A??3, a:b:c: = 0.7473:1:1.1135, Z = 1. The strongest seven reflections in the X-ray powder-diffraction pattern are [d(A??)(I)(hkl)]: 9.433(100)(001); 4.726(30)(002); 3.700(30)(022); 3.173(30b)(122, 113, 120, 003); 3.010(30)(122, 212); 2.896(30)(211); 2.820(50)(022). The mineral occurs on a single specimen collected from the 5,425-foot bench, Gold Quarry mine, Eureka County, Nevada, as isolated clusters of radiating sprays of crystals and as compact parallel crystal aggregates, which are both found on and between breccia fragments. Sprays and aggregates never exceed 3 mm in longest dimension and typically average about 0.5 mm in size. Goldquarryite is a late-stage supergene mineral associated with opal, carbonate-fluorapatite and hewettite, on a host rock composed principally of brecciated and hydrothermally rounded jasperoid fragments which have been lightly cemented by late-stage silicification. Individual euhedral crystals are acicular to bladed, elongate [100], with a length-to-width ratio of approximately 20:1; the maximum size is 1.5 mm but most crystals do not exceed 0.4 mm in length. Forms are {010}, {001} major and {100} very minor. The mineral is pleochroic; translucent (masses) to transparent (crystals); very pale blue to blue-gray (crystals) or blue (masses); with a white streak and a vitreous to glassy luster. Goldquarryite is brittle, lacks cleavage, has an irregular fracture, and is nonfluorescent; hardness (Mohs') is estimated at 3-4; measured density is 2.78(1) g/cm3 (sink-float techniques using methylene iodide-acetone mixtures), calculated density is 2.81 g/cm3 (for formula and unit-cell parameters derived from crystal structure). Optically, it is biaxial positive, ?? = 1.570, ?? = 1.573, ?? = 1.578; 2V (meas.) = ???30??, 2V (calc.) = 76??; dispersion r < v, strong. Average electron-microprobe analysis: K2O = 0.17, CuO = 5.33, CaO = 1.25, NiO = 0.23, ZnO = 0.05, CdO = 26.24, Al2O3 = 15.22, V2O3 = 0.05, P2O5 = 28.04, F = 3.63, H2O (calculated assuming stoichiometry) = [22.19], -O = F = -1.53, total = 100.87 weight %, corresponding to [(Cu0.66Ni0.03Zn0.01) ??0.70.

Mineralogical Record↗
USGS2006

Salinity effects on viability, metabolic activity and proliferation of three Perkinsus species

Little is known regarding the range of conditions in which many Perkinsus species may proliferate, making it difficult to predict conditions favorable for their expansion, to identify conditions inducing mortality, or to identify instances of potential cross-infectivity among sympatric host species. In this study, the effects of salinity on viability, metabolic activity and proliferation of P. marinus, P. olseni and P. chesapeaki were determined. Specifically, this research examined the effects of 5 salinities (7, 11, 15, 25, 35???), (1) without acclimation, on the viability and metabolic activity of 2 isolates of each Perkinsus species, and (2) with acclimation, on the viability, metabolic activity, size and number of 1 isolate of each species. P. chesapeaki showed the widest range of salinity tolerance of the 3 species, with high viability and cell proliferation at all salinities tested. Although P. chesapeaki originated from low salinity areas (i.e. <15???), several measures (i.e. cell number and metabolic activity) indicated that higher salinities (15, 25???) were more favorable for its growth. P. olseni, originating from high salinity areas, had better viability and proliferation at the higher salinities (15, 25, 35???). Distinct differences in acute salinity response of the 2 P. olseni isolates at lower salinities (7, 11???), however, suggest the need for a more expansive comparison of isolates to better define the lower salinity tolerance. Lastly, P. marinus was more tolerant of the lower salinities (7 and 11???) than P. olseni, but exhibited reduced viability at 7???, even after acclimation. ?? Inter-Research 2006.

Diseases of Aquatic Organisms↗
USGS2011

Formulation of a correlated variables methodology for assessment of continuous gas resources with an application to the Woodford play, Arkoma Basin, eastern Oklahoma

Shale gas is a form of continuous unconventional hydrocarbon accumulation whose resource estimation is unfeasible through the inference of pore volume. Under these circumstances, the usual approach is to base the assessment on well productivity through estimated ultimate recovery (EUR). Unconventional resource assessments that consider uncertainty are typically done by applying analytical procedures based on classical statistics theory that ignores geographical location, does not take into account spatial correlation, and assumes independence of EUR from other variables that may enter into the modeling. We formulate a new, more comprehensive approach based on sequential simulation to test methodologies known to be capable of more fully utilizing the data and overcoming unrealistic simplifications. Theoretical requirements demand modeling of EUR as areal density instead of well EUR. The new experimental methodology is illustrated by evaluating a gas play in the Woodford Shale in the Arkoma Basin of Oklahoma. Differently from previous assessments, we used net thickness and vitrinite reflectance as secondary variables correlated to cell EUR. In addition to the traditional probability distribution for undiscovered resources, the new methodology provides maps of EUR density and maps with probabilities to reach any given cell EUR, which are useful to visualize geographical variations in prospectivity.

Oklahoma↗
USGS2012

Salmonid intranuclear microsporidosis

Nucleospora salmonis is an intra-nuclear microsporidian parasite in the family Enterocytozoonidae (Docker et al. 1997). Prespore stages of the parasite were first observed among adult and then juvenile Chinook salmon ( Oncorhynchus tshawytscha ) by Elston et al. (1987) and Morrison et al. (1990), respectively in Washington, U.S.A. The microsporidian nature of the parasite was subsequently confirmed by the observation of spores in lymphoblasts of juvenile Chinook salmon from California (Hedrick et al. 1991). The principal target cell for N. salmonis are hematopoietic cells which, upon infection, undergo proliferative changes leading to a leukemia-like condition with an accompanying anemia (Wongtavatchai et al. 1995).

Book chapter↗
USGS2008

SIM_ADJUST -- A computer code that adjusts simulated equivalents for observations or predictions

This report documents the SIM_ADJUST computer code. SIM_ADJUST surmounts an obstacle that is sometimes encountered when using universal model analysis computer codes such as UCODE_2005 (Poeter and others, 2005), PEST (Doherty, 2004), and OSTRICH (Matott, 2005; Fredrick and others (2007). These codes often read simulated equivalents from a list in a file produced by a process model such as MODFLOW that represents a system of interest. At times values needed by the universal code are missing or assigned default values because the process model could not produce a useful solution. SIM_ADJUST can be used to (1) read a file that lists expected observation or prediction names and possible alternatives for the simulated values; (2) read a file produced by a process model that contains space or tab delimited columns, including a column of simulated values and a column of related observation or prediction names; (3) identify observations or predictions that have been omitted or assigned a default value by the process model; and (4) produce an adjusted file that contains a column of simulated values and a column of associated observation or prediction names. The user may provide alternatives that are constant values or that are alternative simulated values. The user may also provide a sequence of alternatives. For example, the heads from a series of cells may be specified to ensure that a meaningful value is available to compare with an observation located in a cell that may become dry. SIM_ADJUST is constructed using modules from the JUPITER API, and is intended for use on any computer operating system. SIM_ADJUST consists of algorithms programmed in Fortran90, which efficiently performs numerical calculations.

Ground Water Modeling Investigation Report↗