bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Characteristics of Greenback Cutthroat Trout in Streams: Their Relation to Model Predictions andRecovery Criteria
Authors: Young Michael K. , Guenther-Gloss Paula M. 
Published: June 2004

Abstract
Fishes listed under the U.S. Endangered Species Act receive intensive management, but evaluations of population characteristics are rare. We report population and habitat characteristics of federally threatened greenback cutthroat trout Oncorhynchus clarki stomias in 12 streams in north-central Colorado surveyed in 1998 and 1999. Our objectives were to assess population size, structure, and distribution, to evaluate a model developed by Harig and Fausch (2002) to assess translocation success, and to compare population characteristics to those reported in the recovery plan. Allopatric population sizes in 10 streams varied from 170 to 7,347 greenback cutthroat trout at least 75 mm long, whereas the 2 streams with brook trout throughout supported 0–142 greenback cutthroat trout. Populations displayed few upstream–downstream trends in fish abundance or mean length, and the coefficient of variation among sampled reaches within streams averaged 61%. As the density of fish at least 75 mm long increased, the percentage of juvenile (&lt;75 mm) fish in a population increased, the percentage of adult (&gt;125 mm) fish longer than 200 mm decreased, and the average weight of a 200-mm fish declined. The abundance of juvenile fish was positively correlated with summer water temperature. Population estimates were highly correlated with the translocation model index values, suggesting that the translocation model may apply to other cutthroat trout taxa in similar environments. Of the 12 streams for which our extensive field data are available, 4 satisfied the recovery criteria we studied and other criteria in the recovery plan; 8 did not. We conclude that many populations of greenback cutthroat trout, including some that meet recovery criteria, are still at risk of extinction and that a reliable monitoring protocol needs to be established.
A Conditional Constant Catch Policy for Managing the Pacific Halibut Fishery
Authors: Clark William G. , Hare Steven R. 
Published: June 2004

Abstract
Since 1985, the staff of the International Pacific Halibut Commission (IPHC) has used a constant harvest rate policy—currently 20% of exploitable biomass—to estimate the yield currently available from Pacific halibut Hippoglossus stenolepis stock. This paper outlines a more stable alternative policy in which yield is held constant at some ceiling level so long as taking that yield would not result in a total exploitation rate exceeding a specified ceiling rate. During any periods of low abundance, the policy would revert to a constant harvest rate policy at the ceiling rate. The ceiling harvest rate would be chosen so as to assure that spawning biomass remained above a specified minimum. A policy of this kind could produce a yield similar to the present 20% constant harvest rate policy but with much less year-to-year variation attributable to changes in stock abundance, assessment methods, and estimated removals by other fisheries.
Effects of Acoustic Transmitters on Swimming Performance and Predator Avoidance of Juvenile Chinook Salmon
Authors: Anglea Steven M. , Geist David R. , Brown Richard S. , Deters Katherine A. , McDonald Robert D. 
Published: June 2004

Abstract
The objective of this study was to determine whether juvenile Chinook salmon Oncorhynchus tshawytscha are negatively influenced by the intraperitoneal implantation of acoustic transmitters. We evaluated swimming performance and predator avoidance of juvenile salmonids implanted with acoustic transmitters that weighed up to 6.7% of the fish's body weight in air. Critical swimming speeds (Ucrit) of tagged, sham-tagged (surgery but no tag), and control fish were measured in a respirometer to determine tag effects on swimming performance. Swimming performance was similar among treatment groups at 1-d and 21-d postsurgery intervals. Predator avoidance of fish implanted with active tags was evaluated to determine whether tagged fish were impaired by the operation of the tags or predators were attracted to the signals emitted from the tags. Predator avoidance was evaluated by comparing the proportion of each treatment group consumed (active tag, inactive tag, sham, and control) during exposure to piscivorous adult rainbow trout O. mykiss. Surgical implantation of acoustic tags in juvenile fall Chinook salmon did not significantly affect swimming performance. Implantation of acoustic transmitters (active and inactive) did not result in greater predation susceptibility in tagged fish than in untagged fish.
Electrofishing Effort and Fish Species Richness and Relative Abundance in Ozark Highland Streams of Arkansas
Authors: Dauwalter Daniel C. , Pert Edmund J. 
Published: June 2004

Abstract
We sampled 15 stream sites in the Ozark Highlands ecoregion of Arkansas and examined the effect of increased backpack electrofishing effort on the richness and relative abundance estimates of fish species. Each site was 75 mean stream widths (MSWs) long and was divided into 15 consecutive segments that were each 5 MSWs long. For each site the percent of empirical and theoretical species richness and the percent of relative abundance similarity to the entire fish assemblage were calculated by adding consecutive segments using an approach that resulted in 15 accumulation curves per assemblage character for each stream site. On average, a distance of 53.8 MSWs (SD = 7.4) was needed to sample 95% of empirical species richness at a stream site, which was equal to an area of 2,722.0 m2 (SD = 1,967.0). For sampling 95% of theoretical species richness, an average of 101.8 MSWs (SD = 34.5), or 5,055.7 m2 (SD = 3,667.4), was needed. Obtaining 95% relative abundance similarity required an average sampling effort equivalent to 24.0 MSWs (SD = 8.9), or 1,269.7 m2 (SD = 932.1). Mean stream width explained more variance in the reach lengths and areas needed for estimates of species richness and relative abundance than did riffle-pool sequence length or watershed size. Our results should offer insight into species richness and relative abundance accumulation rates when using a one-pass backpack electrofishing sample in Ozark Highland streams of Arkansas.
The Frequency and Cost of Patient‐Initiated Device Removal in the ICU
Authors: Fraser Gilles L. , Riker Richard R. , Prato Stephen , Wilkins Micheline L. 
Published: June 2004

Objective. To determine the frequency and pattern with which patients in the intensive care unit (ICU) remove medical devices on their own, and the costs associated with this problem.Design. Prospective observational study.Setting. Two 10‐bed sections of a multidisciplinary ICU in a tertiary care teaching hospital.Patients. Adults admitted to the ICU for longer than 24 hours during October 1998.Interventions. None.Measurements and Main Results. Medical records were reviewed prospectively for the occurrence of patient‐initiated device removal and the responses to those events by health care providers. Associated costs were estimated using hospital databases and Medicare physician reimbursement schedules. Annual cost estimates were calculated using 1997 admission statistics for 1211 adults in an ICU for more than 24 hours. Thirty‐six patients were studied for 199 patient‐days. Ten patients (28%) removed 42 devices: 88% of these events involved gastrointestinal tubes and vascular catheters. Significant agitation was documented within 2 hours before 74% of the events. Estimated cost associated with device removal was $7606, or $181/event. The estimated annual cost in this 42‐bed ICU was more than $250,000.Conclusions. Patients commonly remove medical devices on their own, and this represents significant consumption of health care resources.
A Multicenter Evaluation of Gentamicin Therapy in the Neonatal Intensive Care Unit
Authors: Glover Mark L. , Shaffer Christopher L. , Rubino Christopher M. , Cuthrell Corey , Schoening Shellie , Cole Erika , Potter David , Ransom J. Laurence , Gal Peter 
Published: June 2004

Study Objective. To evaluate traditional nomogram (TN) versus individualized pharmacokinetic gentamicin dosing practices in neonatal intensive care units, focusing on achieving target therapeutic concentrations (peak > 8 μg/ml, trough < 2 μg/ml), number of dosing changes, number of concentrations obtained, and evidence of nephrotoxicity.Design. Retrospective chart review.Setting. Three neonatal intensive care units.Patients. Three hundred nine infants prescribed gentamicin.Intervention. None.Measurements and Main Results. Sixty‐seven percent of patients receiving pharmacokinetic dosing had initial peak concentrations of 8 μ/ml or greater compared with 7% of patients receiving TN dosing (p<0.001). Trough concentrations exceeding 2 μ/ml were reported in 23% of patients receiving TN dosing compared with 2% of pharmacokinetic‐dosed patients (p<0.001). Forty‐two percent and 6%, respectively, required dosage adjustments (p<0.01). The mean number of concentrations obtained per patient was 2.8 and 2.1, respectively (p<0.01). Neither group had evidence of gentamicin‐related nephrotoxicity.Conclusion. Compared with TN dosing, administering gentamicin loading doses and performing initial pharmacokinetic analysis resulted in rapid attainment of desired concentrations and fewer dosage adjustments, and allowed for a decrease in the number of gentamicin concentrations.
Retrospective Evaluation of the Effect of Valproate Therapy on Transaminase Elevations in Patients with Hepatitis C
Authors: Lott Rex S. , Helmboldt Kristin M. , Madaras‐Kelly Karl J. 
Published: June 2004

Study Objective. To evaluate whether a relationship exists between valproate treatment and transaminase elevations in patients who are positive for hepatitis C virus (HCV).Design. Retrospective medical record review.Setting. Veterans affairs medical center.Patients. A total of 214 HCV‐positive patients; 28 were treated with valproate (study group), 186 were not (control group).Intervention. Demographic characteristics; valproate treatment histories; plasma concentrations of alanine aminotransferase (ALT) and aspartate aminotransferase (AST), albumin, and bilirubin; and exposure to other potentially hepatotoxic drugs, including probable alcohol abuse, were evaluated.Measurements and Main Results. Hepatotoxicity was staged by comparing maximum ALT and AST values against upper limits of normal or patients' mean elevated baseline ALT and AST values. Data were analyzed using a logistic regression model. Control patients and those with longer durations of HCV were more likely (p<0.0171 and p<0.0142, respectively) to exhibit higher stages of hepatotoxicity. More valproate‐treated patients were exposed to other potential hepatotoxins at the time of peak transaminase elevations (50% vs 39%, p<0.005), whereas more control patients received two or more potential hepatotoxins (13% vs 4%, p<0.00005).Conclusion. Valproate treatment, either alone or in the presence of other potential hepatotoxins, does not appear to be related to increased transaminase elevations in patients with HCV.
Establishing and Maintaining System Linearity
Authors: Wood James C. S. 
Published: June 2004

AbstractA flow cytometer system transforms a received optical signal into an electrical signal whose amplitude ideally is directly proportional to the optical signal but in practice is at least related in a linear fashion. Establishment and maintenance of system linearity are prerequisites to accurate quantitative measurements. The many potential sources of offsets and nonlinearity are found in all parts of the detection, amplification, and data acquisition systems of a flow instrument. This unit aims to help investigators evaluate performance of the hardware in flow cytometer detection systems.
Shading Correction: Compensation for Illumination and Sensor Inhomogeneities
Authors: Young Ian T. 
Published: June 2004

AbstractThe interaction between objects in real space, the illumination, and the camera frequently leads to a situation in which a microscope image exhibits significant shading across the field of view. In general this shading effect is undesirable and requires elimination, especially for quantitative microscopy. Starting with a simple mathematical model, this unit develops procedures to correct images for the shading thus introduced in the image‐formation process. Two cases are distinguished: the a priori, which assumes the availability of calibration images in addition to the images of interest; and the a posteriori, which assumes that only the recorded images of interest are available.
High‐Sensitivity Immunofluorescence/Flow Cytometry: Detection of Cytokine Receptors and Other Low‐Abundance Membrane Molecules
Authors: Zola Heddy 
Published: June 2004

AbstractCell marker identification by traditional phenotyping techniques is now considered straight‐forward and relatively uncomplicated. In immunofluorescence/flow cytometry the sensitivity, or detection limit, depends on the reagents, staining, and instrument parameters. The sensitivity of the most commonly used procedures, based on fluorescein‐conjugated antibodies, is about 2,000 molecules of target antigen per cell, which is adequate for most of the widely used leucocyte markers. However, measuring target antigens of low density has proved very difficult indeed. Flow cytometric immunofluorescence is capable of detecting 100 molecules of target antigen per cell in practical applications, provided every step of the staining and analysis procedure is optimized for sensitivity. This level of sensitivity reveals staining not seen using conventional analytical procedures. This unit discusses the underlying principles of high‐sensitivity immunofluorescence and provides an excellent series of protocols for the practical detection of as few as 100 target antigen molecules per cell.
Whole Blood Analysis of Leukocyte‐Platelet Aggregates
Authors: Barnard Marc R. , Krueger Lori A. , Frelinger A.L. , Furman Mark I. , Michelson Alan D. 
Published: June 2004

AbstractIn inflammatory and thrombotic syndromes, platelets aggregate with circulating leukocytes, especially monocytes and neutrophils. The platelet binding is initiated primarily through platelet surface expression of P‐selectin (CD62P) following activation‐dependent degranulation. The levels of P‐selectin involved can be low enough to make direct measurement difficult, but detection of leukocyte‐platelet aggregates is relatively simply by whole‐blood flow cytometry. Light scatter and at least one leukocyte‐specific antibody are used to gate the desired population, and the presence of associated platelets is detected by immunostaining for abundant platelet‐specific markers.
Quality Control in Nucleic Acid Analysis
Authors: Hurley Anne A. 
Published: June 2004

AbstractAll flow cytometry systems require instrument quality control procedures such as are described for phenotyping. However, there are additional considerations for DNA analysis beyond those outlined for other types of analyses. Because flow cytometric analysis of cellular DNA content is an established procedure for measurement of DNA ploidy of tumors and of the fraction of cells in the S phase of the cell cycle two parameters that have prognostic utility in clinical oncology careful quality control of this type of analysis is essential. This unit discusses the quality control issues peculiar to quantitative analysis of cellular DNA content and provides information complementary to many of the units in this chapter.
Analysis of DNA Content and BrdU Incorporation
Authors: Darzynkiewicz Zbigniew , Juan Gloria 
Published: June 2004

AbstractDuring the past two decades, the techniques of analysis of cell cycle kinetics based upon the flow cytometric detection of BrdU incorporation have replaced the cumbersome autoradiographic methodology utilizing tritiated thymidine. This unit distills the knowledge gained over this time into concise and easy to follow protocols for DNA content analysis following thermal denaturation or acid denaturation, as well as a modified method that combines thermal denaturation with washless immunocytochemical detection of BrdU.
Combination DNA/RNA Fish and Immunophenotyping
Authors: Dirks Roeland W. 
Published: June 2004

AbstractThis unit presents methods for combining immunophenotyping with DNA/RNA FISH. The approach is used in so‐called genotype/phenotype analysis to identify chromosomal aberrations in sub‐populations of cells present in heterogenous populations. Combining RNA and DNA detection with identification of cellular proteins is quite difficult. This series of protocols is provided to enable the successful application of the combination of these techniques.
Assays of Natural Killer (NK) Cell Ligation to Target Cells
Authors: Renò Filippo , Papa Stefano , Vitale Marco , Zamai Loris 
Published: June 2004

AbstractAssays for natural killer cells have long been established in the flow repertoire, but successful application of a flow‐based protocol requires attention to many details. This unit provides these details in a comprehensive manner. In particular, the assay is designed for simple bench‐top cytometers, rather than for more complex research instruments. Following this protocol, even a novice user should be able to achieve successful completion of an NK assay.
Flow Cytometric Analysis of Cell Division by Dye Dilution
Authors: Lyons A. Bruce , Doherty Kathleen V. 
Published: June 2004

AbstractThe technique described in this unit uses the intracellular fluorescent label carboxyfluorescein diacetate succinimidyl ester (CFSE) to tag proliferating cells. Covalently bound CFSE is divided equally between daughter cells, allowing discrimination of successive rounds of cell division. The technique is applicable to in vitro cell division as well as to in vivo division of adoptively transferred cells and can resolve up to eight successive generations. CFSE is long lived, permitting analysis for several months after transfer, and has the same spectral characteristics as fluorescein, so monoclonal antibodies conjugated to phycoerythrin or other compatible fluorochromes may be used to immunophenotype the dividing cells.
Reporters of Gene Expression: Autofluorescent Proteins
Authors: Rasko John E.J. 
Published: June 2004

AbstractThis unit on GFP provides clear, detailed, easy‐to‐follow directions for successful transduction of GFP into appropriate cell lines, as well as carefully detailed strategy and trouble‐shooting sections. Instructions for sorting and purification of sucessfully transduced cells and for analysis and re‐analysis of cells together with sample data are all included. The discussion provides data on multiple GFP mutants and lists relevant sources and suggested reading material.
Multidimensional Data Analysis in Immunophenotyping
Authors: Loken Michael R. 
Published: June 2004

AbstractThe complexity of cell populations requires careful selection of reagents to detect cells of interest and distinguish them from other types. Additional reagents are frequently used to provide independent criteria for cell identification. Two or three monoclonal antibodies in combination with forward and right‐angle light scatter generate a data set that is difficult to visualize because the data must be represented in four‐ or five‐dimensional space. The separation between cell populations provided by the multiple characteristics is best visualized by multidimensional analysis using all parameters simultaneously to identify populations within the resulting hyperspace. Groups of cells are distinguished based on a combination of characteristics not apparent in any usual two‐dimensional representation of the data.
Antibiotic Susceptibility Testing by Flow Cytometry
Authors: Mason David J. , Mortimer Fiona C. , Gant Vanya A. 
Published: June 2004

AbstractFlow cytometry can provide a rapid indication of antibiotic susceptibility. This unit describes a number of fluorescent dyes that allow the cytometer to distinguish the heterogeneic nature of populations exposed to antibiotics. No single method can be used for multiple organisms, since it is the interference with the organisms growth and structural integrity that signals the impact of the antibiotic so rapidly. This unit discusses membrane structural changes as well as alterations in nucleic acid and the probes that can be successfully used with flow cytometry.
Functional Assays of Oxidative Stress Using Genetically Engineered Escherichia coli Strains
Authors: Herrera Guadalupe , Martínez Alicia , O'Cornor José‐Enrique , Blanco Manuel 
Published: June 2004

AbstractOxidative stress may be induced in bacteria by exogenous biocidal agents and is involved in endogenous metabolism. The oxyR operon is a main sensor of oxidative stress and oxyR‐deficient bacteria show enhanced sensitivity to oxidative stress and increased accumulation of intracellular reactive oxygen species (ROS). Flow cytometric functional assays in bacteria are limited by the impaired penetration of vital dyes trough the cell wall. Escherichia coli B WP2 strains possess an altered cell‐wall lipopolysaccharide that leads to increased membrane permeability. Flow cytometric analysis of WP2 strains is a convenient alternative for cytometric assays of bacterial function. This unit presents protocols for flow cytometric studies of intracellular oxidative stress in two E. coli B WP2 strains, wild‐type or deficient in the oxyR function, using ROS‐sensitive fluorogenic substrates. Support Protocols describe preparation of phage C21 stock for bacterial verification, verification of the WP2 phenotype, and verification of the deficiency in oxyR function.
Preparation of Human Epidermal Keratinocyte Cultures
Authors: Yamada Susan S. 
Published: June 2004

AbstractCultured keratinocytes have been used by a number of investigators in studies investigating wound repair and carcinogenesis, and they have also proven useful as a model for differentiation. This unit describes a protocol for establishing human keratinocytes in tissue culture. Human newborn foreskins are proteolytically digested to separate the epidermis and the dermis, and keratinocytes are obtained from the epidermis.
Purification of a Crude Mitochondrial Fraction by Density‐Gradient Centrifugation
Authors: Graham John M. 
Published: June 2004

AbstractMost mitochondria prepared by differential centrifugation are contaminated to some extent by lysosomes, peroxisomes, tubular Golgi membranes, and small amounts of endoplasmic reticulum. Density gradient centrifugation using a variety of density media‐‐sucrose, Percoll, Nycodenz, Iodixanol‐‐is described here and is used to prepare purer fractions of mitochondria. The resulting gradient can be analyzed for three marker enzymes: succinate dehydrogenase (mitochondria), b‐galactosidase (lysosomes), and catalase (peroxisomes).
Metabolic Labeling of Prenyl and Carboxyl‐Methyl Groups
Authors: Magee Anthony I. 
Published: June 2004

AbstractThis unit provides protocols for prenylation and carboxy‐methylation of proteins in cultured cells. These modifications often accompany fatty acid acylation. Cultured cells can be labeled biosynthetically using radiolabeled mevalonate, a precursor, to label intermediates that are incorporated as prenoids‐‐e.g., farnesyl and geranylgeranyl. Carboxy‐methylation often accompanies prenylation. The methyl group can be labeled using [3H‐methyl]methionine.
Radioiodination of Cellular Proteins
Authors: Caplan Steve , Baniyash Michal 
Published: June 2004

AbstractDespite the advances of non‐radioactive methods of protein labeling, radioiodination remains an important tool for studying proteins. This unit discusses several commonly used methods for radioiodination of proteins for various purposes. Included are several simple, reliable protocols for radioiodination of cell surface proteins on live cells, radioiodination of purified, solubilized membrane proteins, and radioiodination of purified soluble proteins.