bluuebunny/crossref_metadata_2025_split huggingface dataset:
Penetration of poly(ethylene glycol) into wood cell walls of red pine
Authors: Jeremic Dragica , Cooper Paul , Brodersen Peter 
Published: April 2007

Abstract
Penetration of poly(ethylene glycol) (PEG) with a wide range of molecular weights into cell walls of red pine wood was investigated. The study included bulking measurements and visualization of diffusion of brominated PEG by scanning transmission electron microscopy coupled to an energy-dispersive X-ray analyzer (STEM-EDXA) and a time-of-flight secondary ion mass spectrometer (ToF-SIMS). Both bulking and visualization techniques were in agreement, showing that all molecular weights of the polymer (PEG 1000, PEG 8000, and PEG 20000) are capable of penetrating cell walls. ToF-SIMS was more sensitive than STEM-EDXA, allowing visualization of lower amounts of brominated PEG. A trend to higher concentrations of PEG in the middle lamellae was observed.
The Ethical and Regulatory Problems in the Stem Cell Scandal
Authors: Aera Han 
Published: April 2007

AbstractThe recent stem cell scandal of fabrication of two papers published in Science by Dr. Hwang Woo Suk shocked the world and devastated the South Korean society. Investigations conducted by the South Korean government have revealed a variety of ethical and regulatory failures. In this paper, I first explain the South Korean regulatory background to research conducted on human subjects in general and on biotechnological research in particular, and then analyze the ethical and regulatory problems affecting the research for the two papers published in 2004 and 2005 by Dr. Hwang's team, respectively. These problems can be summarized as: 1) problems regarding egg donation (lack of informed consent and donation by vulnerable subjects), 2) ambiguous record-keeping of research funding, 3) insufficient reviews by the two local IRBs (an already established IRB and a newly established IRB, both deferred to the principal scientist's heavy-handed influence), 4) too close ties between the research team and government officials, and 5) the National Bioethics Committee's inertia and lack of impartiality.
Using Demographic Models to Determine Intrinsic Rate of Increase and Sustainable Fishing for Elasmobranchs: Pitfalls, Advances, and Applications
Authors: Gedamke Todd , Hoenig John M. , Musick John A. , DuPaul William D. , Gruber Samuel H. 
Published: April 2007

Abstract
Leslie matrices and life tables are demographic models commonly used to evaluate the ability of specific elasmobranch life history strategies to sustain given levels and patterns of fishing pressure. These models are generally density independent and provide an instantaneous rate of population growth for a specified set of life history traits that correspond to a specific population size. Many investigators are using these models to compute rates of population growth that they claim are estimates of the maximum population growth rate (rintrinsic); they then use these estimates to compute purported estimates of maximum sustainable fishing mortality. However, neither a Leslie matrix nor a life table can be used to estimate rintrinsic without additional information, except in the special case where a severely depleted population is modeled. Only in a severely depleted population will competition for resources be at a minimum and both density-dependent compensation and the rate of population growth be at a maximum (i.e., at rintrinsic). The fundamental problem is to determine the life history parameters that would occur if the population were extremely depleted because extensive observations on extremely depleted populations are rare. In the absence of such data, rintrinsic can only be estimated from these types of density-independent models by extrapolating observed population growth rates toward zero population size. We illustrate the problems in, and describe methods for, estimating rintrinsic and present information on two species of elasmobranch: barndoor skate Dipturus laevis and lemon shark Negaprion brevirostris
Quantification of the Vital Rates, Abundance, and Status of a Critical, Endemic Population of Bonneville Cutthroat Trout
Authors: Budy Phaedra , Thiede Gary P. , McHugh Peter 
Published: April 2007

Abstract
Most subspecies of cutthroat trout Oncorhynchus clarkii are imperiled or extinct due to the combined effects of habitat degradation and interactions with exotic species. To quantify abundance and vital rates and evaluate trends, we selected a large population of Bonneville cutthroat trout O. clarkii utah from the Logan River of northern Utah, a river characterized by high-quality and connected habitat. Over a 5-year period, we completed a comprehensive population assessment, including depletion-based abundance estimates and a mark–recapture study (1,050 tagged fish) of site fidelity, growth, and survival. Population density exceeded 1,500 cutthroat trout/km at high-elevation sites; this is substantially higher than most other reported densities of inland, stream-type cutthroat trout. Fish demonstrated extremely high rates of site fidelity on average (92%; SE = 6%), and growth rates were also high (up to 0.50 g/d; mean = 0.09 g/d). Cormack–Jolly–Seber survival rates (fish ≥ 100 mm) increased with age-class (group effect) and condition (individual covariate) and ranged from over 64% at high-elevation sites to approximately 30% at lower-elevation sites. Population growth rates (λ) appeared to be declining overall; however, 95% confidence intervals of λ frequently overlapped 1.0, indicating high variability that limited conclusions about future status. Both survival rate and fish density were consistently lower at sites where Bonneville cutthroat trout were sympatric with exotic brown trout Salmo trutta. The continuity, connectedness, and large size of this habitat fragment of the Logan River have clearly contributed to the persistence of this population. Our results provide important conservation and recovery benchmarks for identifying rangewide limiting factors of cutthroat trout. We recommend a precautionary approach to management of this endemic and important population; potential options include habitat protection or restoration and the removal of exotic brown trout.
Otolith Trace Element Chemistry as an Indicator of Anadromy in Yukon River Drainage Coregonine Fishes
Authors: Brown Randy J. , Bickford Nate , Severin Ken 
Published: April 2007

AbstractEight coregonine species have been documented in the Yukon River drainage. They include inconnuStenodus leucichthys, broad whitefishCoregonus nasus, humpback whitefishC. pidschian, Alaska whitefishC. nelsonii, least ciscoC. sardinella, Bering ciscoC. laurettae, round whitefishProsopium cylindracium, and pygmy whitefishP. coulterii. Personal use, sport, and commercial fisheries within the drainage target several of these species. Some species are capable of anadromous life histories, as evidenced by their presence in estuaries, yet few studies have investigated the upstream migrations of anadromous components of these populations. Only inconnu migrations have been previously examined in the Yukon River drainage. We investigated the distribution of anadromous coregonine fish in the Yukon River drainage in Alaska using sampling and otolith chemistry procedures. Six species were identified in sample collections from eight regions of the drainage between 1,200 and 2,000 km upstream from the Bering Sea. Gonadosomatic indices indicated that most sampled fish of all species were mature and preparing to spawn. Anadromous inconnu, broad whitefish, and humpback whitefish were distributed in the Yukon River and its tributaries to a maximum distance of 1,700 km from the sea. Anadromous least cisco were distributed in the Yukon River and its tributaries up to 1,600 km from the sea, whereas anadromous Bering cisco were present in the Yukon River main stem as far upstream as 2,000 km. No anadromous round whitefish were detected. Few coregonine spawning areas have been identified, so the actual migration distances of anadromous species may be greater than presented here.
A Structured Approach for Developing Indices of Biotic Integrity: Three Examples from Streams and Rivers in the Western USA
Authors: Whittier Thomas R. , Hughes Robert M. , Stoddard John L. , Lomnicky Gregg A. , Peck David V. , Herlihy Alan T. 
Published: April 2007

AbstractIn the late 1990s the Environmental Monitoring and Assessment Program of the U.S. Environmental Protection Agency developed a structured set of tests to evaluate and facilitate selection of metrics for indices of biotic integrity (IBIs). These IBIs were designed to be applicable across multistate regions as part of a national assessment of all U.S. waters. Here, we present additional steps in, and refinements to, that IBI development process. We used fish and amphibian assemblage data from 932 stream and river sites in 12 western U.S. states to develop IBIs for Mountains, Xeric, and Plains ecoregions. We divided 237 candidate metrics into nine metric classes representing different attributes of assemblage structure and function. For each ecoregion we sequentially eliminated metrics by testing metric range, signal‐to‐noise ratios, responsiveness to disturbance, and redundancy to select the best metric in each class. The IBIs for the Mountains and Plains each had seven metrics and the Xeric IBI had five. In the Mountains, half of the estimated stream length that could be assessed had IBI scores greater than 62 (out of 100). In the Xeric and Plains, half the stream length had scores no greater than 50 and no greater than 37, respectively. An estimated 16% of Xeric stream length had scores greater than 62 (the median for the Mountains), while 5% of Plains stream length had scores that exceeded 62. This IBI development process is less subjective and more streamlined and has more clearly defined criteria for metric selection and scoring than those used in the past, while maintaining a strong ecological foundation.
Development and Reliability Testing of the Clinical Pharmacist Recommendation Taxonomy
Authors: Hoth Angela B. , Carter Barry L. , Ness Jose , Bhattacharyya Anjan , Shorr Ronald I. , Rosenthal Gary E. , Kaboli Peter J. 
Published: April 2007

Study Objective. To evaluate the reliability of a newly developed taxonomy—the Clinical Pharmacist Recommendation (CPR) taxonomy—to classify clinical pharmacy interventions.Design. The CPR taxonomy was developed and refined in three phases. In each phase, reviewers independently reviewed recommendations made by a clinical pharmacist‐physician team and categorized them into mutually exclusive categories: priority, problem, and response. Interrater reliability was assessed for all categories during each development phase.Setting. Primary care clinics of a Veterans Affairs Medical Center.Patients. Fifty‐three patients enrolled in the Veterans Affairs Enhanced Pharmacy Outpatient Clinic (EPOC) trial.Measurements and Main Results. Interrater reliability was assessed using the κ statistic. A total of 423 recommendations were evaluated during the three testing phases. In the final testing phase, agreement was moderate for pharmacotherapy problem subcategories (κ=0.57), substantial for pharmacotherapy problem primary categories (κ=0.64), and almost perfect for response categories (κ=0.85). Taxonomy completion time/patient averaged 4.6 minutes (range 1–11 min).Conclusion. The CPR taxonomy provides a reliable method to systematically evaluate clinical pharmacy recommendations based on the therapeutic problem identified and specific action recommended to resolve the problem.
Prevalence of Illicit Use and Abuse of Prescription Stimulants, Alcohol, and Other Drugs Among College Students: Relationship with Age at Initiation of Prescription Stimulants
Authors: Kaloyanides Kristy B. , McCabe Sean E. , Cranford James A. , Teter Christian J. 
Published: April 2007

Study Objective. To examine associations between age at initiation of prescription stimulants and illicit use and abuse of prescription stimulants, alcohol, and other drugs among college students in the United States.Design. Web‐based survey of college students.Setting. A large (full‐time undergraduate population > 20,000) university.Intervention. A Web‐based survey was sent to a random sample of 5389 undergraduate college students plus an additional 1530 undergraduate college students of various ethnic backgrounds over a 2‐month period.Measurements and Main Results. Alcohol abuse was assessed by including a modified version of the Cut Down, Annoyance, Guilt, Eye‐opener (CAGE) instrument. Drug use‐related problems were assessed with a slightly modified version of the Drug Abuse Screening Test, short form (DAST‐10). The final sample consisted of 4580 undergraduate students (66% response rate). For the analyses, five subgroups were created based on age at initiation of prescription stimulant use: no prescription stimulant use, grades kindergarten (K)–4, grades 5–8, grades 9–12, and college. Undergraduate students to whom stimulants were prescribed in grades K‐4 reported similar rates of alcohol and other drug use compared with that of the group that had no prescription stimulant use. For example, students who started prescription stimulants in grades K‐4 were no more likely to report coingestion of alcohol and illicit prescription stimulants (odds ratio [OR] 1.4, 95% confidence interval [CI] 0.2–11.5, NS] than the group that had no prescription stimulant use. However, undergraduate students whose prescription stimulant use began in college had significantly higher rates of alcohol and other drug use. For example, students who started a prescription stimulant in college were almost 4 times as likely (OR 3.7, 95% CI 1.9‐7.1, p<0.001) to report at least three positive indicators of drug abuse on the DAST‐10 compared with the group that had no prescription stimulant use.Conclusions. In concordance with results of previous research, these results indicate that initiation of prescription stimulants during childhood is not associated with increased future use of alcohol and other drugs.
Thermal synthesis and characterization of AlχLa1-χ
P3O9
Authors: Bělina Petr , Šulcová Petra , Trojan Miroslav , Mazurek Pavel 
Published: April 2007

Abstract
New binary lanthanum-aluminum triphosphates were synthesized by thermal-condensation method from H3PO4, La2O3 and Al(OH)3. These pigments could be potentially used as special inorganic pigments; their corrosion-inhibition properties were widely studied. Synthesis conditions were determined on the basis of DTA and TG measurements. The products were also characterized by X-ray diffraction analysis. Physical properties — density by pycnometric method, particle size distribution, oil number and critical pigment volume concentration (CPVC), pH and specific conductivity of their aqueous extracts were also determined.
Minimotif Miner: A Computational Tool to Investigate Protein Function, Disease, and Genetic Diversity
Authors: Schiller Martin R. 
Published: April 2007

AbstractThe Minimotif Miner Web site contains information on several hundred short functional motifs in a single database, and allows the user to search protein queries for the presence of these motifs. Scoring based on evolutionary conservation, protein surface prediction, and motif frequency can be used in conjunction with other motif programs and the known biology of the query to reduce false‐positive predictions and select short motifs for experimental pursuit.
Assays for Determination of Protein Concentration
Authors: Olson Bradley J.S.C. , Markwell John 
Published: April 2007

AbstractBiochemical analysis of proteins relies on accurate quantitation of protein concentration. This unit describes how to perform commonly used protein assays, e.g., Lowry, Bradford, BCA, and UV spectroscopic protein assays. The primary focus of the unit is assay selection, emphasizing sample and buffer compatibility. Protein assay standard curves and data processing fundamentals are discussed in detail. This unit also details high‐throughput adaptations of the commonly used protein assays, and also contains a protocol for BCA assay of total protein in SDS‐PAGE sample buffer that is used for equal loading of SDS‐PAGE gels, which is reliable, inexpensive, and quick.
Recombineering: Genetic Engineering in Bacteria Using Homologous Recombination
Authors: Thomason Lynn , Court Donald L. , Bubunenko Mikail , Costantino Nina , Wilson Helen , Datta Simanti , Oppenheim Amos 
Published: April 2007

AbstractThe bacterial chromosome and plasmids can be engineered in vivo by homologous recombination using PCR products and synthetic oligonucleotides as substrates. This is possible because bacteriophage‐encoded recombination functions efficiently to recombine sequences with homologies as short as 35 to 40 bases. This recombineering allows DNA sequences to be inserted or deleted without regard to location of restriction sites. This unit first describes preparation of electrocompetent cells expressing the recombineering functions and their transformation with dsDNA or ssDNA. Support protocols describe a two‐step method of making genetic alterations without leaving any unwanted changes, and a method for retrieving a genetic marker (cloning) from the E. coli chromosome or a co‐electroporated DNA fragment and moving it onto a plasmid. A method is also given to screen for unselected mutations. Additional protocols describe removal of defective prophage, methods for recombineering.
Constructing Recombinant DNA Molecules by PCR
Authors: Elion Elaine A. , Marina Pablo , Yu Lu 
Published: April 2007

AbstractThis unit describes the use of PCR to construct hybrid DNA molecules. The unit provides an overview of how PCR can be exploited to accomplish numerous cloning strategies. The Basic Protocol outlines the PCR amplification and cloning strategies. The Commentary includes a troubleshooting guide for problems most frequently encountered in PCR cloning, plus four specific examples of the application of this technique to create in‐frame fusion proteins, to create recombinant DNA products, to generate deletions and inversions by inverse PCR, and to introduce mutagenized PCR products or specific mutations or fusions by gap repair in yeast.
Strategies for Large‐Insert Cloning and Analysis
Authors: Smith Douglas R. , Moir Donald T. 
Published: April 2007

AbstractThis revised introduction provides an up‐to‐date overview of available resources and methods for identifying, mapping, manipulating, and analyzing large‐insert (BAC, YAC, PAC, and P1) clones from the human genome or from other genomes. The table listing available libraries and clone resources has been updated, emphasizing widely used resources that are readily available and that were also used to map and sequence the human genome. Mapping references have been updated, along with links to web sites that provide online access to integrated mapping and sequencing resources. Additional information is included on restriction endonuclease fingerprinting approaches and on transformation‐associated recombination (TAR) cloning methods for rescue of genes or genomic segments from specific cell types or individuals.
Characterization of Flow Cytometer Instrument Sensitivity
Authors: Hoffman Robert A. , Wood James C.S. 
Published: April 2007

AbstractFluorescence sensitivity, measured in terms of resolution, allows the researcher to more accurately answer the question of how dim a cell can be and still be resolvable from another population. This measure focuses on the width, i.e., the standard deviation, of the population distributions and not on the location, i.e., the mean intensity, of populations on a histogram scale relative to the background. To determine the fluorescence sensitivity in terms of the resolution, both the detection efficiency, Q, and optical background, B, need to be measured. Both factors affect the ability to resolve dimly fluorescent subpopulations, and both factors are required to uniquely characterize the performance of a flow cytometer. Using Q and B, it is possible to determine the minimum fluorescence intensity that is resolvable from the background or from another population. This unit describes a practical and robust approach to measure the critical factors that determine the ability of a flow cytometer to analyze dimly fluorescent particles.
Separation of binary mixtures of carbon dioxide and methane through sulfonated polycarbonate membranes
Authors: Sridhar S. , Aminabhavi Tejraj M. , Ramakrishna M. 
Published: April 2007

AbstractPolycarbonate (PC) was sulfonated to varying degrees using acetyl sulfate. FTIR and NMR experiments were carried out to confirm sulfonation. The membranes were characterized by DSC and TGA to assess thermal stability. Ion exchange capacity (IEC) and degree of sulfonation (DS) were determined and their effect on permeation of CO2 and CH4 gases was investigated. Free volume fractions (FVF) of the membranes were found to decrease from 0.31 to 0.19 as the DS increased from 0 to 39.4%. Single gas permeation studies revealed that sulfonated PC exhibited higher selectivities than unmodified PC at reduced permeability. For a DS of 14.4%, sulfonated PC exhibited a selectivity of 36.1, which was 1.7 times that of unmodified PC, whereas the permeability dropped from 8.4 to 4.7 Barrers. In case of binary CO2/CH4 mixture permeation through PC membrane of the same DS, an increase in CO2 feed concentration from 5 to 40 mol % produced an increase in permeability from 0.24 to 2.0 Barrers and a rise in selectivity from 11.7 to 27.2 at constant feed pressure (20 bar) and temperature (30°C). A rise in the feed pressure from 5 to 30 bar at a constant feed composition of 5% CO2 resulted in a reduction in permeability from 0.38 to 0.2 Barrers and selectivity from 15.6 to 10.2. Sulfonated PC was found to be a promising candidate for separation of CO2 from CH4. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007
Rheological characterization of chitosan matrices: Influence of biopolymer concentration
Authors: Diez‐Sales O. , Dolz M. , Hernández M. J. , Casanovas A. , Herraez M. 
Published: April 2007

AbstractViscoelastic properties of chitosan (CH), chitosan‐poly(ethylene glycol) 400 (CH‐PEG), and chitosan‐poly(ethylene glycol) 400 with glyoxal as crosslinking agent (CH‐PEG‐Gly) systems were studied to analyze the effect of chitosan concentration (from 0.83 to 1.67%). Dynamic moduli increase as chitosan concentration increases for all systems. For CH and CH‐PEG systems the loss modulus (G″) is greater than the storage modulus (G′) with predominance of the viscous over the elastic behavior. This corresponds to the characteristic behavior of solutions (nonstructured systems). The presence of PEG 400 induces a complementary reinforcement of the mechanical properties of the system. Except for the lowest chitosan concentration, when glyoxal was added to the CH‐PEG systems, a gelled matrix was obtained. In this case, G′ is greater than G″, and practically independent of frequency. This behavior is typical of three‐dimensional networks and indicates true gel formation, showing clear elastic behavior (tan δ < 1). In creep and recovery analysis, CH‐PEG‐Gly systems exhibited distinct regions that were mathematically modeled using Burger's model. This analysis shows that the CH‐PEG‐Gly matrices (from 1.25 to 1.67%) recover almost totally (100%). Therefore, these matrices could be useful as systems for the development of films for topical hydrophilic drug delivery, and the levels of the residual viscosity (η0) or the complex viscosity (η*) could be used to control drug release. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007