bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antiprimer Quenching-Based Real-Time PCR and Its Application to the Analysis of Clinical Cancer Samples
Authors: Li Jin , Wang Fengfei , Mamon Harvey , Kulke Matthew H , Harris Lyndsay , Maher Elizabeth , Wang Lilin , Makrigiorgos G Mike 
Published: February 2006

AbstractBackground: Nucleic acid amplification plays an increasingly important role in genetic analysis of clinical samples, medical diagnostics, and drug discovery. We present a novel quantitative PCR technology that combines the advantages of existing methods and allows versatile and flexible nucleic acid target quantification in clinical samples of widely different origin and quality.Methods: We modified one of the 2 PCR primers by use of an oligonucleotide “tail” fluorescently labeled at the 5′ end. An oligonucleotide complementary to this tail, carrying a 3′ quenching molecule (antiprimer), was included in the reaction along with 2 primers. After primer extension, the reaction temperature was lowered such that the antiprimer hybridizes and quenches the fluorescence of the free primer but not the fluorescence of the double-stranded PCR product. The latter provides real-time fluorescent product quantification. This antiprimer-based quantitative real-time PCR method (aQRT-PCR) was used to amplify and quantify minute amounts of input DNA for genes important to cancer.Results: Simplex and multiplex aQRT-PCR demonstrated linear correlation (r2 &gt;0.995) down to a DNA input equivalent to 20 cells. Multiplex aQRT-PCR reliably identified the HER-2 gene in microdissected breast cancer samples; in formalin-fixed, paraffin-embedded specimens; and in plasma circulating DNA from cancer patients. Adaptation to multiplex single-nucleotide polymorphism detection via allele-specific aQRT-PCR allowed correct identification of apolipoprotein B polymorphisms in 51 of 51 human specimens.Conclusion: The simplicity, versatility, reliability, and low cost of aQRT-PCR make it suitable for genetic analysis of clinical specimens.
Utility of Thrombin-Generation Assay in the Screening of Factor V G1691A (Leiden) and Prothrombin G20210A Mutations and Protein S Deficiency
Authors: Hézard Nathalie , Bouaziz-Borgi Lobna , Remy Marie-Geneviève , Nguyen Philippe 
Published: February 2006

Abstract
Background: The thrombin-generation assay has a variety of clinical uses, including diagnosis of thromboembolism-related disease, and particular profiles are associated with thrombophilic risk factors. The aim of this study was to evaluate the use of this assay in screening and identifying patients who require specific thrombophilic testing.
Methods: We used a 2-step approach to perform specific thrombophilic testing and thrombin-generation assays on 169 consecutive patients. The first step was to identify particular profiles of thrombin generation corresponding to each type of thrombophilic risk factor and to determine the pertinent variables related to thrombin generation. We then performed ROC curve analysis for each predefined variable to determine the relevant cutoffs for identification of patients in need of further testing (negative predictive value, 100%).
Results: Suggestive profiles were seen in factor V Leiden (n = 49) and prothrombin (n = 12) mutations and in protein S deficiency (n = 12). ROC curves showed that factor V Leiden may be excluded when the difference between lag times obtained in the absence and presence of activated protein C (APC) is &gt;1.5 min and that prothrombin G20210A may also be excluded when the peak thrombin concentration is ≤426 nmol/L. In addition, protein S deficiency may be excluded when the percentage of APC-induced endogenous thrombin potential inhibition is &gt;63%.
Conclusion: The thrombin-generation assay represents a promising tool for screening thrombophilic risk factors, particularly in patients who are carriers of factor V Leiden or prothrombin G20210A mutations and patients with protein S deficiency.
Influence of Imprecision on ROC Curve Analysis for Cardiac Markers
Authors: Kupchak Peter , Wu Alan HB , Ghani Farooq , Newby L Kristen , Ohman E Magnus , Christenson Robert H 
Published: February 2006

Abstract
Background: There has been considerable debate regarding the impact of assay imprecision on the performance of cardiac biomarkers for diagnosis of acute coronary syndromes (ACS) and risk stratification for future adverse cardiac events.
Methods: Using existing data from 2 published clinical trials, we used a resampling method to statistically introduce 5%, 10%, and 20% imprecision to results for B-type natriuretic peptide (BNP) and cardiac troponin I (cTnI) and examined its impact on ROC curve analysis.
Results: Superimposition of artificial imprecision produced no significant difference in the area under the ROC curve observed for BNP for diagnosis of heart failure or for cTnI for 30-day risk stratification of patients with ACS.
Conclusion: Assay imprecision does not appear to be a critical determinant in the interpretation of cardiac marker results for patients with heart disease.
Allergy testing: the role of recombinant allergens
Authors: Mothes Nadine , Valenta Rudolf , Spitzauer Susanne 
Published: February 2006

AbstractCurrently, diagnosis of type I allergy is performed using crude allergen extracts, which allow the identification of the allergen-containing source responsible for type I allergic symptoms (e.g., allergic rhino-conjunctivitis, asthma) but not the disease-eliciting molecules. With the introduction of recombinant allergens produced by molecular biology techniques, a large panel of allergenic molecules has become available. The application of these recombinant allergens for in vitro tests has led to new forms of component-resolved diagnosis (CRD) and allows the establishment of a patient's individual reactivity profile. The increasing number of recombinant allergens characterized during the last decade has allowed the development of chip-based allergy tests for simultaneous detection of up to 5000 different allergens and epitopes. The introduction of these recombinant allergen-based tests into clinical practice improves the selection of patients for traditional specific immunotherapy and allows monitoring of the immunological efficacy of specific immunotherapy by measuring allergen-specific IgG antibodies. Besides their diagnostic application, recombinant allergens and hypoallergenic derivatives thereof have also been used as vaccines in clinical trials, and recent results have shown their usefulness for the treatment of type I allergy.
Autoimmune diagnostics in diabetes mellitus
Authors: Seissler Jochen , Scherbaum Werner A. 
Published: February 2006

AbstractType 1 diabetes results from a specific destruction of the insulin-producing β-cells of the pancreas. The disease is characterized by the appearance of specific autoantibodies against islet cell antigens. Autoantibodies to insulin, glutamic acid decarboxylase, tyrosine phosphatase IA-2 and cytoplasmic islet cell antibodies are useful markers for the differential diagnosis of type 1 diabetes when clinical and metabolic criteria alone do not allow definite classification. Autoimmune diagnostics is of particular importance in adults to discriminate between type 1 and type 2 diabetes and to assess the diagnosis of latent autoimmune diabetes in adults.
CYP2C8 polymorphism among the Portuguese
Authors: Cavaco Isa , Piedade Rita , Gil J. Pedro , Ribeiro Vera 
Published: February 2006

AbstractCytochrome P450 2C8 (CYP2C8) is a polymorphic phase I drug-metabolising enzyme involved in the metabolism of a wide variety of xenobiotics, as well as a proposed player in the regulation of vascular tone. Polymorphisms in this gene may have an impact on the metabolism of therapeutic drugs such as paclitaxel and verapamil. In this report we have determined the frequencies of the main non-synonymous
Establishment of an indocyanine green test using an automatic chemistry analyzer
Authors: Seong Moon-Woo , Song Sang-Hoon , Oh Joo-Young , Park Joong-Won , Lee Do-Hoon 
Published: February 2006

AbstractThe indocyanine green (ICG) clearance test has been used to assess the reserve of hepatic function. This method is based on the spectrometric measurement of its plasma concentration at maximum wavelength of 805nm, which requires a spectrophotometer and associated maintenance. We established an ICG clearance test using a Toshiba 200FR automatic chemistry analyzer that can be tuned to a wavelength of approximately 805nm. Five pooled sera spiked from 0 to 4.0mg/dL were analyzed for linearity test and precision was determined at five levels in the range 0.1–2.0mg/dL. The ICG retention rate at 15min (R15) was determined for 38 patients using a conventional method and our method. The ICG clearance test using the automatic chemistry analyzer showed good linearity, and precision ranged from 0.3% to 1.0% for within-run CVs and from 0.6% to 4.7% for total CVs. The degree of agreement between the two methods was also acceptable (mean difference of 1.5%). It is expected that the ICG test using the automatic chemistry analyzer can replace the conventional ICG clearance test, considering the excellent agreement, good precision and linearity over a clinically relevant range.
How the Irish Became Protestant in America
Authors: Carroll Michael P. 
Published: February 2006

AbstractIt often comes as a surprise to learn that most contemporary Americans who think of themselves as “Irish” are, in fact, Protestant, not Catholic. While commentators generally agree that these Protestant Irish-Americans are descended mainly from the Irish who settled in the United States prior to the Famine, the story of how theybecamethe Protestants they are is—this article argues—more complicated than first appears. To understand that story, however, one must correct for two historiographical biases. The first has to do with the presumed religiosity of the so-called “Scotch-Irish” in the pre-Famine period; the second involves taking “being Irish” into account in the post-Famine periodonlywith dealing with Catholics, not Protestants. Once these biases are corrected, however, it becomes possible to develop an argument that simultaneously does two things: it provides a new perspective on the contribution made by the Irish (generally) to the rise of the Methodists and Baptists in the early nineteenth century, and it helps us to understand why so many American Protestants continue to retain an Irish identity despite the fact that their link to Ireland is now almost two centuries in the past.
The Preacher Paradigm: Promotional Biographies and the Modern-Made Evangelist
Authors: Lofton Kathryn E. 
Published: February 2006

AbstractBetween 1886 and 1931, Christian publishing houses in the United States offered an unprecedented biographical profile of the contemporary American evangelist as an unambiguously modern figure. Sold at tabernacle tents, Christian bookshops, and church fund-raisers, these texts simultaneously document concerns with the modern landscape as they regale readers with the styles and stories of headlining American Protestants, including Dwight Moody (1837–1899), Sam Jones (1847–1906), Reuben Archer Torrey (1856–1928), J. Wilbur Chapman (1859–1918), Rodney “Gipsy” Smith (1860–1947), Billy Sunday (1862–1935), and Baxter “Cyclone Mac” McClendon (1879–1935). Although it is not difficult to discern distinguishing marks and regional inflections within the anecdotal particularities of these men, the overarching structure and themes of their chronologies is consistent. The purpose of this essay is to produce the beginning of a collective biography of the turn-of-the-century preacher, highlighting the persistent paradigm represented in the promotional products of these preachers. Whereas previous historians have described these men as antiquated proponents of an “old time” religion, this article argues that their narratives reveal a strikingly modern man, poised in an engaged and contradictory conflict with his contemporary moment.
Ultraviolet Radiation Attenuates Thrombospondin 1 Expression via PI3K‐Akt Activation in Human Keratinocytes
Authors: Kim Mi‐Sun , Oh Youn Jin , Lee SeRah , Kim Ji Eun , Kim Kyu Han , Chung Jin Ho 
Published: February 2006

ABSTRACTThrombospondin 1 (TSP1) is an extracellular glycoprotein and a recognized inhibitor of angiogenesis. Recent studies have demonstrated that UV radiation induces an angiogenic switch, by which it alters the balance between pro‐ and anti‐angiogenic factors in the skin. Here we describe the effects of acute UV exposure on TSP1 expression in human skin epidermis, primary keratinocytes and the epidermal cell line HaCaT. We found that protein and mRNA expressions of TSP1 are significantly reduced in human skin in vivo and in keratinocytes in vitro by a single UV exposure. In human skin and keratinocytes, UV exposure induced the phosphorylation of Akt, a downstream target of the PI3K pathways. Specific inhibitors of PI3K, wortmannin and LY294002, completely blocked Akt activation and UV‐induced TSP1 downregulation in keratinocytes. We showed that a specific Akt phosphorylation inhibitor and small interfering RNA‐mediated Akt depletion were also blocked by UV‐induced TSP1 downregulation in keratinocytes. In conclusion, our findings demonstrate that acute UV exposure downregulates TSP1 expression via PI3K‐Akt activation in human keratinocytes. These novel findings may help us understand the regulatory mechanisms of UV‐induced skin angiogenesis.
Density Responses of Subarctic Coastal Marine Fish and Crabs to Artificial Reefs
Authors: Sargent Philip S. , Gregory Robert S. , Schneider David C. 
Published: February 2006

AbstractStructurally complex habitats provide refuge from predators and higher invertebrate prey density—and therefore have higher densities of young fish—than do noncomplex (or barren) sea floors. Artificial reefs are used worldwide to increase seabed complexity in an attempt to increase fish and invertebrate densities and biomass. We employed small‐scale tetrahedral reefs to test three hypotheses: (1) that increased habitat complexity increases the density of individual demersal and epibenthic fish and crab species; (2) that association of affected species will be stronger during the day than at night; and (3) that the density of affected species will attenuate with distance from reefs. We deployed reefs with transects in Newman Sound, Newfoundland, Canada. Each reef transect was paired with a control transect and additional distant control transects along the 15‐m isobath. We estimated the densities of prevalent fish and crab species by means of scuba diving during the autumn of 1999 and summer of 2000. We observed a total of 722 fish and 362 crabs during this study. The densities of cunners Tautogolabrus adspersus in both years and winter flounder Pseudopleuronectes americanus and toad crabs Hyas araneus in 1999 significantly increased near artificial reefs during the day. Atlantic cod Gadus morhua and Greenland cod G. ogac showed some association with artificial reefs but not significantly so due to low daytime observations. For those species that showed an association with reefs, densities attenuated to baseline levels within 20 m from the reefs. None of the species examined were significantly associated with artificial reefs during the night. Yellowtail flounder Limanda ferruginea and rock crabs Cancer irroratus did not associate with reefs at any time.
Effect of soil properties on lead bioavailability and toxicity to earthworms
Authors: Bradham Karen D. , Dayton Elizabeth A. , Basta Nicholas T. , Schroder Jackie , Payton Mark , Lanno Roman P. 
Published: February 2006

Abstract
Soil properties are important factors modifying metal bioavailability to ecological receptors. Twenty-one soils with a wide range of soil properties (USA; http://soils.usda.gov/technical/classification/taxonomy/) were amended with a single concentration of Pb (2,000 mg/kg) to determine the effects of soil properties on Pb bioavailability and toxicity to earthworms. Earthworm mortality ranged from 0 to 100% acute mortality following exposure to the same total concentration of Pb (2,000 mg/kg) in amended field soils. Internal Pb concentrations in earthworms ranged from 28.7 to 782 mg/kg, with a mean of 271 mg/kg. Path analysis was used to partition correlations in an attempt to discern the relative contribution of each soil property. Results of path analysis indicated that pH was the most important soil property affecting earthworm mortality (p &lt; 0.01) and internal Pb (p &lt; 0.05). Soil pH was related inversely to mortality and internal Pb, soil solution Pb, and Pb bioavailability. The most important soil property modifying reproduction was amorphous iron and aluminum oxides (FEAL). Because FEAL is rich in pH-dependent cation-exchange sites, several soil properties, including pH, FEAL, and cation-exchange capacity, have a causal effect on Pb adsorption and soluble Pb. Path analysis is useful for assessing contaminated soils with a wide range of soil properties and can assist in ecological risk assessment and remediation decisions for contaminated sites. Soil properties are important factors modifying metal bioavailability and toxicity and should be considered during the ecological risk assessment of metals in contaminated soils.
How terrestrial snails can be used in risk assessment of soils
Authors: de Vaufleury Annette , Cœurdassier Michael , Pandard Pascal , Scheifler Renaud , Lovy Christiane , Crini Nadia , Badot Pierre-Marie 
Published: February 2006

AbstractAmong soil invertebrates, terrestrial snails are herbivorous and detritivorous organisms exposed to polluted soils by both digestive and cutaneous routes. Using laboratory-reared snails (Helix aspersa aspersa), we describe how the effects of contaminants on survival and growth of snails can be evaluated in laboratory bioassays. A national ring test was performed to assess the effect of Cd added to the soil or to the food. The ecotoxicity of sewage sludge also was evaluated. The present results demonstrate that toxicity depends on both the pollutants and the exposure route. Cadmium was sixfold more toxic for snails exposed via food contamination (median effective concentration [EC50], 68–139 μg/g) than via soil contamination (EC50, 534–877 μg/g), whereas the opposite occurred with the sewage sludge (EC50, 55% of sludge in the food and 10% of waste in the soil). A logistic relationship linked growth inhibition and internal Cd concentrations, which can reach 2,000 μg/g in the viscera of snails exposed to 626 μg/g in the food. No clear trend was found between Cu, Zn, Pb, Cr, and Ni concentrations in the sludge and in snail tissues. These data enabled the development of an international standard, which should enhance the use of terrestrial gastropods for both fundamental research and routine risk assessment in the terrestrial environment.
Developing a critical load approach for national risk assessments of atmospheric metal deposition
Authors: Hall Jane R. , Ashmore Mike , Fawehinmi Joseph , Jordan Crawford , Lofts Stephen , Shotbolt Laura , Spurgeon David J. , Svendsen Claus , Tipping Edward 
Published: February 2006

Abstract
The critical load approach has been proposed for evaluation of the need to reduce atmospheric emissions of metals that lead to transboundary transport and deposition across Europe. The present study demonstrates and evaluates the application of a critical load approach for national-scale risk assessment of metal deposition in the United Kingdom. Critical load maps, calculated using critical limits based on pH-dependent free metal ion activities, are presented. Current concentrations of lead and cadmium in soils are compared with two sets of critical limit values: First, limits based on the reactive soil concentration, and second, a pH-dependent free ion critical limit function, which takes into account variable soil characteristics across the country. The use of these two models leads to different conclusions about which areas of the United Kingdom are at greatest risk, partly because of differences in the range of values of pH and organic matter in soils used in ecotoxicological experiments and in the national database. Critical loads were calculated based on free ion critical limits; the critical loads were lowest in the south and east of the country and were associated with higher soil pH, lower runoff, and lower soil organic matter.
Copper inhibition of soil organic matter decomposition in a seventy-year field exposure
Authors: Sauvé Sébastien 
Published: February 2006

Abstract
On a site contaminated decades ago with Cu from a wood treatment facility, we can observe that the decomposition of soil organic matter has been slowed. This represents an exceptional data set, and it allows us to address many challenges faced by regulators and risk assessors who are trying to derive appropriate soil quality criteria. These data are representative of a field study with a very well-equilibrated contamination and allow the derivation of chronic toxicity threshold values for the inhibition of microbial respiration. Soil respiration is the main determinant of the carbon balance, and it is assessed using the accumulation of soil organic matter (SOM) in this case. Using data derived from a 70-year-old field study also has the advantage of not being subject to risk assessment uncertainty factors arising from the potential aging effects of spiked soil or to the uncertainty caused by laboratory-to-field differences, both of which are very difficult to address. The resulting toxicity thresholds for an inhibition of SOM degradation are 154, 193, and 285 mg Cu/kg dry soil for inhibition levels of 10, 20, and 50%, respectively. Setting those thresholds correctly is critical for a proper risk assessment relative to sustainable development and agriculture.
Effects of humic acid and competing cations on metal uptake byLolium perenne
Authors: Kalis Erwin J. J. , Temminghoff Erwin J. M. , Weng Liping , van Riemsdijk Willem H. 
Published: February 2006

AbstractWithin the bioticl ligand model, which describes relationships between chemical speciation and metal binding at an organism's surface, multicomponent (long-term) metal uptake by plants has seldom been studied. In the present work, we exposed perennial ryegrass to nutrient solutions with two levels of Cd, Cu, Ni, Pb, and Zn (1 and 0.1 μM) and with or without 30 mg/L of humic acid. Iron and Mn concentrations were constant over all treatments. The hypothesis tested was that humic acid lowers the free and labile metal concentration and, therefore, reduces the metal uptake and, finally, the metal content of the plant. The free metal ion concentrations in the nutrient solutions were measured by the Donnan membrane technique and labile metal concentrations by diffusive gradients in thin-films. The metal content of the shoots depends on the metal content of the roots. The metal content of the roots is a function of the adsorption of metals on the root surface. In a multicomponent system at metal concentrations of 1 μM, humic acid decreased Cu, Pb, and Fe adsorption at the root surface, but it increased Cd, Zn, and Mn adsorption at the root surface. Complexation of cations such as Cu, Pb, and Fe with high affinity for (dissolved) organic matter may lead to increased uptake of cations with low affinity for organic matter (Ni, Zn, and Cd) because of competition between cations at the root surface. The results suggest that competition between metal ions can play a major role in multicomponent metal uptake, which has to be taken into account during risk assessments of metal-polluted soils.