bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interface resistive switching effects in bulk manganites
Authors: Belogolovskii Mikhail 
Published: February 2009

Abstract
A physical mechanism driving the resistance switching in heterocontacts, formed by a metal counterelectrode and electrically conducting bulk perovskite manganites, is discussed. The nature of the inelastic, charge-hopping transport inside insulating and strongly inhomogeneous metal/manganite interfaces is studied theoretically. Comparison with measured current-voltage characteristics for a La0.67Ca0.33MnO3/Ag heterostructure in a high-resistance state reveals the presence of one or more charge traps along a conduction path within the interface. In a low-resistance state the main charge-transferring events are direct tunneling ones. The analysis of electrical noise measurements for a La0.82Ca0.18MnO3 single crystal in three different charge-transport regimes shows scattering centers with a broad, flat spectrum of excitation states, independent of manganite electrical and/or magnetic characteristics. All of these results are consistent with an oxygen-drift model for a bistable resistance state in perovskites.
Vitrification of a monatomic 2D simple liquid
Authors: Mizuguchi Tomoko , Odagaki Takashi 
Published: February 2009

Abstract
A monatomic simple liquid in two dimensions, where atoms interact isotropically through the Lennard-Jones-Gauss potential [M. Engel, H.-R. Trebin, Phys. Rev. Lett. 98, 225505 (2007)], is vitrified by the use of a rapid cooling technique in a molecular dynamics simulation. Transformation to a crystalline state is investigated at various temperatures and the time-temperature-transformation (TTT) curve is determined. It is found that the transformation time to a crystalline state is the shortest at a temerature 14% below the melting temperature T
m and that at temperatures below T
v ≡ 0:6T
m the transformation time is much longer than the available CPU time. This indicates that a long-lived glassy state is realized for T ≤ T
v.
Anatomical characteristics and antioxidant properties of Euphorbia nicaeensis ssp. glareosa
Authors: Luković Jadranka , Malenčić Djordje , Zorić Lana , Kiprovski Biljana , Merkulov Ljiljana , Boža Pal 
Published: February 2009

Abstract
Anatomical analyses found that leaves of Euphorbia nicaeensis ssp. glareosa are isolateral, amphistomatous, with two layers of palisade cells on the adaxial and one on the abaxial side. Laticifers are present by vascular bundles, in palisade and spongy tissue. Stem laticifers are located in the pericyclic ring, adjacent to the phloem, in cylinder parenchyma and medullar rays. The structure of pleiochasium and dichasium peduncle is similar to the stem structure. Plants from typical steppe habitat show more xeromorphic features. Phytochemical screening of extracts showed presence of catecholes, flavonoids, tannins, saponins, free quinone derivatives and absence of anthocyanins, leucoanthocyanins, alkaloids, steroid compounds and essential oils. Our results showed that the examined taxon was partially susceptible to the action of reactive oxygen species, such as O2·− and ·OH. The higher quantities of ROS thus provoked an antioxidative response from the plant, both in an enzymatic and non-enzymatic manner. Stable anatomical structure, presence and distribution of laticifers and effective antioxidant properties when exposed to ROS, make Euphorbia nicaeensis subsp. glareosa potentially interesting for further pharmaceutical and phytochemical examinations.
Seasonal dynamics of macrophyte abundance in two regulated streams
Authors: Hrivnák Richard , Oťaheľová Helena , Gömöry Dušan 
Published: February 2009

Abstract
This study analysed seasonal dynamics of macrophyte abundance in two perennial lowland regulated streams (Stream 1 and 2) in the Danube basin (Slovakia). Assessments of macrophyte abundance and environmental characteristics were accomplished 7 times during the vegetation period in 2005 within a 100 m long section. Statistically significant differences in total abundance of macrophytes as well as an abundance of macrophyte groups (hydrophytes, amphiphytes, helophytes) and Potamogeton nodosus were detected among months within the vegetation period. Abundance fluctuations for individual macrophyte groups and species were moderate in Stream 1 and much stronger in Stream 2. Only amphiphytes showed bimodal temporal distribution in Stream 1, but the abundance of this group was low, reflecting more or less random occurrence of species in vegetation period. Multiple linear regression revealed that water depths and air temperature are the most significant environmental variables affecting the seasonal pattern of total as well as dominating group abundance in Stream 1 and 2, respectively. In all cases, abundances are significantly influenced by the abundance of the respective group in the preceding month. Culmination time differed between streams for all macrophyte groups except helophytes. Total abundance culminated 0.57 month later in the Stream 1 compared to Stream 2.
The effects of markedly raised intracellular sphingosine kinase-1 activity in endothelial cells
Authors: Limaye Vidya , Vadas Mathew , Pitson Stuart , Gamble Jennifer 
Published: February 2009

AbstractThe enzyme sphingosine kinase-1 (SK1) promotes the formation of sphingosine-1-phosphate (S1P), which is an important survival factor for endothelial cells (EC). Modest increases in intracellular SK1 activity in the EC are known to confer a survival advantage upon the cells. Here, we investigated the effects of more dramatic increases in intracellular SK1 in the EC. We found that these cells show reduced cell survival under conditions of stress, enhanced caspase-3 activity, cell cycle inhibition, and cell-cell junction disruption. We propose that alterations in the phosphorylation state of the enzyme may explain the differential effects on the phenotype with modest versus high levels of enforced expression of SK1. Our results suggest that SK1 activity is subject to control in the EC, and that this control may be lost in conditions involving vascular regression.
Chronic increases in sphingosine kinase-1 activity induce a pro-inflammatory, pro-angiogenic phenotype in endothelial cells
Authors: Limaye Vidya , Xia Pu , Hahn Chris , Smith Malcolm , Vadas Mathew , Pitson Stuart , Gamble Jennifer 
Published: February 2009

AbstractSphingosine kinase-1 (SK1) promotes the formation of sphingosine-1-phosphate (S1P), which has potent pro-inflammatory and pro-angiogenic effects. We investigated the effects of raised SK1 levels on endothelial cell function and the possibility that this signaling pathway is activated in rheumatoid arthritis. Human umbilical vein endothelial cells with 3- to 5-fold SK1 (ECSK) overexpression were generated by adenoviral and retroviralmediated gene delivery. The activation state of these cells and their ability to undergo angiogenesis was determined. S1P was measured in synovial fluid from patients with RA and OA. ECSK showed an enhanced migratory capacity and a stimulated rate of capillary tube formation. The cells showed constitutive activation as evidenced by the induction of basal VCAM-1 expression, and further showed a more augmented VCAM-1 and E selectin response to TNF compared with empty vector control cells (ECEV). These changes had functional consequences in terms of enhanced neutrophil binding in the basal and TNFstimulated states in ECSK. By contrast, over-expression of a dominant-negative SK inhibited the TNF-induced VCAM-1 and E selectin and inhibited PMN adhesion, confirming that the observed effects were specifically mediated by SK. The synovial fluid levels of S1P were significantly higher in patients with RA than in those with OA. Small chronic increases in SK1 activity in the endothelial cells enhance the ability of the cells to support inflammation and undergo angiogenesis, and sensitize the cells to inflammatory cytokines. The SK1 signaling pathway is activated in RA, suggesting that manipulation of SK1 activity in diseases of aberrant inflammation and angiogenesis may be beneficial.
The expression of COX-2, hTERT, MDM2, LATS2 and S100A2 in different types of non-small cell lung cancer (NSCLC)
Authors: Stražišar Mojca , Mlakar Vid , Glavač Damjan 
Published: February 2009

AbstractSeveral studies have reported different expression levels of certain genes in NSCLC, mostly related to the stage and advancement of the tumours. We investigated 65 stage I-III NSCLC tumours: 32 adenocarcinomas (ADC), 26 squamous cell carcinomas (SCC) and 7 large cell carcinomas (LCC). Using the real-time reverse transcription polymerase chain reaction (RT-PCR), we analysed the expression of the COX-2, hTERT, MDM2, LATS2 and S100A2 genes and researched the relationships between the NSCLC types and the differences in expression levels. The differences in the expression levels of the LATS2, S100A2 and hTERT genes in different types of NSCLC are significant. hTERT and COX-2 were over-expressed and LATS2 under-expressed in all NSCLC. We also detected significant relative differences in the expression of LATS2 and MDM2, hTERT and MDM2 in different types of NSCLC. There was a significant difference in the average expression levels in S100A2 for ADC and SCC. Our study shows differences in the expression patterns within the NSCLC group, which may mimic the expression of the individual NSCLC type, and also new relationships in the expression levels for different NSCLC types.
Use of Medaka in Toxicity Testing
Authors: Padilla Stephanie , Cowden John , Hinton David E. , Yuen Bonny , Law Sheran , Kullman Seth W. , Johnson Rodney , Hardman Ronald C. , Flynn Kevin , Au Doris W.T. 
Published: February 2009

AbstractSmall aquarium fishes are increasingly used as animal models, and one of these, the Japanese Medaka (Oryzias latipes), is frequently utilized for toxicity testing. While these vertebrates have many similarities with their terrestrial counterparts, there are differences that must be considered if these organisms are to be used to their highest potential. Commonly, testing may employ either the developing embryo or adults; both are easy to use and work with. To illustrate the utility and breadth of toxicity testing possible using medaka fish, we present protocols for assessing neurotoxicity in developing embryos, evaluating toxicant effects on sexual phenotype after treatment with endocrine‐disrupting chemicals by sexual genotyping, and measuring hepatotoxicity in adult fish after treatment with a model hepatotoxicant. The methods run the gamut from immunohistology through PCR to basic histological techniques. Curr. Protoc. Toxicol. 39:1.10.1‐1.10.36. © 2009 by John Wiley & Sons, Inc.
Glutamate Cysteine Ligase (GCL) Transgenic and Gene‐Targeted Mice for Controlling Glutathione Synthesis
Authors: Mohar Isaac , Botta Dianne , White Collin C. , McConnachie Lisa A. , Kavanagh Terrance J. 
Published: February 2009

AbstractThe tripeptide glutathione (GSH) has important antioxidant properties, scavenges free radicals, and serves as a cofactor for glutathione S‐transferase conjugation of many xenobiotics. GSH is synthesized in two steps. The first and, often, rate‐limiting step is the formation of γ‐glutamylcysteine, which is catalyzed by the inducible heterodimeric enzyme glutamate cysteine ligase (GCL). The two subunits of GCL are the catalytic subunit (GCLC) and the modifier subunit (GCLM). In this unit, the generation and basic characterization methodologies of transgenic mouse models that have been developed to (1) conditionally over express both GCL subunits; (2) lack GCLM (Gclm null); and (3) create a hybrid between Gclm conditional over‐expressing mice on a Gclm null genetic background are discussed. These models can be used to explore the fundamental role of GCLC and GCLM in GSH synthesis, as well as the toxicological role of GSH and its synthesis in xenobiotic metabolism and response to oxidative stress. Curr. Protoc. Toxicol. 39:6.16.1‐6.16.20. © 2009 by John Wiley & Sons, Inc.
Microvolume Spectrophotometric and Fluorometric Determination of Protein Concentration
Authors: Desjardins Philippe , Hansen Joel B. , Allen Michael 
Published: February 2009

AbstractMethods for determining protein concentration that use progressively smaller amounts of material are continually being developed. A new way of minimizing the amount of sample used for spectroscopic analysis is providing more opportunities for greater quality control. Traditional spectrophotometric and fluorometric methods for determination of protein concentrations have long required placing samples into containment devices such as cuvettes or capillaries. A microsample retention system is changing that paradigm by using natural surface tension properties to capture and hold microvolume samples in place during measurement without traditional containment devices. The advantage of such a system is to dramatically reduce the amount of sample required (1 to 2 µl) while greatly increasing the dynamic range of protein concentrations that can be measured. Modifications to classic protein concentration determination protocols are presented to provide a microvolume alternative to traditional cuvette‐based methods. Curr. Protoc. Protein Sci. 55:3.10.1‐3.10.16. © 2009 by John Wiley & Sons, Inc.
Overview on Concepts and Applications of Fab Antibody Fragments
Authors: Rader Christoph 
Published: February 2009

AbstractIn this overview, the Fab molecule is introduced and discussed as the first generated antibody fragment, which still dominates basic research and clinical applications. The unit contains a concepts section and an applications section. In the concepts section, the two principal methods for producing Fab, as well as the generation and directed evolution of Fab by phage display, are described. The applications section discusses Fab in clinical applications, as well as their increasingly important role in the determination of the three‐dimensional structures of transmembrane proteins. Curr. Protoc. Protein Sci. 55:6.9.1‐6.9.14. © 2009 by John Wiley & Sons, Inc.
E. coli Expression and Purification of Fab Antibody Fragments
Authors: Kwong Ka Yin , Rader Christoph 
Published: February 2009

AbstractThe Fab molecule was the first generated antibody fragment and still dominates basic research and clinical applications. This unit describes the E. coli expression and purification of Fab antibody fragments with and without a His tag, and is designed to yield sufficient protein for the evaluation and characterization of a panel of Fab selected from a Fab library by phage display. Curr. Protoc. Protein Sci. 55:6.10.1‐6.10.14. © 2009 by John Wiley & Sons, Inc.
Analysis of Protein Acylation
Authors: Zeidman Ruth , Jackson Caroline S. , Magee Anthony I. 
Published: February 2009

AbstractProteins can be acylated with a variety of fatty acids attached by different covalent bonds, influencing, among other things, their function and intracellular localization. This unit describes methods to analyze protein acylation, both levels of acylation and also the identification of the fatty acid and the type of bond present in the protein of interest. Protocols are provided for metabolic labeling of proteins with tritiated fatty acids, for exploitation of the differential sensitivity to cleavage of different types of bonds, in order to distinguish between them, and for thin‐layer chromatography to separate and identify the fatty acids associated with proteins.Curr. Protoc. Protein Sci. 55:14.2.1‐14.2.12. © 2009 by John Wiley & Sons, Inc.
Use of the Intracellular Fluorescent Dye CFSE to Monitor Lymphocyte Migration and Proliferation
Authors: Parish Christopher R. , Glidden Megan H. , Quah Ben J. C. , Warren Hilary S. 
Published: February 2009

AbstractThe stable incorporation of the intracellular fluorescent dye 5‐(and ‐6)‐carboxyfluorescein diacetate succinimidyl ester (CFSE) into cells provides a powerful tool to monitor cell migration, and to quantify cell division, because of the sequential decrease in fluorescent labeling in daughter cells. CFSE‐labeled lymphocytes have been used to analyze the relationship between cell division and differentiation of cell function, and cell proliferation versus apoptosis, both in vivo and in vitro, and have allowed analysis of the site of response to antigens in vivo.Curr. Protoc. Immunol. 84:4.9.1‐4.9.13. © 2009 by John Wiley & Sons, Inc.
Laboratory Maintenance of Clostridium difficile
Authors: Sorg Joseph A. , Dineen Sean S. 
Published: February 2009

AbstractClostridium difficile is a Gram‐positive, spore‐forming, anaerobe and is the leading cause of antibiotic‐associated diarrhea, pseudomembranous colitis, and toxic megacolon. Essential to the lifestyle of C. difficile is the ability to form a metabolically dormant spore, germinate, and grow out upon appropriate signals and elicit disease with the secretion of two toxins. To aid in the study of this organism, this unit describes the growth and maintenance of C. difficile. Included are methods to isolate C. difficile from environmental samples, grow in laboratory medium, and produce and purify spores. Curr. Protoc. Microbiol. 12:9A.1.1‐9A.1.10. © 2009 by John Wiley & Sons, Inc.
Cultivation and Laboratory Maintenance of Chlamydia pneumoniae
Authors: Campbell Lee Ann , Kuo Cho‐Chou 
Published: February 2009

AbstractChlamydiae are Gram‐negative obligate intracellular parasites. Chlamydia pneumoniae is a human respiratory pathogen that causes pneumonia, bronchitis, sinusitis, and pharyngitis. C. pneumoniae has also been associated with cardiovascular disease. C. pneumoniae can only be grown in cell culture and is more difficult to isolate from specimens than Chlamydia trachomatis. Commonly used cell lines for isolation of C. trachomatis are not sensitive for C. pneumoniae. The most sensitive cell lines for isolation of C. pneumoniae are HL and HEp‐2. Centrifugation of the inoculum onto the monolayer and inclusion of cycloheximide in the medium enhance isolation. Inclusions are smaller than those of other chlamydiae and are visualized by staining with FITC‐conjugated genus‐ or C. pneumoniae–specific monoclonal antibodies. Slow expansion and use of a small inoculum are key to successful culture. Infectious organisms can be purified by use of Hypaque‐76 gradients to titers >1 × 108/ml. Curr. Protoc. Microbiol. 12:11B.1.1‐11B.1.23. © 2009 by John Wiley & Sons, Inc.
Testing of Transmission of Tobraviruses by Nematodes
Authors: MacFarlane Stuart A. , Neilson Roy 
Published: February 2009

AbstractVirus diseases often are spread between plants by vector organisms, some of which live below ground (e.g., fungi and nematodes) and feed on the plant root system. Tobraviruses are one of only two groups of plant viruses that have nematode vectors. They are primarily viruses of weed plants but can cause significant economic damage in a range of cultivated crops including potato, peas, beans, and many ornamental species. Identifying these viruses and their nematode vectors is a very important part of the struggle to combat disease in crop plants, and requires specialized techniques that will be discussed further in this unit. Curr. Protoc. Microbiol. 12:16B.5.1‐16B.5.16. © 2009 by John Wiley & Sons, Inc.
Novel Approaches to Bacterial Infection Therapy by Interfering with Cell‐to‐Cell Signaling
Authors: Rasko David A. , Sperandio Vanessa 
Published: February 2009

AbstractThe identification of cell‐to‐cell signaling inhibitors among bacteria is a novel mechanism used to control the virulence of pathogens. Signaling inhibitors have a significant potential to be used as therapeutics in that they will exert less biological pressure to develop resistance than classic antibiotics, which attempt to eradicate or significantly inhibit bacterial growth. Decreasing the virulence of pathogens by inhibiting signaling provides a mechanism by which the bacteria will be “misled” into not activating virulence factors. If virulence factors are not activated, these pathogens will either pass through the host without incidence or be controlled by the host's immune system. In this unit, we discuss the general principles for the design and implementation of a high‐throughput screen to identify inhibitors of bacterial cell‐to‐cell communication. We also provide a detailed protocol using a specific example of signaling inhibitor identification using enterohemorrhagic Escherichia coli as a model system. Curr. Protoc. Microbiol. 12:17.3.1‐17.3.11. © 2009 by John Wiley & Sons, Inc.
Nanoporous Copper with Tunable Nanoporosity for SERS Applications
Authors: Chen Lu‐Yang , Yu Jin‐Shan , Fujita Takeshi , Chen Ming‐Wei 
Published: February 2009

AbstractNanostructured materials with designable microstructure and controllable physical and chemical properties are highly desired for practical applications in nanotechnology. In this article, it is reported that nanoporous copper with a tunable nanopore size can be fabricated by controlling the dealloying process. The influence of acid concentration and etching potential on the formation of nanoprosity is systematically investigated. With optimal etching conditions, the nanopore sizes can be tailored from ∼15 to ∼120 nm by controlling the dealloying time. It is found that the tunable nanoporosity leads to significant improvements in surface‐enhanced Raman scattering (SERS) of nanoporous copper and peak values of SERS enhancements for both rhodamine 6G and crystal violet 10B molecules are observed at a pore size of ∼30–50 nm. This study underscores the effect of complex three‐dimensional nanostructures on physical and chemical properties and is helpful in developing inexpensive SERS substrates for sensitive instrumentations in molecular diagnostics.
Biofunctionalization of Vertically Aligned Diamond Nanowires
Authors: Yang Nianjun , Uetsuka Hiroshi , Nebel Christoph E. 
Published: February 2009

AbstractVertically aligned diamond nanowires are biofunctionalized using aminophenyl linker molecules to bond nucleic acid molecules with a well‐defined nanometer‐sized spacing to the transducer. This novel DNA biosensor combines the outstanding electrochemical properties of diamond as a transducer with the controlled bonding of DNA molecules to the tips of nanowires by use of an electrochemical attachment scheme. Nucleic acid molecules are bonded in this way and dispersed to the transducer, giving rise to optimized hybridization kinetics of DNA. Negatively charged redox mediator molecules (Fe(CN)63−/4−) are applied for DNA‐hybridization sensing. Voltammetric detection of DNA hybridization by differential pulse voltammetry is performed with respect to its sensitivity and reproducibility. On a sensor area of 0.03 cm2, a detection limit of 2.0 pM is achieved. As for the chemical stability of the DNA bonding to the diamond nanowires, no degradation over 30 hybridization/denaturation cycles could be detected. By use of this dilute DNA arrangement, single‐base mismatch discrimination is achieved. Under the same conditions, smooth diamond modified with phenyl is not suitable for amperometric DNA sensing.