bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growing and Analyzing Biofilms in Flow Cells
Authors: Sternberg Claus , Tolker‐Nielsen Tim 
Published: January 2006

AbstractThe setup of flow cell systems for the study of microbial biofilms and methods for the analysis of structural biofilm development are described in this unit. Use of flow cells allows direct microscopic investigation of biofilm development. The biofilms in flow cells develop under hydrodynamic conditions, and the environment can be carefully controlled and easily changed. The protocols in this unit include construction of the flow cell and the bubble trap, assembly and sterilization of the flow cell system, inoculation of the flow cells, running of the system, image capture and analysis, and disassembly and cleaning of the system. In addition, embedding and fluorescent in situ hybridization of flow cell–grown biofilms are addressed.
Methods for Analysis of Bacterial Autoinducer‐2 Production
Authors: Taga Michiko E. 
Published: January 2006

AbstractThe quorum‐sensing signal molecule autoinducer‐2 (AI‐2) is produced by over 50 diverse bacterial species and controls many different processes, including antibiotic production, biofilm formation, and virulence. AI‐2 production often varies according to growth phase, media conditions, and the presence of specific factors. This unit describes a biological assay for AI‐2 activity produced by a bacterial strain of interest. The assay employs an AI‐2 reporter strain, Vibrio harveyi BB170, which produces light in response to AI‐2. In the first stage of the assay, culture fluids of the bacterial strain of interest are collected over a time course of growth and filtered to remove cells. In the next stage, these culture fluids are mixed with BB170, and the light produced in response to AI‐2 in the culture fluids is measured using a luminometer. BB170 is exquisitely sensitive to AI‐2, and therefore, even low amounts of AI‐2 can be detected using this bioassay.
Laboratory Maintenance of Anaplasma phagocytophilum
Authors: Carlyon Jason A. 
Published: January 2006

AbstractAnaplasma phagocytophilum is the etiologic agent of human granulocytic anaplasmosis (formerly human granulocytic ehrlichiosis), an emerging and potentially deadly disease in the United States, Europe, and Asia. A. phagocytophilum is an obligate intracellular bacterium that displays a unique tropism for neutrophils. Studying this fascinating organism not only provides insight into microbial invasion and intracellular survival strategies, but also offers a unique approach to understanding neutrophil biology and host defense mechanisms. This unit describes the inoculation and maintenance of A. phagocytophilum from an infected blood sample into eukaryotic cell culture or laboratory mice. Cytological staining and immunofluorescent methods for assessing A. phagocytophilum infection are also presented. In addition, this unit describes isolation of viable, host cell–free bacterial preparations from infected cells, as well as the cryopreservation of infected cultures. Lastly, fluorescent labeling of live A. phagocytophilum for the purpose of tracking infection is provided.
Laboratory Maintenance of Mycobacterium marinum
Authors: Gao Lian‐Yong , Manoranjan Joanna 
Published: January 2006

AbstractM. marinum naturally infects fish and amphibians and causes diseases in these animals with pathological features similar to the human disease caused by M. tuberculosis. At the genetic and biochemical levels, M. marinum is closely related to M. tuberculosis. Because of these and other properties of M. marinum (such as its fast growth rate and convenient laboratory handing on the benchtop), M. marinum has been increasingly used as a model for studying M. tuberculosis pathogenesis. The protocols in this unit describe the methods for laboratory culturing (in liquid and solid media) and maintenance (subculturing, short‐ and long‐term storage) of M. marinum and the methods for processing M. marinum for infection assays. Important parameters for culturing and maintaining M. marinum and its processing for infection assays are discussed in detail.
Cell Culture Assay for Transient Replication of Human and Animal Papillomaviruses
Authors: Wilson Van G. 
Published: January 2006

AbstractThis unit contains protocols for evaluation of replication functionality of papillomavirus genomes or subgenomic fragments. Replication is measured after transient cotransfection of the genome (or subgenomic fragment) with expression vectors encoding the viral E1 and E2 proteins. Input DNA is methylated at the adenine of GATC sequences by propagation in E. coli. DNA that replicates in mammalian cells will lose the adenine methylation and become DpnI‐resistant, while residual methylated input DNA will remain DpnI‐sensitive. After transfection, DNA extraction, and DpnI digestion, replicated DNA can be detected by Southern blotting as a full‐length plasmid, since it is resistant to digestion. This assay can be used to map the genomic location of a functional origin or to evaluate replication activity of mutations in either the origin DNA sequences or the E1 or E2 proteins.
Transfecting Protoplasts by Electroporation to Study Viroid Replication
Authors: Zhong Xuehua , Itaya Asuka , Ding Biao 
Published: January 2006

AbstractProtoplasts have been extensively used to study replication of plant viruses at the cellular level. However, their use in studying viroid replication has been very limited because of various technical barriers. As a result, mechanisms of viroid replication remain poorly understood. The electroporation protocol presented in this unit offers a simple, fast and reproducible method to inoculate protoplasts derived from cultured cells of tobacco (Nicotiana tabacum) and the related species Nicotiana benthamiana to study viroid replication. The protocol has proven to be useful in characterizing sequence/structural features of potato spindle tuber viroid (PSTVd) that are important for replication at the cellular level, and may be adapted to study the replication of other viroids.
Isolation and Cloning of Small RNAs from Virus‐Infected Plants
Authors: Chappell Louise , Baulcombe David , Molnár Attila 
Published: January 2006

AbstractRNA silencing is an evolutionarily conserved, RNA‐mediated, regulatory system of eukaryotic organisms that also acts as an antiviral system in plants and animals. A defining feature of RNA silencing is the presence of 21‐ to 26‐nucleotide small RNAs corresponding to the silencing target sequence, which in virus‐infected plants are derived from the viral genome. The virus‐derived small RNAs have a nonrandom distribution along the viral genome, suggesting hotspots for viral small‐RNA generation. The isolated small RNAs can be used either as probes for hybridization studies or for directional cloning in order to get detailed information about their sizes, origins, and functions. This unit describes an isotope‐free small‐RNA cloning procedure that utilizes unmodified small RNAs and is routinely used to characterize small RNAs from various plant tissues.
Dimerization of α‐methylstyrene (AMS): Kinetic study of the liquid–liquid process
Authors: Ghosh Bhaswati , Chaudhuri Basab 
Published: January 2006

AbstractThe dimerization of α‐methylstyrene (AMS) in the presence of aqueous sulfuric acid catalyst in liquid–liquid (L–L) mode of operation has been studied and the kinetic parameters have been determined. There was no mass transfer limitation in the process and the reaction was found to be intrinsically first‐order. The rate constants, activation energy, and product distribution for the L–L mode of operation have been reported. A plausible explanation for the formation of the industrially important dimer in the presence of alcohols has been presented. The data are new and have not been previously reported in the literature. © 2006 American Institute of Chemical Engineers AIChE J, 2006
Detecting white matter injury in sickle cell disease using voxel‐based morphometry
Authors: Baldeweg Torsten , Hogan Alexandra M. , Saunders Dawn E. , Telfer Paul , Gadian David G. , Vargha‐Khadem Faraneh , Kirkham Fenella J. 
Published: January 2006

AbstractObjectiveSickle cell disease (SCD) is associated with cerebrovascular disease, cerebral infarction, and cognitive dysfunction. This study aimed to detect the presence and extent of white matter abnormalities in individuals with SCD using voxel‐based morphometry (VBM).MethodsThirty‐six children and adolescents with SCD (age range, 9–24 years) and 31 controls (8–25 years) underwent magnetic resonance investigations using T1‐ and T2‐weighted protocols. White and gray matter density maps were obtained from three‐dimensional magnetic resonance imaging (MRI) data sets. Using VBM, we compared the maps between controls and SCD individuals with silent white matter infarct lesions (SCD+L; n = 16), and those without visible abnormality (SCD−L; n = 20).ResultsIn comparison with controls, intelligence quotients (IQs) were lower in both SCD groups irrespective of presence of visible lesions. VBM showed widespread bilateral white matter abnormalities in the SCD+L group, extending beyond the regions of focal infarction in the deep anterior and posterior white matter borderzones. Bilateral white matter abnormalities were also observed in the SCD−L group, in locations similar to those in the SCD+L group.InterpretationVBM is sensitive to detection of widespread white matter injury in SCD patients in borderzones between arterial territories even in the absence of evidence of infarction. Those changes may contribute to cognitive deficits in this population. Ann Neurol 2006
Evolution of cerebral arteriopathies in childhood arterial ischemic stroke
Authors: Danchaivijitr Nasuda , Cox Timothy C. , Saunders Dawn E. , Ganesan Vijeya 
Published: January 2006

AbstractObjectiveTo investigate evolution of cerebral arteriopathy in children with arterial ischemic stroke (AIS) and its influence on recurrence.MethodsArteriopathy severity was graded on serial magnetic resonance angiograms from 50 children with first AIS; diagnostic categories were assigned.ResultsArteriopathy affected 72 arteries in 43 of 50 children. Five had clinical recurrence, with reinfarction in four; another had clinically silent reinfarction. Twelve children (24%; 4 with recurrence) had progressive arteriopathy. Arteriopathy improved in 24 patients (including 1 with recurrent transient ischemic attacks) and was stable in 7 patients. Magnetic resonance angiograms remained normal in seven patients; one had recurrent stroke. Diagnoses were transient cerebral arteriopathy (n = 24), chronic cerebral arteriopathy (n = 11), arterial dissection (n = 3), possible moyamoya (n = 2), primary moyamoya (n = 1), dysplastic arteriopathy (n = 1), and cerebral vasculitis (n = 1). Some of the first two categories could represent thromboembolic arterial occlusion with recanalization. The hazard of recurrence was three times higher when arterial disease had progressed (Cox regression hazard ratio, 3.2; 95% confidence intervals, 0.5–20.3; p = 0.22). After adjustment for age and number of AIS risk factors, the hazard ratio was 3.1 (95% confidence interval, 0.4–22.2; p = 0.27).InterpretationArteriopathy frequently progresses after childhood AIS. Further studies are needed to examine the relationship between progressive arteriopathy and recurrence. Ann Neurol 2006
Synthesis of Naturally Occurring Polyynes
Authors: Shi Shun Annabelle L. K. , Tykwinski Rik R. 
Published: January 2006

AbstractOver the past fifty years, hundreds of polyyne compounds have been isolated from nature. These often unstable molecules are found in sources as common as garden vegetables and as obscure as bacterial cultures. Naturally occurring polyynes feature a wide range of structural diversity and display an equally broad array of biological properties. Early synthetic efforts relied primarily on Cu‐catalyzed, oxidative acetylenic homo‐ and heterocoupling reactions to assemble the polyyne framework. The past 25 years, however, have witnessed a renaissance in the field of polyyne natural product synthesis: transition‐metal‐catalyzed alkynylation reactions and asymmetric transformations have combined to substantially expand access to natural polyynes. This Review recounts these synthetic achievements and also highlights both the natural source(s) and biological relevance for many of these compounds.
Synthesis, crystal structure and electrochemical properties of three isocloso eleven‐vertex ferrocenecarboxylate ruthenaborane clusters
Authors: Dou Jianmin , Guo Qingliang , Wu Libin , Li Dacheng , Wang Daqi , Wang Huaisheng , Li Yantuan 
Published: January 2006

AbstractThe reaction of [RuCl2(PPh3)3] with closo‐[B10H10]2− and C5H5FeC5H4COOH (FcCO2H) in refluxing CH2Cl2 solution affords three ruthenaborane clusters: [PPh3(H2O)(FcCO2)RuB10H8Cl] (1), [(PPh3)2ClRu(PPh3)(FcCO2)RuB10H9]·0.5CH2Cl2 (2 × 0.5CH2Cl2) and [PPh3(FcCO2)2RuB10H8] (3). All of these compounds are characterized by FT‐IR, NMR spectroscopic techniques, elemental analysis and single‐crystal X‐ray analysis. They are all based on a closo‐type 1:2:4:2:2 {RuB10} stack with the metal occupying the unique six‐connected apical position and can be considered as having isocloso structures derived from the complete capping of the open face of an arachano geometry to give a completely closed deltahedral cluster. Compounds 1 and 2 both have an exo‐polyhedral ferrocenecarboxylate that is attached with one {RuO} and one {BO} bond each, resulting in one exo‐cyclic five‐membered RuOCOB ring. There is in addition one exo‐polyhedral ruthenium atom bonded to the center {RuB10} cluster via one {RuRu} linkage and two {RuHµB} bridges, which forms a closed exo‐polyhedral tetrahedron configuration in compound 2. Compound 3 has two exo‐polyhedral ferrocenecarboxylates to form two five‐membered RuOCOB rings engendering a symmetrical conformation. All of these new 11‐vertex ruthenaboranes can be considered as having isocloso structures derived from the complete capping of the open face of an arachano geometry to give a completely closed deltahedral cluster. Copyright © 2006 John Wiley & Sons, Ltd.
Structural study of C,N‐chelated monoorganotin(IV) halides
Authors: Novák Petr , Padělková Zdeňka , Císařová Ivana , Kolářová Lenka , Růžička Aleš , Holeček Jaroslav 
Published: January 2006

AbstractThree monoorganotin(IV) compounds of general formula LCNSnX3, where LCN is a 2‐(dimethylaminomethyl)phenyl‐ group and X = Cl (1), Br (2) and I (3), were prepared and characterized using XRD and NMR techniques. Compound 1 reacts with moisture producing [(LCN)2HSnCl2]+ [LCNSnCl4]−. Compound 3 decomposes to (LCN)2SnI2, SnI2 and I2 when heated. Compound 2 was reacted with NH4F yielding an equilibrium of fluorine‐containing species. The major products were [LCNSnF5]2− and [(LCNSnF3)2(µ2‐F)2]2− (4a). When compound 2 was reacted with another fluorinating agent, LCN(n‐Bu)2SnF, an oligomeric product, [LCNSnF2(µ2‐F)2]n, was observed. Further addition of NH4F led to subsequent formation of 4a. The structure of fluorinated products was investigated by 1H, 19F and 119Sn NMR spectroscopy. Copyright © 2006 John Wiley & Sons, Ltd.
Organotin(IV) and organolead(IV) complexes as biocides and fertility regulators: synthetic, spectroscopic and biological studies
Authors: Chaudhary Ashu , Agarwal Mithlesh , Singh R. V. 
Published: January 2006

AbstractBiocidal, antifertility and spectroscopic aspects of organotin(IV) and organolead(IV) complexes with amino acids(L) and 2,2‐bipyridine(L′) are described with the support of elemental analysis, IR, 1H, 13C, 119Sn and 207Pb NMR spectroscopy. The spectral data suggest that the ligand L acts in a monodentate and ligand L′ in a bidentate manner, coordinating through the nitrogen atoms. The complexes have been characterized on the basis of molecular weight determinations and conductivity measurements. The isolated products are coloured solids, soluble in dimethylsulfoxide (DMSO), dimethylformamide (DMF) and methanol. All the complexes are monomeric in nature, as indicated by their molecular weight determinations. Conductivity measurements in dry DMF show them to be non‐electrolytes. The complexes have been screened against a number of fungi and bacteria to assess their growth inhibiting potential. The results are positive. In addition to these studies, the complexes show good antimicrobial properties as compared with their starting materials. The testicular sperm density, sperm morphology, sperm motility, density of cauda epididymis, spermatozoa and fertility in mating trials and the biochemical parameters of the reproductive organs of rats were examined and are discussed in detail. Copyright © 2006 John Wiley & Sons, Ltd.
Synthesis of novel palladium N‐heterocyclic‐carbene complexes as catalysts for Heck and Suzuki cross‐coupling reactions
Authors: Özdemir Ismail , Yiǧit Murat , Çetinkaya Engin , Çetinkaya Bekir 
Published: January 2006

AbstractNovel palladium‐1,3‐dialkylperhydrobenzimidazolin‐2‐ylidene (2a–c) and palladium‐1,3‐dialkylimidazolin‐2‐ylidene complexes (4a,b) have been prepared and characterized by C, H, N analysis, 1H‐NMR and 13C‐NMR. Styrene or phenylboronic acid reacts with aryl halide derivatives in the presence of catalytic amounts of the new palladium‐carbene complexes, PdCl2(1,3‐dialkylperhydrobenzimidazolin‐2‐ylidene) or PdCl2(1,3‐dialkylimidazolin‐2‐ylidene) to give the corresponding CC coupling products in good yields. Copyright © 2006 John Wiley & Sons, Ltd.
Ring‐opening polymerization of styrene oxide with Maghnite‐H+ as ecocatalyst
Authors: Yahiaoui Ahmed , Belbachir Mohammed 
Published: January 2006

AbstractThe polymerization of styrene oxide was carried out at 20°C in chloroform with an acid‐exchanged montmorillonite as acid solid ecocatalyst (Mag‐H+). The effect of the amount of catalyst, solvent, and concentration of monomer on yield and molecular weight of polymer was studied. A typical reaction product (PSTO) was analyzed by infrared and nuclear magnetic resonance spectroscopy, as well as by gel‐permeation chromatography and MALDI‐TOFMS. The mechanism of the polymerization appears to be cationic. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 1681–1687, 2006
Preparation of cellulose acetate butyrate and poly(ethylene glycol) copolymer to blend with poly(3‐hydroxybutyrate)
Authors: Cheng Guoxiang , Wang Tiezhu , Zhao Qiang , Ma Xiaolu , Zhang Liguang 
Published: January 2006

AbstractA two‐step procedure was used to synthesize the cellulose acetate butyrate and poly(ethylene glycol) graft copolymer (CAB‐g‐PEG). By choosing the appropriate composition, the crosslinked graft copolymer or not could be obtained. Then, the CAB‐g‐PEG copolymer was blended with poly(3‐hydroxybutyrate) (PHB), to further improve the mechanical properties of PHB. The results indicated that PHB and CAB‐g‐PEG that were not crosslinked were miscible over the entire composition range. As the CAB‐g‐PEG copolymer increased in the PHB/CAB‐g‐PEG blends, the melting temperature of the blends decreased, the crystallization of PHB became more difficult, and the crystallinity of the blend and PHB phase all decreased. The tensile properties and impact strength of the PHB/CAB‐g‐PEG blends were superior to the PHB/CAB blends. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 1471–1478, 2006
Effect of bisphenol A on the miscibility, phase morphology, and specific interaction in immiscible biodegradable poly(ε‐caprolactone)/poly(L‐lactide) blends
Authors: Kuo Shiao‐Wei , Huang Chih‐Feng , Tung Yi‐Chih , Chang Feng‐Chih 
Published: January 2006

AbstractWe have investigated the enhancement in miscibility, upon addition of bisphenol A (BPA) of immiscible binary biodegradable blends of poly(ε‐caprolactone) (PCL) and poly(L‐lactide) (PLLA). That BPA is miscible with both PCL and PLLA was proven by the single value of Tg observed by differential scanning calorimetry (DSC) analyses over the entire range of compositions. At various compositions and temperatures, Fourier transform infrared spectroscopy confirmed that intermolecular hydrogen bonding existed between the hydroxyl group of BPA and the carbonyl groups of PCL and PLLA. The addition of BPA enhances the miscibility of the immiscible PCL/PLLA binary blend and transforms it into a miscible blend at room temperature when a sufficient quantity of the BPA is present. In addition, optical microscopy (OM) measurements of the phase morphologies of ternary BPA/PCL/PLLA blends at different temperatures indicated an upper critical solution temperature (UCST) phase diagram, since the ΔK effect became smaller at higher temperature (200°C) than at room temperature. An analysis of infrared spectra recorded at different temperatures correlated well with the OM analyses. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 1146–1161, 2006
Physical properties of natural rubber/organoclay nanocomposites compatibilized with epoxidized natural rubber
Authors: Teh P. L. , Mohd Ishak Z. A. , Hashim A. S. , Karger‐Kocsis J. , Ishiaku U. S. 
Published: January 2006

AbstractOnium ion‐modified montmorillonite (organoclay) was melt compounded with natural rubber (NR) in an internal mixer and cured by using a conventional sulfuric system. Epoxidized natural rubber with 50 mol % epoxidation (ENR 50) was used in 10 parts per hundred rubber (phr) as a compatibilizer. The effect of organoclay with different filler loading up to 10 phr was studied. Cure characteristics were determined by a Monsanto MDR2000 rheometer, whereas the tensile, compression, and tear properties of the nanocomposites were measured according to the related ASTM standards. While the torque maximum and torque minimum increased slightly, both scorch time and cure time reduced with the incorporation of organoclay. The tensile strength, elongation at break, and tear properties went through a maximum (at about 2 phr) as a function of the organoclay content. As expected, the hardness, moduli at 100% (M100) and 300% elongations (M300) increased continuously with increasing organoclay loading. The compression set decreased with incorporation of organoclay. The dispersion of the organoclay in the NR stocks was investigated by X‐ray diffraction and transmission electron microscopy. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 1083–1092, 2006
Local microstructure characterization of rare earth‐doped PMMA with low‐ion content by fluorescence EXAFS
Authors: Zhao Hui , Hu Jun , Zhang Qijin , Bao Jun , Liu Wenhan , Gao Chen , Luo Yanhua 
Published: January 2006

AbstractFluorescence‐extended X‐ray absorption fine structure (EXAFS), and emission spectrum and excitation spectrum (ESES) were used to characterize the local structure of rare earth‐doped poly(methyl methacrylate)s (Re‐PMMAs) with ion concentration of 600–1000 ppm. Fluorescence EXAFS shows that the chemical state of Sm in Sm‐PMMA is the same as that in Sm2O3 and samarium octanoate (SOA), while that of Eu in Eu‐PMMA is different from that in Eu2O3 and europium octanoate. ESES also proves the concomitance of Eu2+ with Eu3+ ions in Eu‐PMMA. And, the almost identical peak positions of Eu L3 edge at ∼6976.7 eV in fluorescence EXAFS of Eu‐PMMA with various Eu content suggests the proportions of Eu2+ to Eu3+ are the same in these samples. The simulation of fluorescence EXAFS shows that the first‐shell coordination number of Sm3+ in Sm‐PMMA is 9.12, and the average first‐shell distance around Sm3+ in Sm‐PMMA is 2.43 Å. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 1294–1298, 2006