bluuebunny/crossref_metadata_2025 huggingface dataset:
Ecotoxicological effects of creosote contamination on benthic microbial populations in an estuarine environment†
Authors: Koepfler Eric T. , Kator Howard I.
Published: October 2006

Ecotoxicological effects of creosote contamination on benthic bacterial communities in the Elizabeth River, Virginia were investigated using both structural and functional microbial parameters. Parameters included direct counts, viable counts of heterotrophs and “cresol‐utilizers”, and bacterial production determined using the tritiated thymidine uptake method. Ancillary data included temperature, salinity, Eh profiles, concentrations of polycyclic aromatic hydrocarbons (PAHs), sediment granulometry and total organic carbon. Two reference stations in relatively nonpolluted areas were sampled for comparative data. Results indicated that cell specific and total heterotrophic bacterial production were depressed in a dose‐dependent manner with increasing sediment PAH concentrations. Sediment properties and seasonal changes in temperature appeared to modify the effects of PAHs on bacterial production. Direct bacterial counts and viable counts of total heterotrophs were depressed in the most contaminated sediments. Evidence of creosote adaptation was equivocal, with cresol‐utilizer densities not significantly elevated at contaminated stations. The presence of creosote was associated with shifts of Eh toward more negative values compared to nonpolluted sediments. Toxicants which reduce benthic bacterial production may indirectly impact other trophic groups through aberrant cycling of carbon or nutrients. Of the parameters examined, the tritiated thymidine production assay was found to be the most sensitive for detection of ecotoxicological effects.
Metals and microbes in toxicity testing
Authors: Cooney J. J. , Pettibone G. W.
Published: October 2006

The use of microorganisms can be a valuable and powerful tool in assessing the toxicity of metals, but a number of factors must be considered if meaningful results are to be obtained. In many instances natural assemblages of microorganisms are preferred to pure cultures as test systems. Similarly, effects on microbial processes such as primary production, respiration, or nitrogen fixation can provide better evaluations of toxicity than are provided by measurements of viability on pure cultures. When possible, more than one measure of activity or viability should be used. In a large number of cases, the toxicity of a metal is influenced by the chemical species of the metal. The chemical species and the availability of a metal can be influenced markedly by physical and chemical conditions, which include conditions in the field and conditions of the assay itself. Thus, those using microorganisms to assay the toxicity of metals should take care to specify the assay conditions in detail, and they should be sure that the assay conditions are as close as possible to in situ conditions. Moreover, caution should be used when extrapolating from laboratory to field situations, or from one field situation to another.
Cadmium uptake by pseudomonas fluorescens cells
Authors: Bauda P. , Garsot P. , Block J. C.
Published: October 2006

Accumulation of 109Cd by Ps. fluorescens has been investigated using the metabolic inhibitors: 1 mM dinitrophenol (DNP) and 100 μM NN′dicyclohexylcarbodiimide (DCCD). Although bacterial uptake of cadmium was reduced by DNP and DCCD, the ability of these inhibitors to complex 109Cd was thought to be the cause, rather than a reduction in metabolic activity. This was substantiated by the absence of effects due to temperature and nutrient conditions. Experiments undertaken with Ca, Mg, Zn, and Mn ions have proven the competitive action of Ca, Mg, and Mn ions on cadmium uptake.
Photobacterium phosphoreumtoxicity bioassay. I. Test procedures and applications
Authors: Ribo Juan M. , Kaiser Klaus L. E.
Published: October 2006

This review ofPhotobacterium phosphoreumtoxicity bioassay, commonly known as the MicrotoxTMtests, consists of two parts. The first part, I. Test Procedures and Applications, is a selective literature review which describes the principle, methodology, experimental conditions and procedures, and the applications of the MicrotoxTMtest. It includes a list of relevant references and tables showing comparisons of Microtox test results with those of various other acute toxicity assays for selected compounds and complex industrial effluents. The second part of this review deals with toxicity data compilation.
Lead, tin, and multiple antibiotic resistant Pseudomonas spp. isolated from polluted sediment
Authors: Belliveau B. H. , Wong P. T. S. , Trevors J. T.
Published: October 2006

Two Pseudomonas spp. were isolated from freshwater sediment by enrichment in nutrient broth amended with either 1000 μg/mL lead or tin. Both organisms also displayed multiple antiobiotic resistance. The tin‐resistant pseudomonad was also resistant to 1000 μg/mL lead, whereas the Iead‐resistant Pseudomonas sp. was not resistant to 1000 μg/mL tin. Vertical and horizontal agarose gel electrophoresis of cleared cell lysates revealed that plasmids were not present in either strain. It therefore appears that lead, tin, and antiobiotic resistance is not plasmid encoded in these organisms.
Toxicity assessment of industrial effluents from S. Paulo state, Brazil, using short‐term microbial assays
Authors: Sanchez Petra S. , Sato Maria I. Z. , Paschoal Clarice M. R. B. , Alves Maria N. , Furlan Eloisa V. , Martins Maria T.
Published: October 2006

Microorganisms have demonstrated several attributes that make them attractive for use in quick screening of effluents and chemicals for toxicity. The aim of this study was to evaluate the acute toxicity and mutagenicity of industrial effluents from São Paulo State using short‐term microbial bioassays. Samples of industrial effluents and receiving waters were analyzed for acute toxicity by the Microtox system, a motility test using Spirillum volutans, growth inhibition of Pseudomonas fluorescens, and dehydrogenase assay; for mutagenicity, these samples were analyzed by Salmonella typhimurium (Ames test), Escherichia coli WP2, and Saccharomyces cerevisiae reversion mutation assays. Among the acute toxicity assays carried out in this study, the Microtox and S. volutans tests showed good sensitivity and general good agreement with the Daphnia similis assay, which demonstrates that these tests are potentially useful as toxicity indicators for the industrial effluents and receiving waters considered. In relation to mutagenicity assays, good results were obtained with the three methods tested. The detection of mutagens in the industrial effluents considered indicates that some constituents of these waste waters discharged in receiving waters can cause adverse biological effects and could be deleterious from a public health standpoint. The data of this research emphasize the importance of acute toxicity and mutagenicity assays as supplementary approaches for a rapid and efficient action in water pollution control, and for evaluation of potential toxic chemical effects.
Microbial toxicity of triclopyr and related herbicides
Authors: Baarschers William H. , Donnelly James G. , Heitland Holger S.
Published: October 2006

Microbial toxicity of triclopyr (3,5,6‐trichloropyridinyloxyacetic acid, Garlon) was measured with several microorganisms in comparison with the related herbicides 2,4‐D (2,4‐dichlorophenoxyacetic acid) and picloram (4‐amino‐3,5,6‐trichloropicolinic acid). Growth inhibition of three fungi (Trichoderma viride, Mortierella isabellina, and Saprolegnia parasitica) was measured in terms of colony size on agar plates and in terms of cell counts for two algae (Chlorella vulgaris and Chlorella pyrenoidosa). Dehydrogenase measurement by a direct 2‐(4‐lodophenyl)‐3‐(4‐nitrophenyl)‐5‐phenyl tetrazolium chloride method was used for the bacteria Pseudomonas pictorum and Arthrobacter globiformis. Dose‐response curves were determined to obtain EC50 values for triclopyr, 2,4‐D, picloram, their commonly used amine salts, and the degradation products, 3,5,6‐trichloro‐2‐pyridinol, 2,4‐dichlorophenol, and decarboxy picloram. Toxicities of triclopyr and 2,4‐D were similar in most cases, and both compounds were more toxic than picloram. The three degradation products were substantially more toxic than the respective parent compounds. The algae were most sensitive and gave much lower EC50 values than the fungi and bacteria.
Metabolism of 1,8‐dinitropyrene by human, rhesus monkey, and rat intestinal microflora
Authors: Cerniglia Carl E. , Lambert Kenneth J. , White Gail L. , Heflich Robert H. , Franklin Wirt , Fifer E. Kim , Beland Frederick A.
Published: October 2006

Dinitropyrenes (DNPs) are highly mutagenic in the Salmonella reversion assay and are tumorigenic in rodents. Bacterial nitroreductases have been implicated in the mutagenic activation of DNPs. In this study, we investigated the metabolism of 1,8‐dinitropyrene (1,8‐DNP) by anaerobic bacterial suspensions derived from human feces, and the intestinal contents of rhesus monkeys and rats. The 1,8‐DNP metabolites were isolated by reversed‐phase high performance liquid chromatography, and identified by comparison of their chromatographic and mass spectral properties with those of authentic compounds. All of the intestinal microflora metabolized 1,8‐DNP to 1‐amino‐8‐nitropyrene and 1,8‐diaminopyrene. The mutagenic activity of samples extracted from incubations of human or rat intestinal microflora cultured with 1,8‐DNP was measured by reversion of Salmonella typhimurium TA98. There was a decrease in the mutagenic activities of the extracts with time of incubation that correlated with increased 1‐amino‐8‐nitropyrene and 1,8‐diaminopyrene formation. The decreased mutagenicity of the 1,8‐DNP metabolites was confirmed by conducting assays with authentic 1‐amino‐8‐nitropyrene and 1,8‐diaminopyrene. Both compounds showed much lower mutagenic activity compared to 1,8‐DNP. The results indicate that intestinal microflora have the ability to metabolize 1,8‐DNP to amine derivatives that are less mutagenic than the parent compound.
Evaluation of surrogate tests in toxicant impact assessments
Authors: Burton G. Allen , Stemmer B. L.
Published: October 2006

A surrogate test battery was evaluated at several stream and landfill sites where toxicant contamination had occurred. The battery consisted of microbial activity assays and macrofaunal organisms: alkaline phosphatase, amylase, arylsulfatase, electron transport system activity, β‐galactosidase, β‐glucosidase, protease, metal resistance, heterotrophic uptake (14C), zooplankton (Daphnia magna, Ceriodaphnia), amphipods (Hyalella azteca), and fathead minnows (Pimephales promelas). Waters, leachates, and sediments were tested for toxicity from sites in 5 states. Surrogate responses were correlated with in situ biological and/or chemical parameters. At each test site, statistically significant relationships were observed between microbial test responses and in situ biological or chemical responses, revealing both toxicant impacts and natural variations. Field validation of this test approach revealed its sensitivity and versatility, supporting its use in routine toxicant impact assessments.
Comparison of three rapid toxicity test procedures: Microtox,® polytox,® and activated sludge respiration inhibition
Authors: Elnabarawy M. T. , Robideau R. R. , Beach S. A.
Published: October 2006

Methods for measuring respiratory activity can detect adverse effects on heterotrophic microorganisms. These methods are useful tools for assessing the impact of chemicals on biological wastewater treatment processes. They are also well suited for evaluating the treatability potential of individual wastes. However, varying results are often reported when using municipal or industrial activated sludge substrate in toxicity assessments. The lack of reproducibility of these tests has also greatly limited efforts to measure the effectiveness of treatment plants in removing toxic contaminants. The toxicity of waste‐waters and chemicals to biological treatment systems can be determined in 30 min with the new Polytox® toxicity procedure. The Polytox® kit utilizes a specialized blend of bacterial cultures. The objective of this paper is to evaluate the relative sensitivity of the new Polytox® toxicity procedure with two accepted microbial assay procedures; namely, the Microtox® bioluminescence assay and the Organization for Economic Cooperation and Development's Activated Sludge Respiration Inhibition test. This paper compares toxicity values for selected inorganic and organic chemicals as determined in the three microbial assay systems. The sensitivity and reliability of the new Polytox® toxicity procedure is discussed.
Biological testing—development, application, and trends in canadian environmental protection laboratories
Authors: Blaise C. , Sergy G. , Wellis P. , Bermingham N. , Van Coillie R.
Published: October 2006

Past and present Canadian experiences with biological tests for controlling the quality of wastewaters are discussed. Test use has evolved from data acquisition on acute toxicities, to physicochemical and biological parameters being regulated and monitored by industrial sector in the 1970s, and hazard assessments conducted by the 1980s. At a time when Environment Canada is reviewing its ecotoxicological procedures, new opportunities for waste assessment with “second generation” biotests are emerging. Recent experiences suggest that small‐scale, sensitive, biological tests can be employed for environmentally and economically effective control of effluents entering aquatic environments. It is also expected that biotesting activities will increase because of new environmental strategies and regulations. These will stimulate biological research and development, and promote a partnership between ecotoxicology, environmental chemistry, and biotechnology.
Coliphage association with coliform indicators: A case study in Peru
Authors: Ratto A. , El‐Shaarawi A. H. , Dutka B. J. , Lopez C. , Vega C.
Published: October 2006

The associations between traditional coliform/fecal coliform indicator tests and coliphage, Presence/Absence (P/A), A‐1 broth, and H2S paper strip tests are evaluated for Peruvian waters.

Drinking water samples showed that the P/A test was the most sensitive, producing the greatest number of positive results. In drinking water, in some of the samples, the only indicator organisms present were coliphage. The incidence of coliphage in these potable water supplies reflects the probability of human pathogenic viruses also surviving the treatment processes accorded those samples.
Effect of Jejunal and Biliary Decompression on Postoperative Complications and Pancreatic Leakage Arising from Pancreatojejunostomy after Pancreatoduodenectomy
Authors: Ishizaki Yoichi , Yoshimoto Jiro , Sugo Hiroyuki , Miwa Ken , Kawasaki Seiji
Published: October 2006

Background

Since its introduction, reconstruction after pancreatoduodenectomy has undergone numerous modifications, leading to a dramatic decline in the mortality rate. However, the reported morbidity rate, due mainly to pancreatic leakage, still remains high.

Methods

Between January 1999 and April 2005, 102 consecutive patients underwent pancreatojejunostomy after pancreatoduodenectomy. Patients treated by biliary decompression alone (n = 58) were compared with patients treated by jejunal decompression alone (n = 40). Four patients who underwent both biliary and jejunal decompression were excluded from the study.

Results

Patients who underwent jejunal decompression had a significantly lower incidence of overall postoperative complications (P = 0.028), pancreatic leakage (P = 0.009), and infection (P = 0.011) than patients who underwent biliary decompression. Only one patient who underwent biliary decompression died as a direct result of pancreatic leakage.

Conclusions

Discontinuation of biliary decompression with postoperative jejunal decompression using tube jejunostomy may be a good option in patients undergoing pancreatoduodenectomy, because it appears to reduce the incidence of overall postoperative complications, pancreatic leakage, and infection.
Water activity and mobility in solutions of glycerol and small molecular weight sugars: Implication for cryo- and lyopreservation
Authors: He Xiaoming , Fowler Alex , Toner Mehmet
Published: October 2006

In this study, the free volume models, originally developed for large molecular weight polymer-solvent systems, were used to study the water activity and mobility in solutions of four small molecular weight cryo-/lyoprotectants, viz., glycerol, a monosaccharide (fructose), and two disaccharides (sucrose and trehalose). The free volume model parameters were determined by fitting the models to available experimental data using a nonlinear optimization procedure. It was found that free volume models could accurately predict the available experimental data, which suggests that the free volume models might be generally applicable to aqueous solutions of small molecular weight cryo-/lyoprotectants. Furthermore, several models for estimating the mutual diffusion coefficient were tested using available experimental data for aqueous solutions of glycerol and a better method to estimate the mutual diffusion coefficient was proposed. Free volume models were used to predict and analyze the water activity and mobility in solutions of four cryo-/lyoprotectants under conditions frequently encountered in cryo-/lyopreservation applications. It was found that the water mobility in the glassy state of the above four solutions is essentially negligible in the case of cryopreservation with storage temperature lower than −110°C. However, the water mobility in a glass at higher temperature (>−80°C) may be significant. As a result, a subcooling of up to 50°C may be necessary for the long-term cryo-/lyopreservation of biomaterials depending on the water content and the type of cryo-/lyoprotectants. It was further shown that trehalose might be the best of the four protectants studied for lyopreservation (water mass fraction ⩽0.1) when the storage temperature is above the room temperature. The results from this study might be useful for the development of more effective protocols for both cryopreservation and lyopreservation of living cells and other biomaterials.
Polymer light emitting diodes and poly(di-n-octylfluorene) thin films as fabricated with a microfluidics applicator
Authors: Cheun H. , Rugheimer P. P. , Larson B. J. , Gopalan P. , Lagally M. G. , Winokur M. J.
Published: October 2006

A microfluidics applicator is used in the fabrication of a polyfluorene based polymer light emitting diode (PLED). This procedure results in a single contiguous polymer trace and, as a consequence of the high deposition speed, shows unusual characteristics in both the film morphology and polymer microstructure. These aspects are studied using fluorescence microscopy, profilometry, and optical absorption and emission spectroscopies. Room temperature analysis of the poly(di-n-octylfluorene) indicates that the combination of high-speed deposition and rapid drying process traps the polymer into a metastable conformational state. Optical spectroscopy at reduced temperature identifies emission from at least two distinct conformational chromophores. At elevated temperature there is an abrupt, irreversible transition to a more conventional structural form. Electroluminesence data from PLED test devices are shown and this demonstrates some of the unique opportunities afforded by this method of polymer film formation and device fabrication. Device operation is not optimized.
Nanostructure and temperature-dependent photoluminescence of Er-doped Y2O3 thin films for micro-optoelectronic integrated circuits
Authors: Van T. T. , Hoang J. , Ostroumov R. , Wang K. L. , Bargar J. R. , Lu J. , Blom H.-O. , Chang J. P.
Published: October 2006

The nanostructure and photoluminescence of polycrystalline Er-doped Y2O3 thin films, deposited by radical-enhanced atomic layer deposition (ALD), were investigated in this study. The controlled distribution of erbium separated by layers of Y2O3, with erbium concentrations varied from 6to14at.%, was confirmed by elemental electron energy loss spectroscopy (EELS) mapping of Er M4 and M5. This unique feature is characteristic of the alternating radical-enhanced ALD of Y2O3 and Er2O3. The results are also consistent with the extended x-ray absorption fine structure (EXAFS) modeling of the Er distribution in the Y2O3 thin films, where the EXAFS data were best fitted to a layer-like structure. X-ray diffraction (XRD) and selected-area electron diffraction (SAED) patterns revealed a preferential film growth in the [111] direction, showing a lattice contraction with increasing Er doping concentration, likely due to Er3+ of a smaller ionic radius replacing the slightly larger Y3+. Room-temperature photoluminescence characteristic of the Er3+ intra-4f transition at 1.54μm was observed for the 500Å, 8at.% Er-doped Y2O3 thin film, showing various well-resolved Stark features due to different spectroscopic transitions from the I13∕24→I15∕24 energy manifold. The result indicates the proper substitution of Y3+ by Er3+ in the Y2O3 lattice, consistent with the EXAFS and XRD analyses. Thus, by using radical-enhanced ALD, a high concentration of optically active Er3+ ions can be incorporated in Y2O3 with controlled distribution at a low temperature, 350°C, making it possible to observe room-temperature photoluminescence for fairly thin films (∼500–900Å) without a high temperature annealing.
Highly efficient organic light-emitting diodes with metal/fullerene anode
Authors: Han Sijin , Yuan Yanyan , Lu Zheng-Hong
Published: October 2006

Metal/fullerene bilayers have been studied as hole injection electrodes for use in organic light-emitting diodes (OLEDs). In the case of a simple emission zone structure, it is found that OLEDs with the Au∕C60 anodes have much lower (∼10V) driving voltages and much higher current efficiencies (five times higher) than OLEDs with a simple Au anode. This anode structure was found to be applicable for all types of light-emitting structures including fluorescent and phosphorescent dye-doped systems. The formation of a primary bond at the Au∕C60 interface is explained as the major cause for efficient hole injection from Au to C60. The hole transfer barrier between C60 and the adjacent hole transport layer is also found critical in selecting suitable matching materials to achieve highly efficient OLEDs.
Flexibility of phenylene oligomers revealed by single molecule spectroscopy
Authors: Fückel Burkhard , Hinze Gerald , Diezemann Gregor , Nolde Fabian , Müllen Klaus , Gauss Jürgen , Basché Thomas
Published: October 2006

The rigidity of a p-phenylene oligomer (p-terphenyl) has been investigated by single molecule confocal fluorescence microscopy. Two different rylene diimide dyes attached to the terminal positions of the oligomer allowed for wavelength selective excitation of the two chromophores. In combination with polarization modulation the spatial orientation of the transition dipoles of both end groups could be determined independently. We have analyzed 597 single molecules in two different polymer hosts, polymethylmethacrylate and Zeonex®. On average we find a 22° deviation from the linear gas phase geometry (T=0K), indicating a rather high flexibility of the p-phenylene oligomer independent of the matrix. To substantiate our experimental results, we have performed quantum chemical calculations at the density functional theory level for the molecular geometry and the electronic excitations. Our findings are in agreement with former experiments on the persistence length of poly(p-phenylenes).
Magnonic crystal theory of the spin-wave frequency gap in low-doped manganites
Authors: Krawczyk M. , Puszkarski H.
Published: October 2006

A theory of three-dimensional (3D) magnonic crystal (conceived as the magnetic counterpart of the photonic crystal) is developed and applied to explain the existence of the spin-wave frequency gap, recently revealed by neutron scattering experiments, in low-doped La1−xCaxMnO3 manganites. A confrontation of the theory with experimental results proves that certain manganites can be regarded as 3D magnonic crystals existing in the nanoscale in nature.
Size mediated control of the optical and magneto-optical properties of Co nanoparticles in ZrO2
Authors: Clavero C. , Sepúlveda B. , Armelles G. , Konstantinović Z. , García del Muro M. , Labarta A. , Batlle X.
Published: October 2006

We present a study of the optical and magneto-optical (MO) properties of Co nanoparticles embedded in ZrO2 in the spectral range from 1.4to4.3eV. The nanostructured films were prepared by pulsed laser deposition in a wide range of Co nanoparticle concentrations varying from 20% to 80%. For Co concentration lower than x∼0.45 the size of the nanoparticles was found to remain almost constant (D∼2.5nm), whereas it increases above it. Differences are found between the optical and MO constant of the Co nanoparticles and those of continuous Co films. Those differences are associated with size effects of the intraband contribution inside the nanoparticles.
Optical properties and local bonding configurations of hydrogenated amorphous silicon nitride thin films
Authors: Mei J. J. , Chen H. , Shen W. Z. , Dekkers H. F. W.
Published: October 2006

We report on the optical properties and local bonding configurations of both as-deposited and postannealed hydrogenated amorphous silicon nitride (a-SiNx:H) thin films grown on crystalline Si substrates with x approximately 1.2±0.1. Ultraviolet optical reflection and infrared (IR) absorption measurements were applied to characterize the films. A method simply based on optical reflection spectra is proposed for accurate determination of the optical band gap, band tail, wavelength-dependent refractive index and extinction coefficient, as well as the film thickness, suggesting that the Tauc-Lorentz [G. E. Jellison, Jr. and F. A. Modine, Appl. Phys. Lett. 69, 371 (1996); 69, 2137 (1996)] model with the inclusion of Urbach tail is the optimal one to describe the optical response of a-SiNx:H films. The yielded optical parameters can be related well to the film microstructure as revealed by the IR absorption analysis. These results have implications for future deposition controlling and device applications.
Investigation of electronic structures of ordered and disordered Ni3Fe by electron energy loss spectroscopy
Authors: Zhong X. Y. , Zhu Jing , Zhang A. H. , Mou S. C.
Published: October 2006

The electronic structures of ordered and disordered Ni3Fe have been investigated by electron energy loss spectroscopy. The threshold energies of the L2,3 edges of Fe, and then Ni, are different in the two phases and the white-line ratios L3∕L2 of Ni and Fe from ordered Ni3Fe are lower than those from disordered Ni3Fe, while the 3d occupancies of Ni and Fe atoms in ordered Ni3Fe are less than those in disordered Ni3Fe. The s-p-d rehybridization and the intraband redistribution of the d-band electrons of Ni and Fe atoms are suggested to explain the authors’ experimental results.
Testing one component plasma models on colloidal overcharging phenomena
Authors: Martín-Molina Alberto , Maroto-Centeno José Alberto , Hidalgo-Álvarez Roque , Quesada-Pérez Manuel
Published: October 2006

In this paper, the mechanisms of overcharging of a colloidal macroion in the presence of multivalent counterions are investigated by means of Monte Carlo simulations. This computational technique appears as a powerful tool for probing the validity of semianalytical models developed for this issue. In particular, the simulations performed are compared with the predictions of two different models based on the one component plasma (OCP) theory. Therein, the multivalent ionic atmosphere confined at the macroion surface is approximated by a two-dimensional Wigner crystal. These kinds of models are largely used in the literature since (in some cases) they present quite simple equations to describe the electric double layer (EDL) of macroions with different geometries in the presence of much smaller (but still multivalent) ions. In this sense, charge inversion phenomena of membranes, polyelectrolytes, DNA molecules, etc., are straightforwardly predicted in terms of these expressions. Unfortunately, comparisons between these predictions and experimental results are scarce, mostly due to the difficulty to reproduce the experimental conditions in the laboratory. Accordingly, the goal of the present paper is to simulate EDLs under real conditions (in which overcharging phenomena are expected to happen) and use the results obtained in this way for comparing with those obtained from OCP models.
First principles calculations of oxygen vacancy passivation by fluorine in hafnium oxide
Authors: Chen Wei , Sun Qing-Qing , Ding Shi-Jin , Zhang David Wei , Wang Li-Kang
Published: October 2006

The fluorine incorporation into HfO2 with oxygen vacancies has been investigated using first principles calculations. The authors show that atomic fluorine can efficiently passivate the neutral oxygen vacancy with excess energies of 4.98 and 4.39eV for threefold- and fourfold-coordinated oxygen vacancy sites, respectively. The introduction of fluorine elevates the vacancy induced state into conduction band by transferring the neutral vacancy state to positively charged state, and thus removes the gap state which causes trap-assisted tunneling. The HfO2 band gap is not narrowed after fluorine incorporation.
Accurate estimation of the density of states from Monte Carlo transition probability data
Authors: Fenwick Michael K.
Published: October 2006

This study develops an efficient approach for calculating the density of states from energy transition probability matrices generated from extended sampling Monte Carlo simulations. Direct and iterative variants of the method are shown to achieve high accuracy when applied to the two-dimensional Ising model for which the density of states function can be determined exactly. They are also used to calculate the density of states of lattice protein and Lennard-Jones models which generate more complex nonzero matrix structures. Whereas the protein simulations test the method on a system exhibiting a rugged free energy landscape, the Lennard-Jones calculations highlight implementation details that arise in applications to continuous energy systems. Density of states results for these two systems agree with estimates from multiple histogram reweighting, demonstrating that the new method provides an alternative approach for computing the thermodynamic properties of complex systems.
Noble metal nanoparticle patterning deposition using pulsed-laser deposition in liquid for surface-enhanced Raman scattering
Authors: Cui H. , Liu P. , Yang G. W.
Published: October 2006

Deposition of noble metal nanoparticle patterning via pulsed-laser deposition in liquid for use as surface-enhanced Raman scattering substrates has been reported. The silver nanoparticle patterning has been deposited on a glass surface in contact with water by the pulsed-laser ablation of a silver target in water, and then found to be a highly effective surface-enhanced Raman scattering substrate. Three advantages of this technique are, respectively, positioning of nanoparticle patterning in devices with limited accessibility for optical sensing by surface-enhanced Raman scattering, chemically simple, and clean for nanoparticle patterning fabrications.
Single-walled carbon nanotube growth from ion implanted Fe catalyst
Authors: Choi Yongho , Sippel-Oakley Jennifer , Ural Ant
Published: October 2006

The authors present experimental evidence that single-walled carbon nanotubes can be grown by chemical vapor deposition from ion implanted iron catalyst. They systematically characterize the effect of ion implantation dose and energy on the catalyst nanoparticles and nanotubes formed at 900°C. They also fabricate a micromachined silicon grid for direct transmission electron microscopy characterization of the as-grown nanotubes. This work opens up the possibility of controlling the origin of single-walled nanotubes at the nanometer scale and of integrating them into nonplanar three-dimensional device structures with precise dose control.
Rapid hot-electron capture in self-assembled quantum dots via phonon processes
Authors: Zhang J.-Z. , Galbraith I.
Published: October 2006

Electron capture induced by carrier heating in InAs∕GaAs quantum dots is studied theoretically. Room temperature capture rates due to single longitudinal-optical (LO) phonons, LO phonons plus acoustic phonons, and two LO phonons are compared. Due to energy broadening from carrier-carrier scattering, single LO-phonon processes are the fastest capture channel. Screening from wetting-layer (WL) carriers is studied comprehensively using a number of screening models. Due to the dispersion of the WL electron-hole plasma and dynamic effects of screening, antiscreening occurs expediting rather than slowing down electron capture, with capture times of several picoseconds when the carrier temperature is 100–200K above room temperature.
Optimized plasmonic nanoparticle distributions for solar spectrum harvesting
Authors: Cole Joseph R. , Halas N. J.
Published: October 2006

The large optical cross sections of metallic nanoparticles at wavelengths corresponding to their plasmon resonance make them highly attractive for harvesting solar energy for a variety of applications. Here the authors determine ideal distributions of spherical metallic nanoparticles, both nanospheres and nanoshells, that match the AM 1.5 solar spectrum in a mixed component, submonolayer geometry. Both absorbing and scattering distributions are determined and their properties compared to conventional broad spectrum absorbing and scattering media.
Paraelectric ceramics/metal dual composites SrTiO3∕Pt system with giant relative permittivity
Authors: Cho Won Woo , Kagomiya Isao , Kakimoto Ken-Ichi , Ohsato Hitoshi
Published: October 2006

Dielectric properties of SrTiO3–Pt (platinum) composites prepared using conventional ceramic method were investigated. Dense complex ceramics were obtained without chemical reaction between SrTiO3 and Pt during sintering processes. The relative permittivity (εr) of SrTiO3 was increased by the addition of Pt particles nearly up to the percolation threshold of 27.8vol% as predicted using normalized percolation theory. The maximum εr of 2150 at 1MHz was obtained for the composite including 27vol% Pt due to the increased electric field around Pt particles. Using finite difference time domain method, the increase of electric field in the direction of applied electric field was confirmed visually in the vicinity of the embedded metal particles.
Oxygen atoms on Si(100)-(2×1): Imaging with scanning tunneling microscopy
Authors: Trenhaile B. R. , Agrawal Abhishek , Weaver J. H.
Published: October 2006

The authors use scanning tunneling microscopy to study the initial stage of oxidation for H2O exposed Si(100). Following H2O dissociation and saturation of the surface with Cl, a mild anneal allows the oxygen to insert into the Si dimer bonds. Bridge-bonded oxygen atoms appear as a dark spot in the center of the dimer. The density of these “split dimer” defects correlates with the c-type defect density on the clean surface. These results also show how to produce nearly defect-free halogen-terminated Si(100).
Myriophyllum (Haloragaceae) in Australasia. 1. New Zealand: A revision of the genus and a synopsis of the family.
Authors: Orchard AE
Published: October 2006

The six species of
Myriophyllum found in New Zealand are described and illustrated. The name M.
triphyllum is proposed as a substitute for M. elatinoides of New Zealand authors and one
new subspecies, M. pedunculatum subsp. novae-zealandiae, is described. A synopsis of
the family Haloragaceae in New Zealand is provided.
A new species of Plagiochila (Hepaticae) from Tasmania.
Authors: Inoue H
Published: October 2006

Plagiochila ratkowskiana Inoue, a new species of the Plagiochilaceae, Hepaticae,
is described and illustrations are presented. This new species belongs to sect. Depexifolia
as the second known species and is related to P. circinalis (Lehm.) Lehm. et Lindenbg.
in New Zealand and Tasmania.
The generic limits of Ixodia R.Br. ex Ait. (Compositae-Inuleae).
Authors: Orchard AE
Published: October 2006

The two Tasmanian species of Ixodia (I. angusta and
I. achlaena) are re-examined in relation to Ixodia achillaeoides, Haeckeria, Cassinia,
Helichrysum and Ammobium. It is concluded that they show as great, if not more, similarity
to Haeckeria and Cassinia (especially sect. Rhynea) as they do to Ixodia achillaeoides,
and it is proposed that they be segregated as a new genus Odixia. Two new combinations
are made: Odixia angusta and 0. achlaena.
Ptilotus pedleyanus, a new species of Amaranthaceae from Queensland.
Authors: Benl G , Eichler H
Published: October 2006

Ptilotus pedleyanus is described, illustrated and compared
with related species in order to show its diagnostic characteristics. Two varieties are
recognized: var. pedleyanus and var. comosus.
A revision of the Australian species of Symplocos (Symplocaceae).
Authors: Nooteboom HP
Published: October 2006

A complete account with full descriptions is given of the
Australian species of Symplocos. Keys to all accepted taxa are provided. The following
new taxa are described: Symplocos hylandii Nooteboom and S. cochinchinensis vars
glaberrima Nooteboom and pilosiuscula Nooteboom. A new combination is S.
cochinchinensis var. candelabrum (Brand) Nooteboom for a taxon endemic to Lord Howe
Island.
Descriptions and notes for Mycena galopus var. mellea and Mycena sanguinolenta.
Authors: Grgurinovic CA , Holland AA
Published: October 2006

A new variety of Mycena
galopus (Pers. ex Fr.) Kummer is described. A detailed description of Mycena
sanguinolenta (Alb. & Schw. ex Fr.) Kummer is also provided and its similarities and
dissimilarities to its European and North American counterparts are discussed. Camera
lucida drawings of basidiospores, cystidia and pileal cuticles are provided.
A review of the genus Helicia Lour. (Proteaceae) in Australia.
Authors: Foreman DB
Published: October 2006

The genus Helicia in Australia is reviewed. A key to the
species is given. Three new species, Helicia grayi, Helicia blakei arid Helicia lewisensis
are described. Helicia glabrescens C. T. White and Helicia dentellata Sleumer are reduced
to synonyms si Helicia australasica F. Muell. Distribution maps are given for all species.
Only those specimens of particular significance, type specimens and specimens seen of
the new species are fully cited; a separate species identification list has been lodged with
the journal.
Eucalyptus wilcoxii (Myrtaceae), a new species from Sout-eastern NSW.
Authors: Boland DJ , Kleinig DA
Published: October 2006

A new species, Eucalyptus
wilcoxii Boland & Kleinig, is described. Its taxonomic position is in subgenus
Symphyomyrtus, series Viminales following the informal classification of eucalypts
proposed by Pryor and Johnson. In adult characters it superficially resembles E.
baeuerlenii F. Muell. but differs markedly from that species in its shortly petiolate and
narrow-elliptical seedling and juvenile leaves and in its smaller and shortly pedicellate
fruit. The species is known only from the vicinity of Mother Woila Mountain in Deua
National Park, New South Wales. Evidence for recognition of this taxon was gathered
from the comparative morphology of E. wilcoxii and E. baeuerlenii. The oil composition
of adult leaves and isozyme analyses of seeds showed clear differences although the wood
anatomy was not distinguishable between the two species. The ecology, distribution,
taxonomic status, natural affinities and conservation status of E. wilcoxii are discussed.
Australian liverworts (Hepaticae): annotated list of binomials and checklist of published species with bibliography.
Authors: Scott GAM , Bradshaw JA
Published: October 2006

All names (binomials) of liverworts (Hepaticae) recorded for Australia in published
works, supplemented by some unpublished data, are listed in alphabetical order, with
details of publication and an interpretation of present taxonomic status; where appropriate,
annotations clarify the nomenclature. The species known to occur in Australia, and those
about which no opinion is yet possible, are included in a check-list arranged in taxonomic
order, with details of the States from which they have been recorded and the sources of
the records. An exhaustive bibliography of references is provided.
A revised natural regions map for Australia.
Authors: Barlow BA
Published: October 2006

A previously published proposal for delineation of botanical regions in Australia is
emended in response to comments and suggestions received. Thirty-three natural regions
are distinguished in a grid cell framework, and are grouped into six floristic zones.
Regelia punicea (N.Byrnes) Barlow, comb.nov. (Myrtaceae) from the Northern Territory: Phytogeographic implications.
Authors: Barlow BA
Published: October 2006

On the
basis of habit, habitat and floral characters, Melaleuca punicea N. Byrnes from Arnhem
Land is more satisfactorily placed in the genus Regelia, which otherwise is confined to the
south-west of Western Australia. This disjunct occurrence of a relatively unspecialized
member of its group of genera indicates that it is relictual, and that the origin of the group
may not have been in the south-west of Western Australia.
Franciscodendron (Sterculiaceae), a new tree genus from Queensland.
Authors: Myland BPM , van Steenis CGGJ
Published: October 2006

A new monotypic genus,
Franciscodendron B. Hyland & Steenis is described for the first time, based on Sterculia
laurifolia F. Muell. A comparison with nine genera of the tribe Sterculieae indicates that
Franciscodendron has its closest relationship with Hildegardia.
Galectin-1 is essential in tumor angiogenesis and is a target for antiangiogenesis therapy
Authors: Thijssen Victor L. J. L. , Postel Ruben , Brandwijk Ricardo J. M. G. E. , Dings Ruud P. M. , Nesmelova Irina , Satijn Sietske , Verhofstad Nicole , Nakabeppu Yusaku , Baum Linda G. , Bakkers Jeroen , Mayo Kevin H. , Poirier Françoise , Griffioen Arjan W.
Published: October 2006

We describe that galectin-1 (gal-1) is a receptor for the angiogenesis inhibitor anginex, and that the protein is crucial for tumor angiogenesis. gal-1 is overexpressed in endothelial cells of different human tumors. Expression knockdown in cultured endothelial cells inhibits cell proliferation and migration. The importance of gal-1 in angiogenesis is illustrated in the zebrafish model, where expression knockdown results in impaired vascular guidance and growth of dysfunctional vessels. The role of gal-1 in tumor angiogenesis is demonstrated in gal-1-null mice, in which tumor growth is markedly impaired because of insufficient tumor angiogenesis. Furthermore, tumor growth in gal-1-null mice no longer responds to antiangiogenesis treatment by anginex. Thus, gal-1 regulates tumor angiogenesis and is a target for angiostatic cancer therapy.
A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change
Authors: Li Caroline M. , Klevecz Robert R.
Published: October 2006

Perturbation of the gated-synchrony system in yeast with phenelzine, an antidepressant drug used in the treatment of affective disorders in humans, leads to a rapid lengthening in the period of the genome-wide transcriptional oscillation. The effect is a concerted, genome-scale change in expression that is first seen in genes maximally expressed in the late-reductive phase of the cycle, doubling the length of the reductive phase within two cycles after treatment. Clustering of genes based on their temporal patterns of expression yielded just three super clusters whose trajectories through time could then be mapped into a simple 3D figure. In contrast to transcripts in the late-reductive phase, most transcripts do not show transients in expression relative to others in their temporal cluster but change their period in a concerted fashion. Mapping the trajectories of the transcripts into low-dimensional surfaces that can be represented by simple systems of differential equations provides a readily testable model of the dynamic architecture of phenotype. In this system, period doubling may be a preferred pathway for phenotypic change. As a practical matter, low-amplitude, genome-wide oscillations, a ubiquitous but often unrecognized attribute of phenotype, could be a source of seemingly intractable biological noise in microarray studies.
Protective immunity to lethal challenge of the 1918 pandemic influenza virus by vaccination
Authors: Kong Wing-pui , Hood Chantelle , Yang Zhi-yong , Wei Chih-Jen , Xu Ling , García-Sastre Adolfo , Tumpey Terrence M. , Nabel Gary J.
Published: October 2006

The remarkable infectivity and virulence of the 1918 influenza virus resulted in an unprecedented pandemic, raising the question of whether it is possible to develop protective immunity to this virus and whether immune evasion may have contributed to its spread. Here, we report that the highly lethal 1918 virus is susceptible to immune protection by a preventive vaccine, and we define its mechanism of action. Immunization with plasmid expression vectors encoding hemagglutinin (HA) elicited potent CD4 and CD8 cellular responses as well as neutralizing antibodies. Antibody specificity and titer were defined by a microneutralization and a pseudotype assay that could assess antibody specificity without the need for high-level biocontainment. This pseudotype inhibition assay can define evolving serotypes of influenza viruses and facilitate the development of immune sera and neutralizing monoclonal antibodies that may help contain pandemic influenza. Notably, mice vaccinated with 1918 HA plasmid DNAs showed complete protection to lethal challenge. T cell depletion had no effect on immunity, but passive transfer of purified IgG from anti-H1(1918) immunized mice provided protective immunity for naïve mice challenged with infectious 1918 virus. Thus, humoral immunity directed at the viral HA can protect against the 1918 pandemic virus.
SEL1L, the homologue of yeast Hrd3p, is involved in protein dislocation from the mammalian ER
Authors: Mueller Britta , Lilley Brendan N. , Ploegh Hidde L.
Published: October 2006

Protein quality control in the endoplasmic reticulum (ER) involves recognition of misfolded proteins and dislocation from the ER lumen into the cytosol, followed by proteasomal degradation. Viruses have co-opted this pathway to destroy proteins that are crucial for host defense. Examination of dislocation of class I major histocompatibility complex (MHC) heavy chains (HCs) catalyzed by the human cytomegalovirus (HCMV) immunoevasin US11 uncovered a conserved complex of the mammalian dislocation machinery. We analyze the contributions of a novel complex member, SEL1L, mammalian homologue of yHrd3p, to the dislocation process. Perturbation of SEL1L function discriminates between the dislocation pathways used by US11 and US2, which is a second HCMV protein that catalyzes dislocation of class I MHC HCs. Furthermore, reduction of the level of SEL1L by small hairpin RNA (shRNA) inhibits the degradation of a misfolded ribophorin fragment (RI332) independently of the presence of viral accessories. These results allow us to place SEL1L in the broader context of glycoprotein degradation, and imply the existence of multiple independent modes of extraction of misfolded substrates from the mammalian ER.