bluuebunny/crossref_metadata_2025 huggingface dataset:
Sustainable Coastal Development: The Dual Mandate and a Recommendation for “Commerce Managed Areas”
Authors: Weinstein M.P. , Reed De.J.
Published: March 2005

Pitting the dynamicism and uncertainty inherent in undisturbed coastal ecosystems against the stability and predictability required of human‐dominated landscapes creates the paradox of the dual mandate. We describe a gradient of estuarine types ranging from systems that experience little human intrusion—conservation estuaries—to those that are dominated by people or extractive uses—production and urban‐industrial estuaries. Future approaches to managing these estuarine resources will require a division of the concept of marine protected areas into at least two subcategories: “conservation” managed areas (CConservationMAs) and “commerce” managed areas (CCommerceMAs). The latter includes conditions where humans are not only a core feature of the landscape but also where extractive uses drive a large part of the local, regional, and even national economy. System reliability and predictability of ecosystem services are integral components of any management scheme in CCommerceMAs. By recognizing this division managers can construct appropriate baselines that encompass the biodiversity and ecological integrity inherent in relatively undisturbed estuaries (or portions thereof), or the ecosystem health and system reliability that characterize urban‐industrial systems. The terms ecosystem restoration and ecosystem rehabilitation are also distinguished; the former term is used to describe practices that return ecosystems to optimum biological integrity, whereas the latter term is applied to the health of human‐dominated estuaries where the goal is to manage natural processes and functions. Our proposed approach does not mean that ecosystem quality is sacrificed in urban‐industrial or production systems; to the contrary, contaminant source control, suitable sediment and water quality, and the human endeavors to address them are just as important to sustaining commercial activity as they are to the well‐being of extant biota. So too, are the conservation and preservation of existing critical habitat (proximate reservoirs of biodiversity) in urban‐industrial systems, and rehabilitation of habitats that support species coadapted to the presence of humans.
The interaction Between Science and Policy in the Control of Phragmites in Oligohaline Marshes of Delaware Bay
Authors: Teal J.M. , Peterson S
Published: March 2005

Public Service Enterprise Group of New Jersey (PSEG) restored Delaware Bay marshes to enhance fish production as part of a mitigation negotiated in the company's New Jersey Pollutant Discharge Elimination System permit. Restoration meant control of an introduced type of the common reed, Phragmites, which had displaced Spartina alterniflora and S. patens. Phragmites dominance altered the function and structure of the brackish marshes and reduced habitat value by raising and flattening marsh surface and covering smaller tidal creeks. A common control technique is to use an herbicide—glyphosate. Public concern about herbicide use led to public meetings where the concerns were discussed and data provided. The scientific information regarding the herbicide did not satisfy the public. PSEG and New Jersey regulators agreed to test other methods for reed control and limit the amount of herbicide used. Experiments with methods of Phragmites control indicate that herbicide application over three or more growing seasons, concentrating in an area until control was complete, is the most effective control method.
No additional effect of topical calcipotriol on narrow‐band UVB phototherapy in patients with generalized vitiligo
Authors: Ada Simin , Şahin Sedef , Boztepe Gonca , Karaduman Ayşen , Kölemen Fikret
Published: March 2005

Background/Purpose: There is no definite cure for vitiligo; however, treatment responses with photobiological modalities are quite acceptable. Of all these, narrow‐band UVB phototherapy was proposed rather recently. Calcipotriol has been shown to have stimulating activity on melanogenesis besides immunomodulatory and anti‐inflammatory effects. This study was performed to determine whether adding topical calcipotriol to narrow‐band UVB phototherapy enhances the efficacy of treatment.

Methods: In this prospective, single‐blinded (investigator), right–left comparison clinical study, 20 patients with generalized vitiligo were enrolled. Symmetrical lesions with similar sizes, bilaterally distributed on arms, legs, hands, feet or trunk were selected as reference lesions. In addition to narrow‐band UVB, totally 96 treatment sessions, received two or three times weekly, the patients were asked to apply 0.005% topical calcipotriol on the selected side of the reference lesions twice daily. Then, they were monitored at the end of every 24‐session interval.

Results: Cosmetically acceptable repigmentation was observed in 55% (11/20) of the patients without taking calcipotriol into account. There was statistically significant better response on the side that calcipotriol was not applied at the 24th session (P<0.05). No statistically significant difference was found between the calcipotriol‐treated and non‐treated sides at 48th, 72th, and 96th sessions (P>0.05).

Conclusion: Our data confirm that, narrow‐band UVB phototherapy is effective by itself in vitiligo, and show that adding topical calcipotriol does not improve treatment outcome.
A case of toxic epidermal necrolysis with lesions mostly on sun‐exposed skin
Authors: Mansur A. T. , Aydıngöz İ. A.
Published: March 2005

Toxic epidermal necrolysis (TEN) is a cutaneous, mostly drug‐induced reaction pattern characterized by a widespread necrosis and exfoliation of epidermis, involving more than 30% of the body surface area. Photo‐induced Stevens–Johnson syndrome and erythema multiforme, which belong to the same spectrum of TEN, have been described before. However, there is only one case of TEN limited to sun‐exposed areas, which was caused by clobazam. In this report a second case of TEN because of naproxen, with lesions showing clear‐cut borders on sun‐exposed body areas resembling a sun‐burn reaction, is presented.
UVA‐1 cold light therapy in the treatment of atopic dermatitis: 61 patients treated in the Leiden University Medical Center
Authors: Polderman Marloes C. A. , Wintzen Marjolein , Cessie Saskia le , Pavel Stan
Published: March 2005

Background: UVA‐1 has been shown to be effective in the treatment of patients with atopic dermatitis. However, its optimal therapeutic conditions are not yet fully established.

Methods: In an open prospective study we retrospectively compared the effect of 4 weeks therapy (32 patients) with the effect of the usual 3 weeks therapy (29 patients) in patients with atopic dermatitis, using a medium dose UVA‐1 cold light (45 J/cm2), 5 days a week.

Results: Scoring atopic dermatitis index (SCORAD) and dermatology life quality index (DLQI) quality of life indexes improved significantly during both 3 and 4 weeks UVA‐1. Patients who were treated for 4 weeks showed a superior improvement of the SCORAD index [23.12 points, 95% confidence interval (CI) 16.09–30.16, vs. 13.32 points, 95% CI 5.61–21.04, P=0.059], and the DLQI (5.41 points, 95% CI 2.38–7.88, vs. 3.86 points, 95% CI 1.88–5.84, P=0.360), compared with patients who were treated for 3 weeks. However, the differences did not reach statistical significance. Only patients who were treated for 4 weeks were able to maintain their improvement 6 weeks after therapy. In both groups 50% of patients had intermittently used mild topical corticosteroids in the follow‐up period.

Conclusion: Extension of UVA‐1 therapy from 3 to 4 weeks results in a clinically relevant improvement of the outcome, and more prolonged therapeutic effects, measured by the SCORAD index.
The Cellular Pathway of CD1e in Immature and Maturing Dendritic Cells
Authors: Angénieux Catherine , Fraisier Vincent , Maître Blandine , Racine Victor , van der Wel Nicole , Fricker Dominique , Proamer Fabienne , Sachse Martin , Cazenave Jean‐Pierre , Peters Peter , Goud Bruno , Hanau Daniel , Sibarita Jean‐Baptiste , Salamero Jean , de la Salle Henri
Published: March 2005

Dendritic cells (DCs) present antigens to T cells via CD1, HLA class I or class II molecules. During maturation, HLA class II‐restricted presentation is optimized. The relocalization of CD1e from Golgi to endosomal compartments during DC maturation suggests also an optimization of the antigen‐presentation pathway via CD1 molecules. We here detail the biosynthesis and cellular pathway of CD1e in immature and maturing DCs. Unlike the other CD1 molecules, CD1e was found to reach late endosomes through sorting endosomes, without passing through the plasma membrane in either immature or maturing cells. After induction of DC maturation, CD1e disappeared rapidly from the Golgi and was transiently localized in HLA‐DR+ vesicles, while the number of CD1e+/CD1b+ compartments increased for at least 20 h. High‐resolution light microscopy showed that, in immature DCs, CD1e+ vesicles were often in close apposition to EEA1+ or HLA‐DR+ compartments, while CD1e displayed a nearly exclusive distribution in the lysosomes of mature DCs, a finding corroborated by immunoelectron microscopy. During maturation, CD1e synthesis progressively declined, while the endosomal cleavage of CD1e still occurred. Thus, CD1e displays peculiar properties, suggesting an unexpected role among the family of CD1 antigen‐presenting molecules.
Molecular Basis for Dissimilar Nuclear Trafficking of the Actin‐Bundling Protein Isoforms T‐ and L‐Plastin
Authors: Delanote Veerle , Van Impe Katrien , De Corte Veerle , Bruyneel Erik , Vetter Guillaume , Boucherie Ciska , Mareel Marc , Vandekerckhove Joël , Friederich Evelyne , Gettemans Jan
Published: March 2005

T‐ and L‐plastin are highly similar actin‐bundling proteins implicated in the regulation of cell morphology, lamellipodium protrusion, bacterial invasion and tumor progression. We show that T‐plastin localizes predominantly to the cytoplasm, whereas L‐plastin distributes between nucleus and cytoplasm in HeLa or Cos cells. T‐plastin shows nuclear accumulation upon incubation of cells with the CRM1 antagonist leptomycin B (LMB). We identified a Rev‐like nuclear export sequence (NES) in T‐plastin that is able to export an otherwise nuclear protein in an LMB‐dependent manner. Deletion of the NES promotes nuclear accumulation of T‐plastin. Mutation of residues L17, F21 or L26 in the T‐plastin NES inhibits nuclear efflux. L‐plastin harbors a less conserved NES and lacks the F21 T‐plastin residue. Insertion of a Phe residue in the L‐plastin NES specifically enhances its export activity. These findings explain why both isoforms exhibit specific distribution patterns in eukaryotic cells.
N‐terminal deletion of the γ subunit affects the stabilization and activity of chloroplast ATP synthase
Authors: Ni Zhang‐Lin , Dong Hui , Wei Jia‐Mian
Published: March 2005

Five truncation mutants of chloroplast ATP synthase γ subunit from spinach (Spinacia oleracea) lacking 8, 12, 16, 20 or 60 N‐terminal amino acids were generated by PCR by a mutagenesis method. The recombinant γ genes were overexpressed in Escherichia coli and assembled with αβ subunits into a native complex. The wild‐type (WT) αβγ assembly i.e. αβγWT exhibited high Mg2+‐dependent and Ca2+‐dependent ATP hydrolytic activity. Deletions of eight residues of the γ subunit N‐terminus caused a decrease in rates of ATP hydrolysis to 30% of that of the αβWT assembly. Furthermore, only ≈ 6% of ATP hydrolytic activity was retained with the sequential deletions of γ subunit up to 20 residues compared with the activity of the αβWT assembly. The inhibitory effect of the ε subunit on ATP hydrolysis of these αβγ assemblies varied to a large extent. These observations indicate that the N‐terminus οf the γ subunit is very important, together with other regions of the γ subunit, in stabilization of the enzyme complex or during cooperative catalysis. In addition, the in vitro binding assay showed that the γ subunit N‐terminus is not a crucial region in binding of the ε subunit.
Characterization of α‐synuclein aggregation and synergistic toxicity with protein tau in yeast
Authors: Zabrocki Piotr , Pellens Klaartje , Vanhelmont Thomas , Vandebroek Tom , Griffioen Gerard , Wera Stefaan , Van Leuven Fred , Winderickx Joris
Published: March 2005

A yeast model was generated to study the mechanisms and phenotypical repercussions of expression of α‐synuclein as well as the coexpression of protein tau. The data show that aggregation of α‐synuclein is a nucleation–elongation process initiated at the plasma membrane. Aggregation is consistently enhanced by dimethyl sulfoxide, which is known to increase the level of phospholipids and membranes in yeast cells. Aggregation of α‐synuclein was also triggered by treatment of the yeast cells with ferrous ions, which are known to increase oxidative stress. In addition, data are presented in support of the hypothesis that degradation of α‐synuclein occurs via autophagy and proteasomes and that aggregation of α‐synuclein disturbs endocytosis. Reminiscent of observations in double‐transgenic mice, coexpression of α‐synuclein and protein tau in yeast cells is synergistically toxic, as exemplified by inhibition of proliferation. Taken together, the data show that these yeast models recapitulate major aspects of α‐synuclein aggregation and cytotoxicity, and offer great potential for defining the underlying mechanisms of toxicity and synergistic actions of α‐synuclein and protein tau.
Identification of the heparin‐binding domains of the interferon‐induced protein kinase, PKR
Authors: Fasciano Stephen , Hutchins Brian , Handy Indhira , Patel Rekha C.
Published: March 2005

PKR is an interferon‐induced serine‐threonine protein kinase that plays an important role in the mediation of the antiviral and antiproliferative actions of interferons. PKR is present at low basal levels in cells and its expression is induced at the transcriptional level by interferons. PKR's kinase activity stays latent until it binds to its activator. In the case of virally infected cells, double‐stranded (ds) RNA serves as PKR's activator. The dsRNA binds to PKR via two copies of an evolutionarily conserved motif, thus inducing a conformational change, unmasking the ATP‐binding site and leading to autophosphorylation of PKR. Activated PKR then phosphorylates the α‐subunit of the protein synthesis initiation factor 2 (eIF2α) thereby inducing a general block in the initiation of protein synthesis. In addition to dsRNA, polyanionic agents such as heparin can also activate PKR. In contrast to dsRNA‐induced activation of PKR, heparin‐dependent PKR activation has so far remained uncharacterized. In order to understand the mechanism of heparin‐induced PKR activation, we have mapped the heparin‐binding domains of PKR. Our results indicate that PKR has two heparin‐binding domains that are nonoverlapping with its dsRNA‐binding domains. Although both these domains can function independently of each other, they function cooperatively when present together. Point mutations created within these domains rendered PKR defective in heparin‐binding, thereby confirming their essential role. In addition, these mutants were defective in kinase activity as determined by both in vitro and in vivo assays.
Allosteric properties of the GTP activated and CTP inhibited uracil phosphoribosyltransferase from the thermoacidophilic archaeon Sulfolobus solfataricus
Authors: Jensen Kaj F. , Arent Susan , Larsen Sine , Schack Lise
Published: March 2005

The upp gene, encoding uracil phosphoribosyltransferase (UPRTase) from the thermoacidophilic archaeon Sulfolobus solfataricus, was cloned and expressed in Escherichia coli. The enzyme was purified to homogeneity. It behaved as a tetramer in solution and showed optimal activity at pH 5.5 when assayed at 60 °C. Enzyme activity was strongly stimulated by GTP and inhibited by CTP. GTP caused an approximately 20‐fold increase in the turnover number kcat and raised the Km values for 5‐phosphoribosyl‐1‐diphosphate (PRPP) and uracil by two‐ and >10‐fold, respectively. The inhibition by CTP was complex as it depended on the presence of the reaction product UMP. Neither CTP nor UMP were strong inhibitors of the enzyme, but when present in combination their inhibition was extremely powerful. Ligand binding analyses showed that GTP and PRPP bind cooperatively to the enzyme and that the inhibitors CTP and UMP can be bound simultaneously (KD equal to 2 and 0.5 µm, respectively). The binding of each of the inhibitors was incompatible with binding of PRPP or GTP. The data indicate that UPRTase undergoes a transition from a weakly active or inactive T‐state, favored by binding of UMP and CTP, to an active R‐state, favored by binding of GTP and PRPP.
Functional analysis of the methylmalonyl‐CoA epimerase from Caenorhabditis elegans
Authors: Kühnl Jochen , Bobik Thomas , Procter James B , Burmeister Cora , Höppner Jana , Wilde Inga , Lüersen Kai , Torda Andrew E. , Walter Rolf D. , Liebau Eva
Published: March 2005

Methylmalonyl‐CoA epimerase (MCE) is an enzyme involved in the propionyl‐CoA metabolism that is responsible for the degradation of branched amino acids and odd‐chain fatty acids. This pathway typically functions in the reversible conversion of propionyl‐CoA to succinyl‐CoA. The Caenorhabditis elegans genome contains a single gene encoding MCE (mce‐1) corresponding to a 15 kDa protein. This was expressed in Escherichia coli and the enzymatic activity was determined. Analysis of the protein expression pattern at both the tissue and subcellular level by microinjection of green fluorescent protein constructs revealed expression in the pharynx, hypodermis and, most prominently in body wall muscles. The subcellular pattern agrees with predictions of mitochondrial localization. The sequence similarity to an MCE of known structure was high enough to permit a three‐dimensional model to be built, suggesting conservation of ligand and metal binding sites. Comparison with corresponding sequences from a variety of organisms shows more than 1/6 of the sequence is completely conserved. Mutants allelic to mce‐1 showed no obvious phenotypic alterations, demonstrating that the enzyme is not essential for normal worm development under laboratory conditions. However, survival of the knockout mutants was altered when exposed to stress conditions, with mutants surprisingly showing an increased resistance to oxidative stress.
Autonomous oscillations in Saccharomyces cerevisiae during batch cultures on trehalose
Authors: Jules Matthieu , François Jean , Parrou Jean Luc
Published: March 2005

We report that autonomous oscillations, which usually happen in aerobic glucose‐limited continuous cultures of yeast at low dilution rate, were also observed in trehalose discontinuous cultures of Saccharomyces cerevisiae. This unexpected oscillatory behaviour was therefore examined using fast Fourier transformation of online gas measurements. This robust mathematical analysis underlined the existence of two types of oscillation. The first was found to be linked to the cell cycle because (a) the periodicity corresponded to a fraction of the generation time and (b) the oscillations were accompanied by a transient increase in the budding index, mobilization of storage carbohydrates, and fermentative activity. Moreover, these oscillations occurred in a range of specific growth rates between 0.04 and 0.15 h−1. All these criteria were consistent with the cell‐cycle‐related metabolic oscillations observed in the same range of growth rates in glucose‐limited continuous cultures. The second type were short‐period respiratory oscillations, independent of the specific growth rate. Both types of oscillation were found to take place consecutively and/or simultaneously during batch culture on trehalose. In addition, mobilization of intracellular trehalose emerged as a key parameter for the sustainability of these autonomous oscillations as they were no longer observed in a mutant defective in neutral trehalase activity. We propose that batch culture on trehalose may be an excellent device for further investigation of the molecular mechanisms that underlie autonomous oscillations in yeast.
Structural characterization of Ca2+/CaM in complex with the phosphorylase kinase PhK5 peptide
Authors: Cook Atlanta G. , Johnson Louise N. , McDonnell James M.
Published: March 2005

Phosphorylase kinase (PhK) is a large hexadecameric enzyme consisting of four copies of four subunits: (αβγδ)4. An intrinsic calmodulin (CaM, the δ subunit) binds directly to the γ protein kinase chain. The interaction site of CaM on γ has been localized to a C‐terminal extension of the kinase domain. Two 25‐mer peptides derived from this region, PhK5 and PhK13, were identified previously as potential CaM‐binding sites. Complex formation between Ca2+/CaM with these two peptides was characterized using analytical gel filtration and NMR methods. NMR chemical shift perturbation studies showed that while PhK5 forms a robust complex with Ca2+/CaM, no interactions with PhK13 were observed. 15N relaxation characteristics of Ca2+/CaM and Ca2+/CaM/PhK5 complexes were compared with the experimentally determined structures of several Ca2+/CaM/peptide complexes. Good fits were observed between Ca2+/CaM/PhK5 and three structures: Ca2+/CaM complexes with peptides from endothelial nitric oxide synthase, with smooth muscle myosin light chain kinase and CaM kinase I. We conclude that the PhK5 site is likely to have a direct role in Ca2+‐regulated control of PhK activity through the formation of a classical ‘compact’ CaM complex.
Experimental and Numerical Study of Coupled Dynamic Response of a Mini Tension Leg Platform
Authors: Joseph Anitha , Idichandy V. G. , Bhattacharyya S. K.
Published: March 2005

Role of mini tension leg platforms (TLP) in oil exploration and production in marginal deepwater fields is becoming increasingly important. Mini TLP combines the simplicity of a spar and favorable response features of a TLP. In this paper, the results of a detailed experimental and numerical investigation of the coupled dynamic behavior of a mini TLP are reported with special attention to hull-tether coupling. The experimental study has been carried out using a scaled model in wave flume with specially designed tethers whose first two “string” natural frequencies are excited by waves, thus achieving strong hull-tether coupling. The numerical study has been carried out using a nonlinear time domain finite element method specifically addressed to compliant offshore platforms using a combination of potential theory based wave loading and Morison-type wave loading. Extensive comparisons between numerical and experimental results have been made both for platform motions and deflected shapes of the tethers and conclusions drawn.
Reliability Based Assessment of Deck Elevations for Offshore Jacket Platforms
Authors: Heredia-Zavoni Ernesto , Campos Dante , Ramı´rez Gallegher
Published: March 2005

Structural reliability analyses of fixed marine platforms subjected to storm wave loading are performed to assess deck elevations. Platforms are modeled as a series system consisting of the deck and jacket bays. The structural reliability analyses are carried out assuming dominant failure modes for the system components. Upper and lower bounds of the probability of failure are computed. The variation of the reliability index per bay component as a function of wave height, with a focus on those wave heights that generate forces on the deck, is analyzed. A comparison is given for the deck probability of failure and the lower bound probability of failure of the jacket in order to assess how the deck or the jacket controls the probability of failure of the system. Results are also given for reliability analyses considering different deck elevations. Finally, an analysis of the total probabilities of failure, unconditioned on wave heights, is given.
First-Generation Wave Power Plants: Current Status and R&D Requirements
Authors: Falca˜o A. F. de O.
Published: March 2005

The paper concentrates on the wave energy devices developed to be located on the shoreline or near shore (the so-called first generation devices) that have reached the stage of full-sized prototype deployed in open sea waters, including in special the oscillating water column. The principal factors affecting the technological development and the economics are identified and analyzed, taking into consideration the experience from existing prototypes: device siting, hydrodynamics and structure geometry, structural design and construction, power take-off equipment (turbine, electrical generator) and control.
Plasma control using neural network and optical emission spectroscopy
Authors: Kim Byungwhan , Bae Jung Ki , Hong Wan-Shick
Published: March 2005

Due to high sensitivity to process parameters, plasma processes should be tightly controlled. For plasma control, a predictive model was constructed using a neural network and optical emission spectroscopy (OES). Principal component analysis (PCA) was used to reduce OES dimensionality. This approach was applied to an oxide plasma etching conducted in a CHF3∕CF4 magnetically enhanced reactive ion plasma. The etch process was systematically characterized by means of a statistical experimental design. Three etch outputs (etch rate, profile angle, and etch rate nonuniformity) were modeled using three different approaches, including conventional, OES, and PCA-OES models. For all etch outputs, OES models demonstrated improved predictions over the conventional or PCA-OES models. Compared to conventional models, OES models yielded an improvement of more than 25% in modeling profile angle and etch rate nonuniformtiy. More than 40% improvement over PCA-OES model was achieved in modeling etch rate and profile angle. These results demonstrate that nonreduced in situ data are more beneficial than reduced one in constructing plasma control model.
Reactions of water and ethanol with polycrystalline TiC surfaces
Authors: Chen Zhiying , Perry Scott S. , Savan Alan , Adams Paul M. , Didziulis Stephen V.
Published: March 2005

The adsorption and reaction of water and ethanol with polycrystalline TiC coatings have been investigated and compared with those of the nonpolar (100) face of single crystal TiC. This work is pursued to develop a fundamental understanding of the surface bonding and reaction properties, thus enabling the use of TiC as a tribological coating material. Temperature-programmed desorption has been used to characterize the desorption behavior of these model adsorbates as well as that of products resulting from their reaction with the TiC surface. Following adsorption at 100K, molecular desorption as well as desorption of reaction products is evident for both water and ethanol. Approximately 70% of the water in the monolayer is judged to irreversibly react with the TiC surface, producing a surface oxide and gaseous hydrogen and carbon monoxide. Approximately 92% of the ethanol in an adsorbed monolayer reacts, predominantly producing gaseous ethene. These results are similar to those on TiC(100) surfaces, although a greater extent of surface reactivity is observed on the polycrystalline surface.
Role of hydrogen on the deposition and properties of fluorinated silicon-nitride films prepared by inductively coupled plasma enhanced chemical vapor deposition using SiF4∕N2∕H2 mixtures
Authors: Fandiño J. , Santana G. , Rodríguez-Fernández L. , Cheang-Wong J. C. , Ortiz A. , Alonso J. C.
Published: March 2005

Fluorinated silicon-nitride films have been prepared at low temperature (250°C) by remote plasma enhanced chemical vapor deposition using mixtures of SiF4, N2, Ar, and various H2 flow rates. The deposited films were characterized by means of single wavelength ellipsometry, infrared transmission, resonant nuclear reactions, Rutherford backscattering analysis, and current-voltage measurements. It was found that films deposited without hydrogen grow with the highest deposition rate, however, they result with the highest fluorine content (∼27at.%) and excess of silicon (Si∕Nratio≈1.75). These films also have the lowest refractive index and the highest etch rate, and exhibit very poor dielectric properties. As a consequence of the high fluorine content, these films hydrolize rapidly upon exposure to the ambient moisture, forming Si–H and N–H bonds, however, they do not oxidize completely. The addition of hydrogen to the deposition process reduces the deposition rate but improves systematically the stability and insulating properties of the films by reducing the amount of both silicon and fluorine incorporated during growth. All the fluorinated silicon-nitride films deposited at hydrogen flow rates higher than 3.5sccm resulted free of Si–H bonds. In spite of the fact that films obtained at the highest hydrogen flow rate used in this work are still silicon rich (Si∕Nratio≈1.0) and contain a considerable amount of fluorine (∼16at.%), they are chemically stable and show acceptable dielectric properties.
Reaction kinetics of CuInSe2 thin films grown from bilayer InSe/CuSe precursors
Authors: Kim S. , Kim W. K. , Kaczynski R. M. , Acher R. D. , Yoon S. , Anderson T. J. , Crisalle O. D. , Payzant E. A. , Li S. S.
Published: March 2005

The reaction kinetics for the formation of CuInSe2 thin films from a stacked bilayer precursor consisting of InSe and CuSe was studied by means of in situ high-temperature x-ray diffraction. In particular, the isothermal phase evolution of the glass/InSe/CuSe precursor was observed at different temperatures. The pathway produces a CuInSe2 diffusion barrier layer that also functions as a nucleation barrier. Hence, amorphous and crystalline phases simultaneously grow during isothermal processing. The shape of the time-resolved fractional reaction curve exhibits a deceleratory behavior, consistent with the presence of a diffusion-controlled reaction mechanism. Analyses based on Avrami and parabolic-rate laws were conducted. The Avrami exponent for each isothermal reaction is in the range 0.5–0.8, which indicates that the growth reaction is dominantly one-dimensional diffusion controlled. The estimated apparent activation energy for this reaction is 66.0 kJ/mol. The results based on the parabolic rate model are consistent with the Avrami analysis, yielding a similar apparent activation energy value, and thus supporting the conclusion that the process is one-dimensional diffusion controlled.
Growth modes of InN (000-1) on GaN buffer layers on sapphire
Authors: Liu Bing , Kitajima Takeshi , Chen Dongxue , Leone Stephen R.
Published: March 2005

In this work, using atomic force microscopy and scanning tunneling microscopy, we study the surface morphologies of epitaxial InN films grown by plasma-assisted molecular beam epitaxy with intervening GaN buffer layers on sapphire substrates. On smooth GaN buffer layers, nucleation and evolution of three-dimensional InN islands at various coverages and growth temperatures are investigated. The shapes of the InN islands are observed to be predominantly mesalike with large flat (000-1) tops, which suggests a possible role of indium as a surfactant. Rough GaN buffer layers composed of dense small GaN islands are found to significantly improve uniform InN wetting of the substrates, on which atomically smooth InN films are obtained that show the characteristics of step-flow growth. Scanning tunneling microscopy imaging reveals the defect-mediated surface morphology of smooth InN films, including surface terminations of screw dislocations and a high density of shallow surface pits with depths less than 0.3 nm. The mechanisms of the three-dimensional island size and shape evolution and formation of defects on smooth surfaces are considered.
In situ real-time monitoring of profile evolution during plasma etching of mesoporous low-dielectric-constant SiO2
Authors: Gerung Henry , Brinker C. Jeffrey , Brueck Steven R. J. , Han Sang M.
Published: March 2005

We have employed attenuated total reflection Fourier transforms infrared spectroscopy (ATR-FTIRS) to monitor the profile evolution of patterned mesoporous, low-dielectric-constant SiO2 films in situ and in real time during plasma etching. A stack of patterned photoresist, anti-reflective coating, and mesoporous SiO2 is etched in an inductively coupled plasma reactor, using CHF3 and Ar. During etching, the IR absorbance of Si–O–Si stretching modes near 1080cm−1 decreases, and the rate of decrease in Si–O–Si absorbance translates to the SiO2 removal rate. When corrected for the exponentially decaying evanescent electric field, the removal rate helps monitor the profile evolution and predict the final etch profile. The predicted profiles are in excellent agreement with the cross-sectional images taken by scanning electron microscopy. In a similar approach, we calculate the absolute total number of C–F bonds in the sidewall passivation and observe its formation rate as a function of time. Assuming that the thickness of the sidewall passivation tapers down towards the trench bottom, we deduce that C–F formation occurs mostly in the final stage of etching when the trench bottom meets the Ge ATR crystal and that a critical amount of C–F buildup is necessary to maintain the anisotropic etch profile.
Evaluation of Three Immunoassay Kits for Rapid Detection of Influenza Virus A and B
Authors: Weinberg Adriana , Walker Miranda L.
Published: March 2005

Influenza causes high morbidity and mortality in very young and elderly individuals, which can be controlled with antivirals and/or vaccines. The success of therapeutic measures is predicated on the rapid and precise diagnosis of the infection. We compared three rapid influenza immunoassay (RIIA) kits for the diagnosis of influenza virus A and B using 178 respiratory specimens submitted for routine testing. BD Directigen Flu A+B (Directigen), Directigen EZ Flu A+B (EZ), and NOW Flu A NOW Flu B (NOW; Binax) tests had comparable combined influenza virus A and B specificities, varying from 94 to 98%. In contrast, the sensitivity of EZ was significantly lower (39%) than that of NOW (76%) and marginally lower than that of Directigen (56%). The differences in sensitivity were most evident in patients who were >9 years old (Directigen, 53%; EZ, 32%; and NOW, 69%). Among specimens, bronchoalveolar lavage fluids yielded the most discrepant results, with sensitivities varying from 0 (EZ) to 100% (NOW), followed by nasopharyngeal swabs (sensitivities of 27 to 100%) and nasal washes (50 to 81%). The Directigen kit format allowed for faster completion but more cumbersome performance and more difficult interpretation compared with the other two kits. Overall, NOW provided the most accurate diagnoses and had user-friendly technical characteristics. However, the low overall sensitivity of the RIIAs indicates that these can be used as screening tools only.
Comparison of Antibody Repertoires against
Staphylococcus aureus
in Healthy Individuals and in Acutely Infected Patients
Authors: Dryla Agnieszka , Prustomersky Sonja , Gelbmann Dieter , Hanner Markus , Bettinger Edith , Kocsis Béla , Kustos Tamás , Henics Tamás , Meinke Andreas , Nagy Eszter
Published: March 2005

The management of staphylococcal diseases is increasingly difficult with present medical approaches. Preventive and therapeutic vaccination is considered to be a promising alternative; however, little is known about immune correlates of protection and disease susceptibility. To better understand the immune recognition of
Staphylococcus aureus
by the human host, we studied the antistaphylococcal humoral responses in healthy people in comparison to those of patients with invasive diseases. In a series of enzyme-linked immunosorbent assay analyses performed using 19 recombinant staphylococcal cell surface and secreted proteins, we measured a wide range of antibody levels, finding a pronounced heterogeneity among individuals in both donor groups. The analysis revealed marked differences in the antibody repertoires of healthy individuals with or without
S. aureus
carriage, as well as in those of patients in the acute phase of infection. Most importantly, we identified antigenic proteins for which specific antibodies were missing or underrepresented in infected patients. In contrast to the well-described transient nature of disease-induced antistaphylococcal immune response, it was demonstrated that high-titer antistaphylococcal antibodies are stable for years in healthy individuals. In addition, we provide evidence obtained on the basis of opsonophagocytic and neutralizing activity in vitro assays that circulating antistaphylococcal serum antibodies in healthy donors are functional. In light of these data we suggest that proper serological analysis comparing the preexisting antibody repertoires of hospitalized patients with different outcomes for nosocomial staphylococcal infections could be extremely useful for the evaluation of candidate vaccine antigens in addition to protection data generated with animal models.
Development of a Nanoparticle-Labeled Microfluidic Immunoassay for Detection of Pathogenic Microorganisms
Authors: Lin Frank Y. H. , Sabri Mahdi , Alirezaie Javad , Li Dongqing , Sherman Philip M.
Published: March 2005

The light-scattering properties of submicroscopic metal particles ranging from 40 to 120 nm in diameter have recently been investigated. These particles scatter incident white light to generate monochromatic light, which can be seen either by the naked eye or by dark-field microscopy. The nanoparticles are well suited for detection in microchannel-based immunoassays. The goal of the present study was to detect
Helicobacter pylori
- and
Escherichia coli
O157:H7-specific antigens with biotinylated polyclonal antibodies. Gold particles (diameter, 80 nm) functionalized with a secondary antibiotin antibody were then used as the readout. A dark-field stereomicroscope was used for particle visualization in poly(dimethylsiloxane) microchannels. A colorimetric quantification scheme was developed for the detection of the visual color changes resulting from immune reactions in the microchannels. The microchannel immunoassays reliably detected
H. pylori
and
E. coli
O157:H7 antigens in quantities on the order of 10 ng, which provides a sensitivity of detection comparable to those of conventional dot blot assays. In addition, the nanoparticles within the microchannels can be stored for at least 8 months without a loss of signal intensity. This strategy provides a means for the detection of nanoparticles in microchannels without the use of sophisticated equipment. In addition, the approach has the potential for use for further miniaturization of immunoassays and can be used for long-term archiving of immunoassays.
Drifting bumble bee (Hymenoptera: Apidae) workers in commercial greenhouses may be social parasites
Authors: Birmingham Anna L , Hoover Shelley E , Winston Mark L , Ydenberg Ron C
Published: March 2005

Commercial greenhouses require high densities of managed bumble bee (Bombus occidentalis Greene, 1858 and Bombus impatiens Cresson, 1863) colonies to pollinate crops such as tomatoes (Lycopersicon esculentum Miller). We examined drifting, a behavioural consequence of introducing closely aggregated colonies into greenhouse habitats, to determine possible explanations for observed drifting frequencies. Bee drift is normally associated with increased individual mortality and disease transfer between colonies. In this study, individual bees frequently drifted into and remained within foreign colonies. More drifting bees were found in colonies with higher worker and brood populations and greater pollen stores. Increased intracolony aggressive interactions were not associated with a higher number of drifting bees. Drifting bees had a significantly greater number of mature eggs in their ovaries than did resident worker bees residing in colonies hosting drifters, suggesting that drifting could potentially increase the fitness of individual worker bees and may not be solely a function of disorientation and (or) nectar robbing. Taken together, our results suggest that drifting of workers into foreign colonies within greenhouses may demonstrate a predisposition to social parasitism. This selfish worker reproduction challenges our previous understanding of social insect societies as being cooperative societies.
Dispersal characteristics of swift foxes
Authors: Kamler Jan F , Ballard Warren B , Gese Eric M , Harrison Robert L , Karki Seija M
Published: March 2005

From 1997 to 2001, we monitored movements of 109 adult and 114 juvenile swift foxes, Vulpes velox (Say, 1823), at study sites in Colorado, New Mexico, and Texas to determine patterns of dispersal. Significantly more male (93%) than female (58%) juveniles dispersed, and both sexes had similar bimodal dispersal patterns with peaks in September–October and January–February. Adult dispersal occurred more evenly throughout the year, and significantly more male (32%) than female (5%) adults dispersed. Adult males tended to disperse after the death of their mate. Of dispersing foxes with known fates, settlement percentages in new territories were similar between juvenile males and females (40% overall), but they were significantly lower than for adults (89%). All other dispersing foxes with known fates died. Among juvenile females with known fates, similar percentages of philopatric and dispersing foxes reproduced as yearlings (50% overall), so the benefits of dispersal versus philopatry were not clear. Although rarely reported for other species, adult males were an important dispersal cohort in swift foxes (43% of male dispersals and 25% of all dispersals). Because of the female-biased philopatry among swift foxes, dispersal of adult males likely decreased the chances for inbreeding (e.g., father–daughter breeding).
Beneficial effects of urokinase on lipopolysaccharide-induced disseminated intravascular coagulation in rats
Authors: Asamura Risa , Ontachi Yasuo , Hayashi Tomoe , Omote Mika , Arahata Masahisa , Kadohira Yasuko , Maekawa Mio , Yamazaki Masahide , Morishita Eriko , Yoshida Tomotaka , Miyamoto Ken-Ichi , Nakao Shinji , Asakura Hidesaku
Published: March 2005

In a rat model of lipopolysaccharide (LPS)-induced disseminated intravascular coagulation (DIC), we used urokinase (UK) in an attempt to clarify the role of fibrinolysis and to investigate changes in plasma endothelin levels. Two kinds of experiment were performed. The first one: experimental DIC was induced by sustained infusion of 30 mg/kg LPS for 4 h via the tail vein, and two doses of UK (2.0 or 10.0 IU/g/4.5 h) were administered to rats 30 min before infusion of LPS, after which UK infusion was continued for a further 4 h. The second one: experimental DIC was induced by sustained infusion of 1 mg/kg/10 min LPS for 10 min, and two doses of UK (2.0 or 10.0 IU/g/4 h) were administered to rats at 30 min after LPS infusion. The parameters described below were determined at 4 h in the first experiment, at 4 h and 8 h in the second one. The similar results were observed in both kinds of experiment. There were no significant differences in plasma thrombin-antithrombin complex, fibrinogen or platelet number among the three DIC groups, in both kinds of experiment. Plasma levels of D-dimer were significantly increased in the LPS + higher dose of UK group when compared with the LPS group. The increased plasma plasminogen activator inhibitor (PAI) activity seen in the LPS group was significantly suppressed in the groups receiving UK (especially higher dose of UK). In addition, the increased plasma levels of creatinine and alanine aminotransferase seen in the LPS group were significantly suppressed in the groups receiving UK (especially higher dose of UK). Plasma levels of endothelin, known to be a potent vasoconstrictive agent, were markedly elevated by LPS infusion, and were significantly suppressed in the groups receiving UK of both kinds of experiment, in a dose-dependent fashion compared with LPS group. Glomerular fibrin deposition was significantly suppressed in the groups receiving UK when compared with the LPS group. No manifestations of bleeding were observed in any of the groups. Enhanced fibrinolysis and depressed endothelin induced by UK thus appear to play an important role in preventing the development of organ failure in the LPS-induced DIC model.
Mycobacterium tuberculosis inducing disseminated intravascular coagulation
Authors: Wang Jann-Yuan , Hsueh Po-Ren , Liaw Yuang-Shuang , Shau Wen-Yi , Yang Pan-Chyr , Luh Kwen-Tay , Lee Li-Na
Published: March 2005

Disseminated intravascular coagulation (DIC) can develop infrequently in patients with tuberculosis and has a very high mortality rate. We conducted a retrospective study to evaluate the incidence of tuberculosis-induced DIC and to investigate the clinical manifestation, outcome, and prognostic factors of such patients. From January 2002 to December 2003, all culture-proven tuberculosis patients who developed DIC before starting anti-tuberculosis treatments were selected for this study. Patients who had other clinical conditions or were infected by other pathogens that may have been responsible for their DIC were excluded. Survival analysis was performed for each variable with possible prognostic significance. Our results showed that 27 (3.2%) out of the 833 patients with culture-proven tuberculosis had tuberculosis-induced DIC with a mortality rate of 63.0%. The most common clinical manifestations were fever (63.0%) and multiple patches of pulmonary consolidation (59.3%). Seven (25.9%) patients had disseminated tuberculosis. Twelve (44.4%) developed acute respiratory distress syndrome and three (11.1%) were associated with hemophagocytosis. Twenty-four (88.9%) patients had findings that were unusual for an acute bacterial infection, such as positive acid-fast smear, miliary pulmonary lesions, lymphocytotic exudative pleural effusion, and mediastinal lymphadenopathy. Early anti-tuberculosis treatment significantly improved survival. In conclusion, tuberculosis can cause DIC. Patients with non-miliary, non-disseminated tuberculosis could also develop the rare clinical manifestation. Since the prognosis was very poor in patients not treated at an early stage, a high index of suspicion is required, especially in those with clinical findings suggestive of tuberculosis.
Glycoprotein VI is associated with GPIb-IX-V on the membrane of resting and activated platelets
Authors: Gardiner Elizabeth E. , Matzaris Maria , Taylor Simon G. , Wijeyewickrema Lakshmi , Ozaki Yukio , Kahn Mark L. , Andrews Robert K. , Berndt Michael C. , Arthur Jane F.
Published: March 2005

The platelet collagen receptor, glycoprotein (GP)VI, initiates platelet aggregation at low shear stress while GPIb-IX-V, which binds von Willebrand factor, elicits platelet aggregation under high shear conditions. To investigate the possibility that GPIb-IX-V and GPVI are associated on the platelet surface, we first ascertained that aggregation induced by a GPVI-specific agonist, collagen-related peptide, like collagen, is markedly cross-blocked by a GPIbα-specific monoclonal antibody, SZ2. Immunoprecipitation of GPIb-IX with anti-GPIbα from the 1% (v/v) Triton-soluble fraction of unstimulated platelets and immunoblot-ting with anti-GPVI demonstrated association between GPIb-IX and GPVI. This association was maintained when platelets were activated by thrombin. Pre-treatment of platelets with methyl-β-cyclodextrin to disrupt lipid rafts did not affect association in resting platelets under these conditions of detergent lysis. The association is also independent of cytoskeletal attachment, since it was unaffected by treatment with N-ethylmaleimide or DNaseI, which dissociate GPIb-IX from filamin and the actin-containing cytoskeleton, respectively. Finally, the association involves an interaction between the ectodomains of GPIbα and GPVI, since soluble fragments of GPIbα (glycocalicin) and GPVI are co-precipitated from the platelet supernatant under conditions where GPVI is shed. A contribution of GPIb-IX-V to GPVI-induced platelet responses, and vice versa, therefore warrants further investigation.