bluuebunny/crossref_metadata_2025 huggingface dataset:
Invertebrate traits for the biomonitoring of large European rivers: an initial assessment of alternative metrics
Authors: Gayraud Sébastien , Statzner Bernhard , Bady Pierre , Haybachp Arne , Schöll Franz , Usseglio‐Polatera Philippe , Bacchi Michel
Published: October 2003

1. The application of environmental policy and legislation across large‐scale administrative units creates a growing need for standard tools to assess and monitor the ‘ecological health’ of rivers, a requirement that can be achieved through the description of ecological functions of lotic invertebrate species in river communities.

2. To assess alternative metrics, we tested how the functional structure (described by 14 biological traits) of invertebrate communities in 190 large river reaches differed with respect to differences in taxonomic resolution (species, genus, family), taxa weighting of traits (raw abundance, ln‐transformed abundance, presence–absence data) and consideration of alien species (inclusion or exclusion), and how these differences influenced the potential of functional descriptions to discriminate river reaches across a gradient of multiple human impacts.

3. Functional descriptions derived at the level of species, genera and families were very similar, whereas functional descriptions derived from raw abundances differed significantly from those derived from both ln‐transformed abundances and presence–absence data. Functional descriptions after the exclusion of alien species differed considerably from those including alien species.

4. Generally, the functional descriptions significantly discriminated river reaches according to the level of human impact. Taxonomic resolution scarcely influenced the discrimination of impact levels, whereas the use of raw abundances decreased impact discrimination in comparison with ln‐transformed abundances and presence–absence data. Exclusion of alien species also decreased discrimination of impact levels.

5. When considered separately, individual biological traits describing maximal size, number of descendants per reproductive cycle, number of reproductive cycles per individual, life duration of adults, reproductive method, parental care, body form and feeding habits had the highest potential to discriminate the level of human impact.

6. Our findings indicate that genus or perhaps family identifications are sufficient for large‐river biomonitoring using invertebrate traits. Although raw abundances could provide a better discrimination of low levels of human impact, presence–absence data should be sufficient to discriminate functional community changes caused by elevated levels of human impact across Europe.
Ocoidae, a new family of asiloid flies (Diptera: Brachycera: Asiloidea), based on Ocoa chilensis gen. and sp.n. from Chile, South America
Authors: Yeates David K. , Irwin Michael E. , Wiegmann Brian M.
Published: October 2003

Abstract.  The monotypic new family Ocoidae is described to accommodate Ocoa gen.n., small, elongate, delicate, asiloid flies known from west‐central Chile, South America. Both sexes of adult O. chilensis sp.n. are described and illustrated; immature stages are unknown. Diagnostic morphological features of adults include the antennal postpedicel comprising a single, undivided structure consisting of a bulbous base and a long, threadlike terminal element; vein M3 lacking, anal vein complete; acropod heterodactylus; spurs lacking on all tibiae; and anterior surface of hind coxa with strong, knoblike, bulbous projection; and abdominal tergite 2 lacking sensory patches of hairs. The epandrium of the male terminalia is divided along the midline into two sicklelike sections; gonostyli articulate in a horizontal plane. The female terminalia has well‐developed acanthophorite spines; posterior margin of hypoproct with several ventrally projecting, elongate, needlelike setae; two large, poorly sclerotized spermathecae; and a spermathecal sac that is smaller than each spermatheca. The relationships of this enigmatic family are discussed in relation to recent findings on the phylogeny and classification of the Asiloidea. Ocoidae are similar to Therevidae and close relatives Scenopinidae and Apsilocephalidae, comprising the therevoid group of families; however, they lack defining synapomorphies of those families. Morphological evidence supports a sister‐group relationship between Ocoidae and Scenopinidae. Molecular evidence from 28S rDNA provides further support for the monophyly of the therevoid group of families, and suggests that Ocoidae belongs within this clade, in agreement with the morphological data. The nucleotide data place Ocoidae as sister to the Scenopinidae + Therevidae, but the morphology‐based hypothesis of relationships (Ocoidae + Scenopinidae) is only two additional steps (0.2%) on the optimal trees from the molecular data.
Evolution, mitochondrial DNA phylogeny and systematic position of the Macaronesian endemic Hydrotarsus Falkenström (Coleoptera: Dytiscidae)
Authors: Ribera Ignacio , Bilton David T. , Balke Michael , Hendrich Lars
Published: October 2003

Abstract.  Hydrotarsus Falkenström (Coleoptera, Dytiscidae) is the only genus of aquatic beetle considered to be endemic to the Atlantic islands of Macaronesia. Its three known species (H. lundbladi Falkenström from Madeira, and H. compunctus (Wollaston) and H. pilosus Guignot from the Canary Islands) are revised, and their phylogenetic position studied based on sequences of the 16S rRNA and Cytochrome Oxidase I genes of mitochondrial DNA. Our results clearly indicate that the species of Hydrotarsus fall deep within the genus Hydroporus Clairville, in a clade formed by (in addition to Hydrotarsus) species currently included in the H. fuscipennis, marginatus, nigrita and tessellatus groups, and in consequence a new synonymy is proposed: Hydrotarsus Falkenström = Hydroporus Clairville syn.n. The origin of the species of ‘Hydrotarsus’, based on molecular clock estimations, is late Miocene, relatively recent in the history of the Atlantic islands. They are therefore not palaeoendemics but highly derived, recently evolved elements in the Macaronesian fauna. The estimated ages of divergence among species are much more recent than the emergence of any of the islands on which they are found, suggesting rare long‐range dispersal as the mechanism driving the diversification of the lineage. Morphological modifications of the species of ‘Hydrotarsus’ are discussed, as well as those of other dytiscids from hygropetric habitats.
Charged amino‐acid residues in transmembrane domains of the plastidic ATP/ADP transporter from Arabidopsis are important for transport efficiency, substrate specificity, and counter exchange properties
Authors: Trentmann Oliver , Decker Corina , Winkler Herbert H. , Neuhaus H. Ekkehard
Published: October 2003

Structure–function relationships of the plastidic ATP/ADP transporter from Arabidopsis thaliana have been determined using site‐directed mutants at positions K155, E245, E385, and K527. These charged residues are found within highly conserved domains of homologous transport proteins from plants and bacteria and are located in predicted transmembrane regions. Mutants of K155 to K155E, K155R, or K155Q reduced ATP transport to values between 4 and 16% of wild‐type uptake, whereas ADP transport was always less then 3% of the wild‐type value. Site‐directed mutations in which glutamate at positions 245 or 385 was replaced with lysine, abolished transport. However, conservative (E245D, E385D) or neutral (E245Q, E385Q) replacement at these two positions allowed transport. The fourth reciprocal exchange, K527E, also abolished uptake of both adenylates. K527R and K527Q were unable to transport ATP, but ADP transport remained at 35 and 27%, respectively, of the wild‐type activity. There was a 70‐fold decreased apparent affinity of K527R for ATP, but only a twofold decrease for ADP. The efflux of ATP, but not ADP, was also greatly reduced in K527R. These observations show strikingly that K527 plays a role in substrate specificity that is manifest in both the influx and efflux components of this antiporter.
Formation of acyl radical in lipid peroxidation of linoleic acid by manganese‐dependent peroxidase from Ceriporiopsis subvermispora and Bjerkandera adusta
Authors: Watanabe Takashi , Katayama Shihoko , Enoki Makiko , Honda Yoichi , Kuwahara Masaaki
Published: October 2003

Lipid peroxidation by managanese peroxidase (MnP) is reported to decompose recalcitrant polycyclic aromatic hydrocabon (PAH) and nonphenolic lignin models. To elucidate the oxidative process, linoleic acid and 13(S)‐hydroperoxy‐9Z,11E‐octadecadienoic acid [13(S)‐HPODE] were reacted with MnPs from Ceriporiopsis subvermispora and Bjerkandera adusta and the free radicals produced were analyzed by ESR. When the MnPs were reacted with 13(S)‐HPODE in the presence of Mn(II), H2O2 and tert‐nitrosobutane (t‐NB), the ESR spectrum contained a sharp triplet of acyl radical (aN = 0.81 mT). Formation of acyl radical was also observed in the reactions of Mn(III)‐tartrate with 13(S)‐HPODE and with linoleic acid, but the latter reaction occurred explosively after an induction period of around 30 min. Reactions of MnP with linoleic acid in the presence of Mn(II), H2O2 and t‐NB gave no spin adducts while addition of t‐NB after preincubation of linoleic acid with MnP/Mn(II)/H2O2 for 2 h gave spin adducts of carbon‐centered (aN = 1.53 mT, aH = 0.21 mT) and acyl (aN = 0.81 mT) radicals. In contrast to linoleic acid, methyl linoleate and oleic acid were not peroxidized by MnP and chelated Mn(III) within a few hours, indicating that structures containing both the 1,4‐pentadienyl moiety and a free carboxyl group are necessary for inducing the peroxidation in a short reaction time. These results indicate that MnP‐dependent lipid peroxidation is not initiated by direct abstraction of hydrogen from the bis‐allylic position during turnover but proceeds by a Mn(III)‐dependent hydrogen abstraction from enols and subsequent propagation reactions involving the formation of acyl radical from lipid hydroperoxide. This finding expands the role of chelated Mn(III) from a phenol oxidant to a strong generator of free radicals from lipids and lipid hydroperoxides in lignin biodegradation.
Thermodynamics and dynamics of histidine‐binding protein, the water‐soluble receptor of histidine permease
Authors: Kreimer David I. , Malak Henrik , Lakowicz Joseph R. , Trakhanov Sergei , Villar Enrique , Shnyrov Valery L.
Published: October 2003

The bacterial histidine permease is a model system for ABC transporters (traffic ATPases). The water‐soluble receptor of this permease, HisJ, binds l‐histidine and l‐arginine (tightly) and l‐lysine and l‐ornithine (less tightly) in the periplasm, interacts with the membrane‐bound complex (HisQMP2) and induces its ATPase activity, which results in ligand translocation. HisJ is a two‐domain protein; in the absence of ligand, the cleft between two domains is open and binding of substrate stabilizes the closed conformation. Surprisingly, various liganded HisJ forms display substantial differences in their physicochemical characteristics and capacity to induce the ATPase. This is due to either different effects of the individual ligands on the respective closed structures, or to different equilibria being reached for each ligand between the open liganded form and the closed liganded form [Wolf, A., Lee, K.C., Kirsch, J.F. & Ames, G.F.‐L. (1996) J. Biol. Chem.271, 21243–21250]. In this work, time‐resolved measurements of the decay of intrinsic HisJ fluorescence and of the decay of the anisotropy of the fluorescence, as well as the analysis of the steady‐state near UV CD and fluorescence spectra, rule out the model in which the differences between liganded complexes reflect different equilibria. The decay of the anisotropy of the fluorescence shows that liganded complexes differ dramatically in their large‐scale conformational dynamics. Differential scanning calorimetry (DSC) curves for the HisJ thermal unfolding are well described by a scheme of equilibrium two‐state unfolding of two independent domains, which can be ascribed to the two‐domain structure of HisJ. This is true both for apo‐HisJ at various pH values, and for HisJ in the presence of its ligands at varying concentrations, at pH 8.3. The DSC and structural data suggest that all ligands interact more extensively with the larger domain. A qualitative model for the HisJ conformational dynamics employing the idea of a twisting movement of the domains is proposed, which explains the difference in the efficacy of the ATPase induction by the various liganded HisJ forms.
Cytochrome c6 from Cyanophora paradoxa
Authors: Steiner Jürgen M. , Serrano Aurelio , Allmaier Günter , Jakowitsch Johannes , Löffelhardt Wolfgang
Published: October 2003

In the eukaryotic alga Cyanophora paradoxa, which does not contain plastocyanin, photosynthetic electron transport from the cytochrome b6/f complex to photosystem I is mediated by cytochrome c6. Cytochrome c6 was purified to homogeneity by column chromatography and FPLC. The relative molecular mass of the holoprotein was determined by two different mass spectrometric methods (californium‐252 plasma desorption and UV matrix‐assisted laser desorption ionization) giving 9251 ± 3.3 Da. N‐terminal Edman microsequencing yielded information on approx. 30 amino acid residues. Based on these data and on highly conserved regions of cytochromes c6, degenerate oligonucleotides were designed and used for PCR to amplify the genomic DNA of C. paradoxa. Screening of a C. paradoxa cDNA library yielded several clones coding for preapo‐cytochrome c6. The deduced sequence of the mature protein was verified by plasma desorption mass spectrometric peptide mapping and shows high similarity to those of cytochromes c6 from cyanobacteria and algae. Cytochrome c6 appears to be encoded by a single nuclear gene (petJ) in C. paradoxa. As the mature protein is located in the lumen of the thylakoid membrane, it has to traverse three biological membranes as well as the unique peptidoglycan layer of the cyanelles before it reaches its final subcellular locale. Thus the transit sequence is composed of two different targeting signals: a stroma targeting peptide resembling those of higher plants with respect to hydropathy plots and amino acid composition and a hydrophobic signal peptide functioning as a thylakoid‐traversing domain. There are indications for alternative sorting of part of the cyanelle cytochrome c6 pool to the periplasmic space. This is the first known bipartite transit sequence of a cyanelle precursor protein from C. paradoxa, a model organism concerning the endosymbiotic origin of plastids. Labeled precursor is efficiently imported into isolated cyanelles, then routed into thylakoids and processed to the mature protein. Hitherto, in vitro protein translocation was not reported for cyanobacterial‐type thylakoids.
Conserved aromatic residues in the transmembrane region VI of the V1a vasopressin receptor differentiate agonist vs. antagonist ligand binding
Authors: Cotte Nathalie , Balestre Marie‐Noëlle , Aumelas André , Mahé Eve , Phalipou Sylvie , Morin Denis , Hibert Marcel , Manning Maurice , Durroux Thierry , Barberis Claude , Mouillac Bernard
Published: October 2003

Despite their opposite effects on signal transduction, the nonapeptide hormone arginine‐vasopressin (AVP) and its V1a receptor‐selective cyclic peptide antagonist d(CH2)5[Tyr(Me)2]AVP display homologous primary structures, differing only at residues 1 and 2. These structural similarities led us to hypothesize that both ligands could interact with the same binding pocket in the V1a receptor. To determine receptor residues responsible for discriminating binding of agonist and antagonist ligands, we performed site‐directed mutagenesis of conserved aromatic and hydrophilic residues as well as nonconserved residues, all located in the transmembrane binding pocket of the V1a receptor. Mutation of aromatic residues of transmembrane region VI (W304, F307, F308) reduced affinity for the d(CH2)5[Tyr(Me)2]AVP and markedly decreased affinity for the unrelated strongly hydrophobic V1a‐selective nonpeptide antagonist SR 49059. Replacement of these aromatic residues had no effect on AVP binding, but increased AVP‐induced coupling efficacy of the receptor for its G protein. Mutating hydrophilic residues Q108, K128 and Q185 in transmembrane regions II, III and IV, respectively, led to a decrease in affinity for both agonists and antagonists. Finally, the nonconserved residues T333 and A334 in transmembrane region VII, controlled the V1a/V2 binding selectivity for both nonpeptide and cyclic peptide antagonists. Thus, because conserved aromatic residues of the V1a receptor binding pocket seem essential for antagonists and do not contribute at all to the binding of agonists, we propose that these residues differentiate agonist vs. antagonist ligand binding.
Linking autotrophic activity in environmental samples with specific bacterial taxa by detection of 13C‐labelled fatty acids
Authors: Knief Claudia , Altendorf Karlheinz , Lipski André
Published: October 2003

A method for the detection of physiologically active autotrophic bacteria in complex microbial communities was developed based on labelling with the stable isotope 13C. Labelling of autotrophic nitrifying, sulphur‐oxidizing and iron‐oxidizing populations was performed in situ by incubation with NaH[13C]O3. Incorporated label into fatty acid methyl esters (FAMEs) was detected and quantified using gas chromatography‐mass spectrometry in single ion monitoring mode. Before the analyses of different environmental samples, the protocol was evaluated in pure culture experiments. In different environmental samples a selective labelling of fatty acids demonstrated which microbial taxa were responsible for the respective chemolithoautotrophic activity. The most strongly labelled fatty acids of a sample from a sulphide treating biofilter from an animal rendering plant were cis‐7‐hexadecenoic acid (16:1 cis7) and 11‐methyl hexadecanoic acid (16:0 11methyl), which are as‐yet not known for any sulphide‐oxidizing autotroph. The fatty acid labelling pattern of an experimental biotrickling filter sample supplied with dimethyl disulphide clearly indicated the presence and activity of sulphide‐oxidizing bacteria of the genus Thiobacillus. For a third environmental sample from an acid mining lake sediment, the assignment of autotrophic activity to bacteria of the genus Leptospirillum but not to Acidithiobacillus could be made by this method, as the fatty acid patterns of these bacteria show clear differences.
Microsite‐dependent changes in methanogenic populations in a boreal oligotrophic fen
Authors: Galand Pierre E. , Fritze Hannu , Yrjälä Kim
Published: October 2003

Wetlands, including peatlands, are the main source of natural methane emission. Well‐defined fen microsites have different methane emissions rates, but it is not known whether the methane‐producing Archaea communities vary at these sites. Possible horizontal variations of communities, in a natural oligotrophic fen, were analysed by characterizing the methanogens from two well‐defined microsites: Eriophorum lawn and Hummock. Community structures were studied at two different layers of the fen, showing, respectively, high and low methane production. The structure of methanogen populations was determined using molecular techniques targeting the 16SrRNA gene and combined denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) analysis. Results subjected to non‐metric multidimensional scaling (MDS), diversity indices calculation and phylogenetic analysis revealed that upper layer communities changed with site while deeper layer communities remained the same. Phylogenetic analyses revealed six different clusters of sequences grouping with only two known orders of methanogens. Upper layers of Hummock were dominated by sequences clustering with members of Methanomicrobiales and sequences dominating the upper part of the Eriophorum lawn were related to members of the order Methanosarcinales. Novel methanogenic sequences were found at both sites at both depths. Vegetation characterizing the microsites probably influences the microbial communities in the layers of the fen where methane is produced.
Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities
Authors: Ranjard Lionel , Lejon David P. H. , Mougel Christophe , Schehrer Lucie , Merdinoglu Didier , Chaussod Rémi
Published: October 2003

Assessing soil microbial community structure by the use of molecular techniques requires a satisfactory sampling strategy that takes into account the high microbial diversity and the heterogeneous distribution of microorganisms in the soil matrix. The influence of the sample size of three different soil types (sand, silt and clay soils) on the DNA yield and analysis of bacterial and fungal community structure were investigated. Six sample sizes from 0.125 g to 4 g were evaluated. The genetic community structure was assessed by automated ribosomal intergenic spacer analysis (A‐RISA fingerprint). Variations between bacterial (B‐ARISA) and fungal (F‐ARISA) community structure were quantified by using principal component analysis (PCA). DNA yields were positively correlated with the sample size for the sandy and silty soils, suggesting an influence of the sample size on DNA recovery, whereas no correlation was observed in the clay soil. B‐ARISA was shown to be consistent between the different sample sizes for each soil type indicating that the sampling procedure has no influence on the assessment of bacterial community structure. On the contrary for F‐ARISA profiles, strong variations were observed between replicates of the smaller samples (<1 g). Principal component analysis analysis revealed that sampling aliquots of soil ≥1 g are required to obtain robust and reproducible fingerprinting analysis of the genetic structure of fungal communities. However, the smallest samples could be adequate for the detection of minor populations masked by dominant ones in larger samples. The sampling strategy should therefore be different according to the objectives: rather large soil samples (≥1 g) for a global description of the genetic community structure, or a large number of small soil samples for a more complete inventory of microbial diversity.
Diversity of fungi in organic soils under a moorland – Scots pine (Pinus sylvestris L.) gradient
Authors: Anderson Ian C. , Campbell Colin D. , Prosser James I.
Published: October 2003

The conservation and regeneration of native Scots pine (Pinus sylvestris L.) woodlands is being actively encouraged by conservation agencies in the UK because of their high biodiversity value. In the present study, the consequences of regeneration on terrestrial fungal communities was determined in three parallel transects running from open moorland, through an intermediate zone showing seedling colonization, into a mature Scots pine forest at Abernethy Forest, Cairngorm, Scotland. Soil cores were taken at 18 m intervals along each 180 m transect, and the diversity of the soil fungal community was investigated by DGGE and sequence analysis of ITS fragments PCR‐amplified from DNA extracted from soil. Analysis of DGGE profiles generated for two of the three transects indicates a clear shift in the community from the moorland region of the transects to the forest region. Whereas a few bands were present at all sampling points across the transects, the majority of bands were unique to either the moorland or forest samples. FASTA database searches of ITS sequence data generated from excised DGGE bands revealed the closest species match for each band. In some cases, the similarity of ITS sequences to database sequences was poor, but the remaining sequences were most closely related to ITS sequences of both mycorrhizal and non‐mycorrhizal fungi. The data are discussed in relation to the effect of native pine woodland expansion on the soil fungal community.
The efficacy and safety of terbinafine in children
Authors: Gupta AK , Adamiak A , Cooper EA
Published: October 2003

Terbinafine is an allylamine antifungal agent that has been effective and safe in the treatment of superficial and some deep mycotic infections in adults. An increasing amount of data is available where terbinafine has been used in the paediatric population to treat superficial fungal infections, in particular tinea capitis. The data suggest that terbinafine is effective and safe using treatment regimens that involve short duration therapy, leading to an increased compliance and providing a cost‐effective means of treating paediatric superficial fungal infections such as tinea capitis. Terbinafine has been approved for the treatment of tinea capitis in many countries worldwide, and provides good efficacy rates for Trichophyton tinea capitis using shorter regimens than the gold standard griseofulvin. The adverse events profile for children is similar to that in adults with few adverse effects associated with its use. The evidence favours the use of terbinafine in the treatment of superficial infections in children.
Effect of tree host species on fungal community composition in a tropical rain forest in Panama
Authors: Ferrer Astrid , Gilbert Gregory S.
Published: October 2003

Abstract.  To determine whether host species influence the composition of fungal communities, the ascomycetes and basidiomycetes present on three tree species (Prioria copaifera (Fabaceae), Quararibea asterolepis (Bombacaceae), and Trichilia tuberculata (Meliaceae)) were sampled on the 50‐ha Forest Dynamics Project plot in lowland moist tropical forest on Barro Colorado Island, Panama. The most abundant fungal morphotypes of both ascomycetes and basidiomycetes were generalists found on all three hosts, but detrended correspondence analysis revealed distinct differences in fungal community composition among host trees. These differences among hosts were constant across census years. Randomization tests revealed that there were significantly fewer host‐generalist fungi than expected for ascomycetes but not for basidiomycetes. These results indicate that host composition plays a role in structuring both ascomycete and basidiomycete fungal communities, but that the most successful fungal morphotypes are capable of colonizing multiple host species.
WORTHWHILE READING ON GLOBAL CHANGE BIOLOGY
Authors: Kerr Jeremy
Published: October 2003

Books reviewed:

Chapin, F.S. III, Sala, O.E. & Huber‐Sannwald, E. (eds), Global biodiversity in a changing environment. Scenarios for the 21st century.
Growth and spectroscopic analysis of Yb3+-doped Y3Al5O12 fiber single crystals
Authors: Yoshikawa A. , Boulon G. , Laversenne L. , Canibano H. , Lebbou K. , Collombet A. , Guyot Y. , Fukuda T.
Published: October 2003

Two major fiber crystal growth methods have been applied for the synthesis and spectroscopic characterizations of Yb3+-doped Y3Al5O12 (Yb:YAG) to show the feasibility of a flexible single crystal fiber laser. One is the micropulling-down (μ-PD) method and the other is the laser heated pedestal growth (LHPG) method. 500 mm length fiber with no Yb segregation has been grown by the μ-PD method. A detailed analysis of Yb:YAG spectroscopy is made to contribute to the discussion on the determination of energy levels. On the other hand, a combinatorial chemistry approach has been applied on concentration gradient crystal fibers grown by the LHPG method allowing the measurement of the intrinsic radiative lifetime and the analysis of concentration quenching processes of Yb3+ ions in YAG.
Crystallographic features of oriented nanocrystals induced by focused-ion-beam irradiation of an amorphous alloy
Authors: Tarumi Ryuichi , Takashima Kazuki , Higo Yakichi
Published: October 2003

We have formed crystallographically oriented nanosized crystals (NCs) in a Ni–P amorphous alloy using focused-ion-beam (FIB) irradiation at room temperature. Transmission electron microscopy observations of the irradiated plane revealed the formation of NCs throughout the irradiated area. From a series of electron diffraction analyses, the structure of the formed NCs was determined to be face-centered cubic (fcc) of Ni and the following orientation of the formed NCs was confirmed: Irradiated plane normal ∥〈111〉fcc, and FIB direction ∥〈110〉fcc. The formed NCs consisted of two variants which have a twin relation, the twinning plane being the irradiated plane. These twin related crystals have a domainlike microstructure with an average domain size of approximately 200 nm. The elastic anisotropy of the amorphous alloy does not affect the crystallographic features of the formed NCs. The features which control the orientation of the formed NCs are discussed from crystallographic and geometrical points of view.
Low incident angle and classical x-ray diffraction analysis of residual stresses in diamond coated Si3N4
Authors: Soares M. R. , Belmonte M. , Silva R. F.
Published: October 2003

The overall residual stresses and the stress distribution on chemical vapor deposition diamond coated silicon nitride (Si3N4) are investigated by x-ray diffraction using the classical sin2 ψ method and the low incident beam angle diffraction technique, respectively. The deposition time and the substrate surface roughness evidence a clear effect on the film texture and residual stress generation on the diamond coatings. For the roughest substrate, 15 μm polished diamond, as the deposition time increases from 2 to 6 h, a remarkable improvement of the (220) texture and compressive stress relaxation occur from −0.75 to −0.14 GPa. A change to less compressive and even to slight tensile stress takes place for the smoothest substrate, colloidal finished silica, giving stress values of −0.40 and 0.21 GPa for 2 and 6 h of deposition time, respectively. The stress profile along the film thickness for the 6 h grown diamond film on the 15 μm polished substrate exhibits a linear decrease, in absolute values, from a compressive residual stress of −3.7 GPa, in the upper layer of the film, to almost zero stress at the film/substrate interface.
Hierarchy of random chaotic maps with an invariant measure
Authors: Jafarizadeh M. A. , Behnia S.
Published: October 2003

Hierarchy of one and many-parameter families of random chaotic maps and one-parameter random elliptic maps of cn type with an invariant measure have been introduced. Using the invariant measure (Sinai–Ruelle–Bowen measure), the Kolmogorov–Sinai entropy of the random chaotic maps have been calculated analytically, where the numerical simulations support the results.
Piezoelectrically enhanced capacitive strain sensors using GaN metal-insulator-semiconductor diodes
Authors: Strittmatter R. P. , Beach R. A. , Picus G. S. , McGill T. C.
Published: October 2003

We report on the use of metal-insulator-semiconductor (MIS) diodes, formed on n-GaN with SiO2, for capacitive strain sensing. These diodes, when subjected to static strain, were found to exhibit a steady-state change in capacitance. As a result, they can be used to detect strain with frequencies all the way down to dc. We formulate a model to explain the action of piezoelectricity in the diode and obtain excellent agreement with measurements. The model is then used to develop design criteria which optimize the sensitivity of the diode to detect strain. The sensitivity of the devices tested here rivals that of the best silicon piezoresistive sensors, but could attain nearly tenfold improvement with only minor design changes. Finally, we consider the effects of interface states on sensor performance and demonstrate how static strain sensing in GaN MIS diodes is enabled by the high quality of the oxide interface.
Optimal design of manufacturable three-dimensional composites with multifunctional characteristics
Authors: Torquato S. , Hyun S. , Donev A.
Published: October 2003

We present an optimization method to design three-dimensional composite microstructures with multifunctional characteristics. To illustrate the fascinating types of microstructures that can arise in multifunctional optimization, we apply our methodology to the study the simultaneous transport of heat and electricity in three-dimensional, two-phase composites. We assume that phase 1 has a high thermal conductivity but low electrical conductivity and phase 2 has a low thermal conductivity but high electrical conductivity. The objective functions consist of different combinations of the dimensionless effective thermal and electrical conductivities. When the sum of the effective thermal and electrical conductivities is maximized, we find that the optimal three-dimensional microstructures are triply periodic bicontinuous composites with interfaces that are the Schwartz primitive (P) and diamond (D) minimal surfaces. Maximizing the effective thermal conductivity and minimizing the effective electrical conductivity results in a special dispersion of inclusions in a connected matrix. The effective properties of both the bicontinuous and singly connected microstructures lie on known optimal cross-property bounds. When the sum of the effective thermal and electrical conductivities is minimized, the result is the three-dimensional checkerboard, which is the optimal single-scale microstructure. It is important to note that current fabrication techniques enable one to manufacture all of the aforementioned optimal single-scale composites.
Strain behavior of thin film PbZr0.3Ti0.7O3 (30/70) examined through piezoforce microscopy
Authors: Dunn S.
Published: October 2003

Using an atomic force microscope (AFM) modified to perform piezo-AFM we have investigated the piezoelectric response of sol-gel thin film lead zirconate titanate (PZT 30/70, PbZr0.3Ti0.7O3) on Pt-Ti/SiO2/Si to a quasi-dc electric field. By applying a sinusoidal 2 Hz ac waveform between the AFM cantilever and ground we have generated strain field, or butterfly loops for the PZT film. Coercive fields for the thin films have been calculated from the minimum point of the strain before reversal for the system and are shown to be −30 and +32 V/μm in absolute terms and −23 and +39 V/μm in terms relative to the charge trapped at the electrode interface. The maximum strain of the system was shown at applied biases of ±10 V and was 0.3% at a bias of +10 V, although at this bias the sample was not showing saturated behavior. By relating the offset of the butterfly loops to the charge density generated by defects at the PZT–electrode interface, calculated to be 0.025 Cm−2, an estimate of the number of defects at the interface has been calculated to be one defect for every 6 nm2 of surface, or one defect in every 40 unit cells.
Charge separation effects in magnetized electron–ion plasma expansion into a vacuum
Authors: Nishimura Kazumi , Liang Edison , Gary S. Peter
Published: October 2003

Charge separation effects in the expansion of magnetized relativistic electron–ion plasmas into a vacuum are examined using 212-dimensional particle-in-cell plasma simulations. The electrostatic field at the plasma surface decelerates electrons and accelerates ions. A fraction of the surface electrons is trapped and accelerated by the pondermotive force of the propagating electromagnetic pulse, a mechanism we call the diamagnetic relativistic pulse accelerator. This charge separation is enhanced as the initial plasma temperature is decreased. The overall energy gain of the plasma particles through the expansion strongly depends on the initial plasma temperature. Moreover, the electrons become relatively less energized and the ions more energized as the plasma temperature decreases.
Geometric phase and modulus relations for probability amplitudes as functions on complex parameter spaces
Authors: Botero Alonso
Published: October 2003

We investigate general differential relations connecting the respective behaviors of the phase and modulus of probability amplitudes of the form 〈ψf|ψ〉, where |ψf〉 is a fixed state in Hilbert space and |ψ〉 is a variable state, treated as a section of a U(1) bundle over a complex subspace of the corresponding ray space R=CPn. Amplitude functions on such holomorphic line bundles, while not strictly holomorphic, nevertheless satisfy generalized Cauchy–Riemann conditions involving the U(1) Berry–Simon connection on the parameter space. These conditions entail invertible relations between the gradients of the phase and modulus, therefore allowing for the reconstruction of the phase from the modulus (or vice versa) and other conditions on the behavior of either polar component of the amplitude. As a special case, we consider amplitude functions valued on the space of pure states, the ray space R=CPn, where transition probabilities have a geometric interpretation in terms of geodesic distances as measured with the Fubini–Study metric. In conjunction with the generalized Cauchy–Riemann conditions, this geodesic interpretation leads to additional relations, in particular, a novel connection between the modulus of the amplitude and the phase gradient, somewhat reminiscent of the WKB formula. Finally, a connection with geometric phases is established.
Theoretical study of photoinduced electron transfer from tetramethylethylene to tetracyanoethylene
Authors: Yi Hai-Bo , Duan Xiao-Hui , Lee Jin Yong , Lee Han Myoung , Li Xiang-Yuan , Kim Kwang S.
Published: October 2003

Using ab initio and density functional calculations, we studied photoexcitation of a charge-balanced electron donor–acceptor (DA) complex comprised of tetracyanoethylene (TCE) and tetramethylethylene (TME). We considered both the TCE-TME stacked conformer and a possible conformer with a solvent molecule (dichloromethane) inserted between TCE and TME. The photoexcitation of the DA complex can directly form a charge transfer (CT) state. Our theoretical investigations show that the CT state can also be produced from the decay of higher excited states. Using the continuum model, we investigated the solvent effects on CT absorption, local excitation, and CT emission in the polar solvent. The equilibrium solvation energies of the ground and excited states of the DA complex were calculated using the self-consistent reaction field method, and then the correction of nonequilibrium solvation energies for the vertical transitions was made. The transition energies (i.e., CT absorption for the DA complexes and CT emission for the contact ion pair complexes) in the polar solvent show redshifts relative to those in the gas phase.
Close look at charge carrier injection in polymer field-effect transistors
Authors: Bürgi L. , Richards T. J. , Friend R. H. , Sirringhaus H.
Published: October 2003

Parasitic contact resistance effects are becoming a major issue in organic transistors in that they can severely limit or even dominate their overall transistor performance. We present a systematic study of the contact resistance in bottom-contact polymer field-effect transistors made from poly(3-hexylthiophene) (P3HT) as well as poly-9,9′dioctyl-fluorene-co-bithiophene (F8T2). A microscopic approach based on noncontact scanning-probe potentiometry was used to directly separate the transport properties of the transistor channel and the electrode/polymer contacts, giving very accurate experimental access to both the source and drain contact resistance. The influence of the relevant parameters (temperature, electrode work function, ionization potential of the polymer, charge carrier mobility) on the source/drain contact resistance is investigated. We find that for “good” source/drain contacts that give rise to relatively small overall contact resistances (⩽50 kΩ cm), e.g., P3HT with chromium–gold electrodes, the source and the drain contact resistances are almost identical and are governed by bulk transport through the conjugated polymer. However, for “bad” contacts with a Schottky barrier for hole injection φb⩾0.3 eV, e.g., F8T2 with gold electrodes, the source contact resistance is considerably larger than the drain contact resistance and is dominated by charge-carrier injection at the source. Surprisingly small activation energies of 60–140 meV have been found for the source contact resistance, which are smaller than both φb and the activation energy of the mobility. From this we conclude that the commonly assumed (diffusion-limited) thermionic-emission models do not adequately describe the charge injection process in bottom-contact polymer transistors. On the basis of our results we propose a simple model, in which the source contact resistance is assumed to be the sum of resistance arising from the injection process and resistance due to bulk transport through a depletion region, whereas only the latter contributes to the drain contact resistance.
Fracture strength of ultrananocrystalline diamond thin films—identification of Weibull parameters
Authors: Espinosa H. D. , Peng B. , Prorok B. C. , Moldovan N. , Auciello O. , Carlisle J. A. , Gruen D. M. , Mancini D. C.
Published: October 2003

The fracture strength of ultrananocrystalline diamond (UNCD) has been investigated using tensile testing of freestanding submicron films. Specifically, the fracture strength of UNCD membranes, grown by microwave plasma chemical vapor deposition (MPCVD), was measured using the membrane deflection experiment developed by Espinosa and co-workers. The data show that fracture strength follows a Weibull distribution. Furthermore, we show that the Weibull parameters are highly dependent on the seeding process used in the growth of the films. When seeding was performed with microsized diamond particles, using mechanical polishing, the stress resulting in a probability of failure of 63% was found to be 1.74 GPa, and the Weibull modulus was 5.74. By contrast, when seeding was performed with nanosized diamond particles, using ultrasonic agitation, the stress resulting in a probability of failure of 63%, increased to 4.13 GPa, and the Weibull modulus was 10.76. The tests also provided the elastic modulus of UNCD, which was found to vary from 940 to 970 GPa for both micro- and nanoseeding. The investigation highlights the role of microfabrication defects on material properties and reliability, as a function of seeding technique, when identical MPCVD chemistry is employed. The parameters identified in this study are expected to aid the designer of microelectromechanical systems devices employing UNCD films.
All-SrTiO3 field effect devices made by anodic oxidation of epitaxial semiconducting thin films
Authors: Bellingeri E. , Pellegrino L. , Marré D. , Pallecchi I. , Siri A. S.
Published: October 2003

We report a field effect device fully made of strontium titanate (STO). This perovskite-type material is very attractive for oxide electronics both for its notable dielectric properties as well as for its semiconducting properties in the doped state. We exploit both of these properties by developing a field effect device in which oxygen deficient STO acts as a conducting channel and stoichiometric STO as a dielectric barrier. Such a barrier is obtained by electrochemical oxidation of the surface of an oxygen deficient semiconducting STO film, deposited by pulsed laser ablation in ultrahigh vacuum conditions. The channel conductivity is varied by the application of an electric field between the channel itself and a metallic gate deposited onto the dielectric barrier. Modulation capability of more than 60% is achieved by applying potential lower than 1 V. Conductivity changes are due to electrostatic induced variations of the charge carrier density (n). This result is confirmed by Hall effect measurements during gate biasing. The very good agreement of the measured n with the value calculated from the device capacitance proves the electrostatic origin of the effect observed.
Canonical factorization and diagonalization of Baxterized braid matrices: Explicit constructions and applications
Authors: Chakrabarti A.
Published: October 2003

Braid matrices R̂(θ), corresponding to vector representations, are spectrally decomposed obtaining a ratio fi(θ)/fi(−θ) for the coefficient of each projector Pi appearing in the decomposition. This directly yields a factorization (F(−θ))−1F(θ) for the braid matrix, implying also the relation R̂(−θ)R̂(θ)=I. This is achieved for GLq(n), SOq(2n+1), SOq(2n), Spq(2n) for all n and also for various other interesting cases including the eight-vertex matrix. We explain how the limits θ→±∞ can be interpreted to provide factorizations of the standard (non-Baxterized) braid matrices. A systematic approach to diagonalization of projectors and hence of braid matrices is presented with explicit constructions for GLq(2), GLq(3), SOq(3), SOq(4), Spq(4) and various other cases such as the eight-vertex one. For a specific nested sequence of projectors diagonalization is obtained for all dimensions. The canonical property implemented in the diagonalizers is mutual orthogonality of the rows. In each factor F(θ) our diagonalizer again factors out all dependence on the spectral parameter θ as a diagonal matrix. Applications of our formalism to the construction of L-operators and transfer matrices are indicated. In an Appendix our type of factorization is compared to another one proposed by other authors.
Ab initio studies of ClOx reactions. IX. Combination and disproportionation reactions of ClO and s-ClO3 radicals
Authors: Xu Z. F. , Lin M. C.
Published: October 2003

The mechanism for the reaction ClO+ClO3 on both singlet and triplet state potential surfaces has been investigated with the modified Gaussian-2 method based on the B3LYP/6-311+G(3df ) optimized stationary-point geometries. The result shows that the barrierless association reaction producing ClOClO3 and two lower barrier O-atom abstraction reactions take place primarily on the singlet state potential surface; they are energetically more favorable than those occurring on the triplet state surface. Rate constants calculated by variational transition state and Rice–Ramsperger–Kassel–Marcus theories suggest that the major products are ClOClO3 at low temperatures (<700 K) and OClO+ClOO at high temperatures. The following rate constants are recommended for atmospheric chemistry and combustion applications: k1∞(ClOClO3)=1.43×10−10 T0.094exp(−82/T) cm3 molecule−1 s−1 (200–3000 K) and k10(ClOClO3)=0.14 T−10.19exp(−1597/T) cm6 molecule−2 s−1 (200–800 K) for He as the third-body. In addition, a potential high-temperature reverse reaction involving Cl and ClO4 has been predicted to yield exclusively the ClO and ClO3 products; its rate constant is predicted to be: k4(ClO+ClO3)=8.05×10−11 T0.158 exp(−49/T) cm3 molecule−1 s−1 (200–3000 K). The heats of formation at 0 K for s-ClO3, ClO4, and ClOClO3 have been predicted to be 46.7, 59.4, and 38.3 kcal/mol with about 1 kcal/mol uncertainty using the new heat of formation of OClO, 24.1±0.1 kcal/mol, based on the most recent bond dissociation energy of O–ClO reported in the literature.
Nonequilibrium translational effects in evaporation and condensation
Authors: Bedeaux D. , Kjelstrup S. , Rubi J. M.
Published: October 2003

This paper shows how mesoscopic nonequilibrium thermodynamics can be applied to condensation and evaporation. By extending the normal set of thermodynamic variables with two internal variables, we are able to give a new theoretical foundation for a mechanism of condensation that has been proposed from molecular simulation results. The flux does not follow a simple Arrhenius formula for small activation energies which are relevant here.