bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparative study of daytime mesopause temperatures obtained using unique ground based optical and meteor wind radar techniques over the magnetic equator
Authors: Vineeth C. , Pant Tarun Kumar , Antonita Maria , Ramkumar Geetha , Devasia C. V. , Sridharan R.
Published: October 2005

This paper presents the first ever comparison of daytime Mesopause OH rotational temperatures as determined using Meinel (8‐3) dayglow emissions with those obtained using the recently established and collocated, meteor radar (SKiYMET) over the magnetic equator in India. The measurements were made over Thiruvananthapuram (8.5°N, 76.5°E, 0.5°N diplat.) for January–May 2005 period. Overall agreement had been good (±20 K) with all the gross features coming out fairly well. Further, the temperatures estimated using these two techniques, exhibit significant wavelike modulations with periods spanning ∼3–65 days with varying phase differences, presumably due to their interaction with the longer period waves like the semiannual oscillation (SAO). The consistency of the temperature variabilities at two different altitudes viz. 87 and 94 km enables investigation of the mesosphere lower thermosphere dynamic coupling.
The OH-stretching and OOH-bending overtone spectrum of HOONO
Authors: Schofield Daniel P. , Kjaergaard Henrik G. , Matthews Jamie , Sinha Amitabha
Published: October 2005

We have simulated the HOONO vibrational overtone spectrum with use of a local mode Hamiltonian that includes the OH-stretching, OOH-bending, and NOOH-torsional modes and coupling between all three modes. The local mode parameters and the dipole moment function are calculated with coupled-cluster ab initio theory and an augmented Dunning-type triple-zeta basis set. We investigate the accuracy of the local mode parameters obtained from two different potential-energy fitting routines, as well as the sensitivity of these parameters to the basis set employed. We compare our simulated spectra to previously published action spectra in the first and second OH-stretching overtone regions. In addition we have recorded the spectrum in the OH-stretch and OOH-bend combination region around 7700cm−1 and we also compare to this. Our simulated spectrum is in qualitative agreement with experiment in the first and second OH-stretching overtone and in the stretch-bend regions.
Theoretical study of isomerization and dissociation of acetylene dication in the ground and excited electronic states
Authors: Zyubina T. S. , Dyakov Y. A. , Lin S. H. , Bandrauk A. D. , Mebel A. M.
Published: October 2005

Ab initio calculations employing the configuration interaction method including Davidson’s corrections for quadruple excitations have been carried out to unravel the dissociation mechanism of acetylene dication in various electronic states and to elucidate ultrafast acetylene-vinylidene isomerization recently observed experimentally. Both in the ground triplet and the lowest singlet electronic states of C2H22+ the proton migration barrier is shown to remain high, in the range of 50kcal∕mol. On the other hand, the barrier in the excited 2A″3 and 1A′3 states decreases to about 15 and 34kcal∕mol, respectively, indicating that the ultrafast proton migration is possible in these states, especially, in 2A″3, even at relatively low available vibrational energies. Rice-Ramsperger-Kassel-Marcus calculations of individual reaction-rate constants and product branching ratios indicate that if C2H22+ dissociates from the ground triplet state, the major reaction products should be CCH+(Σ−3)+H+ followed by CH+(Π3)+CH+(Σ+1) and with a minor contribution (∼1%) of C2H+(A12)+C+(P2). In the lowest singlet state, C2H+(A12)+C+(P2) are the major dissociation products at low available energies when the other channels are closed, whereas at Eint>5eV, the CCH+(A′1)+H+ products have the largest branching ratio, up to 70% and higher, that of CH+(Σ+1)+CH+(Σ+1) is in the range of 25%–27%, and the yield of C2H++C+ is only 2%–3%. The calculated product branching ratios at Eint≈17eV are in qualitative agreement with the available experimental data. The appearance thresholds calculated for the CCH++H+, CH++CH+, and C2H++C+ products are 34.25, 35.12, and 34.55 eV. The results of calculations in the presence of strong electric field show that the field can make the vinylidene isomer unstable and the proton elimination spontaneous, but is unlikely to significantly reduce the barrier for the acetylene-vinylidene isomerization and to render the acetylene configuration unstable or metastable with respect to proton migration.
Selective self-assembly at room temperature of individual freestanding Ag2Ga alloy nanoneedles
Authors: Yazdanpanah Mehdi M. , Harfenist Steven A. , Safir Abdelilah , Cohn Robert W.
Published: October 2005

Liquid gallium drops placed on thick Ag films at room temperature spontaneously form faceted nanoneedles of Ag2Ga alloy oriented nearly normal to the surface. This observation suggests that single nanoneedles can be selectively grown by drawing silver-coated microcantilevers from gallium. Needles from 25 nm to microns in diameter and up to 33μm long were grown by this method. These metal-tipped cantilevers have been used to perform atomic force microscopy (AFM) and AFM voltage lithography.
Interdiffusion in InGaAsSb∕AlGaAsSb quantum wells
Authors: Wang Y. , Djie H. S. , Ooi B. S.
Published: October 2005

We modeled the effect of atomic interdiffusion in InGaAsSb∕AlGaAsSb quantum well grown on GaSb substrate. The material modification after interdiffusion has been calculated using Fick’s second law of diffusion and the rationalized biquadratic quinary interpolation algorithm. Our results show that both the group-III and group-V atomic interdiffusions lead to blueshifts of ground-state transition energies. For identical diffusion lengths, the group-III interdiffusion produces a larger ground-state blueshift than the group-V interdiffusion. A wavelength blueshift as large as 772nm is predicted from a 10-nm-wide interdiffused quantum well with an identical diffusion length of 5nm for both the group-III and group-V sublattices. The large wavelength tuning range indicates that the interdiffusion method can be potentially used to trim the emission wavelengths of InGaAsSb∕AlGaAsSb quantum-well structures for various mid-infrared-based photonics devices. Our results will also serve as useful references for a better process control of the epitaxial growth of Sb-based systems.
Spin-polarized current in a ferromagnetic/organic system
Authors: Ren J. F. , Fu J. Y. , Liu D. S. , Mei L. M. , Xie S. J.
Published: October 2005

Spin-polarized current through a ferromagnetic/organic interface was studied theoretically. This study was stimulated by recent experiments on La1−xSrxMnO3∕Alq3∕Co and La1−xSrxMnO3∕sexithienyl∕La1−xSrxMnO3 structures. According to the spin-diffusion equation, the current spin polarization was obtained by assuming that spin polarons as well as spinless bipolarons to be the carriers in the organic semiconductor. It was found that polarons are the effective spin carriers of a spin-polarized current, even though they constitute only a fraction of all carriers. Effects of interfacial electrochemical-potential difference and conductivity matching on spin polarization of the current are discussed.
Kinetics of the reaction between diamond and silicon at high pressure and temperature
Authors: Pantea C. , Voronin G. A. , Zerda T. W.
Published: October 2005

Diamond-silicon carbide composites were sintered from diamond powder and liquid silicon at high pressure-high temperature (HPHT) conditions. Experiments were conducted in the diamond-stable region and then repeated in the graphite-stable region. X-ray diffractograms of the specimens sintered for different time periods provided information on the SiC formation rate and activation energy. Only the late stage of the reaction was investigated, and in the diamond-stable region it was shown that SiC growth was controlled by the diffusion rate of silicon and carbon atoms though the existing layer of SiC. This process is characterized by an activation energy of 264kJ∕mol. At 2GPa, where graphite is the stable form of carbon, in addition to the direct reaction, diamond may first spontaneously transform into graphite, which next reacts with silicon. A combination of these two processes results in a higher activation energy of 410kJ∕mol.
Carbon nanotube gated lateral resonant tunneling field-effect transistors
Authors: Wang D. P. , Perkins B. R. , Yin A. J. , Zaslavsky A. , Xu J. M. , Beresford R. , Snider G. L.
Published: October 2005

We have produced a lateral resonant tunneling field-effect transistor using a Y-junction multiwalled carbon nanotube as the dual gate on a narrow channel etched from a modulation-doped GaAs∕AlGaAs heterostructure. When the Y-junction nanotube is negatively biased, electrons traveling from source to drain along the channel face a voltage-tunable electrostatic double-barrier potential. We measured the three-terminal IDS(VDS,VGS) characteristics of the device at 4.2 K and observed gate-induced structure in the transconductance and negative differential resistance in the drain current. We interpret the data in terms of resonant tunneling through one-dimensional subbands confined by a self-consistently calculated electrostatic potential.
Time-resolved x-ray laser induced photoelectron spectroscopy of isochoric heated copper
Authors: Nelson A. J. , Dunn J. , Hunter J. , Widmann K.
Published: October 2005

Time-resolved x-ray photoelectron spectroscopy is used to probe the nonsteady-state evolution of the valence band electronic structure of laser heated ultrathin (50nm) copper. A metastable phase is studied using a 527nm wavelength 400fs laser pulse containing 0.1–2.5mJ laser energy focused in a large 500×700μm2 spot to create heated conditions of 0.07–1.8×1012Wcm−2 intensity. Valence band photoemission spectra are presented showing the changing occupancy of the Cu 3d level with heating are presented. These picosecond x-ray laser induced time-resolved photoemission spectra of laser-heated ultrathin Cu foil show dynamic changes in the electronic structure. The ultrafast nature of this technique lends itself to true single-state measurements of shocked and heated materials.
Postfabrication fine-tuning of photonic crystal microcavities in InAs∕InP quantum dot membranes
Authors: Dalacu Dan , Frédérick Simon , Poole Philip J. , Aers Geof C. , Williams Robin L.
Published: October 2005

A method to fine-tune photonic crystal defect cavities is developed based on successive oxidation and wet etching cycles. Photonic crystal microcavities based on InP membranes are oxidized using an ultraviolet (UV)/ozone treatment, and the oxide is subsequently removed using a hydrofluoric acid solution. Each oxidation/etch cycle consumes a thin layer of InP directly exposed to the UV/ozone, enlarging the radius of holes in the photonic crystal and decreasing the membrane thickness. The method is applied to single missing air-hole defect cavities with embedded InAs quantum dots, permitting measurement of the resonant frequency tuning in emission. Defect mode energies were found to blueshift 1.74meVpercycle, consistent with finite-difference time-domain simulations. A tuning range of 33meV was obtained after 20cycles.
1.55
μ
m
emission from InAs quantum dots grown on GaAs
Authors: Hsieh Tung-Po , Chiu Pei-Chin , Chyi Jen-Inn , Yeh Nien-Tze , Ho Wen-Jeng , Chang Wen-Hao , Hsu Tzu-Min
Published: October 2005

We report a comparative study on the growth of InAs quantum dots (QDs) on GaAs by metalorganic chemical vapor deposition using triethylgallium (TEGa) and trimethylgallium (TMGa) for the GaAs cap layer. QDs exhibit 1.3μm photoluminescence (PL) at room temperature, as the GaAs cap layer is directly grown on the QDs. The PL emission can be extended to 1.49μm when an In0.25Ga0.75As overgrown layer is inserted between the cap layer and the InAs QDs. The use of TMGa or TEGa for the growth of the GaAs cap layer is essential for a further increase in the emission wavelength of the InAs QDs. Strong PL emission at 1.55μm with a linewidth of 28meV can be obtained as the GaAs cap layer is grown by TEGa, while the optical properties degrade severely when using TMGa.
Radiation-induced trapping and charge transport in a smectic liquid crystal
Authors: Hudson Katherine , Ellman Brett , Gettwert Volker , Getmanenko Yulia , Twieg Robert J.
Published: October 2005

We have studied changes in the hole transport properties of a smectic liquid crystalline semiconductor resulting from high-energy electron irradiation. The “radiation doping” results in sharply increased shallow trap densities and the onset of nearly trap-limited hopping conduction. A simple semiquantitative model provides estimates of the trap lifetime and the irradiation energy required to create a single trap. Experimental techniques to overcome parasitic effects due to increased molecular ion densities in irradiated samples are also discussed.
Molecular identification of fungi isolated from stem tissue of Upland cotton (Gossypium hirsutum)
Authors: Becerra-LopezLavalle L. Augusto , Saleeba Jennifer A. , Lyon Bruce R.
Published: October 2005

Molecular techniques such as restriction fragment length polymorphism (RFLP) analysis, random amplification of polymorphic DNA (RAPD) fingerprinting, and DNA sequencing and database comparison, were employed to identify fungi isolated from field-grown cotton plants (Gossypium hirsutum L.). DNA fragments of between 510 and 590 bp, representing the two rDNA (rDNA) internal transcribed spacers (ITS1 and ITS2) and the intervening 5.8S rRNA gene, were amplified from the fungi with eukaryotic consensus primers. Subsequent digestion with the restriction endonucleases AluI, CfoI, HaeIII, HinfI and HpaII enabled the allotment of all 57 isolates to 13 different groups. Restriction analysis was supported by RAPD–PCR analysis of multiple isolates and rDNA sequencing of representative fungi from each group. Sequence alignment and comparison with rDNA sequences of other fungi available in GenBank allowed for putative identification of three different taxa of Fusarium, two taxa each of Cladosporium, Diaporthe and Nectria, and one taxon each of Alternaria, Ampelomyces, Bartalinia, Phaeosphaeria and Rhizoctonia. Many of the stem-colonising fungi identified in this study are either pathogenic on cotton or have elsewhere been found to act as biocontrol agents.
Conservation implications of clonality and limited sexual reproduction in the endangered shrub Acanthocladium dockeri (Asteraceae)
Authors: Jusaitis Manfred , Adams Mark
Published: October 2005

Allozyme electrophoresis was used to determine the extent of clonality in four naturally occurring populations of Acanthocladium dockeri F.Muell. from the mid-north of South Australia. A total of 33 loci was scored for at least 16 plants from each population. The four known populations of A. dockeri represent four quite distinct genetic clones. Each natural population consists of a single genet, and no indication of any correlation between geographical proximity and genetic similarity was found. Seed set in flowers was very low (0.6% of florets), probably owing to low pollen germinability. Seedlings raised from A. dockeri seed collected at Hart displayed obvious genetic affinities to their parent, but were nevertheless genetically distinct. Differences were consistent with the derivation of this seed by selfing of the Hart genet. A. dockeri is considered at high risk of extinction because of its low genetic diversity, poor seed production, lack of seedling recruitment and population growth by clonal reproduction alone. On the basis of the outcomes of this research, the following recommendations for conservation management of A. dockeri are made: (1) all four extant genets should be preserved in their respective habitats; (2) at least one ex situ collection of all four extant genets should be maintained at a secure site as an insurance against population loss; (3) further surveys are required to potentially locate new populations with superior fertility; and (4) mixing of clones or seed provenances into a single population should be avoided until appropriately designed experimental translocations have evaluated the possible consequences of such mixing on competitive, reproductive and genetic responses of populations.
Plant cover and composition in relation to density of Callitris glaucophylla (white cypress pine) along a rainfall gradient in eastern Australia
Authors: Thompson W. A. , Eldridge D. J.
Published: October 2005

Despite the widespread distribution of Callitris glaucophylla J.Thompson & L.Johnson (white cypress pine) over large areas of eastern Australia, little is known about its impact on the diversity and cover of understorey plants. We examined C. glaucophylla woodlands to see whether stand density and land management influenced the cover and composition of the understorey vegetation. The cover and diversity of understorey plant communities were measured at 83 sites along a gradient in average annual rainfall (215–532 mm) in eastern Australia. The diversity and cover of understorey plants and the cover of trees increased, and the composition of the understorey community changed with increases in average annual rainfall. There were no clear relationships, however, between tree cover or density, and the cover or diversity of understorey plants. Sites that had not been logged contained significantly greater proportions of native and perennial vascular plants, and sites with extant eucalypts had a significantly higher proportion of shrubs than those sites without eucalypts. We attributed these differences to past forestry disturbance regimes which are correlated with the presence of mature eucalypts. Our results do not support the proposition that dense stands of C. glaucophylla suppress the understorey vegetation.
Effects of irrigation on seedling emergence and seedling survival of a desert shrub Haloxylon ammodendron (Chenopodiaceae)
Authors: Tobe Kazuo , Li Xiaoming , Omasa Kenji
Published: October 2005

Haloxylon ammodendron (C.A. Mey) Bunge (Chenopodiaceae) is a shrub occurring on desert sand dunes in China. Seedling emergence and seedling survival were investigated by sowing seeds at different depths (0, 2.5, 5.0 or 10 mm) in fine or coarse sand in pots irrigated under different regimes. Seed burial in sand was required for seedling establishment of this species. Seedling emergence depended greatly on seed burial depth, sand type, and irrigation regime; this appeared to be due to (1) seeds or seedlings suffering from oxygen or moisture deficiency depending on the air : moisture ratio in sand, and/or (2) higher moisture content in sand resulting in hardening of the sand and obstruction of seedling growth. Increased irrigation resulted in longer survival of emerging seedlings because sand was moistened more deeply, and moisture in deeper sand persisted longer. The results suggest that the infrequent and light precipitation common in desert environments is likely to cause germination of many of the buried seeds, but is insufficient for emerging seedlings to survive. It is suggested that water from melting snow in early spring is crucial in enabling seedling establishment of this species in the deserts of China.
Cytolytic granule polarization and degranulation controlled by different receptors in resting NK cells
Authors: Bryceson Yenan T. , March Michael E. , Barber Domingo F. , Ljunggren Hans-Gustaf , Long Eric O.
Published: October 2005

The relative contribution to cytotoxicity of each of the multiple NK cell activation receptors has been difficult to assess. Using Drosophila insect cells, which express ligands of human NK cell receptors, we show that target cell lysis by resting NK cells is controlled by different receptor signals for cytolytic granule polarization and degranulation. Intercellular adhesion molecule (ICAM)-1 on insect cells was sufficient to induce polarization of granules, but not degranulation, in resting NK cells. Conversely, engagement of the Fc receptor CD16 by rabbit IgG on insect cells induced degranulation without specific polarization. Lysis by resting NK cells occurred when polarization and degranulation were induced by the combined presence of ICAM-1 and IgG on insect cells. Engagement of receptor 2B4 by CD48 on insect cells induced weak polarization and no degranulation. However, coengagement of 2B4 and CD16 by their respective ligands resulted in granule polarization and cytotoxicity in the absence of leukocyte functional antigen-1–mediated adhesion to target cells. These data show that cytotoxicity by resting NK cells is controlled tightly by separate or cooperative signals from different receptors for granule polarization and degranulation.
DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus
Authors: Casillas Sònia , Petit Natalia , Barbadilla Antonio
Published: October 2005

Motivation: Polymorphism studies are one of the main research areas of this genomic era. To date, however, no comprehensive secondary databases have been designed to provide searchable collections of polymorphic sequences with their associated diversity measures.

Results: We define a data model for the storage, representation and analysis of genotypic and haplotypic data. Under this model we have created DPDB, ‘Drosophila Polymorphism Database’, a web site that provides a daily updated repository of all well-annotated polymorphic sequences in the Drosophila genus. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity, linkage disequilibrium and codon bias. For data collection, analysis and updating we use PDA, a pipeline that automates the process of sequence retrieval, grouping, alignment and estimation of nucleotide diversity from Genbank sequences in different functional regions. The web site also includes analysis tools for sequence comparison and the estimation of genetic diversity, a page with real-time statistics of the database contents, a help section and a collection of selected links.

Availability: DPDB is freely available at http://dpdb.uab.es and can be downloaded via FTP.

Contact:  antonio.barbadilla@uab.es
Design of a description language for generating wrapper to collect biological data
Authors: Lim Myungeun , Chung Myunggeun , Bae Myungnam , Park Sunhee
Published: October 2005

Summary: The biological data are scattered in various areas with various formats and they are changing continuously. Therefore, data integration becomes an important issue to provide researcher a dynamic access of data. In the data integration process, the method of extracting heterogeneous data dynamically from the data source is an essential part. Data extraction method using wrapper can provide flexibility and extensibility to an integration system.

Contact:  melim@etri.re.kr
The fragment assembly string graph
Authors: Myers Eugene W.
Published: October 2005

We present a concept and formalism, the string graph, which represents all that is inferable about a DNA sequence from a collection of shotgun sequencing reads collected from it. We give time and space efficient algorithms for constructing a string graph given the collection of overlaps between the reads and, in particular, present a novel linear expected time algorithm for transitive reduction in this context. The result demonstrates that the decomposition of reads into kmers employed in the de Bruijn graph approach described earlier is not essential, and exposes its close connection to the unitig approach we developed at Celera. This paper is a preliminary piece giving the basic algorithm and results that demonstrate the efficiency and scalability of the method. These ideas are being used to build a next-generation whole genome assembler called BOA (Berkeley Open Assembler) that will easily scale to mammalian genomes.

Contact:  gene@eecs.berkeley.edu
Association Cluster Detector: a tool for heuristic detection of significance clusters in whole-genome scans
Authors: Marquès-Bonet Tomàs , Lao Oscar , Goertsches Robert , Comabella Manuel , Montalban Xavier , Navarro Arcadi
Published: October 2005

Summary: Whole genome scans analyze large sets of genetic markers, mainly single nucleotide polymorphisms, over the entire genome in order to find variants and regions associated with complex traits so these can be further investigated. Analyzing the results of such scans becomes difficult due to multiple testing problems and to the genomic distributions of recombination, linkage disequilibrium and true associations, which generate an extremely complex network of dependences between markers. Here we present Association Cluster Detector (ACD), a simple tool aiming to ease the analysis of the results of whole genome scans. ACD facilitates correction for multiple tests using several standard procedures and implements a sliding-window heuristic method that helps in detecting potentially interesting candidate regions by exploiting the property of non-random distribution of significantly associated markers.

Availability: The tool can be downloaded from http://www.upf.es/cexs/recerca/bioevo/softanddata.htm

Contact:  arcadi.navarro@upf.edu
Data-adaptive test statistics for microarray data
Authors: Mukherjee Sach , Roberts Stephen J. , van der Laan Mark J.
Published: October 2005

Motivation: An important task in microarray data analysis is the selection of genes that are differentially expressed between different tissue samples, such as healthy and diseased. However, microarray data contain an enormous number of dimensions (genes) and very few samples (arrays), a mismatch which poses fundamental statistical problems for the selection process that have defied easy resolution.

Results: In this paper, we present a novel approach to the selection of differentially expressed genes in which test statistics are learned from data using a simple notion of reproducibility in selection results as the learning criterion. Reproducibility, as we define it, can be computed without any knowledge of the ‘ground-truth’, but takes advantage of certain properties of microarray data to provide an asymptotically valid guide to expected loss under the true data-generating distribution. We are therefore able to indirectly minimize expected loss, and obtain results substantially more robust than conventional methods. We apply our method to simulated and oligonucleotide array data.

Availability: By request to the corresponding author.

Contact:  sach@robots.ox.ac.uk
Model-P: a basecalling method for resequencing microarrays of diploid samples
Authors: Zhan Yiping , Kulp David
Published: October 2005

Motivation: Basecalling is a critical step of the analysis of DNA resequencing microarray data for single nucleotide polymorphism discovery and genotyping. For microarrays hybridized with DNA derived from diploid organisms, basecalling with high accuracy at high call rates is a challenging task. Current methods sometimes do not produce satisfactory results.

Results: We explored using physical models based on the sequences of the probe and the target to predict feature intensities in resequencing microarrays. Based on these intensity-predicting models, a new basecalling method (Model-P), which takes into consideration the expected feature intensities for different potential genotypes, was developed. Model-P is shown to have better performance at high call rates compared with ABACUS, the current state-of-the-art method, on a test dataset and on relatively AT-rich regions.

Availability: Model-P is available upon request.

Contact:  dkulp@cs.umass.edu
Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli
Authors: Simão E. , Remy E. , Thieffry D. , Chaouiya C.
Published: October 2005

Motivation: The integrated dynamical modelling of mixed metabolic/genetic networks constitutes one of the challenges of systems biology. Furthermore, as most of available data about genetic and metabolic regulations are qualitative, there is a pressing need for rigorous qualitative mathematical approaches.

Results: On the basis of two established formalisms, the logical modelling of genetic regulatory networks and the Petri net modelling of metabolic networks, we propose a systematic approach for the modelling of regulated metabolic networks. This approach leans on previous work defining a systematic procedure to translate logical regulatory graphs into standard (discrete) Petri nets (PNs). This approach is illustrated by the qualitative modelling of the biosynthesis of tryptophan (Trp) in Escherichia coli, taking into account two types of regulatory feedbacks: the direct inhibition of the first enzyme of the pathway by the final product of the pathway, and the transcriptional inhibition of the Trp operon by the Trp–repressor complex. On the basis of this integrated PN model, we further indicate how available dynamical analysis tools can be applied to obtain significant insights in the behaviour of the system.

Availability: The software GINsim for the logical modelling of genetic regulatory networks together with the PN model of the regulated Trp biosynthesis pathway are available at: http://gin.univ-mrs.fr/GINsim.

Contact:  chaouiya@ibdm.univ-mrs.fr
RNA secondary structural alignment with conditional random fields
Authors: Sato Kengo , Sakakibara Yasubumi
Published: October 2005

Motivation: The computational identification of non-coding RNA regions on the genome is currently receiving much attention. However, it is essentially harder than gene-finding problems for protein-coding regions because non-coding RNA sequences do not have strong statistical signals. Since comparative sequence analysis is effective for non-coding RNA detection, efficient computational methods are expected for structural alignment of RNA sequences. Several methods have been proposed to accomplish the structural alignment tasks for RNA sequences, and we found that one of the most important points is to estimate an accurate score matrix for calculating structural alignments.

Results: We propose a novel approach for RNA structural alignment based on conditional random fields (CRFs). Our approach has some specific features compared with previous methods in the sense that the parameters for structural alignment are estimated such that the model can most probably discriminate between correct alignments and incorrect alignments, and has the generalization ability so that a satisfiable score matrix can be obtained even with a small number of sample data without overfitting. Experimental results clearly show that the parameter estimation with CRFs can outperform all the other existing methods for structural alignments of RNA sequences. Furthermore, structural alignment search based on CRFs is more accurate for predicting non-coding RNA regions than the other scoring methods. These experimental results strongly support our discriminative method employing CRFs to estimate the score matrix parameters.

Availability: The program which is implemented in C++ is available at http://phmmts.dna.bio.keio.ac.jp/ under the GNU public license.

Contact:  satoken@bio.keio.ac.jp
Implementing the iHOP concept for navigation of biomedical literature
Authors: Hoffmann Robert , Valencia Alfonso
Published: October 2005

Motivation: The World Wide Web has profoundly changed the way in which we access information. Searching the internet is easy and fast, but more importantly, the interconnection of related contents makes it intuitive and closer to the associative organization of human memory. However, the information retrieval tools currently available to researchers in biology and medicine lag far behind the possibilities that the layman has come to expect from the internet.

Results: By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource. iHOP (Information Hyperlinked over Proteins) is an online service that provides this gene-guided network as a natural way of accessing millions of PubMed abstracts and brings all the advantages of the internet to scientific literature research. Navigating across interrelated sentences within this network is closer to human intuition than the use of conventional keyword searches and allows for stepwise and controlled acquisition of information. Moreover, this literature network can be superimposed upon experimental interaction data to facilitate the simultaneous analysis of novel and existing knowledge. The network presented in iHOP currently contains5 million sentences and 40 000 genes from Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.

Availability: iHOP is freely accessible at http://www.pdg.cnb.uam.es/UniPub/iHOP/

Contact:  hoffmann@cbio.mskcc.org

Supplementary Information: Supplementary data are available at Bioinformatics online.
Dancing around the divisome: asymmetric chromosome segregation in Escherichia coli
Authors: Wang Xindan , Possoz Christophe , Sherratt David J.
Published: October 2005

By simultaneously tracking pairs of specific genetic regions and divisome proteins in live Escherichia coli, we develop a new scheme for the relationship between DNA replication-segregation, chromosome organization, and cell division. A remarkable asymmetric pattern of segregation of different loci in the replication termination region (ter) suggests that individual replichores segregate to distinct nucleoid positions, consistent with an asymmetric segregation of leading and lagging strand templates after replication. Cells growing with a generation time of 100 min are born with a nonreplicating chromosome and have their origin region close to mid-cell and their ter polar. After replication initiation, the two newly replicated origin regions move away from mid-cell to opposite cell halves. By mid-S phase, FtsZ forms a ring at mid-cell at the time of initiation of nucleoid separation; ter remains polar. In the latter half of S phase, ter moves quickly toward mid-cell. FtsK, which coordinates the late stages of chromosome segregation with cell division, forms a ring coincident with the FtsZ ring as S phase completes, ∼50 min after its initiation. As ter duplicates at mid-cell, sister nucleoid separation appears complete. After initiation of invagination, the FtsZ ring disassembles, leaving FtsK to complete chromosome segregation and cytokinesis.
Detection and characterization of two strains of Grapevine fanleaf nepovirus in Tunisia
Authors: Fattouch S. , Acheche H. , M’hirsi S. , Marrakchi M. , Marzouki N.
Published: October 2005

The nematode‐borne Grapevine fanleaf nepovirus (GFLV) causes severe degeneration of grapevines in vineyards worldwide. In a recent survey of the sanitary status of grapevine plants in north Tunisian vineyards, we were interested to study the polymorphism of GFLV. Purified virus, from mechanically inoculated Chenopodium quinoa, was used to produce anti‐GFLV antiserum, which specifically recognized GFLV in different Tunisian grapevine samples using the DAS‐ELISA technique. Positive samples were subjected to oligoprobe‐RT‐PCR to amplify a 606 bp region of the viral coat protein sequence. PCR products used for RFLP analysis after digestion with endonuclease AluI produced 3 restriction profiles. RFLP data allowed clear distinction of two GFLV strains in Tunisia. The nucleotide sequence of the PCR‐generated amplicons from each strain was determined showing 93.4% identity at the nucleic acid level and 97.5% similarity at the aminoacid sequence level compared to the previously characterized GFLV‐F13 French isolate. This paper is the first report on molecular variability of GFLV in Tunisia.
First report ofPythium diclinumin Morocco
Authors: El Androusse A. , El Aissami A. , Rahouti M. , Lahlou H. , Bouloud A. , Murandi F. Seigle
Published: October 2005

Pythium diclinumwas isolated from a reservoir near the city of Rabat (Morocco). This is the first report of its presence in this country. Taxonomic and morphological details of the fungus are presented. The isolate grew on potato carrot agar (PCA) containing various concentrations of NaCl, up to 700 mm. Pathogenicity of the Moroccan isolate was demonstratedin vitroon lucerne seeds and seedlings.
Ecological stoichiometry in freshwater benthic ecosystems: an introduction
Authors: FROST PAUL C. , CROSS WYATT F. , BENSTEAD JONATHAN P.
Published: October 2005

1. Ecological stoichiometry is a conceptual framework that considers how the balance of energy and elements affects and is affected by organisms in the environment. This perspective has seen recent development primarily in marine and freshwater pelagic ecosystems but its widescale application to freshwater benthic ecosystems remains limited.

2. This paper briefly introduces the concept of ecological stoichiometry, its potential application to freshwater benthic ecosystems, and it provides an overview of a series of papers that use a stoichiometric approach to illustrate the utility of this concept for studying a range of central questions about benthic ecosystems.

3. Papers in this issue include a detailed description of the elemental composition of stream benthic invertebrates, an analysis of the algal content of and its effects on C : P stoichiometry of periphyton, two reports exploring the stoichiometry of stromatolites and their snail consumers in a stream fed by thermal springs, an examination of the stoichiometric effects on stream periphyton and macroinvertebrates of slight nutrient enrichment resulting from treated sewage effluents, a study of nutrient release ratios and their control from crayfish and snails, a paper addressing the stoichiometric effects on fish and plankton that result from benthic food subsidies to fish, a study of the stoichiometry of tree leaves and litter and floodplain arthropods in the riparian zone of the Rio Grande, and a synthesis examining the current state and future potential of benthic stoichiometry.

4. The insights from these and other studies suggest that ecological stoichiometry has great potential to guide scientific thought and resolve long‐standing problems in ecology. Increasing use of this stoichiometric perspective should thus lead to a deeper understanding of important ecological processes in freshwater benthic ecosystems.
Diet quality affects egg size and number but does not reduce maternal antibody transmission in Japanese quailCoturnix japonica
Authors: GRINDSTAFF JENNIFER L. , DEMAS GREGORY E. , KETTERSON ELLEN D.
Published: October 2005

The ability to resist infection is an important component of survival and lifetime reproductive success. Mounting and maintaining an immunological defence is assumed to be energetically costly and nutritional resources expended on immune function may induce trade‐offs with other energetically expensive functions, including reproduction. Resource limitation may even have transgenerational effects on immune function during reproduction because mothers are the primary source of humoral immunity in young vertebrates.

To determine whether protein restriction affects humoral immunity, either within or across generations, we fed adult Japanese quailCoturnix japonicaisocaloric diets containing either the recommended protein content for reproducing adults (20%), or a low protein diet (12%).

Females fed the low protein diet weighed less than control females and produced fewer eggs that were smaller in size. However, dietary treatment did not affect the antibody response to a novel antigen (SRBCs) or immunoglobulin concentration (IgG = IgY) in either females or their eggs.

This suggests that the magnitude of the humoral immune response is either not constrained by protein availability or that birds can compensate for low dietary protein intake when fedad libitum. Maternal protein reserves may be catabolized to support egg production and antibody formation under protein restriction such that only very severe malnutrition would affect immune function. Future work should address whether other resources mediate the trade‐off between immunity and reproduction or whether other components of the immune response are impacted by resource limitation.
Significance of the dorsal zigzag pattern of Vipera latastei gaditana against avian predators
Authors: NISKANEN MARTTI , MAPPES JOHANNA
Published: October 2005

Aposematism is an antipredatory strategy in which prey animals conspicuously signal their noxiousness to potential predators. This successful strategy is based on avoidance learning of predators.

Most species in the viperid genus Vipera have a characteristic dorsal zigzag pattern. It has previously been suggested that the dorsal zigzag pattern of Vipera berus (the adder) has a cryptic function and thus makes the snake less conspicuous to avian predators. However, a recent experiment suggested that the pattern may function as an aposematic signal rather than being cryptic, and therefore induces active avoidance in avian predators.

We conducted a field experiment in Doñana national park in Spain, testing whether the zigzag pattern gives survival value to Vipera latastei gaditana against avian predators. We used two sizes of plasticine models with a zigzag pattern vs. without a zigzag pattern to record attacks by avian predators. The background was controlled (white vs. natural) to exclude the possibility that one morph would be more cryptic to predators than the other one. We also tested size‐dependent mortality against the signalling and nonsignalling snakes as aposematic signal is expected to enhance the survival of the aposematic species in a size‐dependent manner.

Predation pressure against snakes was severe, and on average 39% of models were attacked. Coloration did not enhance the survival of juvenile‐sized zigzag‐patterned snakes, but significantly increased the survival of adult‐sized zigzag‐patterned snakes on both backgrounds.

Our results provide further support for the aposematism hypothesis of zigzag‐patterned noxious snakes, although the advantage due to disruptive coloration is not mutually exclusive.
Formulating a general statistical model for Betula spp. invasion of lowland heath ecosystems
Authors: MANNING P. , PUTWAIN P. D. , WEBB N. R.
Published: October 2005

Numerous studies describe thresholds at which transitions between alternate ecosystem states occur but few quantitatively delimit these conditions and present them in simple frameworks that are of use in ecosystem management. Previous research on heathland ecosystems has provided a site‐specific statistical model that describes the determinants of the threshold point in heath–scrub vegetation transition, but the wider applicability, and thus utility, of this model was unknown.

Multi‐site experimental manipulations were conducted to assess whether a consistent set of factors limited the recruitment of Betula species into heathland vegetation. Data were pooled and used to fit a single general statistical model. The applicability of this model to a wider range of environments was tested using two independent data sets.

The identity of the factors controlling Betula colonization, which include Betula seed bank density, phosphorus (P) availability and disturbance effects, were broadly similar between sites, but the strength of their effect varied widely.

The general model (explained deviance 59·8%) described Betula seedling densities as a function of biomass and necromass density, vegetation height, Betula seed bank density, P availability and soil water content. These relationships were complex, with numerous interaction and polynomial terms.

Although the model was derived from data from a single community type it was reasonably accurate in the prediction of seedling densities over a wider range of heath conditions. However, data capable of validating predictions of high seedling densities were not available.

Synthesis and applications. The apparent success of the general statistical model suggests that an approach incorporating multi‐site experiments and statistical modelling can facilitate our understanding of ecosystem state transitions and inform the management of invasive species. By describing Betula invasion as a function of variables that are simple, general descriptions of the environment, the model can potentially inform management in a wide range of conditions. The results suggest that heaths close to seed sources and in the degenerate state of the dwarf shrub cycle are the most vulnerable to invasion, and management should target such sites as a priority. At regional scales, these conditions are probably most common in high soil phosphorus sorption capacity areas, where management should be prioritized.
Survival rate, fracture strength and failure mode of ceramic implant abutments after chewing simulation
Authors: BUTZ F. , HEYDECKE G. , OKUTAN M. , STRUB J. R.
Published: October 2005

summary  The aim of this study was to compare titanium‐reinforced ZrO2 and pure Al2O3 abutments regarding their outcome after chewing simulation and static loading. Forty‐eight standard diameter implants with an external hexagon were divided into three groups of 16 implants each and restored with three different types of abutments (group A: ZrO2 abutments with titanium inserts; group B: Al2O3 abutments; group C: titanium abutments). All abutments were fixated on the implants with gold‐alloy screws at 32 Ncm torque, and metal crowns were adhesively cemented onto the abutments. The specimens were exposed to 1·2 million cycles in a chewing simulator. Surviving specimens were subsequently loaded until fracture in a static testing device. Fracture loads (N) and fracture modes were recorded. A Wilcoxon Rank test to compare fracture loads among the three groups and a Fisher exact test to detect group differences in fracture modes were used for statistical evaluation (P < 0·05). All specimens but one of group B survived chewing simulation. No screw loosening occurred. The median fracture loads (±s.d.) were as follows: group A, 294 N (±53); group B, 239 N (±83), and group C, 324 N (±85). The smaller fracture loads in group B were statistically significant. The use of pure Al2O3 abutments resulted in significantly more abutment fractures. It is proposed that titanium‐reinforced ZrO2 abutments perform similar to metal abutments, and can therefore be recommended as an aesthetic alternative for the restoration of single implants in the anterior region. All‐ceramic abutments made of Al2O3 possess less favourable properties.
Teeth and gingival display in the premolar area during smiling in relation to gender and age
Authors: KAPAGIANNIDIS D. , KONTONASAKI E. , BIKOS P. , KOIDIS P.
Published: October 2005

summary  There is limited knowledge concerning tooth and gingival display in the maxillary premolar area during smiling. The purpose of this study was to investigate maxillary premolar and associated gingival display during smiling, and to reveal possible differences related to gender and age. The study consisted of 90 males and 113 females (mean age 38 years, s.d. = 13·83) receiving regular dental care. Two pictures of each subject, one with lips in maximum smile, and the other a retracted frontal view, were made. Clinical crown length, tooth and gingival display were measured for the left maxillary premolars. Central incisors and canines were used as controls. anova with Bonferroni post hoc multiple comparisons tests was used to assess any statistically significant impact of gender and age on tooth and gingival display, and determine differences among gender and age groups (at 5% significance level). Premolars were partially visible in more than 80% of the smiles, and displayed more than 65% of their clinical crown length during smiling. The least display (P < 0·001) was recorded for first and the greatest for second premolars. Tooth display was greater in females, but statistically significant only in central incisors (P < 0·05). No significant differences were revealed between age subgroups. Gingival display was greater for premolars compared with both central incisors (P < 0·001) and canines (P < 0·05). Displayed gingiva was found in first and second premolars in 44 and 49% of subjects, respectively. More gingival display was recorded in females and in younger subjects.