bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel infrared spectra for intermolecular dihydrogen bonding of the phenol-borane-trimethylamine complex in electronically excited state
Authors: Zhao Guang-Jiu , Han Ke-Li
Published: July 2007

The intermolecular dihydrogen bonding in the electronically excited states of the dihydrogen-bonded phenol-BTMA complex in gas phase was theoretically investigated using the time-dependent density functional theory method for the first time. It was theoretically demonstrated that the S1 state of the dihydrogen-bonded phenol-BTMA complex is a locally excited state, in which only the phenol moiety is electronically excited. The infrared spectra of the dihydrogen-bonded phenol-BTMA complex in ground state and the S1 state were calculated at both the O–H and B–H stretching vibrational regions. A novel infrared spectrum of the dihydrogen-bonded phenol-BTMA complex in the electronically excited state was found. The stretching vibrational absorption bands of the dihydrogen-bonded O–H and B–H groups are very strong in the ground state, while they are disappeared in the S1 state. At the same time, a new strong absorption band appears at the CO stretching region. From the calculated bond lengths, it was found that both the O–H and B–H bonds in the dihydrogen bond O–H⋯H–B are significantly lengthened in the S1 state of the dihydrogen-bonded phenol-BTMA complex. However, the C–O bond in the phenol moiety is markedly shortened in the excited state, and then has the characteristics of CO group. Furthermore, it was demonstrated that the intermolecular dihydrogen bonds in the electronically excited state of the dihydrogen-bonded phenol-BTMA complex are strengthened, since calculated H⋯H distance is drastically shortened in the S1 state.
Diffusion of chain molecules and mixtures in carbon nanotubes: The effect of host lattice flexibility and theory of diffusion in the Knudsen regime
Authors: Jakobtorweihen S. , Lowe C. P. , Keil F. J. , Smit B.
Published: July 2007

A novel algorithm for modeling the influence of the host lattice flexibility in molecular dynamics simulations is extended to chain-like molecules and mixtures. This technique, based on a Lowe-Andersen thermostat, maintains the advantages of both simplicity and efficiency. The same diffusivities and other properties of the flexible framework system are reproduced. Advantageously, the computationally demanding flexible host lattice simulations can be avoided. Using this methodology we study the influence of flexibility on diffusion of n-alkanes inside single-walled carbon nanotubes. Furthermore, results are shown for diffusion of two mixtures (methane-helium and ethane-butane). Using these results we investigate the accuracy of theories describing diffusion in the Knudsen regime. For the dynamics in carbon nanotubes the Knudsen diffusivities are much too low. The Smoluchowski model gives better results. Interestingly, the extended Smoluchowski model can reproduce our simulation results obtained with a rigid host lattice. We modify this model to also treat collisions with a flexible interface correctly. As the tangential momentum accommodation coefficient is needed for the theoretical models, we introduce a simple concept to calculate it.
Direct measurement of increased light intensity in optical waveguides coupled to a surface plasmon spectroscopy setup
Authors: Dürr M. , Menges B. , Knoll W. , Yasuda A. , Nelles G.
Published: July 2007

The local increase of light intensity in waveguide structures was monitored by a combination of conventional surface plasmon spectroscopy and a dye-sensitized solar cell (DSSC). The sensitized nanoporous TiO2 layer of the DSSC served both as waveguide structure and light absorber in the DSSC. If the conditions for the excitation of guided modes in the TiO2 waveguide structure were fulfilled, increased light intensity in the porous layer was monitored by an increase of short circuit current in the DSSC. Comparison with direct illumination yields an increase of intensity by a factor of 19±6, in good agreement with transfer matrix calculations.
Ultrafast optical generation and remote detection of terahertz sound using semiconductor superlattices
Authors: Trigo M. , Eckhause T. A. , Wahlstrand J. K. , Merlin R. , Reason M. , Goldman R. S.
Published: July 2007

The authors introduce an all-optical approach to study the propagation of high frequency acoustic phonons in which the generation and detection involves two spatially separated superlattices ∼1μm apart. Propagating modes of frequencies up to ∼1THz escape from the superlattice where they are generated and reach the second superlattice where they are detected and spectrally resolved using pump-probe techniques. The measured frequency spectrum reveals finite size effects, which can be accounted for by a continuum elastic model.
Relaxor behavior of (K0.5Bi0.5)TiO3 ceramics derived from molten salt synthesized single-crystalline nanowires
Authors: Yang Jianfeng , Hou Yudong , Wang Chao , Zhu Mankang , Yan Hui
Published: July 2007

Single-crystalline K0.5Bi0.5TiO3 nanowires have been fabricated by a large scale and facile molten salt synthetic method in a KCl medium. Pristine nanowires have diameters of about 40nm and lengths exceeding 4μm, and they possess tetragonal perovskite structure. The K0.5Bi0.5TiO3 ceramics with a relative density above 98% can be fabricated from high quality nanowires. A broad dielectric peak with frequency dependent dielectric maximum temperature was observed, which can be well fitted by a modified Curie-Weiss law and a Vogel-Fulcher relationship. The suggested relaxor behavior in K0.5Bi0.5TiO3 composition is possibly due to the A-site compositional fluctuations at the nanolevel.
Wireless resonant sensor array for high-throughput screening of materials
Authors: Potyrailo Radislav A. , Morris William G.
Published: July 2007

Screening of materials arrays for their viscoelastic, gas-sorbing, and dielectric properties is important in a wide variety of combinatorial materials science applications. Impedance analysis is an attractive approach to analyze these materials properties and to generate the required new knowledge. Often, these measurements are performed by applying a material onto a suitable sensor and monitoring the changes in materials properties. However, when such a sensor is positioned into a test cell, a direct-wired connection to the analyzer becomes complicated. These complications further increase dramatically when a whole array of sensors is being tested in the test cell. To eliminate these complications, we developed a wireless proximity resonant sensor array system. In the developed system, tested materials are applied onto an array of thickness-shear mode (TSM) resonators operating at 10MHz and arranged for performance testing in a test chamber. Each TSM resonator is coupled to a receiver coil (antenna). An array of these coils is read with a single scanning transmitter coil or an array of transmitter coils. This high-throughput screening approach of sensing materials permits their evaluation in complex environments where additional wiring is not desirable or adds a prohibitively complex design. We demonstrated the applicability of the wireless sensor materials screening approach for the rapid evaluation of the effects of conditioning of polymeric sensing films at different temperatures on the vapor-response patterns to several vapors of industrial, health, law enforcement, and security interest (ethanol, acetonitrile, and water vapors).
Dielectric functions and critical points of PbTiO3, PbZrO3, and PbZr0.57Ti0.43O3 grown on SrTiO3 substrate
Authors: Kang T. D. , Lee Hosun , Xing G. , Izumskaya N. , Avrutin V. , Xiao B. , Morkoç H.
Published: July 2007

Single crystalline PbTiO3, PbZrO3, and PbZr0.57Ti0.43O3 thin films on SrTiO3 (001) substrates were grown by a combination of molecular beam epitaxy and rf sputtering methods. The authors measured the dielectric functions of the thin films using spectroscopic ellipsometry and determined the interband critical point energies using standard critical point model. They compared the critical point energies to the band structure calculations in the literature. The data suggest that anticrossing behavior occurs between Ea and Eb near Zr=0.17. This phenomenon is attributed to a coupling between X1c and X3c bands caused by intrinsic alloy disorder.
Characterization of biaxial stress and its effect on optical properties of ZnO thin films
Authors: Li Y. F. , Yao B. , Lu Y. M. , Cong C. X. , Zhang Z. Z. , Gai Y. Q. , Zheng C. J. , Li B. H. , Wei Z. P. , Shen D. Z. , Fan X. W. , Xiao L. , Xu S. C. , Liu Y.
Published: July 2007

Biaxial stress of ZnO film deposited on quartz was measured by side-inclination x-ray diffraction technique, indicating that the film is subjected to a tensile stress. One part of the stress is induced by thermal mismatch between the ZnO and the quartz and increases with annealing temperature, while another part results from lattice mismatch and is about 1.03GPa. The optical band gap of the ZnO film shows a blueshift with increasing biaxial tensile stress, opposed to the change of the band gap with biaxial tensile stress for GaN. The mechanism of the stress-dependent band gap is suggested in the present work.
Lasing characteristics of a GaN photonic crystal nanocavity light source
Authors: Lai Chun-Feng , Yu Peichen , Wang Te-Chung , Kuo Hao-Chung , Lu Tien-Chang , Wang Shing-Chung , Lee Chao-Kuei
Published: July 2007

Lasing characteristics from photonic crystal defects fabricated on bulk GaN are investigated. The device demonstrates multimode lasing with linewidths as narrow as 2–3Å, and an enhanced spontaneous emission factor β∼0.045. The emission spectra indicate that the laser emission is initiated horizontally in the defect nanocavity and then coupled to the vertical radiation, possibly via photonic crystal Bloch modes or by scattering.
Spatially confined light output of a crystalline zinc oxide nanonet laser
Authors: Liao Qing , Wang Yu , Li Jianlong , Wu Kai , Ai Xi-Cheng , Zhang Jian-Ping
Published: July 2007

A well ordered large-area (>40mm2) crystalline ZnO nanonet on anodic aluminum oxide template was fabricated via a simple approach combining interfacial reaction growth and epitaxial growth. Its optically pumped light output in far field was found to be spatially confined within 5° of its surface normal direction. Theoretical simulation showed that the spatial confinement of the light output was due to the interference and diffraction effects of the periodically aligned air cylinders in the nanonet.
Smad-interacting protein-1 (Zfhx1b) acts upstream of Wnt signaling in the mouse hippocampus and controls its formation
Authors: Miquelajauregui Amaya , Van de Putte Tom , Polyakov Alexander , Nityanandam Anjana , Boppana Sridhar , Seuntjens Eve , Karabinos Anton , Higashi Yujiro , Huylebroeck Danny , Tarabykin Victor
Published: July 2007

Smad-interacting protein-1 (Sip1) [Zinc finger homeobox (Zfhx1b)] is a transcription factor implicated in the genesis of Mowat–Wilson syndrome in humans.
Sip1
expression in the dorsal telencephalon of mouse embryos was documented from E12.5. We inactivated the gene specifically in cortical precursors. This resulted in the lack of the entire hippocampal formation.
Sip1
mutant mice exhibited death of differentiating cells and decreased proliferation in the region of the prospective hippocampus and dentate gyrus. The expression of the Wnt antagonist
Sfrp1
was ectopically activated, whereas the activity of the noncanonical Wnt effector, JNK, was down-regulated in the embryonic hippocampus of mutant mice. In cortical cells, Sip1 protein was detected on the promoter of
Sfrp1
gene and both genes showed a mutually exclusive pattern of expression suggesting that
Sfrp1
expression is negatively regulated by Sip1. Sip1 is therefore essential to the development of the hippocampus and dentate gyrus, and is able to modulate Wnt signaling in these regions.
Chimpanzees are vengeful but not spiteful
Authors: Jensen Keith , Call Josep , Tomasello Michael
Published: July 2007

People are willing to punish others at a personal cost, and this apparently antisocial tendency can stabilize cooperation. What motivates humans to punish noncooperators is likely a combination of aversion to both unfair outcomes and unfair intentions. Here we report a pair of studies in which captive chimpanzees (
Pan troglodytes
) did not inflict costs on conspecifics by knocking food away if the outcome alone was personally disadvantageous but did retaliate against conspecifics who actually stole the food from them. Like humans, chimpanzees retaliate against personally harmful actions, but unlike humans, they are indifferent to simply personally disadvantageous outcomes and are therefore not spiteful.
Nested effects models for high-dimensional phenotyping screens
Authors: Markowetz Florian , Kostka Dennis , Troyanskaya Olga G. , Spang Rainer
Published: July 2007

Motivation: In high-dimensional phenotyping screens, a large number of cellular features is observed after perturbing genes by knockouts or RNA interference. Comprehensive analysis of perturbation effects is one of the most powerful techniques for attributing functions to genes, but not much work has been done so far to adapt statistical and computational methodology to the specific needs of large-scale and high-dimensional phenotyping screens.

Results: We introduce and compare probabilistic methods to efficiently infer a genetic hierarchy from the nested structure of observed perturbation effects. These hierarchies elucidate the structures of signaling pathways and regulatory networks. Our methods achieve two goals: (1) they reveal clusters of genes with highly similar phenotypic profiles, and (2) they order (clusters of) genes according to subset relationships between phenotypes. We evaluate our algorithms in the controlled setting of simulation studies and show their practical use in two experimental scenarios: (1) a data set investigating the response to microbial challenge in Drosophila melanogaster, and (2) a compendium of expression profiles of Saccharomyces cerevisiae knockout strains. We show that our methods identify biologically justified genetic hierarchies of perturbation effects.

Availability: The software used in our analysis is freely available in the R package ‘nem’ from www.bioconductor.org

Contact: ogt@cs.princeton.edu
A Chado case study: an ontology-based modular schema for representing genome-associated biological information
Authors: Mungall Christopher J. , Emmert David B. ,   The FlyBase Consortium
Published: July 2007

Motivation: A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability. Our question was whether we could create a relational database schema that would be successfully reused.

Results: Chado is a relational database schema now being used to manage biological knowledge for a wide variety of organisms, from human to pathogens, especially the classes of information that directly or indirectly can be associated with genome sequences or the primary RNA and protein products encoded by a genome. Biological databases that conform to this schema can interoperate with one another, and with application software from the Generic Model Organism Database (GMOD) toolkit. Chado is distinctive because its design is driven by ontologies. The use of ontologies (or controlled vocabularies) is ubiquitous across the schema, as they are used as a means of typing entities. The Chado schema is partitioned into integrated subschemas (modules), each encapsulating a different biological domain, and each described using representations in appropriate ontologies. To illustrate this methodology, we describe here the Chado modules used for describing genomic sequences.

Availability: GMOD is a collaboration of several model organism database groups, including FlyBase, to develop a set of open-source software for managing model organism data. The Chado schema is freely distributed under the terms of the Artistic License (http://www.opensource.org/licenses/artistic-license.php) from GMOD (www.gmod.org).

Contact: cjm@fruitfly.org or emmert@morgan.harvard.edu.
Automatic genome-wide reconstruction of phylogenetic gene trees
Authors: Wapinski Ilan , Pfeffer Avi , Friedman Nir , Regev Aviv
Published: July 2007

Gene duplication and divergence is a major evolutionary force. Despite the growing number of fully sequenced genomes, methods for investigating these events on a genome-wide scale are still in their infancy. Here, we present SYNERGY, a novel and scalable algorithm that uses sequence similarity and a given species phylogeny to reconstruct the underlying evolutionary history of all genes in a large group of species. In doing so, SYNERGY resolves homology relations and accurately distinguishes orthologs from paralogs. We applied our approach to a set of nine fully sequenced fungal genomes spanning 150 million years, generating a genome-wide catalog of orthologous groups and corresponding gene trees. Our results are highly accurate when compared to a manually curated gold standard, and are robust to the quality of input according to a novel jackknife confidence scoring. The reconstructed gene trees provide a comprehensive view of gene evolution on a genomic scale. Our approach can be applied to any set of sequenced eukaryotic species with a known phylogeny, and opens the way to systematic studies of the evolution of individual genes, molecular systems and whole genomes.

Contact: aregev@broad.mit.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Identification of new drug classification terms in textual resources
Authors: Kolářik Corinna , Hofmann-Apitius Martin , Zimmermann Marc , Fluck Juliane
Published: July 2007

Knowledge about biological effects of small molecules helps in the understanding of biological processes and supports the development of new therapeutic agents. DrugBank is a high quality database providing such information about drugs that contains annotation of drug effects and classification of therapeutic effects. However, to broaden the scope of such a database in classifying and annotating drugs, systems for automatic extraction of classification terms and the corresponding annotation of drugs are needed. We have developed an approach for the identification of new terms used in unstructured text that provide information about drug properties. It is based on the identification and extraction of phrases corresponding to lexico-syntactic patterns - so-called Hearst patterns that contain drug names and directly related drug annotation terms. Such phrases could be identified with a high performance in DrugBank text (0.89 F-score) and in Medline abstracts (0.83 F-score). In comparison to DrugBank annotation terminology, a huge amount of new drug annotation terms could be found. The evaluation of terms extracted from Medline showed that 29–53% of them are new valid drug property terms. They could be assigned to existing and new drug property classes not provided by the DrugBank drug annotation. We come to the conclusion that our system can support database content update by providing additionally drug descriptions of pharmacological effects not yet found in databases like DrugBank. Moreover, we propose that automatic normalization of terms improves the annotation and the retrieval of relevant database entries.

Contact: corinna.kolarik@scai.fraunhofer.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Dead-End Elimination with Backbone Flexibility
Authors: Georgiev Ivelin , Donald Bruce R.
Published: July 2007

Motivation: Dead-End Elimination (DEE) is a powerful algorithm capable of reducing the search space for structure-based protein design by a combinatorial factor. By using a fixed backbone template, a rotamer library, and a potential energy function, DEE identifies and prunes rotamer choices that are provably not part of the Global Minimum Energy Conformation (GMEC), effectively eliminating the majority of the conformations that must be subsequently enumerated to obtain the GMEC. Since a fixed-backbone model biases the algorithm predictions against protein sequences for which even small backbone movements may result in a significantly enhanced stability, the incorporation of backbone flexibility can improve the accuracy of the design predictions. If explicit backbone flexibility is incorporated into the model, however, the traditional DEE criteria can no longer guarantee that the flexible-backbone GMEC, the lowest-energy conformation when the backbone is allowed to flex, will not be pruned.

Results: We derive a novel DEE pruning criterion, flexible-backbone DEE (BD), that is provably accurate with backbone flexibility, guaranteeing that no rotamers belonging to the flexible-backbone GMEC are pruned; we also present further enhancements to BD for improved pruning efficiency. The results from applying our novel algorithms to redesign the β1 domain of protein G and to switch the substrate specificity of the NRPS enzyme GrsA-PheA are then compared against the results from previous fixed-backbone DEE algorithms. We confirm experimentally that traditional-DEE is indeed not provably-accurate with backbone flexibility and that BD is capable of generating conformations with significantly lower energies, thus confirming the feasibility of our novel algorithms.

Availability: Contact authors for source code.

Contact: brd+ismb07@cs.duke.edu
Supervised reconstruction of biological networks with local models
Authors: Bleakley Kevin , Biau Gérard , Vert Jean-Philippe
Published: July 2007

Motivation: Inference and reconstruction of biological networks from heterogeneous data is currently an active research subject with several important applications in systems biology. The problem has been attacked from many different points of view with varying degrees of success. In particular, predicting new edges with a reasonable false discovery rate is highly demanded for practical applications, but remains extremely challenging due to the sparsity of the networks of interest.

Results: While most previous approaches based on the partial knowledge of the network to be inferred build global models to predict new edges over the network, we introduce here a novel method which predicts whether there is an edge from a newly added vertex to each of the vertices of a known network using local models. This involves learning individually a certain subnetwork associated with each vertex of the known network, then using the discovered classification rule associated with only that vertex to predict the edge to the new vertex. Excellent experimental results are shown in the case of metabolic and protein–protein interaction network reconstruction from a variety of genomic data.

Availability: An implementation of the proposed algorithm is available upon request from the authors.

Contact: Jean-Philippe.Vert@ensmp.fr
Computational modeling of Caenorhabditis elegans vulval induction
Authors: Sun Xiaoyun , Hong Pengyu
Published: July 2007

Motivation: Caenorhabditis elegans vulval development is a paradigmatic example of animal organogenesis with extensive experimental data. During vulval induction, each of the six multipotent vulval precursor cells (VPCs) commits to one of three fates (1°, 2°, 3°). The precise 1°-2°-3° formation of VPC fates is controlled by a network of intercellular signaling, intracellular signal transduction and transcriptional regulation. The construction of mathematical models for this network will enable hypothesis generation, biological mechanism discovery and system behavior analysis.

Results: We have developed a mathematical model based on dynamic Bayesian networks to model the biological network that governs the VPC 1°-2°-3° pattern formation process. Our model has six interconnected subnetworks corresponding to six VPCs. Each VPC subnetwork contains 20 components. The causal relationships among network components are quantitatively encoded in the structure and parameters of the model. Statistical machine learning techniques were developed to automatically learn both the structure and parameters of the model from data collected from literatures. The learned model is capable of simulating vulval induction under 36 different genetic conditions. Our model also contains a few hypothetical causal relationships between network components, and hence can serve as guidance for designing future experiments. The statistical learning nature of our methodology makes it easy to not only handle noise in data but also automatically incorporate new experimental data to refine the model.

Contact: hong@cs.brandeis.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Homology search for genes
Authors: Cui Xuefeng , Vinař Tomáš , Brejová Broňa , Shasha Dennis , Li Ming
Published: July 2007

Motivation: Life science researchers often require an exhaustive list of protein coding genes similar to a given query gene. To find such genes, homology search tools, such as BLAST or PatternHunter, return a set of high-scoring pairs (HSPs). These HSPs then need to be correlated with existing sequence annotations, or assembled manually into putative gene structures. This process is error-prone and labor-intensive, especially in genomes without reliable gene annotation.

Results: We have developed a homology search solution that automates this process, and instead of HSPs returns complete gene structures. We achieve better sensitivity and specificity by adapting a hidden Markov model for gene finding to reflect features of the query gene. Compared to traditional homology search, our novel approach identifies splice sites much more reliably and can even locate exons that were lost in the query gene.

On a testing set of 400 mouse query genes, we report 79% exon sensitivity and 80% exon specificity in the human genome based on orthologous genes annotated in NCBI HomoloGene. In the same set, we also found 50 (12%) gene structures with better protein alignment scores than the ones identified in HomoloGene.

Availability: The Java implementation is available for download from http://www.bioinformatics.uwaterloo.ca/software

Contact: mli@uwaterloo.ca
GSEA-P: a desktop application for Gene Set Enrichment Analysis
Authors: Subramanian Aravind , Kuehn Heidi , Gould Joshua , Tamayo Pablo , Mesirov Jill P.
Published: July 2007

Gene Set Enrichment Analysis (GSEA) is a computational method that assesses whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. We report the availability of a new version of the Java based software (GSEA-P 2.0) that represents a major improvement on the previous release through the addition of a leading edge analysis component, seamless integration with the Molecular Signature Database (MSigDB) and an embedded browser that allows users to search for gene sets and map them to a variety of microarray platform formats. This functionality makes it possible for users to directly import gene sets from MSigDB for analysis with GSEA. We have also improved the visualizations in GSEA-P 2.0 and added links to a new form of concise gene set annotations called Gene Set Cards. These additions, as well as other improvements suggested by over 3500 users who have downloaded the software over the past year have been incorporated into this new release of the GSEA-P Java desktop program.

Availability:  GSEA-P 2.0 is freely available for academic and commercial users and can be downloaded from http://www.broad.mit.edu/GSEA

Contact:  mesirov@broad.mit.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Exploring biological network structure using exponential random graph models
Authors: Saul Zachary M. , Filkov Vladimir
Published: July 2007

Motivation: The functioning of biological networks depends in large part on their complex underlying structure. When studying their systemic nature many modeling approaches focus on identifying simple, but prominent, structural components, as such components are easier to understand, and, once identified, can be used as building blocks to succinctly describe the network.

Results: In recent social network studies, exponential random graph models have been used extensively to model global social network structure as a function of their ‘local features’. Starting from those studies, we describe the exponential random graph models and demonstrate their utility in modeling the architecture of biological networks as a function of the prominence of local features. We argue that the flexibility, in terms of the number of available local feature choices, and scalability, in terms of the network sizes, make this approach ideal for statistical modeling of biological networks. We illustrate the modeling on both genetic and metabolic networks and provide a novel way of classifying biological networks based on the prevalence of their local features.

Contact:  saul@cs.ucdavis.edu
Escape ring selectivity, bycatch, and discard survivability in the New England fishery for deep-water red crab, Chaceon quinquedens
Authors: Tallack S. M. L.
Published: July 2007

Tallack, S. M. L. 2007. Escape ring selectivity, bycatch, and discard survivability in the New England fishery for deep-water red crab, Chaceon quinquedens. – ICES Journal of Marine Science, 64: 1579–1586. The trap fishery for red crab, Chaceon quinquedens, occurs at depths of 600–800 m along the continental slope of New England. The target product is a male crab with a carapace width of ∼105 mm or greater. Selectivity was tested at two discrete depths (600 and 800 m), for four different escape ring scenarios: control trap with no escape rings, and escape rings with internal diameters of 9, 10, and 11 cm. Proportions of non-marketable C. quinquedens were large (71–100%) at both depths for all traps, but were smallest in traps with escape rings. Discard mortality was estimated at ∼5% through caging experiments across three haul frequency conditions (every 24 h, every 4 d, and after 8 d), which represented the likely reality of multiple recaptures during a commercial trip. The impact of discarding techniques (low and high impact) was also assessed. If discard proportion estimates of >71% are realistic, and if an estimated ∼5% of these discards die, the recommendation must be made for fishery participants to improve gear selectivity, and thereby to minimize discard mortality rates. On the management side, stock assessments will be more accurate if estimates of discard mortality are incorporated.
Temporal requirement of C/EBPβ in the amygdala following reactivation but not acquisition of inhibitory avoidance
Authors: Milekic Maria H. , Pollonini Gabriella , Alberini Cristina M.
Published: July 2007

Following learning, a memory is fragile and undergoes a protein synthesis-dependent consolidation process in order to become stable. Established memories can again become transiently sensitive to disruption if reactivated and require another protein synthesis-dependent process, known as reconsolidation, in order to persist. Here, we show that, in the basolateral amygdala (BLA), protein synthesis is necessary for both consolidation and reconsolidation of inhibitory avoidance (IA) memory, while the expression of the transcription factor CCAAT enhancer binding protein β (C/EBPβ) is essential only for the reconsolidation process. Moreover, the critical roles of both protein synthesis and C/EBPβ following IA reactivation are temporally restricted, as they are necessary only for recent but not old IA memories. These results, together with previous findings showing that in the hippocampus both protein synthesis and C/EBPβ expression are required for consolidation but not reconsolidation of IA indicate that the stabilization process that takes place either after training or memory retrieval engages distinct neural circuits. Within these circuits, the C/EBPβ-dependent molecular pathway appears to be differentially recruited.
Enzymatic Properties and Subcellular Localization of Arabidopsis β-N-Acetylhexosaminidases
Authors: Strasser Richard , Bondili Jayakumar Singh , Schoberer Jennifer , Svoboda Barbara , Liebminger Eva , Glössl Josef , Altmann Friedrich , Steinkellner Herta , Mach Lukas
Published: July 2007

Plant glycoproteins contain substantial amounts of paucimannosidic N-glycans lacking terminal GlcNAc residues at their nonreducing ends. It has been proposed that this is due to the action of β-hexosaminidases during late stages of N-glycan processing or in the course of N-glycan turnover. We have now cloned the three putative β-hexosaminidase sequences present in the Arabidopsis (Arabidopsis thaliana) genome. When heterologously expressed as soluble forms in Spodoptera frugiperda cells, the enzymes (termed HEXO1–3) could all hydrolyze the synthetic substrates p-nitrophenyl-2-acetamido-2-deoxy-β-d-glucopyranoside, p-nitrophenyl-2-acetamido-2-deoxy-β-d-galactopyranoside, 4-methylumbelliferyl-2-acetamido-2-deoxy-β-d-glucopyranoside, and 4-methylumbelliferyl-6-sulfo-2-acetamido-2-deoxy-β-d-glucopyranoside, albeit to a varying extent. HEXO1 to HEXO3 were further able to degrade pyridylaminated chitotriose, whereas pyridylaminated chitobiose was only cleaved by HEXO1. With N-glycan substrates, HEXO1 displayed a much higher specific activity than HEXO2 and HEXO3. Nevertheless, all three enzymes were capable of removing terminal GlcNAc residues from the α1,3- and α1,6-mannosyl branches of biantennary N-glycans without any strict branch preference. Subcellular localization studies with HEXO-fluorescent protein fusions transiently expressed in Nicotiana benthamiana plants showed that HEXO1 is a vacuolar protein. In contrast, HEXO2 and HEXO3 are mainly located at the plasma membrane. These results indicate that HEXO1 participates in N-glycan trimming in the vacuole, whereas HEXO2 and/or HEXO3 could be responsible for the processing of N-glycans present on secretory glycoproteins.
RTE1 Is a Golgi-Associated and ETR1-Dependent Negative Regulator of Ethylene Responses
Authors: Zhou Xin , Liu Qian , Xie Fang , Wen Chi-Kuang
Published: July 2007

Arabidopsis (Arabidopsis thaliana) RTE1 encodes a membrane protein and negatively regulates ethylene responses. Genetic and transformation studies suggest that the function of the wild-type RTE1 is primarily dependent on ETR1 and can be independent on the other receptors. Ethylene insensitivity caused by the overexpression of RTE1 is largely masked by the etr1-7 mutation, but not by any other receptor mutations. The wild-type ETR1 N terminus is sufficient to the activation of the RTE1 function and the ectopic expression of etr1(1–349) restored ethylene insensitivity conferred by 35S∷gRTE1 in etr1-7. The RTE1 N terminus is not essential to the etr1-2 function and the expression of rte1(NΔ49), which has an N-terminal deletion of 49 amino acid residues, restored ethylene insensitivity in etr1-2 rte1-2. The ectopic expression of GREEN FLUORESCENT PROTEIN (GFP)-RTE1 conferred ethylene insensitivity in wild type and the GFP fusion displayed fast movement within the cytoplasm. The GFP-RTE1 and EYFP-NAG proteins colocalized and the Brefeldin A treatment caused aggregation of GFP-RTE1, suggesting RTE1 is a Golgi-associated protein. Our results suggest specificity of the RTE1 function to ETR1 and that endomembranes may play a role in the ethylene signal transduction.
Molecular Interactions of a Soluble Gibberellin Receptor, GID1, with a Rice DELLA Protein, SLR1, and Gibberellin
Authors: Ueguchi-Tanaka Miyako , Nakajima Masatoshi , Katoh Etsuko , Ohmiya Hiroko , Asano Kenji , Saji Shoko , Hongyu Xiang , Ashikari Motoyuki , Kitano Hidemi , Yamaguchi Isomaro , Matsuoka Makoto
Published: July 2007

GIBBERELLIN INSENSITIVE DWARF1 (GID1) encodes a soluble gibberellin (GA) receptor that shares sequence similarity with a hormone-sensitive lipase (HSL). Previously, a yeast two-hybrid (Y2H) assay revealed that the GID1-GA complex directly interacts with SLENDER RICE1 (SLR1), a DELLA repressor protein in GA signaling. Here, we demonstrated, by pull-down and bimolecular fluorescence complementation (BiFC) experiments, that the GA-dependent GID1–SLR1 interaction also occurs in planta. GA4 was found to have the highest affinity to GID1 in Y2H assays and is the most effective form of GA in planta. Domain analyses of SLR1 using Y2H, gel filtration, and BiFC methods revealed that the DELLA and TVHYNP domains of SLR1 are required for the GID1–SLR1 interaction. To identify the important regions of GID1 for GA and SLR1 interactions, we used many different mutant versions of GID1, such as the spontaneous mutant GID1s, N- and C-terminal truncated GID1s, and mutagenized GID1 proteins with conserved amino acids replaced with Ala. The amino acid residues important for SLR1 interaction completely overlapped the residues required for GA binding that were scattered throughout the GID1 molecule. When we plotted these residues on the GID1 structure predicted by analogy with HSL tertiary structure, many residues were located at regions corresponding to the substrate binding pocket and lid. Furthermore, the GA–GID1 interaction was stabilized by SLR1. Based on these observations, we proposed a molecular model for interaction between GA, GID1, and SLR1.
Functional Analysis of the Epidermal-Specific MYB GenesCAPRICEandWEREWOLFinArabidopsis
Authors: Tominaga Rumi , Iwata Mineko , Okada Kiyotaka , Wada Takuji
Published: July 2007

Epidermis cell differentiation in Arabidopsis thaliana is a model system for understanding the developmental end state of plant cells. Two types of MYB transcription factors, R2R3-MYB and R3-MYB, are involved in cell fate determination. To examine the molecular basis of this process, we analyzed the functional relationship of the R2R3-type MYB gene WEREWOLF (WER) and the R3-type MYB gene CAPRICE (CPC). Chimeric constructs made from the R3 MYB regions of WER and CPC used in reciprocal complementation experiments showed that the CPC R3 region cannot functionally substitute for the WER R3 region in the differentiation of hairless cells. However, WER R3 can substantially substitute for CPC R3. There are no differences in yeast interaction assays of WER or WER chimera proteins with GLABRA3 (GL3) or ENHANCER OF GLABRA3 (EGL3). CPC and CPC chimera proteins also have similar activity in preventing GL3 WER and EGL3 WER interactions. Furthermore, we showed by gel mobility shift assays that WER chimera proteins do not bind to the GL2 promoter region. However, a CPC chimera protein, which harbors the WER R3 motif, still binds to the GL2 promoter region.
Information systems and creativity: an empirical study
Authors: Eaglestone Barry , Ford Nigel , Brown Guy J. , Moore Adrian
Published: July 2007

Purpose

The purpose of this paper is to report research that sought to understand the requirements of information systems designed to support people engaged in creative intellectual activity. The research aimed to provide empirical evidence based on a case study of a particular arena of creativity, namely electro‐acoustic music composition. However, it also sought to identify issues that may apply more widely to other arenas of human creativity.

Design/methodology/approach

The research was based on a related series of three in‐depth studies of electro‐acoustic music composers at work. These studies entailed the collection of qualitative data from interviews, observations and “think aloud” protocols. These data were analysed inductively to reveal concepts and relationships that formed the basis for a model of interactions between the composers and the information systems with which they were working.

Findings

The paper presents a model of relationships between information system features and use, and the resulting effects in terms of the extent to which creativity was perceived by the composers to have been facilitated and inhibited. In particular, a number of tensions were identified which suggest that conventional “best practice” in the design of data‐intensive information systems may be fundamentally at odds with the requirements of such systems to support important aspects of creativity.

Research limitations/implications

The limitations associated with in‐depth qualitative research based on small samples is acknowledged, relating in particular to its lack of ability to generalise on the basis of statistical probability. However, such an approach arguably offers the complementary strength of being particularly suited to exploratory research aimed essentially at charting new territory and identifying rich and possibly unanticipated constructs rather than testing hypotheses based on existing theory. The resultant findings, however, must remain tentative and provisional pending further systematic investigation designed to establish the extent to which they are generalisable.

Practical implications

As well as identifying limitations in conventional approaches to designing data‐intensive information systems, an alternative architecture is proposed which seeks better to map onto the requirements of creativity support. It is hoped that both the criticisms of conventional approaches and the proposed novel architecture may be of practical use to those engaged in the design of data‐intensive creativity support systems.

Originality/value

The research reported here offers a novel perspective on the design of information systems in that it identifies a tension between conventional “best practice” in system design and the requirements of important aspects of creativity support. It has the advantage of being based on the in‐depth observation of real composers in action over protracted periods of time. It also proposes a novel system architecture which seeks to avoid reduce such tensions.
Let's get natural
Authors: Lampel Joseph , Bhalla Ajay
Published: July 2007

Purpose

The purpose of this paper is to argue that the influence of Japanese management practices has led organizations towards a “naturalized” view aiming to resolve the ontological dilemmas that exist between communalism and individualism.

Design/methodology/approach

Having conducted an extensive literature review, the paper draws on literature and examples to construct the argument that for organizations to benefit from Communities of Practice they need to balance the tension between practice and process of such initiatives.

Findings

The influence of Japanese knowledge management practices on the more general phenomenon of transferring practices is twofold. On the one hand, the Japanese precedent has legitimized radical rethinking of management practices which were strongly influenced by rational views of organizations, and on the other hand it provided models which experimenters could emulate.

Practical implications

Looking to the future of KM, it is important that researchers and practitioners acquire deeper understanding of how practices are translated from one context to another. This does not only apply to transferring practices between contexts that are clearly as different as Japan and the USA, or Europe, but also between industries that may appear to operate in the same context. Second, following the Japanese economic crises in the 1990s we are witnessing the fascinating phenomenon of Japanese firms seeking to revitalize their innovative capacity by looking to Western knowledge management practices (Kodama).

Originality value

This paper explores the issue of how the management of knowledge has increasingly become “naturalized” by importing Japanese (or even Eastern) management practices to resolve the ontological dilemmas that exist between communalism and individualism.
Transmitting the entrepreneurial spirit to the work team in SMEs: the importance of leadership
Authors: Ribeiro Soriano Domingo , Manuel Comeche Martínez José
Published: July 2007

Purpose

To establish the extent of the influence of variables which, under a particular style of leadership, form the necessary basis for encouraging and developing group, entrepreneurial activities carried out within the context of small to medium‐sized enterprises (SMEs) thus explaining the transmission of the entrepreneurial spirit to the work team and, consequently, the existence of collective entrepreneurship in the firm.

Design/methodology/approach

From the results of a questionnaire carried out via personal interviews with over 100 firms, a confirmatory factorial analysis was carried out that provided us with the variables to be studied. The cause/effect relationships and their implications were obtained from applying a LISREL8 analysis.

Findings

A leadership based on relationships shows a positive impact, with an intensity of more than double that of participative leadership. A task‐oriented leadership style reduces the chances of transmitting the entrepreneurial spirit to the work team by having a negative influence on the generation of collective entrepreneurship in the firm.

Research limitations/implications

The models contain the relations of “causality” between these latent variables, assuming that the variables observed therein are indicators or symptoms of those other variables. This could be considered as a limitation to our analysis as the study of covariance.

Practical implications

The model has important applications for the process of incorporating new CEOs into the organization.

Originality/value

This paper presents confirmation of the need for aspects traditionally associated with the figure of the entrepreneur to be transmitted to the organization's collective as a whole and for the existence of collective entrepreneurship: an area of management that has thus far received relatively little attention and which could have important practical implications.
New product development management issues and decision‐making approaches
Authors: Yahaya Shahrul‐Yazid , Abu‐Bakar Nooh
Published: July 2007

Purpose

The purpose of this paper is to report findings related to new product development (NPD) management issues and their corresponding decision‐making approaches undertaken by senior managers.

Design/methodology/approach

The study adopts grounded theory research method using interview as the primary data source. 100 NPD management issues, sourced from 16 senior managers from six technology‐based organizations in Malaysia, were investigated and analyzed.

Findings

The study revealed four categories of NPD management issues; strategic NPD management issues, NPD project management issues, NPD process and structural issues, and NPD people management issues. The study also found that senior managers apply different patterns of decision‐making approaches in dealing with each category of NPD management issues.

Research limitations/implications

Although the findings from this study are within the specific context of technology‐based organizations in Malaysia, this exploratory study opens up a number of questions for further investigation.

Practical implications

The discussion from this paper should also stimulate senior managers from other organizations or from other locations to reexamine categories of management issues in their organizations and how they approach them from a decision‐making perspective. This reflection could help identify areas which need further decision‐making skills development.

Originality/value

The classification of NPD management issues provides description of NPD management issues and the corresponding common decision‐making approaches. The study which was carried out at technology‐based organizations in Malaysia contributed to narrow down the geographical imbalances of NPD literatures, contributed to the body of NPD management literatures by bridging it with decision‐making theoretical perspective, and contributed to the naturalistic decision research stream.