bluuebunny/crossref_metadata_2025 huggingface dataset:
Characteristic optical properties of transparent color conversion film prepared from YAG:Ce3+ nanoparticles
Authors: Kasuya R. , Kawano A. , Isobe T. , Kuma H. , Katano J.
Published: September 2007

The authors produced the transparent color conversion thick film which is composed of a high concentration of YAG:Ce3+ nanoparticles prepared by glycothermal method, and characterized its optical properties. The transmittance of the 200μm thick film with the nanoparticle content 70.7wt% was 82% at 525nm corresponding to the emission peak of YAG:Ce3+. The intensity of photoluminescence due to the 5d→4f transition of Ce3+ in YAG:Ce3+ nanoparticles was doubled by placing a reflection mirror at the back of the transparent film. Judging from this result, the transparent film of YAG:Ce3+ nanoparticles has markedly low scattering loss.
Development of a nano-Al∕CuO based energetic material on silicon substrate
Authors: Zhang Kaili , Rossi Carole , Ardila Rodriguez G. A. , Tenailleau Christophe , Alphonse Pierre
Published: September 2007

Nanoenergetic materials (nEMs) have improved performances compared to their bulk counterpart or microcounterpart. The authors propose an approach to synthesize an Al∕CuO based nEM that has several advantages over previous investigations such as enhanced contact, reduced impurities and Al oxidation, tailored dimensions, and easier integration into microsystem. CuO nanowires are synthesized by thermally annealing Cu film deposited onto silicon. Nano-Al is integrated with the nanowires to realize an Al∕CuO based nEM. The synthesized nEM is characterized by scanning electron microscopy, high resolution transmission electron microscopy, x-ray diffraction, differential thermal analysis, and differential scanning calorimetry.
Spectral characterization of transparent (Nd0.01Y0.94La0.05)2O3 laser ceramics
Authors: Yang Qiuhong , Dou C. G. , Ding J. , Hu X. M. , Xu J.
Published: September 2007

The spectrum properties of transparent (Nd0.01Y0.94La0.05)2O3 ceramics were investigated. It was found that all absorption bands of (Nd0.01Y0.94La0.05)2O3 ceramics are broadened, of which the full width at half maximum of the peak centered at 804nm is 8nm and its absorption cross section is 1.02×10−20cm2. The emission cross section of (Nd0.01Y0.94La0.05)2O3 ceramics located at 1078nm is 5.71×10−20cm2 and its fluorescent lifetime is 0.214ms, which are similar to those of 1.0at.%Nd:Y2O3 ceramics. These indicate that (Nd0.01Y0.94La0.05)2O3 transparent ceramics has excellent spectroscopic properties.
Growth parameter-property phase diagram for pulsed laser deposited transparent oxide conductor anatase Nb:TiO2
Authors: Zhang S. X. , Dhar S. , Yu W. , Xu H. , Ogale S. B. , Venkatesan T.
Published: September 2007

The authors performed a systematic study of the structural and electrical properties of Nb:TiO2 thin films by varying the substrate temperature (TS) and oxygen partial pressure (PO2). Niobium is found to incorporate easily and substitutionally into titanium lattice site as indicated by its low activation energy. By increasing TS, the carrier concentration (n) increases in the same way that niobium substitution fraction (s) increases, and the mobility increases as the structural quality is improved. With increasing PO2, n decreases dramatically though s does not change considerably. This may indicate that a large number of p-type native defects form, which “kill” the electrons produced by the Nb donors.
Yield stress of monocrystalline rhenium nanowires
Authors: Philippe L. , Peyrot I. , Michler J. , Hassel A. W. , Milenkovic S.
Published: September 2007

The yield stress of monocrystalline Rhenium nanowires grown by directional solidification was measured by nanobending testing. The average yield stress calculated from the deflection was between 10 and 60GPa, which represents roughly 10% of the rhenium Young modulus along the nanowire’s direction. Analytical results are compared to the ones obtained with a more complex finite element simulation. Origins of the experimental observed yield stress values variations are discussed in terms of experimental measurement errors, elastic anisotropy, and the presence of an oxide layer on the nanowire surface.
Magnetic excitation of magnetic resonance in metamaterials at far-infrared frequencies
Authors: Ishikawa Atsushi , Tanaka Takuo , Kawata Satoshi
Published: September 2007

The authors experimentally demonstrated magnetically excited magnetic resonances with negative magnetic permeability in a metamaterial composed of an array of silver rod pairs. In transmission spectroscopy of the metamaterial, by employing oblique incidence, an incident-magnetic-field-dependent absorption feature was clearly observed at 18THz. The experimental results directly prove that the rod pair structure interacted with the magnetic field of the incident light, producing magnetic resonance. The experimental results were in good agreement with a numerical simulation suggesting that the value of μRe of the silver rod pair array changes from −0.29 to 2.26 at resonance.
Enhanced stability by field cooling in superconducting levitation with translational symmetry
Authors: Del Valle Nuria , Sanchez Alvaro , Pardo Enric , Navau Carles , Chen Du-Xing
Published: September 2007

The force and stability of a levitating system consisting of an infinitely long superconductor and different arrangements of infinitely long parallel permanent magnets are theoretically analyzed for two different cooling processes, field and zero-field cooling, by using a model based on the critical-state model and a magnetic energy minimization procedure. The authors find that by cooling the superconductor near the magnets, one can obtain improved lateral stability as compared to the case of zero-field cooling.
Molecular orientation of 3, 4, 9, 10-perylene-tetracarboxylic-dianhydride thin films at organic heterojunction interfaces
Authors: Chen Wei , Huang Han , Chen Shi , Chen Lan , Zhang Hong Liang , Gao Xing Yu , Wee Andrew Thye Shen
Published: September 2007

In situ low-temperature scanning tunneling microscopy and near-edge x-ray absorption spectroscopy measurements have been used to investigate the molecular orientation of 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) thin films at the interface of organic heterojunctions of PTCDA on copper(II) phthalocyanine (CuPc). On the CuPc monolayer on highly oriented pyrolitic graphite, PTCDA molecules form a well-ordered in-plane herringbone structure with their molecular plane parallel to the substrate surface. The formation of multiple in-plane hydrogen bonding between neighboring PTCDA molecules is responsible for the flat-lying PTCDA on CuPc monolayer, and gives rise to the lying-down orientation of PTCDA thin films on both standing-up and lying-down CuPc thin films, as well as on Au(111) passivated by a self-assembled monolayer of octane-1-thiol.
In situ encapsulation of copper nanoparticles by the dielectric barrier discharge
Authors: Lei Haile , Tang Yongjian , Li Jun , Luo Jiangshan , Zhang Jingmin
Published: September 2007

An experimental investigation is reported on in situ encapsulating copper nanoparticles with a nanolayer of hydrocarbon coating. Copper nanoparticles produced by the flow-levitation method are in situ encapsulated by the dielectric barrier discharge, which generates carbon and hydrogen plasmas for forming a polymerized nanolayer of hydrocarbon at the surface of Cu nanoparticles. The structural, chemical components and optical properties of the encapsulated Cu nanoparticles are characterized by transmission electron microscopy, energy dispersive x-ray spectra, x-ray diffraction, x-ray photoelectron spectra, and UV-visible absorption.
Frenkel-Poole trap energy extraction of atomic layer deposited Al2O3 and HfxAlyO thin films
Authors: Yeh Chun-Chen , Ma T. P. , Ramaswamy Nirmal , Rocklein Noel , Gealy Dan , Graettinger Thomas , Min Kyu
Published: September 2007

Frenkel-Poole (FP) trap energies of atomic layer deposited Al2O3 and HfxAlyO thin films with various Hf∕Al compositions have been extracted. Using a method based on the field and temperature dependence of FP conduction, intrinsic trap energies under zero electric field can be extrapolated. Results indicate that FP trap energies increase from 0.56to1.48eV when adding more and more Al to HfO2. The trap energy seems to be inversely proportional to the square of the dielectric constant of the film, suggesting that traps may originate from the same type of defect, whose energy level is mediated by the dielectric constant.
MicroRNAs regulate synthesis of the neurotransmitter substance P in human mesenchymal stem cell-derived neuronal cells
Authors: Greco Steven J. , Rameshwar Pranela
Published: September 2007

MicroRNAs (miRNAs) are a class of 19- to 23-nt, small, noncoding RNAs, which bind the 3′ UTR of target mRNAs to mediate translational repression in animals. miRNAs have been shown to regulate developmental processes, such as self-renewal of stem cells, neuronal differentiation, myogenesis, and cancer. A functional role of miRNAs in the regulation of neurotransmitter synthesis has yet to be ascribed. We used mesenchymal stem cells (MSCs) as a model to study miRNA-mediated neurotransmitter regulation in developing neuronal cells. MSCs are mesoderm-derived cells, primarily resident in adult bone marrow, which can generate functional neuronal cells. We have previously shown that human MSC-derived neuronal cells express the neurotransmitter gene,
Tac1
, but do not synthesize the gene's encoded peptide, the neurotransmitter substance P (SP), unless stimulated with the inflammatory mediator IL-1α. These findings suggested a potential role for miRNAs in the regulation of SP synthesis. Here, we report on the miRNA profile of undifferentiated human MSCs and MSC-derived neuronal cells by using miRNA-specific bioarrays. miRNAs that were increased in the neuronal cells and decreased after IL-1α stimulation were analyzed by the miRanda algorithm to predict
Tac1
mRNA targets. Putative miR-130a, miR-206, and miR-302a binding sites were predicted within the 3′ UTR of
Tac1
. Target validation using a luciferase reporter system confirmed the miR-130a and miR-206 sites. Specific inhibition of miR-130a and miR-206 in the neuronal cells resulted in SP synthesis and release. The studies provide a different approach in ascribing a new regulatory role for miRNAs in regulating neurotransmitter synthesis.
Strong coupling of predation intensity and diversity in the Phanerozoic fossil record
Authors: Huntley John Warren , Kowalewski Michał
Published: September 2007

The importance of ecological interactions in driving the evolution of animals has been the focus of intense debate among paleontologists, evolutionary biologists, and macroecologists. To test whether the intensity of such interactions covaries with the secular evolutionary trend in global biodiversity, we compiled a species-level database of predation intensity, as measured by the frequency of common predation traces (drillings and repair scars ranging in age from Ediacaran to Holocene). The results indicate that the frequency of predation traces increased notably by the Ordovician, and not in the mid-Paleozoic as suggested by multiple previous studies. Importantly, these estimates of predation intensity and global diversity of marine metazoans correlate throughout the Phanerozoic fossil record regardless of corrections and methods applied. This concordance may represent (
i
) an ecological signal: long-term coupling of diversity and predation; (
ii
) a diversity-driven diffusion of predatory behaviors: an increased probability of more complex predatory strategies to appear at higher diversity levels; or (
iii
) a spurious concordance in signal capture: an artifact where rare species and less-frequent (e.g., trace-producing) predatory behaviors are both more detectable at times when sampling improves. The coupling of predation and diversity records suggests that macroevolutionary and macroecological patterns share common causative mechanisms that may reflect either historical processes or sampling artifacts.
Activation of naturally occurring lung CD4+CD25+regulatory T cells requires CD8 and MHC I interaction
Authors: Joetham Anthony , Takeda Katsuyuki , Miyahara Nobuaki , Matsubara Shigeki , Ohnishi Hiroshi , Koya Toshiyuki , Dakhama Azzeddine , Gelfand Erwin W.
Published: September 2007

Naturally occurring Foxp3+CD4+CD25+T cells (nTregs) isolated from lungs of naive mice regulate allergic airway hyperresponsiveness (AHR) and inflammation. Here, we demonstrate the critical requirement for engagement of MHC class I on CD4+CD25+T cells by CD8 for the functional activation of these nTregs. Suppression of allergen-induced AHR and inflammation by nTregs was abolished in mice treated with anti-CD8. Correspondingly, decreased levels of IL-10 and TGF-β and increased levels of Th2 cytokines in bronchoalveolar lavage were detected in these treated mice. Similarly, nTregs isolated from β2m−/−mice or from mice treated with anti-MHC I antibodyin vitrobefore intratracheal transfer failed to modulate AHR or inflammation. Coculture of nTregs with CD8+T cells increased IL-10 and TGF-β. Addition of anti-MHC I or anti-CD8 reduced IL-10 and TGF-β. These results demonstrate that functional activation of nTregs requires the interaction between MHC I on CD4+CD25+T cells and CD8.
Inhibition of histone deacetylase activity induces developmental plasticity in oligodendrocyte precursor cells
Authors: Lyssiotis Costas A. , Walker John , Wu Chunlei , Kondo Toru , Schultz Peter G. , Wu Xu
Published: September 2007

Recently, it was demonstrated that lineage-committed oligodendrocyte precursor cells (OPCs) can be converted to multipotent neural stem-like cells, capable of generating both neurons and glia after exposure to bone morphogenetic proteins. In an effort to understand and control the developmental plasticity of OPCs, we developed a high-throughput screen to identify novel chemical inducers of OPC reprogramming. Using this system, we discovered that inhibition of histone deacetylase (HDAC) activity in OPCs acts as a priming event in the induction of developmental plasticity, thereby expanding the differentiation potential to include the neuronal lineage. This conversion was found to be mediated, in part, through reactivation of
sox2
and was highly reproducible at the clonal level. Further, genome-wide expression analysis demonstrated that HDAC inhibitor treatment activated
sox2
and 12 other genes that identify or maintain the neural stem cell state while simultaneously silencing a large group of oligodendrocyte lineage-specific genes. This series of experiments demonstrates that global histone acetylation, induced by HDAC inhibition, can partially reverse the lineage restriction of OPCs, thereby inducing developmental plasticity.
Direct Repression of Cyclin D1 by SIP1 Attenuates Cell Cycle Progression in Cells Undergoing an Epithelial Mesenchymal Transition
Authors: Mejlvang Jakob , Kriajevska Marina , Vandewalle Cindy , Chernova Tatyana , Sayan A. Emre , Berx Geert , Mellon J. Kilian , Tulchinsky Eugene
Published: September 2007

Zinc finger transcription factors of the Snail/Slug and ZEB-1/SIP1 families control epithelial-mesenchymal transitions in development in cancer. Here, we studied SIP1-regulated mesenchymal conversion of epidermoid A431 cells. We found that concomitant with inducing invasive phenotype, SIP1 inhibited expression of cyclin D1 and induced hypophosphorylation of the Rb tumor suppressor protein. Repression of cyclin D1 was caused by direct binding of SIP1 to three sequence elements in the cyclin D1 gene promoter. By expressing exogenous cyclin D1 in A431/SIP1 cells and using RNA interference, we demonstrated that the repression of cyclin D1 gene by SIP1 was necessary and sufficient for Rb hypophosphorylation and accumulation of cells in G1 phase. A431 cells expressing SIP1 along with exogenous cyclin D1 were highly invasive, indicating that SIP1-regulated invasion is independent of attenuation of G1/S progression. However, in another epithelial-mesenchymal transition model, gradual mesenchymal conversion of A431 cells induced by a dominant negative mutant of E-cadherin produced no effect on the cell cycle. We suggest that impaired G1/S phase progression is a general feature of cells that have undergone EMT induced by transcription factors of the Snail/Slug and ZEB-1/SIP1 families.
Src-mediated Phosphorylation of Hsp90 in Response to Vascular Endothelial Growth Factor (VEGF) Is Required for VEGF Receptor-2 Signaling to Endothelial NO Synthase
Authors: Duval Martine , Le Bœuf Fabrice , Huot Jacques , Gratton Jean-Philippe
Published: September 2007

Nitric oxide (NO) release from endothelial cells, via endothelial NO synthase (eNOS) activation, is central to the proangiogenic actions of vascular endothelial growth factor (VEGF). VEGF signaling to eNOS is principally mediated by an Akt-dependent phosphorylation of eNOS and by increased association of eNOS to the molecular chaperone, heat-shock protein 90 kDa (Hsp90). Herein, we report that VEGFR-2 activation induces tyrosine phosphorylation of VEGF receptor 2 (VEGFR-2)-associated Hsp90β. Tyrosine phosphorylation of Hsp90β in response to VEGF is dependent on internalization of the VEGFR-2 and on Src kinase activation. Furthermore, we demonstrate that c-Src directly phosphorylates Hsp90 on tyrosine 300 residue and that this event is essential for VEGF-stimulated eNOS association to Hsp90 and thus NO release from endothelial cells. Our work identifies Y300 phosphorylation of Hsp90 as a novel regulated posttranslational modification of the chaperone and demonstrates its importance in the proangiogenic actions of VEGF, namely by regulating NO release from endothelial cells.
Tristetraprolin Inhibits Ras-dependent Tumor Vascularization by Inducing Vascular Endothelial Growth Factor mRNA Degradation
Authors: Essafi-Benkhadir Khadija , Onesto Cercina , Stebe Emmanuelle , Moroni Christoph , Pagès Gilles
Published: September 2007

Vascular endothelial growth factor (VEGF) is one of the most important regulators of physiological and pathological angiogenesis. Constitutive activation of the extracellular signal-regulated kinase (ERK) pathway and overexpression of VEGF are common denominators of tumors from different origins. We have established a new link between these two fundamental observations converging on VEGF mRNA stability. In this complex phenomenon, tristetraprolin (TTP), an adenylate and uridylate-rich element-associated protein that binds to VEGF mRNA 3′-untranslated region, plays a key role by inducing VEGF mRNA degradation, thus maintaining basal VEGF mRNA amounts in normal cells. ERKs activation results in the accumulation of TTP mRNA. However, ERKs reduce the VEGF mRNA-destabilizing effect of TTP, leading to an increase in VEGF expression that favors the angiogenic switch. Moreover, TTP decreases RasVal12-dependent VEGF expression and development of vascularized tumors in nude mice. As a consequence, TTP might represent a novel antiangiogenic and antitumor agent acting through its destabilizing activity on VEGF mRNA. Determination of TTP and ERKs status would provide useful information for the evaluation of the angiogenic potential in human tumors.
Analysis of De Novo Golgi Complex Formation after Enzyme-based Inactivation
Authors: Jollivet Florence , Raposo Graça , Dimitrov Ariane , Sougrat Rachid , Goud Bruno , Perez Franck
Published: September 2007

The Golgi complex is characterized by its unique morphology of closely apposed flattened cisternae that persists despite the large quantity of lipids and proteins that transit bidirectionally. Whether such a structure is maintained through endoplasmic reticulum (ER)-based recycling and auto-organization or whether it depends on a permanent Golgi structure is strongly debated. To further study Golgi maintenance in interphase cells, we developed a method allowing for a drug-free inactivation of Golgi dynamics and function in living cells. After Golgi inactivation, a new Golgi-like structure, containing only certain Golgi markers and newly synthesized cargos, was produced. However, this structure did not acquire a normal Golgi architecture and was unable to ensure a normal trafficking activity. This suggests an integrative model for Golgi maintenance in interphase where the ER is able to autonomously produce Golgi-like structures that need pre-existing Golgi complexes to be organized as morphologically normal and active Golgi elements.
FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes
Authors: Borziak Kirill , Zhulin Igor B.
Published: September 2007

Motivation: Sensory domains that are conserved among Bacteria, Archaea and Eucarya are important detectors of common signals detected by living cells. Due to their high sequence divergence, sensory domains are difficult to identify. We systematically look for novel sensory domains using sensitive profile-based searches initiated with regions of signal transduction proteins where no known domains can be identified by current domain models.

Results: Using profile searches followed by multiple sequence alignment, structure prediction and domain architecture analysis, we have identified a novel sensory domain termed FIST, which is present in signal transduction proteins from Bacteria, Archaea and Eucarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids.

Contact:  joulineib@ornl.gov

Supplementary information:  http://genomics.ornl.gov/research/pubs/fist
Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes
Authors: Sedwards Sean , Mazza Tommaso
Published: September 2007

Motivation: Compartments and membranes are the basis of cell topology and more than 30% of the human genome codes for membrane proteins. While it is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, few, if any, explicitly model the topology of the membranes themselves.

Discrete stochastic simulation potentially offers the most accurate representation of cell dynamics. Since the details of every molecular interaction in a pathway are often not known, the relationship between chemical species in not necessarily best described at the lowest level, i.e. by mass action.

Simulation is a form of computer-aided analysis, relying on human interpretation to derive meaning. To improve efficiency and gain meaning in an automatic way, it is necessary to have a formalism based on a model which has decidable properties.

Results: We present Cyto-Sim, a stochastic simulator of membrane-enclosed hierarchies of biochemical processes, where the membranes comprise an inner, outer and integral layer. The underlying model is based on formal language theory and has been shown to have decidable properties (Cavaliere and Sedwards, 2006), allowing formal analysis in addition to simulation. The simulator provides variable levels of abstraction via arbitrary chemical kinetics which link to ordinary differential equations.

In addition to its compact native syntax, Cyto-Sim currently supports models described as Petri nets, can import all versions of SBML and can export SBML and MATLAB® m-files.

Availability: Cyto-Sim is available free, either as an applet or a stand-alone Java program via the web page (http://www.cosbi.eu/Rpty_Soft_CytoSim.php). Other versions can be made available upon request.

Contact:  t.mazza@unicz.it
Evolutionary analysis of enzymes using Chisel
Authors: Rodriguez Alexis A. , Bompada Tanuja , Syed Mustafa , Shah Parantu K. , Maltsev Natalia
Published: September 2007

Motivation: Availability of large volumes of genomic and enzymatic data for taxonomically and phenotypically diverse organisms allows for exploration of the adaptive mechanisms that led to diversification of enzymatic functions. We present Chisel, a computational framework and a pipeline for an automated, high-resolution analysis of evolutionary variations of enzymes. Chisel allows automatic as well as interactive identification, and characterization of enzymatic sequences. Such knowledge can be utilized for comparative genomics, microbial diagnostics, metabolic engineering, drug design and analysis of metagenomes.

Results: Chisel is a comprehensive resource that contains 8575 clusters and subsequent computational models specific for 939 distinct enzymatic functions and, when data is sufficient, their taxonomic variations. Application of Chisel to identification of enzymatic sequences in newly sequenced genomes, analysis of organism-specific metabolic networks, ‘binning’ of metagenomes and other biological problems are presented. We also provide a thorough analysis of Chisel performance with other similar resources and manual annotations on Shewanella oneidensis MR1 genome.

Availability: Chisel is available for interactive use at http://compbio.mcs.anl.gov/CHISEL. The website also provides a user manual, clusters and function-specific computational models.

Contact:  arodri7@mcs.anl.gov or maltsev@mcs.anl.gov

Supplementary information: Additional data can be found at http://compbio.mcs.anl.gov/CHISEL/htmls/refs.html
Accurate prediction of deleterious protein kinase polymorphisms
Authors: Torkamani Ali , Schork Nicholas J.
Published: September 2007

Motivation: Contemporary, high-throughput sequencing efforts have identified a rich source of naturally occurring single nucleotide polymorphisms (SNPs), a subset of which occur in the coding region of genes and result in a change in the encoded amino acid sequence (non-synonymous coding SNPs or ‘nsSNPs’). It is hypothesized that a subset of these nsSNPs may underlie common human disease. Testing all these polymorphisms for disease association would be time consuming and expensive. Thus, computational methods have been developed to both prioritize candidate nsSNPs and make sense of their likely molecular physiologic impact.

Results: We have developed a method to prioritize nsSNPs and have applied it to the human protein kinase gene family. The results of our analyses provide high quality predictions and outperform available whole genome prediction methods (74% versus 83% prediction accuracy). Our analyses and methods consider both DNA sequence conservation, which most traditional methods are based on, as well unique structural and functional features of kinases. We provide a ranked list of common kinase nsSNPs that have a higher probability of impacting human disease based on our analyses.

Contact:  nschork@scripps.edu

Supplementary information: Supplementary data are available on Bioinformatics online.
RagPools: RNA-As-Graph-Pools—a web server for assisting the design of structured RNA pools forin vitroselection
Authors: Kim Namhee , Shin Jin Sup , Elmetwaly Shereef , Gan Hin Hark , Schlick Tamar
Published: September 2007

Summary: Our RNA-As-Graph-Pools (RagPools) web server offers a theoretical companion tool for RNA in vitro selection and related problems. Specifically, it suggests how to construct RNA sequence/structure pools with user-specified properties and assists in analyzing resulting distributions. This utility follows our recently developed approach for engineering sequence pools that links RNA sequence space regions with corresponding structural distributions via a ‘mixing matrix’ approach combined with a graph theory analysis of RNA secondary-structure space; the mixing matrix specifies nucleotide transition rates, and graph theory links sequences to simple graphical objects representing RNA motifs. The companion RagPools web server (‘Designer’ component) provides optimized starting sequences, mixing matrices and associated weights in response to a user-specified target pool structure distribution. In addition, RagPools (‘Analyzer’ component) analyzes the motif distribution of pools generated from user-specified starting sequences and mixing matrices. Thus, RagPools serves as a guide to researchers who aim to synthesize RNA pools with desired properties and/or experiment in silico with various designs by our approach.

Availability: The web server is accessible on the web at http://rubin2.biomath.nyu.edu

Contact:  schlick@nyu.edu
Functional profiling of microarray experiments using text-mining derived bioentities
Authors: Minguez Pablo , Al-Shahrour Fátima , Montaner David , Dopazo Joaquín
Published: September 2007

Motivation: The increasing use of microarray technologies brought about a parallel demand in methods for the functional interpretation of the results. Beyond the conventional functional annotations for genes, such as gene ontology, pathways, etc. other sources of information are still to be exploited. Text-mining methods allow extracting informative terms (bioentities) with different functional, chemical, clinical, etc. meanings, that can be associated to genes. We show how to use these associations within an appropriate statistical framework and how to apply them through easy-to-use, web-based environments to the functional interpretation of microarray experiments. Functional enrichment and gene set enrichment tests using bioentities are presented.

Availability: Marmite and MarmiteScan can be found in the Babelomics suite: http://www.babelomics.org

Contact:  jdopazo@cipf.es

Supplementary information: Supplementary data are available at Bioinformatics online.
Blinding Techniques in Randomized Controlled Trials of Laser Therapy: An Overview and Possible Solution
Authors: Relf Ian , Chow Roberta , Pirotta Marie
Published: September 2007

Low‐level laser therapy has evidence accumulating about its effectiveness in a variety of medical conditions. We reviewed 51 double blind randomized controlled trials (RCTs) of laser treatment. Analysis revealed 58% of trials showed benefit of laser over placebo. However, less than 5% of the trials had addressed beam disguise or allocation concealment in the laser machines used. Many of the trials used blinding methods that rely on staff cooperation and are therefore open to interference or bias. This indicates significant deficiencies in laser trial methodology. We report the development and preliminary testing of a novel laser machine that can blind both patient and operator to treatment allocation without staff participation. The new laser machine combines sealed preset and non‐bypassable randomization codes, decoy lights and sound, and a conical perspex tip to overcome laser diode glow detection.
Evaluations of New and Current Management Strategies to Control Phomopsis Cane and Leaf Spot of Grape
Authors: Nita Mizuho , Ellis Michael A. , Wilson Leslie L. , Madden Laurence V.
Published: September 2007

To extend our understanding of the epidemiology and control of Phomopsis cane and leaf spot of grape, caused by Phomopsis viticola, studies were conducted to: (i) determine efficacy of a dormant fungicide spray program for controlling the disease in its early stage of development (e.g., spring); (ii) evaluate a disease warning system by applying fungicides and fungicide-adjuvant combinations in response to predicted infection periods based on weather conditions; and (iii) correlate commercial control practices and environmental conditions with disease incidence based on a state-wide survey of commercial fields. With the warning system, control was equal to that obtained with a 7-day protectant fungicide program, but with fewer fungicide applications per season. A dormant application provided consistent, yet only moderate, control of the disease. Growers who applied a dormant-season application or early spring protectant fungicides tended to have lower disease incidence than those who did not. There was high variability in disease incidence within vineyards and farms, but no significant difference in incidence among regions of the state. Overall, early season application of protective fungicides was shown to be a key factor for successful management of P. viticola.

Accepted for publication 29 March 2007. Published 26 July 2007.
Spatiotemporal Spread of Potato virus S and Potato virus X in Seed Potato in Tasmania, Australia
Authors: Lambert Susan J. , Hay Frank S. , Pethybridge Sarah J. , Wilson Calum R.
Published: September 2007

The spatial and temporal distribution of Potato virus S (PVS) and Potato virus X (PVX) was studied in two trials within each of four commercial fields of seed potato var. Russet Burbank in Tasmania, Australia. In the first trial (plots) 20 leaflets were collected from each of 49 plots (each approximately 8 m wide by 10 m long), with plots arranged in a 7-×-7 lattice. In the second trial (transects), leaflets were collected at 1-m intervals along seven adjacent, 50-m long rows. The mean incidence of PVS increased during the season by 5.2% in one of four plot trials and 25.5% in one of four transect trials. The mean incidence of PVX increased during the season by 10.1%, in one of two transect trials. Spatial Analysis by Distance IndicEs and ordinary runs analysis detected aggregation of PVS infected plants early in the season in one and two fields respectively, suggesting transmission during seed-cutting or during planting. An increase in PVS incidence mid- to late season in one field was associated with aggregation of PVS along, but not across rows, which may be related to the closer plant spacing within rows and hence increased potential for mechanical transmission along rows. Results suggested limited spread of PVS and PVX occurred within crops during the season.

Accepted for publication 9 April 2007. Published 26 July 2007.
High Recovery Rate of Phytophthora from Containerized Nursery Stock Pots at a Retail Nursery Highlights Potential For Spreading Exotic Oomycetes
Authors: Dart Norman L. , Chastagner Gary A.
Published: September 2007

Containerized nursery stock asymptomatic for Phytophthora leaf, stem and root diseases were sampled from a nursery in western Washington state directly over areas soil tested positive for Phytophthora ramorum during nursery surveys conducted. Phytophthora was recovered from the soil collected below 90% of the containerized plant pots. The study underscores the potential for exotic and endemic Oomycetes to be transported on asymptomatic nursery stock.

Accepted for publication 9 April 2007. Published 16 August 2007.
Evaluation of Phytophthora ramorum in Nursery Crop Tissue Culture Propagation
Authors: Linderman Robert G. , Davis E. Anne
Published: September 2007

Phytophthora ramorum, cause of Ramorum blight on numerous woody ornamental shrubs, is a regulated pathogen in the US and internationally. Currently, nurseries are inspected to detect infected plants; however, many plants are propagated by tissue culture nurseries and the behavior of P. ramorum in this system is unknown. Pathogen growth and sporulation in propagation vessels containing different multiplication and rooting media, with a range of plants and without plants, was evaluated with regard to pathogen visibility and induction of disease symptoms. Within 2 weeks, the pathogen colonies were visible to the naked eye on all 26 multiplication media and on 9 of 11 rooting media tested (without plants). The appearance of colonies on different media was variable and no sporangia but occasional chlamydospores were produced. The pathogen growth was very visible on multiplication media containing susceptible plants, inoculated plants exhibiting obvious discoloration and mortality. The pathogen was reisolated from terminal shoot tissue and roots of symptomatic plants. Variability occurred in susceptibility of different cultivars of a plant species, in virulence of the two isolates of the pathogen, and in recovery from shoot tissue. We conclude that fungal growth on the media, with or without plants, and symptoms of disease were apparent enough that contaminated vessels would be destroyed.

Accepted for publication 9 April 2007. Published 22 August 2007.
Plant Pathogens at Work: Improving Weed Control Efficacy
Authors: Yandoc-Ables C. B. , Rosskopf E. N. , Charudattan R.
Published: September 2007

Research in the area of the use of plant pathogens as biological control agents for weeds is conducted using either the classical or the bioherbicidal approach. In the classical approach, a pathogen is typically imported from a foreign location to control an introduced weed target. In the inundative or bioherbicide strategy, an indigenous pathogen is cultured to produce large quantities of inoculum that are applied at high rates to the entire target weed population. Research on the development of plant pathogens for biological control using the inundative or bioherbicide approach has moved from determining host range and demonstrating pathogenicity to investigating systems that enhance the efficacy of these agents.

Accepted for publication 9 April 2007. Published 22 August 2007.
Citrus Huanglongbing: The Pathogen and Its Impact
Authors: Gottwald Tim R. , Graça John V. da , Bassanezi Renato B.
Published: September 2007

Citrus Huanglongbing, aka greening disease, has been the subject of several reviews in recent years. In this article, the author presents a concise compilation of the main features and symptoms of the disease, the causal organisms and the vectors including impacts for Florida and Brazil, two relatively new areas where the disease has been discovered, as well as implications for California, Texas, and Arizona citrus industries, which are threatened by the close proximity to the new Florida epidemic, and the rest of the western hemisphere.

Accepted for publication 19 June 2007. Published 6 September 2007.
The future of scientific ballooning
Authors: Pagitz Markus
Published: September 2007

This paper gives a brief overview of the historical development of scientific balloons and their capabilities. Furthermore, a recent programme by NASA is introduced that aims to develop balloons capable of carrying payloads of several tonnes to above 99% of the Earth's atmosphere for up to 100 days. It is shown that the currently investigated balloons suffer from instabilities that can be minimized using a different design paradigm for the cutting patterns. Finally, a novel balloon design, similar to the topology of radiolarians, is introduced that is potentially superior to existing designs.
Diamond at the nanoscale: applications of diamond nanoparticles from cellular biomarkers to quantum computing
Authors: Holt Katherine B
Published: September 2007

Although nanocrystalline diamond powders have been produced in industrial quantities, mainly by detonation synthesis, for many decades their use in applications other than traditional polishing and grinding have been limited, until recently. This paper presents the wide-ranging applications of nanodiamond particles to date and discusses future research directions in this field. Owing to the recent commercial availability of these powders and the present interest in nanotechnology, one can predict a huge increase in research with these materials in the very near future. However, to fully exploit these materials, fundamental as well as applied research is required to understand the transition between bulk and surface properties as the size of particles decreases.
Brain architecture: a design for natural computation
Authors: Kaiser Marcus
Published: September 2007

Fifty years ago, John von Neumann compared the architecture of the brain with that of the computers he invented and which are still in use today. In those days, the organization of computers was based on concepts of brain organization. Here, we give an update on current results on the global organization of neural systems. For neural systems, we outline how the spatial and topological architecture of neuronal and cortical networks facilitates robustness against failures, fast processing and balanced network activation. Finally, we discuss mechanisms of self-organization for such architectures. After all, the organization of the brain might again inspire computer architecture.
Re-engineering cities: a framework for adaptation to global change
Authors: Dawson Richard
Published: September 2007

Urban areas are expected to continue their rapid growth in the twenty-first century. Globally, cities are major sources of greenhouse gases emissions and their high population densities make them potential focal points of vulnerability to global environmental change. Moreover, their reach, in terms of flows of materials and resources, extends far outside their borders. Evidently, it is no longer tenable to consider urban systems to be static artefacts constructed in a stable environment, nor continue to divorce them from the global context that influences many of the climatic and socio-economic changes within cities. Furthermore, the uncertainty in the future climatic and socio-economic conditions poses significant challenges for planners. A framework is proposed for analysing urban systems with evidence-based tools over extended time scales. This forms the basis of a manifesto for future challenges and research directions for this critical subject area, which ultimately will help engineers and urban planners to better understand the areas for which they are responsible and to develop adaptation strategies that can tackle the challenges posed by long-term global change and lead to more sustainable cities.
Four-stranded DNA: cancer, gene regulation and drug development
Authors: Huppert Julian Leon
Published: September 2007

DNA can form many structures other than the famous double helix. In particular, guanine-rich DNA of particular sequences can form four-stranded structures, called G-quadruplexes. This article describes the structural form of these sequences, techniques for predicting which sequences can fold up in this manner and efforts towards stability prediction. It then discusses the biological significance of these structures, focusing on their importance in telomeric regions at the end of chromosomes, and their existence in gene promoters and mRNA, where they may be involved with regulating transcription and translation, respectively. Ligands that are capable of selectively binding to these structures are introduced and described, as are DNA aptamers that form G-quadruplex structures; both of these classes of compound have been investigated as anticancer agents in clinical trials. The growing use of G-quadruplexes in the nanotechnology field is also outlined. The article concludes with an analysis of future directions the field may take, with some proposals for further important studies.
The engineering options for mitigating the climate impacts of aviation
Authors: Williams Victoria
Published: September 2007

Aviation is a growing contributor to climate change, with unique impacts due to the altitude of emissions. If existing traffic growth rates continue, radical engineering solutions will be required to prevent aviation becoming one of the dominant contributors to climate change. This paper reviews the engineering options for mitigating the climate impacts of aviation using aircraft and airspace technologies. These options include not only improvements in fuel efficiency, which would reduce carbon dioxide (CO
2
) emissions, but also measures to reduce non-CO
2
impacts including the formation of persistent contrails. Integrated solutions to optimize environmental performance will require changes to airframes, engines, avionics, air traffic control systems and airspace design.

While market-based measures, such as offset schemes and emissions trading, receive growing attention, this paper sets out the crucial role of engineering in the challenge to develop a ‘green air traffic system’.
Advances in solid dosage form manufacturing technology
Authors: Andrews Gavin P
Published: September 2007

Currently, the pharmaceutical and healthcare industries are moving through a period of unparalleled change. Major multinational pharmaceutical companies are restructuring, consolidating, merging and more importantly critically assessing their competitiveness to ensure constant growth in an ever-more demanding market where the cost of developing novel products is continuously increasing. The pharmaceutical manufacturing processes currently in existence for the production of solid oral dosage forms are associated with significant disadvantages and in many instances provide many processing problems. Therefore, it is well accepted that there is an increasing need for alternative processes to dramatically improve powder processing, and more importantly to ensure that acceptable, reproducible solid dosage forms can be manufactured. Consequently, pharmaceutical companies are beginning to invest in innovative processes capable of producing solid dosage forms that better meet the needs of the patient while providing efficient manufacturing operations. This article discusses two emerging solid dosage form manufacturing technologies, namely hot-melt extrusion and fluidized hot-melt granulation.
Chemistry across scales: from molecules to cells
Authors: Yaliraki Sophia N , Barahona Mauricio
Published: September 2007

Many important biological functions are strongly dependent on specific chemical interactions. Modelling how the physicochemical molecular details emerge at much larger scales is an active area of research, currently pursued with a variety of methods. We describe a series of theoretical and computational approaches that aim to derive bottom-up descriptions that capture the specificity that ensues from atomistic detail by extracting relevant features at the different scales. The multiscale models integrate the descriptions at different length and time scales by exploiting the idea of mechanical responses. The methodologies bring together concepts and tools developed in seemingly unrelated areas of mathematics such as algebraic geometry, model reduction, structural graph theory and non-convex optimization. We showcase the applicability of the framework with examples from protein engineering and enzyme catalysis, protein assembly, and with the description of lipid bilayers at different scales. Many challenges remain as it is clear that no single methodology will answer all questions in such multidimensional complex problems.
Ten years of science in
Philosophical Transactions A
: with the University Research Fellows
Authors: Thompson J.Michael T
Published: September 2007

In this brief paper, I review my 10 years as the Editor of the
Philosophical Transactions of the Royal Society A
. I look at the content of the journal over the years, relating it to a full classification of the physical sciences based on the interests of fellows and research fellows of the Royal Society. I show that the journal has performed well in terms of downloads, citations and impact factors. Innovations such as the Millennium and Christmas Issues for young scientists have stimulated a close and enjoyable interaction with the Society's research fellows. In addition to authoring papers and organizing themes, they have always been keen to help with the refereeing processes. They provided exciting demonstrations for a Summer Science exhibit that I organized to highlight the work of the journal, and five of the research fellows now sit on the Editorial Board. Looking to the future, I describe the new subject clusters that are being introduced as the journal steps up its publication rate from one issue per month to two, starting in January 2008.
Modelling interwall interactions in carbon nanotubes: fundamentals and device applications
Authors: Bichoutskaia Elena
Published: September 2007

Carbon nanotubes are the most commonly used ‘building blocks’ of modern nanotechnology. Their unique mechanical and electronic properties, stability and functionality show great promise in creating functional devices on the nanometre scale. One of the great challenges in using this scale is the ability of physical manipulation of the components, such as their positioning and assembling. Strong correlation between the structure and mechanical interactions of the walls of carbon nanotubes provides self-regulation of their relative motion. This can be further exploited in low-friction and high-stiffness devices. In this paper, we present a condensed overview of the recent progress in fundamental understanding of nanomechanical and nanoelectromechanical behaviour of carbon nanotubes and their applications in nanodevices.