bluuebunny/crossref_metadata_2025 huggingface dataset:
Syntactically cued text facilitates oral reading fluency in developing readers
Authors: LEVASSEUR VALERIE MARCIARILLE , MACARUSO PAUL , PALUMBO LAURA CONWAY , SHANKWEILER DONALD
Published: March 2008

Can fluency in oral reading be facilitated by formatting text to preserve major syntactic boundaries? Seven-, 8-, and 9-year-old children read aloud passages under two text format conditions. In the structure-preserving condition, the ends of lines coincided with ends of clauses; in the phrase-disrupting condition, line breaks always interrupted a phrasal unit. Experiment 1 showed that oral reading fluency, as indexed by skill in phrasal reading, was rated higher when children were reading in the structure-preserving condition. In addition, the structure-preserving condition resulted in significantly fewer false starts at the beginning of lines following a return sweep. The results of Experiment 2, in which texts of varying levels of difficulty were read by slightly older readers, confirmed both findings. Measures of fluency were correlated with other language and reading measures; however, no effects of format were obtained on oral reading rate (words correct per minute). Taken as a whole, these findings indicate a benefit of keeping clausal units intact in promoting fluent reading by facilitating the transition from one line to the next.
Pedestal temperature models based on first and second stability
limits of ballooning modes
Authors: ONJUN THAWATCHAI
Published: March 2008

Models for the prediction of electron pedestal temperatures at the
edge of type I ELMy H-mode plasmas are developed. These models are based
on theory motivated concepts for pedestal width and pressure gradient. The
pedestal pressure gradient is assumed to be limited by high n
ballooning mode instabilities, where both the first and second stability
limits are considered. The effect of the bootstrap current, which reduces
the magnetic shear in the steep pressure gradient region at the edge of
the H-mode plasma, can result in access to the second stability of
ballooning mode. In these pedestal models, the magnetic shear and safety
factor are calculated at one pedestal width away from separatrix. The
predictions of these models are compared with the experimental electron
pedestal temperatures for type I ELMy H-mode discharges obtained from the
latest public version (version 3.2) in the International Tokamak Physics
Activity Edge (ITPA) Pedestal Database.
Charge state of Zn projectile ions in partially ionized plasma:
Simulations
Authors: NARDI ERAN , FISHER DIMITRI V. , ROTH MARKUS , BLAZEVIC ABEL , HOFFMANN DIETER H.H.
Published: March 2008

This study deals with the simulation of the experimental study of Roth
et al. (2000) on the interaction of
energetic Zn projectiles in partially ionized laser produced carbon
targets, and with similar type experiments. Particular attention is paid
to the specific contributions of the K and L shell target electrons to
electron recombination in the energetic Zn ionic projectile. The classical
Bohr–Lindhard model was used for describing recombination, while
quantum mechanical models were also introduced for scaling the L to K
cross-section ratios. It was found that even for a hydrogen-like carbon
target, the effect of the missing five bound electrons brings about an
increase of only 0.6 charge units in the equilibrium charge state as
compared to the cold target value of 23. A collisional radiative
calculation was employed for analyzing the type of plasma produced in the
experimental study. It was found that for the plasma conditions
characteristic of this experiment, some fully ionized target plasma atoms
should be present. However in order to explain the experimentally observed
large increase in the projectile charge state a very dominant component of
the fully ionized plasma must comprise the target plasma. A procedure for
calculating the dynamic evolvement of the projectile charge state within
partially ionized plasma is also presented and applied to the type of
plasma encountered in the experiment of Roth et al. (2000). The low temperature and density tail on the
back of the target brings about a decrease in the exiting charge state,
while the value of the average charge state within the target is dependent
on the absolute value of the cross-sections.
Ion focusing effect of electron cloud produced by laser-plasma
interaction
Authors: MIYAZAKI SHUJI , OKAZAKI NOBUYASU , SONOBE RYO , KONG QING , KAWATA SHIGEO , ANDREEV A.A. , LIMPOUCH JIRI
Published: March 2008

We propose a focusing mechanism of high-energy ions by an electron
cloud produced by a laser interaction with slab plasma. In our
2.5-dimensional (2.5D) particle-in-cell simulations, the laser intensity
is 2 × 1020 W/cm2, the laser wavelength
λ is 1.053 μm, and the laser spot size is 2.5λ. When the high
intensity laser irradiates slab plasma, electrons are accelerated,
oscillate around the plasma and produce the electron cloud locally at the
sides of the plasma. Because the electrons are localized transversely, a
static electric potential is formed to focus ions and at the same time the
ions are accelerated longitudinally. Though the longitudinal ion
acceleration has been studied well, the ion focusing effect is reported
for the first time in this paper. In our calculations, the maximum energy
and intensity of the protons are 8.61 MeV and 1.89 × 1017
W/cm2, and the diameter of the proton bunch accelerated are
focused to 71.2% of its initial size.
End‐to‐end flood risk assessment: A coupled model cascade with uncertainty estimation
Authors: McMillan Hilary K. , Brasington James
Published: March 2008

This paper presents the case for an ‘End‐to‐End’ flood inundation modeling strategy: the creation of a coupled system of models to allow continuous simulation methodology to be used to predict the magnitude and simulate the effects of high return period flood events. The framework brings together the best in current thinking on reduced complexity modeling to formulate an efficient, process‐based methodology which meets the needs of today's flood mitigation strategies. The model chain is subject to stochasticity and parameter uncertainty, and integral methods to allow the propagation and quantification of uncertainty are essential in order to produce robust estimates of flood risk. Results from an experimental application are considered in terms of their implications for successful floodplain management, and compared against the deterministic methodology more commonly in use for flood risk assessment applications. The provenance of predictive uncertainty is also considered in order to identify those areas where future effort in terms of data collection or model refinement might best be directed in order to narrow prediction bounds and produce a more precise forecast.
The magneto-optical Barnett effect in metals (invited)
Authors: Rebei A. , Hohlfeld J.
Published: March 2008

The interaction of polarized light with a spin in the presence of dissipation and fluctuations is shown to be equivalent to a spin transfer process that can cause switching. In high energy plasmas, the spin transfer is dominated by a spin-spin exchange term while at lower energy densities it is dominated by an optical Barnett-like effect and dissipation. This latter effect is used in conjunction with optical boson modes to predict femtosecond magnetization reversal believed to be recently measured in GdCoFe thin films. Conventional approaches based on the Bloch and the Landau–Lifshitz equations are valid only for weak coupling to the environment and hence are unable to reproduce this ultrafast switching.
Low-voltage organic thin-film transistors with π-σ-phosphonic acid molecular dielectric monolayers
Authors: Ma Hong , Acton Orb , Ting Guy , Ka Jae Won , Yip Hin-Lap , Tucker Neil , Schofield Richard , Jen Alex K.-Y.
Published: March 2008

Pentacene-based organic thin-film transistors (OTFTs) have been fabricated using π-σ-phosphonic acid self-assembled monolayers (SAMs) on top of aluminum oxide as the gate dielectrics. With ultrathin dielectrics, high capacitances up to 760nF∕cm2 and low leakage current densities of 10−8A∕cm2 at 2V could be obtained, allowing operation of OTFTs within −3V. Vast improvements in the gate leakage current (∼2 orders), on/off current ratio (1 order), and subthreshold slope down to 85mV∕decade are achieved compared to control devices without SAMs. The OTFTs with pentacene vapor deposited at room temperature on SAM dielectrics-modified substrates exhibit mobilities of 0.14–0.30cm2∕Vs, on/off current ratios of 105, and threshold voltages of −(1.3–1.5)V.
Cathodoluminescence defect characterization of hydrothermally grown SnO2 nanoparticles
Authors: Pal U. , Pérez-Centeno A. , Herrera-Zaldívar M.
Published: March 2008

Sn O 2 nanoparticles in the 50–150nm size range were grown by a low temperature hydrothermal process, using SnCl4⋅5H2O as precursor and CH3(CH2)15N(Br)(CH3)3 as stabilizing agent. The as-grown samples were mostly amorphous and their crystallinity improved either by prolonged hydrothermal process or by air annealing at high temperatures. The absence of near-band-edge emission and appearance of a broad visible emission related mainly to oxygen vacancies and crystalline defects were the main characteristics of their room temperature cathodoluminescence (CL) spectra. A luminescent band in the 1.79–1.83eV spectral region was also detected. The intensity of the defect bands reduces both on prolonged hydrothermal treatment and air annealing at high temperatures, indicating a net decrease of defect content on thermal treatments. Panchromatic CL images revealed that most of the defect emissions come from smaller SnO2 nanoparticles.
Magnetic field induced ferroelectric loop in Bi0.75Sr0.25FeO3−δ
Authors: Kundys Bohdan , Maignan Antoine , Martin Christine , Nguyen Ninh , Simon Charles
Published: March 2008

Magnetic field induced ferroelectric hysteresis loop observed in Bi0.75Sr0.25FeO3−δ is of prime importance. The coexistence of antiferromagnetism and weak ferromagnetism is responsible for the original magnetoelastic and magnetoferroelectric properties. Upon external magnetic field application, the existence of a magnetostrictive effect supports a structural transition toward a homogeneous antiferromagnetic and ferroelectric phase. The magnetic field induced polarization is among the highest reported for BiFeO3 based systems in either thin film or bulk form (Pr=96μC∕cm2 at 10T) while the ferroelectric coercive field is among the lowest reported (Hc=661V∕cm at 10T). These properties make this material very attractive for technical applications.
Transmission electron microscopy characterization of nanorods in BaNb2O6-doped ErBa2Cu3O7−δ films
Authors: Yamada K. , Mukaida M. , Kai H. , Teranishi R. , Ichinose A. , Kita R. , Kato S. , Horii S. , Yoshida Y. , Matsumoto K. , Toh S.
Published: March 2008

Ba Nb 2 O 6 -doped microstructures as artificial pinning centers in ErBa2Cu3O7−δ films were studied by transmission electron microscopy. The presence of nanorods, which contain niobium, was confirmed from bright-field images and elemental map images. The crystal structure of the nanorod was determined to be cubic perovskite. The lattice constant of nanorods in the ErBa2Cu3O7−δ film was in good agreement with the lattice constant of Ba(Er0.5Nb0.5)O3. Furthermore, parallel Moiré fringes were observed in the bright-field images. It has never been confirmed by any other researchers that BaNb2O6 doped into the ErBa2Cu3O7−δ film transforms to Ba(Er0.5Nb0.5)O3 nanorods with a perovskite structure.
The shock-densification behavior of three distinct Ni+Al powder mixtures
Authors: Eakins Daniel E. , Thadhani Naresh N.
Published: March 2008

The shock-densification response of equivolumetric mixtures of Ni+Al powders of varying particle size and morphology has been determined through instrumented parallel-plate impact experiments. The results reveal a variation in the densification response, with crush strengths (stress at full density) ranging from 0.5 to nearly 6GPa. A modified Fischmeister–Artz contact model was proposed to predict the crush strength of configurationally varying Ni+Al powder mixtures.
Quantitative analysis of individual metal-CdSe-metal nanowire field-effect transistors
Authors: Skinner Kwan , Dwyer Chris , Washburn Sean
Published: March 2008

Heterostructured metal-CdSe-metal nanowires were fabricated by sequential electrochemical deposition of layers of Au and the semiconductor CdSe. Nonlinear I-V curves were observed, and a parameter retrieval model was used to extract the majority carrier mobility of 0.5cm2V−1s−1 for nanowires fabricated with zero deposition current during the exchange of the final CdSe and Au segments. This improved threefold with the application of a small current during the solution exchange. Values for the resistance and the electron density for these nanowires were determined.
Impact of soil consolidation and solution composition on the hydraulic properties of coastal acid sulfate soils
Authors: Le Thi Minh Hue , Pham An Ninh , Collins Richard N. , Waite T. David
Published: March 2008

Acid sulfate soils (ASS) are distributed worldwide on coastal floodplains, presenting a great challenge to coastal development and urbanisation. Upon oxidation, these soils become stratified with visibly distinguishable soil strata that are progressively less oxidised with depth. In this study, the geotechnical properties, quantified by hydraulic conductivity and consolidation coefficient, of an ASS profile from the Tweed River floodplain, north-eastern New South Wales, Australia, were investigated at a laboratory scale and compared with results obtained from the field. Measurements were conducted with a Rowe cell (or hydraulic consolidometer) by controlled compressive and pore water pressures. The results indicated that hydraulic conductivity and consolidation coefficient values gradually decreased with increasing consolidation pressure or decreasing void ratio, but were significantly higher for the more oxidised ASS horizons. These results suggest that controlled soil consolidation along ASS drainage banks may prove to be effective at reducing acid discharge. Passing low pH (pH 3) or high cation concentration (50 mm CaCl2) solutions through intact consolidated potential ASS samples did not induce changes in the hydraulic conductivity or consolidation coefficient of this material indicating that ASS soil ripening involves more than acidification reactions, and the practice of flushing drains with high ionic strength estuarine tidal waters is unlikely to induce soil subsidence as a result of ASS structural change and clay flocculation.
Population genomics of the wild yeast
Saccharomyces paradoxus
: Quantifying the life cycle
Authors: Tsai Isheng J. , Bensasson Douda , Burt Austin , Koufopanou Vassiliki
Published: March 2008

Most microbes have complex life cycles with multiple modes of reproduction that differ in their effects on DNA sequence variation. Population genomic analyses can therefore be used to estimate the relative frequencies of these different modes in nature. The life cycle of the wild yeast
Saccharomyces paradoxus
is complex, including clonal reproduction, outcrossing, and two different modes of inbreeding. To quantify these different aspects we analyzed DNA sequence variation in the third chromosome among 20 isolates from two populations. Measures of mutational and recombinational diversity were used to make two independent estimates of the population size. In an obligately sexual population these values should be approximately equal. Instead there is a discrepancy of about three orders of magnitude between our two estimates of population size, indicating that
S. paradoxus
goes through a sexual cycle approximately once in every 1,000 asexual generations. Chromosome III also contains the mating type locus (
MAT
), which is the most outbred part in the entire genome, and by comparing recombinational diversity as a function of distance from
MAT
we estimate the frequency of matings to be ≈94% from within the same tetrad, 5% with a clonemate after switching the mating type, and 1% outcrossed. Our study illustrates the utility of population genomic data in quantifying life cycles.
RXLR effector reservoir in two
Phytophthora
species is dominated by a single rapidly evolving superfamily with more than 700 members
Authors: Jiang Rays H. Y. , Tripathy Sucheta , Govers Francine , Tyler Brett M.
Published: March 2008

Pathogens secrete effector molecules that facilitate the infection of their hosts. A number of effectors identified in plant pathogenic
Phytophthora
species possess N-terminal motifs (RXLR-dEER) required for targeting these effectors into host cells. Here, we bioinformatically identify >370 candidate effector genes in each of the genomes of
P. sojae
and
P. ramorum
. A single superfamily, termed avirulence homolog (
Avh
) genes, accounts for most of the effectors. The Avh proteins show extensive sequence divergence but are all related and likely evolved from a common ancestor by rapid duplication and divergence. More than half of the Avh proteins contain conserved C-terminal motifs (termed W, Y, and L) that are usually arranged as a module that can be repeated up to eight times. The
Avh
genes belong to the most rapidly evolving part of the genome, and they are nearly always located at synteny breakpoints. The superfamily includes all experimentally identified oomycete effector and avirulence genes, and its rapid pace of evolution is consistent with a role for Avh proteins in interaction with plant hosts.
Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource
Authors: Herrel Anthony , Huyghe Katleen , Vanhooydonck Bieke , Backeljau Thierry , Breugelmans Karin , Grbac Irena , Van Damme Raoul , Irschick Duncan J.
Published: March 2008

Although rapid adaptive changes in morphology on ecological time scales are now well documented in natural populations, the effects of such changes on whole-organism performance capacity and the consequences on ecological dynamics at the population level are often unclear. Here we show how lizards have rapidly evolved differences in head morphology, bite strength, and digestive tract structure after experimental introduction into a novel environment. Despite the short time scale (≈36 years) since this introduction, these changes in morphology and performance parallel those typically documented among species and even families of lizards in both the type and extent of their specialization. Moreover, these changes have occurred side-by-side with dramatic changes in population density and social structure, providing a compelling example of how the invasion of a novel habitat can evolutionarily drive multiple aspects of the phenotype.
Dissection of mechanisms of Chinese medicinal formula Realgar-
Indigo naturalis
as an effective treatment for promyelocytic leukemia
Authors: Wang Lan , Zhou Guang-Biao , Liu Ping , Song Jun-Hong , Liang Yang , Yan Xiao-Jing , Xu Fang , Wang Bing-Shun , Mao Jian-Hua , Shen Zhi-Xiang , Chen Sai-Juan , Chen Zhu
Published: March 2008

To enhance therapeutic efficacy and reduce adverse effects, practitioners of traditional Chinese medicine (TCM) prescribe a combination of plant species/minerals, called formulae, based on clinical experience. Nearly 100,000 formulae have been recorded, but the working mechanisms of most remain unknown. In trying to address the possible beneficial effects of formulae with current biomedical approaches, we use Realgar-
Indigo naturalis
formula (RIF), which has been proven to be very effective in treating human acute promyelocytic leukemia (APL) as a model. The main components of RIF are realgar,
Indigo naturalis
, and
Salvia miltiorrhiza
, with tetraarsenic tetrasulfide (A), indirubin (I), and tanshinone IIA (T) as major active ingredients, respectively. Here, we report that the ATI combination yields synergy in the treatment of a murine APL model
in vivo
and in the induction of APL cell differentiation
in vitro
. ATI causes intensified ubiquitination/degradation of promyelocytic leukemia (PML)-retinoic acid receptor α (RARα) oncoprotein, stronger reprogramming of myeloid differentiation regulators, and enhanced G
1
/G
0
arrest in APL cells through hitting multiple targets compared with the effects of mono- or biagents. Furthermore, ATI intensifies the expression of Aquaglyceroporin 9 and facilitates the transportation of A into APL cells, which in turn enhances A-mediated PML-RARα degradation and therapeutic efficacy. Our data also indicate A as the principal component of the formula, whereas T and I serve as adjuvant ingredients. We therefore suggest that dissecting the mode of action of clinically effective formulae at the molecular, cellular, and organism levels may be a good strategy in exploring the value of traditional medicine.
Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR
Authors: Franks W. Trent , Wylie Benjamin J. , Schmidt Heather L. Frericks , Nieuwkoop Andrew J. , Mayrhofer Rebecca-Maria , Shah Gautam J. , Graesser Daniel T. , Rienstra Chad M.
Published: March 2008

Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of ≈1 Å, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 ± 0.13 Å (1.52 ± 0.12 Å for all heavy atoms), which improved to 0.49 ± 0.05 Å (1.19 ± 0.07 Å) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 ± 0.06 Å bbRMSD (1.06 ± 0.07 Å); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 ± 0.09 Å; 1.29 ± 0.07 Å) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.
Immunization by a bacterial aerosol
Authors: Garcia-Contreras Lucila , Wong Yun-Ling , Muttil Pavan , Padilla Danielle , Sadoff Jerry , DeRousse Jessica , Germishuizen Willem Andreas , Goonesekera Sunali , Elbert Katharina , Bloom Barry R. , Miller Rich , Fourie P. Bernard , Hickey Anthony , Edwards David
Published: March 2008

By manufacturing a single-particle system in two particulate forms (i.e., micrometer size and nanometer size), we have designed a bacterial vaccine form that exhibits improved efficacy of immunization. Microstructural properties are adapted to alter dispersive and aerosol properties independently. Dried “nanomicroparticle” vaccines possess two axes of nanoscale dimensions and a third axis of micrometer dimension; the last one permits effective micrometer-like physical dispersion, and the former provides alignment of the principal nanodimension particle axes with the direction of airflow. Particles formed with this combination of nano- and micrometer-scale dimensions possess a greater ability to aerosolize than particles of standard spherical isotropic shape and of similar geometric diameter. Here, we demonstrate effective application of this biomaterial by using the live attenuated tuberculosis vaccine bacille Calmette–Guérin (BCG). Prepared as a spray-dried nanomicroparticle aerosol, BCG vaccine exhibited high-efficiency delivery and peripheral lung targeting capacity from a low-cost and technically simple delivery system. Aerosol delivery of the BCG nanomicroparticle to normal guinea pigs subsequently challenged with virulent
Mycobacterium tuberculosis
significantly reduced bacterial burden and lung pathology both relative to untreated animals and to control animals immunized with the standard parenteral BCG.
Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene
CCA1
Authors: Gutiérrez Rodrigo A. , Stokes Trevor L. , Thum Karen , Xu Xiaodong , Obertello Mariana , Katari Manpreet S. , Tanurdzic Milos , Dean Alexis , Nero Damion C. , McClung C. Robertson , Coruzzi Gloria M.
Published: March 2008

Understanding how nutrients affect gene expression will help us to understand the mechanisms controlling plant growth and development as a function of nutrient availability. Nitrate has been shown to serve as a signal for the control of gene expression in
Arabidopsis
. There is also evidence, on a gene-by-gene basis, that downstream products of nitrogen (N) assimilation such as glutamate (Glu) or glutamine (Gln) might serve as signals of organic N status that in turn regulate gene expression. To identify genome-wide responses to such organic N signals,
Arabidopsis
seedlings were transiently treated with ammonium nitrate in the presence or absence of MSX, an inhibitor of glutamine synthetase, resulting in a block of Glu/Gln synthesis. Genes that responded to organic N were identified as those whose response to ammonium nitrate treatment was blocked in the presence of MSX. We showed that some genes previously identified to be regulated by nitrate are under the control of an organic N-metabolite. Using an integrated network model of molecular interactions, we uncovered a subnetwork regulated by organic N that included
CCA1
and target genes involved in N-assimilation. We validated some of the predicted interactions and showed that regulation of the master clock control gene
CCA1
by Glu or a Glu-derived metabolite in turn regulates the expression of key N-assimilatory genes. Phase response curve analysis shows that distinct N-metabolites can advance or delay the
CCA1
phase. Regulation of
CCA1
by organic N signals may represent a novel input mechanism for N-nutrients to affect plant circadian clock function.
Curriculum wars: national identity in education
Authors: Murray Helen
Published: March 2008

This paper explores the politics of education in countries affected by conflict. Drawing particularly on the Palestinian experience, it looks at the power relations among internal and external actors that shape the curriculum-building process. In the increasingly politicised world of
international aid, especially in the Middle East, it challenges the idea that international agencies and donors can take a neutral approach to education. Unlike the other three pillars of humanitarian response – food, health and shelter – education is never neutral, it is intrinsically
ideological and political.
Classification of eight-dimensional perfect forms
Authors: Sikirić Mathieu , Schürmann Achill , Vallentin Frank
Published: March 2008

In this paper, we classify the perfect lattices in dimension88. There are1091610916of them. Our classification heavily relies on exploiting symmetry in polyhedral computations. Here we describe algorithms making the classification possible.
Fitting a geometric graph to a protein–protein interaction network
Authors: Higham Desmond J. , Rašajski Marija , Pržulj Nataša
Published: March 2008

Motivation: Finding a good network null model for protein–protein interaction (PPI) networks is a fundamental issue. Such a model would provide insights into the interplay between network structure and biological function as well as into evolution. Also, network (graph) models are used to guide biological experiments and discover new biological features. It has been proposed that geometric random graphs are a good model for PPI networks. In a geometric random graph, nodes correspond to uniformly randomly distributed points in a metric space and edges (links) exist between pairs of nodes for which the corresponding points in the metric space are close enough according to some distance norm. Computational experiments have revealed close matches between key topological properties of PPI networks and geometric random graph models. In this work, we push the comparison further by exploiting the fact that the geometric property can be tested for directly. To this end, we develop an algorithm that takes PPI interaction data and embeds proteins into a low-dimensional Euclidean space, under the premise that connectivity information corresponds to Euclidean proximity, as in geometric-random graphs. We judge the sensitivity and specificity of the fit by computing the area under the Receiver Operator Characteristic (ROC) curve. The network embedding algorithm is based on multi-dimensional scaling, with the square root of the path length in a network playing the role of the Euclidean distance in the Euclidean space. The algorithm exploits sparsity for computational efficiency, and requires only a few sparse matrix multiplications, giving a complexity of O(N2) where N is the number of proteins.

Results: The algorithm has been verified in the sense that it successfully rediscovers the geometric structure in artificially constructed geometric networks, even when noise is added by re-wiring some links. Applying the algorithm to 19 publicly available PPI networks of various organisms indicated that: (a) geometric effects are present and (b) two-dimensional Euclidean space is generally as effective as higher dimensional Euclidean space for explaining the connectivity. Testing on a high-confidence yeast data set produced a very strong indication of geometric structure (area under the ROC curve of 0.89), with this network being essentially indistinguishable from a noisy geometric network. Overall, the results add support to the hypothesis that PPI networks have a geometric structure.

Availability: MATLAB code implementing the algorithm is available upon request.

Contact:  natasha@ics.uci.edu
Biological sequence classification utilizing positive and unlabeled data
Authors: Xiao Yuanyuan , Segal Mark R.
Published: March 2008

Motivation: In the genomics setting, an increasingly common data configuration consists of a small set of sequences possessing a targeted property (positive instances) amongst a large set of sequences for which class membership is unknown (unlabeled instances). Traditional two-class classification methods do not effectively handle such data.

Results: Here, we develop a novel method, likely positive-iterative classification (LP-IC) for this problem, and contrast its performance with the few existing methods, most of which were devised and utilized in the text classification context. LP-IC employs an iterative classification scheme and introduces a class dispersion measure, adopted from unsupervised clustering approaches, to monitor the model selection process. Using two case studies—prediction of HLA binding, and alternative splicing conservation between human and mouse—we show that LP-IC provides superior performance to existing methodologies in terms of: (i) combined accuracy and precision in positive identification from the unlabeled set; and (ii) predictive performance of the resultant classifiers on independent test data.

Contact:  mark@biostat.ucsf.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Impact of climate change on long-term zooplankton biomass in the upwelling region of the Gulf of Guinea
Authors: Wiafe George , Yaqub Hawa B. , Mensah Martin A. , Frid Christopher L. J.
Published: March 2008

Wiafe, G., Yaqub, H. B., Mensah, M. A., and Frid, C. L. J. 2008. Impact of climate change on long-term zooplankton biomass in the upwelling region of the Gulf of Guinea. – ICES Journal of Marine Science, 65: 318–324. We investigated long-term changes in coastal zooplankton in the upwelling region in the Gulf of Guinea, 1969–1992, in relation to climatic and biotic factors. We considered the role of hydrographic and climatic factors, i.e. sea surface temperature (SST), salinity, sea level pressure, windfield, and Southern Oscillation Index (SOI), in the long-term variation of zooplankton in a multiple regression analysis, along with the abundance of Sardinella. Annual variation in zooplankton biomass was cyclical, with the annual peak occurring during the major upwelling season, July–September. Over the 24-year period, there was a downward trend in zooplankton biomass (equivalent to 6.33 ml per 1000 m3 per year). The decomposed trend in SST during the major upwelling revealed gradual warming of surface waters. This trend was believed to be the main influence on the abundance of the large copepod Calanoides carinatus (sensitive to temperatures above 23°C), which appears in the coastal waters only during the major upwelling season. The warming trend associated with global climate change could affect zooplankton community structure, especially during the major upwelling season. Global warming coupled with “top–down” (predation) control by Sardinella might be responsible for the long-term decline in zooplankton biomass in the upwelling region of the Gulf of Guinea.
Cell Wall Modifications in Arabidopsis Plants with Altered α-l-Arabinofuranosidase Activity
Authors: Chávez Montes Ricardo A. , Ranocha Philippe , Martinez Yves , Minic Zoran , Jouanin Lise , Marquis Mélanie , Saulnier Luc , Fulton Lynette M. , Cobbett Christopher S. , Bitton Frédérique , Renou Jean-Pierre , Jauneau Alain , Goffner Deborah
Published: March 2008

Although cell wall remodeling is an essential feature of plant growth and development, the underlying molecular mechanisms are poorly understood. This work describes the characterization of Arabidopsis (Arabidopsis thaliana) plants with altered expression of ARAF1, a bifunctional α-l-arabinofuranosidase/β-d-xylosidase (At3g10740) belonging to family 51 glycosyl-hydrolases. ARAF1 was localized in several cell types in the vascular system of roots and stems, including xylem vessels and parenchyma cells surrounding the vessels, the cambium, and the phloem. araf1 T-DNA insertional mutants showed no visible phenotype, whereas transgenic plants that overexpressed ARAF1 exhibited a delay in inflorescence emergence and altered stem architecture. Although global monosaccharide analysis indicated only slight differences in cell wall composition in both mutant and overexpressing lines, immunolocalization experiments using anti-arabinan (LM6) and anti-xylan (LM10) antibodies indicated cell type-specific alterations in cell wall structure. In araf1 mutants, an increase in LM6 signal intensity was observed in the phloem, cambium, and xylem parenchyma in stems and roots, largely coinciding with ARAF1 expression sites. The ectopic overexpression of ARAF1 resulted in an increase in LM10 labeling in the secondary walls of interfascicular fibers and xylem vessels. The combined ARAF1 gene expression and immunolocalization studies suggest that arabinan-containing pectins are potential in vivo substrates of ARAF1 in Arabidopsis.
Sucrose Synthase Is Associated with the Cell Wall of Tobacco Pollen Tubes
Authors: Persia Diana , Cai Giampiero , Del Casino Cecilia , Faleri Claudia , Willemse Michiel T.M. , Cresti Mauro
Published: March 2008

Sucrose synthase (Sus; EC 2.4.1.13) is a key enzyme of sucrose metabolism in plant cells, providing carbon for respiration and for the synthesis of cell wall polymers and starch. Since Sus is important for plant cell growth, insights into its structure, localization, and features are useful for defining the relationships between nutrients, growth, and cell morphogenesis. We used the pollen tube of tobacco (Nicotiana tabacum) as a cell model to characterize the main features of Sus with regard to cell growth and cell wall synthesis. Apart from its role during sexual reproduction, the pollen tube is a typical tip-growing cell, and the proper construction of its cell wall is essential for correct shaping and direction of growth. The outer cell wall layer of pollen tubes consists of pectins, but the inner layer is composed of cellulose and callose; both polymers require metabolic precursors in the form of UDP-glucose, which is synthesized by Sus. We identified an 88-kD polypeptide in the soluble, plasma membrane and Golgi fraction of pollen tubes. The protein was also found in association with the cell wall. After purification, the protein showed an enzyme activity similar to that of maize (Zea mays) Sus. Distribution of Sus was affected by brefeldin A and depended on the nutrition status of the pollen tube, because an absence of metabolic sugars in the growth medium caused Sus to distribute differently during tube elongation. Analysis by bidimensional electrophoresis indicated that Sus exists as two isoforms, one of which is phosphorylated and more abundant in the cytoplasm and cell wall and the other of which is not phosphorylated and is specific to the plasma membrane. Results indicate that the protein has a role in the construction of the extracellular matrix and thus in the morphogenesis of pollen tubes.
Comparison of the Dynamics and Functional Redundancy of the Arabidopsis Dynamin-Related Isoforms DRP1A and DRP1C during Plant Development
Authors: Konopka Catherine A. , Bednarek Sebastian Y.
Published: March 2008

Members of the Arabidopsis (Arabidopsis thaliana) DYNAMIN-RELATED PROTEIN1 (DRP1) family are required for cytokinesis and cell expansion. Two isoforms, DRP1A and DRP1C, are required for plasma membrane maintenance during stigmatic papillae expansion and pollen development, respectively. It is unknown whether the DRP1s function interchangeably or if they have distinct roles during cell division and expansion. DRP1C was previously shown to form dynamic foci in the cell cortex, which colocalize with part of the clathrin endocytic machinery in plants. DRP1A localizes to the plasma membrane, but its cortical organization and dynamics have not been determined. Using dual color labeling with live cell imaging techniques, we showed that DRP1A also forms discreet dynamic foci in the epidermal cell cortex. Although the foci overlap with those formed by DRP1C and clathrin light chain, there are clear differences in behavior and response to pharmacological inhibitors between DRP1A and DRP1C foci. Possible functional or regulatory differences between DRP1A and DRP1C were supported by the failure of DRP1C to functionally compensate for the absence of DRP1A. Our studies indicated that the DRP1 isoforms function or are regulated differently during cell expansion.
Characterization of an Amino Acid Permease from the Endomycorrhizal Fungus Glomus mosseae
Authors: Cappellazzo Gilda , Lanfranco Luisa , Fitz Michael , Wipf Daniel , Bonfante Paola
Published: March 2008

Arbuscular mycorrhizal (AM) fungi are capable of exploiting organic nitrogen sources, but the molecular mechanisms that control such an uptake are still unknown. Polymerase chain reaction-based approaches, bioinformatic tools, and a heterologous expression system have been used to characterize a sequence coding for an amino acid permease (GmosAAP1) from the AM fungus Glomus mosseae. The GmosAAP1 shows primary and secondary structures that are similar to those of other fungal amino acid permeases. Functional complementation and uptake experiments in a yeast mutant that was defective in the multiple amino acid uptake system demonstrated that GmosAAP1 is able to transport proline through a proton-coupled, pH- and energy-dependent process. A competitive test showed that GmosAAP1 binds nonpolar and hydrophobic amino acids, thus indicating a relatively specific substrate spectrum. GmosAAP1 mRNAs were detected in the extraradical fungal structures. Transcript abundance was increased upon exposure to organic nitrogen, in particular when supplied at 2 mm concentrations. These findings suggest that GmosAAP1 plays a role in the first steps of amino acid acquisition, allowing direct amino acid uptake from the soil and extending the molecular tools by which AM fungi exploit soil resources.
TheArabidopsisP4-ATPase ALA3 Localizes to the Golgi and Requires a β-Subunit to Function in Lipid Translocation and Secretory Vesicle Formation
Authors: Poulsen Lisbeth Rosager , López-Marqués Rosa Laura , McDowell Stephen C. , Okkeri Juha , Licht Dirk , Schulz Alexander , Pomorski Thomas , Harper Jeffrey F. , Palmgren Michael Gjedde
Published: March 2008

Vesicle budding in eukaryotes depends on the activity of lipid translocases (P4-ATPases) that have been implicated in generating lipid asymmetry between the two leaflets of the membrane and in inducing membrane curvature. We show that Aminophospholipid ATPase3 (ALA3), a member of the P4-ATPase subfamily in Arabidopsis thaliana, localizes to the Golgi apparatus and that mutations of ALA3 result in impaired growth of roots and shoots. The growth defect is accompanied by failure of the root cap to release border cells involved in the secretion of molecules required for efficient root interaction with the environment, and ala3 mutants are devoid of the characteristic trans-Golgi proliferation of slime vesicles containing polysaccharides and enzymes for secretion. In yeast complementation experiments, ALA3 function requires interaction with members of a novel family of plant membrane-bound proteins, ALIS1 to ALIS5 (for ALA-Interacting Subunit), and in this host ALA3 and ALIS1 show strong affinity for each other. In planta, ALIS1, like ALA3, localizes to Golgi-like structures and is expressed in root peripheral columella cells. We propose that the ALIS1 protein is a β-subunit of ALA3 and that this protein complex forms an important part of the Golgi machinery required for secretory processes during plant development.
EMB2473/MIRO1, anArabidopsisMiro GTPase, Is Required for Embryogenesis and Influences Mitochondrial Morphology in Pollen
Authors: Yamaoka Shohei , Leaver Christopher J.
Published: March 2008

The regulation of mitochondrial biogenesis, subcellular distribution, morphology, and metabolism are essential for all aspects of plant growth and development. However, the molecular mechanisms involved are still unclear. Here, we describe an analysis of the three Arabidopsis thaliana orthologs of the evolutionarily conserved Miro GTPases. Two of the genes, MIRO1 and MIRO2, are transcribed ubiquitously throughout the plant tissues, and their gene products localize to mitochondria via their C-terminal transmembrane domains. While insertional mutations in the MIRO2 gene do not have any visible impact on plant development, an insertional mutation in the MIRO1 gene is lethal during embryogenesis at the zygote to four-terminal-cell embryo stage. It also substantially impairs pollen germination and tube growth. Laser confocal and transmission electron microscopy revealed that the miro1 mutant pollen exhibits abnormally enlarged or tube-like mitochondrial morphology, leading to the disruption of continuous streaming of mitochondria in the growing pollen tube. Our findings suggest that mitochondrial morphology is influenced by MIRO1 and plays a vital role during embryogenesis and pollen tube growth.
The Coiled-Coil and Nucleotide Binding Domains of the Potato Rx Disease Resistance Protein Function in Pathogen Recognition and Signaling
Authors: Rairdan Gregory J. , Collier Sarah M. , Sacco Melanie A. , Baldwin Thomas T. , Boettrich Teresa , Moffett Peter
Published: March 2008

Plant genomes encode large numbers of nucleotide binding and leucine-rich repeat (NB-LRR) proteins, some of which mediate the recognition of pathogen-encoded proteins. Following recognition, the initiation of a resistance response is thought to be mediated by the domains present at the N termini of NB-LRR proteins, either a Toll and Interleukin-1 Receptor or a coiled-coil (CC) domain. In order to understand the role of the CC domain in NB-LRR function, we have undertaken a systematic structure–function analysis of the CC domain of the potato (Solanum tuberosum) CC-NB-LRR protein Rx, which confers resistance to Potato virus X. We show that the highly conserved EDVID motif of the CC domain mediates an intramolecular interaction that is dependent on several domains within the rest of the Rx protein, including the NB and LRR domains. Other conserved and nonconserved regions of the CC domain mediate the interaction with the Ran GTPase–activating protein, RanGAP2, a protein required for Rx function. Furthermore, we show that the Rx NB domain is sufficient for inducing cell death typical of hypersensitive plant resistance responses. We describe a model of CC-NB-LRR function wherein the LRR and CC domains coregulate the signaling activity of the NB domain in a recognition-specific manner.
Survey and field of application of Lead Free Anti‐Corrosive Pigments
Authors: Pantzer R.
Published: March 2008

The technical and economic importance of anti‐corrosion is demonstrated by the English investigation “Report of the Committee on Corrosion and Protection”.
Introduction: A Tribute to a Scholar and Teacher Extraordinaire
Authors: Conway O'Brien John
Published: March 2008

John E. Elliott has been a professor of economics at the University of Southern California in Los Angeles since 1956 when he graduated from Harvard University with a doctorate in economics. In that position at USC, John has distinguished himself not only as a scholar and prolific writer but also as an outstanding teacher. He has received every teaching honour which USC has within its power to bestow. Moreover, John has distinguished himself for his contribution to the wellbeing of the faculty and to the advancement of its efforts to preserve and extend the concept of academic freedom. John E. Elliott was born in the year 1931 and the essays which comprise this Festschrift are written in celebration of his sixtieth birthday. The numerous awards he has received for the high quality of his teaching, for his creativity and innovation in the dissemination of knowledge, his record of books published, articles contributed to scholarly journals, and book reviews, are to be found in his curriculum vitae printed at the end of this work.
Introduction: A Tribute to a Teacher and Scholar Extraordinaire
Authors: Conway O'Brien John
Published: March 2008

John E. Elliott has been a professor of economics at the University of Southern California in Los Angeles since 1956 when he graduated from Harvard University with a doctorate in economics. In that position at USC, John has distinguished himself not only as a scholar and prolific writer but also as an outstanding teacher. He has received every teaching honour which USC has within its power to bestow. Moreover, John has distinguished himself for his contribution to the well‐being of the faculty and to the advancement of its efforts to preserve and extend the concept of academic freedom. John E. Elliott was born in the year 1931 and the essays which comprise this Festschriftare written in celebration of his sixtieth birthday. The numerous awards he has received for the high quality of his teaching, for his creativity and innovation in the dissemination of knowledge, his record of books published, articles contributed to scholarly journals and book reviews are to be found in his curriculum vitae printed at the end of this work.
Editorial
Authors: WYNN ELEANOR
Published: March 2008

The guest editor's editorial speaks for itself in introducing the scope of this special issue on prototyping. As a general overview of the contribution, from a farther perspective than the authors—all system developers or prototyping practitioners—I submit the following brief comments.