bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrashallow defect states at SiO2∕4H–SiC interfaces
Authors: Dhar S. , Chen X. D. , Mooney P. M. , Williams J. R. , Feldman L. C.
Published: March 2008

Interface state density (Dit) at SiO2∕4H–SiC interfaces are reported for states lying energetically within ∼0.05–0.2eV of the conduction band edge (EC) of 4H–SiC using capacitance-voltage characterization as a function of temperature. Comparison of as-grown dry oxidized and nitrided interfaces confirms the significant reduction of Dit associated with nitridation. In the as-oxidized case (no nitridation), the Dit in the energy range ∼0.05–0.2eV below EC is found to consist of a broad Dit peak at about ∼0.1eV below EC with an energy width of about ∼0.2eV and a peak magnitude of ∼2×1013cm−2eV−1 superimposed on an exponentially decaying background distribution. Interfacial nitridation completely eliminates the broad peak but does not strongly affect the background.
Heparan sulfate biosynthesis enzymes EXT1 and EXT2 affect NDST1 expression and heparan sulfate sulfation
Authors: Presto Jenny , Thuveson Maria , Carlsson Pernilla , Busse Marta , Wilén Maria , Eriksson Inger , Kusche-Gullberg Marion , Kjellén Lena
Published: March 2008

Heparan sulfate (HS) proteoglycans influence embryonic development and adult physiology through interactions with protein ligands. The interactions depend on HS structure, which is determined largely during biosynthesis by Golgi enzymes. How biosynthesis is regulated is more or less unknown. During polymerization of the HS chain, carried out by a complex of the exostosin proteins EXT1 and EXT2, the first modification enzyme, glucosaminyl
N
-deacetylase/
N
-sulfotransferase (NDST), introduces
N
-sulfate groups into the growing polymer. Unexpectedly, we found that the level of expression of EXT1 and EXT2 affected the amount of NDST1 present in the cell, which, in turn, greatly influenced HS structure. Whereas overexpression of EXT2 in HEK 293 cells enhanced NDST1 expression, increased NDST1 N-glycosylation, and resulted in elevated HS sulfation, overexpression of EXT1 had opposite effects. Accordingly, heart tissue from transgenic mice overexpressing EXT2 showed increased NDST activity. Immunoprecipitaion experiments suggested an interaction between EXT2 and NDST1. We speculate that NDST1 competes with EXT1 for binding to EXT2. Increased NDST activity in fibroblasts with a gene trap mutation in EXT1 supports this notion. These results support a model in which the enzymes of HS biosynthesis form a complex, or a GAGosome.
A simple and exact Laplacian clustering of complex networking phenomena: Application to gene expression profiles
Authors: Kim Choongrak , Cheon Mookyung , Kang Minho , Chang Iksoo
Published: March 2008

Unraveling of the unified networking characteristics of complex networking phenomena is of great interest yet a formidable task. There is currently no simple strategy with a rigorous framework. Using an analogy to the exact algebraic property for a transition matrix of a master equation in statistical physics, we propose a method based on a Laplacian matrix for the discovery and prediction of new classes in the unsupervised complex networking phenomena where the class of each sample is completely unknown. Using this proposed Laplacian approach, we can simultaneously discover different classes and determine the identity of each class. Through an illustrative test of the Laplacian approach applied to real datasets of gene expression profiles, leukemia data [Golub TR,
et al.
(1999)
Science
286:531–537], and lymphoma data [Alizadeh AA,
et al.
(2000)
Nature
403:503–511], we demonstrate that this approach is accurate and robust with a mathematical and physical realization. It offers a general framework for characterizing any kind of complex networking phenomenon in broad areas irrespective of whether they are supervised or unsupervised.
Temporal compression mediated by short-term synaptic plasticity
Authors: Leibold Christian , Gundlfinger Anja , Schmidt Robert , Thurley Kay , Schmitz Dietmar , Kempter Richard
Published: March 2008

Time scales of cortical neuronal dynamics range from few milliseconds to hundreds of milliseconds. In contrast, behavior occurs on the time scale of seconds or longer. How can behavioral time then be neuronally represented in cortical networks? Here, using electrophysiology and modeling, we offer a hypothesis on how to bridge the gap between behavioral and cellular time scales. The core idea is to use a long time constant of decay of synaptic facilitation to translate slow behaviorally induced temporal correlations into a distribution of synaptic response amplitudes. These amplitudes can then be transferred to a sequence of action potentials in a population of neurons. These sequences provide temporal correlations on a millisecond time scale that are able to induce persistent synaptic changes. As a proof of concept, we provide simulations of a neuron that learns to discriminate temporal patterns on a time scale of seconds by synaptic learning rules with a millisecond memory buffer. We find that the conversion from synaptic amplitudes to millisecond correlations can be strongly facilitated by subthreshold oscillations both in terms of information transmission and success of learning.
Factors promoting marine invasions: A chemoecological approach
Authors: Mollo Ernesto , Gavagnin Margherita , Carbone Marianna , Castelluccio Francesco , Pozone Ferdinando , Roussis Vassilios , Templado José , Ghiselin Michael T. , Cimino Guido
Published: March 2008

The Mediterranean Sea is losing its biological distinctiveness, and the same phenomenon is occurring in other seas. It gives urgency to a better understanding of the factors that affect marine biological invasions. A chemoecological approach is proposed here to define biotic conditions that promote biological invasions in terms of enemy escape and resource opportunities. Research has focused on the secondary metabolite composition of three exotic sea slugs found in Greece that have most probably entered the Mediterranean basin by Lessepsian migration, an exchange that contributes significantly to Mediterranean biodiversity. We have found toxic compounds with significant activity as feeding deterrents both in the cephalaspidean
Haminoea cyanomarginata
and in the nudibranch
Melibe viridis
. These findings led us to propose aposematism in the former and dietary autonomy in producing defensive metabolites in the latter case, as predisposing factors to the migration. In the third mollusk investigated, the anaspidean
Syphonota geographica
, the topic of marine invasions has been approached through a study of its feeding biology. The identification of the same compounds from both the viscera of each individual, separately analyzed, and their food, the seagrass
Halophila stipulacea
, implies a dietary dependency. The survival of
S. geographica
in the Mediterranean seems to be related to the presence of
H. stipulacea
. The initial invasion of this exotic pest would seem to have paved the way for the subsequent invasion of a trophic specialist that takes advantage of niche opportunities.
Controlling the rates of biochemical reactions and signaling networks by shape and volume changes
Authors: Lizana L. , Bauer B. , Orwar O.
Published: March 2008

In biological systems, chemical activity takes place in micrometer- and nanometer-sized compartments that constantly change in shape and volume. These ever-changing cellular compartments embed chemical reactions, and we demonstrate that the rates of such incorporated reactions are directly affected by the ongoing shape reconfigurations. First, we show that the rate of product formation in an enzymatic reaction can be regulated by simple volume contraction–dilation transitions. The results suggest that mitochondria may regulate the dynamics of interior reaction pathways (e.g., the Krebs cycle) by volume changes. We then show the effect of shape changes on reactions occurring in more complex and structured systems by using biomimetic networks composed of micrometer-sized compartments joined together by nanotubes. Chemical activity was measured by implementing an enzymatic reaction–diffusion system. During ongoing reactions, the network connectivity is changed suddenly (similar to the dynamic tube formations found inside Golgi stacks, for example), and the effect on the reaction is registered. We show that spatiotemporal properties of the reaction–diffusion system are extremely sensitive to sudden changes in network topology and that chemical reactions can be initiated, or boosted, in certain nodes as a function of connectivity.
Size, foraging, and food web structure
Authors: Petchey Owen L. , Beckerman Andrew P. , Riede Jens O. , Warren Philip H.
Published: March 2008

Understanding what structures ecological communities is vital to answering questions about extinctions, environmental change, trophic cascades, and ecosystem functioning. Optimal foraging theory was conceived to increase such understanding by providing a framework with which to predict species interactions and resulting community structure. Here, we use an optimal foraging model and allometries of foraging variables to predict the structure of real food webs. The qualitative structure of the resulting model provides a more mechanistic basis for the phenomenological rules of previous models. Quantitative analyses show that the model predicts up to 65% of the links in real food webs. The deterministic nature of the model allows analysis of the model's successes and failures in predicting particular interactions. Predacious and herbivorous feeding interactions are better predicted than pathogenic, parasitoid, and parasitic interactions. Results also indicate that accurate prediction and modeling of some food webs will require incorporating traits other than body size and diet choice models specific to different types of feeding interaction. The model results support the hypothesis that individual behavior, subject to natural selection, determines individual diets and that food web structure is the sum of these individual decisions.
NFAR-1 and -2 modulate translation and are required for efficient host defense
Authors: Pfeifer Ingrid , Elsby Rachel , Fernandez Marilyn , Faria Paula A. , Nussenzveig Daniel R. , Lossos Izidor S. , Fontoura Beatriz M. A. , Martin W. David , Barber Glen N.
Published: March 2008

We report here that the alternatively spliced nuclear factors associated with double-stranded RNA, NFAR-1 (90 kDa) and -2 (110 kDa), are involved in retaining cellular transcripts in intranuclear foci and can regulate the export of mRNA to the cytoplasm. Furthermore, the NFAR proteins were found to remain associated with exported ribonucleoprotein complexes. Loss of NFAR function, which was embryonic-lethal, caused an increase in protein synthesis rates, an effect augmented by the presence of the mRNA export factors TAP, p15, or Rae1. Significantly, NFAR depletion in normal murine fibroblasts rendered these cells dramatically susceptible to vesicular stomatitis virus replication. Collectively, our data demonstrate that the NFARs exert influence on mRNA trafficking and the modulation of translation rates and may constitute an innate immune translational surveillance mechanism important in host defense countermeasures against virus infection.
Comparative lesion sequencing provides insights into tumor evolution
Authors: Jones Siân , Chen Wei-dong , Parmigiani Giovanni , Diehl Frank , Beerenwinkel Niko , Antal Tibor , Traulsen Arne , Nowak Martin A. , Siegel Christopher , Velculescu Victor E. , Kinzler Kenneth W. , Vogelstein Bert , Willis Joseph , Markowitz Sanford D.
Published: March 2008

We show that the times separating the birth of benign, invasive, and metastatic tumor cells can be determined by analysis of the mutations they have in common. When combined with prior clinical observations, these analyses suggest the following general conclusions about colorectal tumorigenesis: (
i
) It takes ≈17 years for a large benign tumor to evolve into an advanced cancer but <2 years for cells within that cancer to acquire the ability to metastasize; (
ii
) it requires few, if any, selective events to transform a highly invasive cancer cell into one with the capacity to metastasize; (
iii
) the process of cell culture
ex vivo
does not introduce new clonal mutations into colorectal tumor cell populations; and (
iv
) the rates at which point mutations develop in advanced cancers are similar to those of normal cells. These results have important implications for understanding human tumor pathogenesis, particularly those associated with metastasis.
Fluorescence resonance energy transfer in near-infrared fluorescent oligonucleotide probes for detecting protein–DNA interactions
Authors: Zhang Surong , Metelev Valeri , Tabatadze David , Zamecnik Paul C. , Bogdanov Alexei
Published: March 2008

Optical imaging in the near-infrared (NIR) range enables detecting ligand-receptor interactions and enzymatic activity
in vivo
due to lower scattering and absorption of NIR photons in the tissue. We designed and tested prototype NIR fluorescent oligodeoxyribonucleotide (ODN) reporters that can sense transcription factor NF-κB p50 protein binding. The reporter duplexes included donor NIR Cy5.5 indodicarbocyanine fluorochrome linked to the 3′ end of the first ODN and NIR acceptor fluorochromes (indodicarbocyanine Cy7 or, alternatively, a heptamethine cyanine IRDye 800CW) that were linked at the positions +8 and +12 to the complementary ODN that encoded p50 binding sites. Both Cy7 and 800CW fluorochromes were linked by using hydrophilic internucleoside phosphate linkers that enable interaction between the donor and the acceptor with no base-pairing interference. We observed efficient fluorescence resonance energy transfer (FRET) both in the case of Cy5.5–Cy7 and Cy5.5–800CW pairs of fluorochromes, which was sensitive to the relative position of the dyes. Higher FRET efficiency observed in the case of Cy5.5–Cy7 pair was due to a larger overlap between the ODN-linked Cy5.5 emission and Cy7 excitation spectra. Fluorescent mobility shift assay showed that the addition of human recombinant p50 to ODN duplexes resulted in p50 binding and measurable increase of Cy5.5 emission. In addition, p50 binding provided a concomitant protection of FRET effect from exonuclease-mediated hydrolysis. We conclude that NIR FRET effect can be potentially used for detecting protein–DNA interactions and that the feasibility of detection depends on FRET efficacy and relative fluorochrome positions within ODN binding sites.
Calculation of stochastic thermal transport due to resonant magnetic perturbations in DIII-D*
Authors: Joseph I. , Evans T.E. , Runov A.M. , Fenstermacher M.E. , Groth M. , Kasilov S.V. , Lasnier C.J. , Moyer R.A. , Porter G.D. , Schaffer M.J. , Schneider R. , Watkins J.G.
Published: March 2008

The effect of resonant magnetic perturbations on heat transport in DIII-D H-mode plasmas has been calculated by combining the TRIP3D field line tracing code with the E3D two-fluid transport code. Simulations show that the divertor heat flux distribution becomes non-axisymmetric because heat flux is efficiently guided to the divertor along the three-dimensional invariant manifolds of the magnetic field. Calculations demonstrate that heat flux is spread over a wider area of the divertor target, thereby reducing the peak heat flux delivered during steady-state operation. Filtered optical cameras have observed non-axisymmetric particle fluxes at the strike point and Langmuir probes have observed non-axisymmetric floating potentials. On the other hand, the predicted magnitude of stochastic thermal transport is too large to match the pedestal plasma profiles measured by Thomson scattering and charge exchange recombination spectroscopy. The Braginskii thermal conductivity overestimates the experimental heat transport in the pedestal because the mean free paths of both species are longer than estimates of the parallel thermal correlation lengths, and collisionless transport models are probably required for accurate description. However, even the collisionless estimates for electron thermal transport are too large by one to two orders of magnitude. Thus, it is likely that another mechanism such as rotational screening of resonant perturbations limits the stochastic region and reduces transport inside of the pedestal.
Geometric braid group action on derived categories of coherent sheaves
Authors: Riche Simon
Published: March 2008

In this paper we give, for semi-simple groups without factors of type

G

2

\mathbf {G}_2

, a geometric construction of a braid group action on

D

b

Coh
⁡
(

g

~

)

\mathcal {D}^b \operatorname {Coh}(\widetilde {\mathfrak {g}})

extending the action constructed by Bezrukavnikov, Mirković and Rumynin in the context of localization in positive characteristic. It follows that this action extends to characteristic zero, where it also has some nice representation-theoretic interpretations. The argument uses a presentation of the affine braid group analogous to the “Bernstein presentation” of the corresponding Hecke algebra (this presentation was suggested by Lusztig; it is worked out in the appendix, written jointly with Roman Bezrukavnikov).
Apical Accumulation of Rho in the Neural Plate Is Important for Neural Plate Cell Shape Change and Neural Tube Formation
Authors: Kinoshita Nagatoki , Sasai Noriaki , Misaki Kazuyo , Yonemura Shigenobu
Published: March 2008

Although Rho-GTPases are well-known regulators of cytoskeletal reorganization, their in vivo distribution and physiological functions have remained elusive. In this study, we found marked apical accumulation of Rho in developing chick embryos undergoing folding of the neural plate during neural tube formation, with similar accumulation of activated myosin II. The timing of accumulation and biochemical activation of both Rho and myosin II was coincident with the dynamics of neural tube formation. Inhibition of Rho disrupted its apical accumulation and led to defects in neural tube formation, with abnormal morphology of the neural plate. Continuous activation of Rho also altered neural tube formation. These results indicate that correct spatiotemporal regulation of Rho is essential for neural tube morphogenesis. Furthermore, we found that a key morphogenetic signaling pathway, the Wnt/PCP pathway, was implicated in the apical accumulation of Rho and regulation of cell shape in the neural plate, suggesting that this signal may be the spatiotemporal regulator of Rho in neural tube formation.
A pattern recognition approach to infer time-lagged genetic interactions
Authors: Chuang Cheng-Long , Jen Chih-Hung , Chen Chung-Ming , Shieh Grace S.
Published: March 2008

Motivation: For any time-course microarray data in which the gene interactions and the associated paired patterns are dependent, the proposed pattern recognition (PARE) approach can infer time-lagged genetic interactions, a challenging task due to the small number of time points and large number of genes. PARE utilizes a non-linear score to identify subclasses of gene pairs with different time lags. In each subclass, PARE extracts non-linear characteristics of paired gene-expression curves and learns weights of the decision score applying an optimization algorithm to microarray gene-expression data (MGED) of some known interactions, from biological experiments or published literature. Namely, PARE integrates both MGED and existing knowledge via machine learning, and subsequently predicts the other genetic interactions in the subclass.

Results: PARE, a time-lagged correlation approach and the latest advance in graphical Gaussian models were applied to predict 112 (132) pairs of TC/TD (transcriptional regulatory) interactions. Checked against qRT-PCR results (published literature), their true positive rates are 73% (77%), 46% (51%), and 52% (59%), respectively. The false positive rates of predicting TC and TD (AT and RT) interactions in the yeast genome are bounded by 13 and 10% (10 and 14%), respectively. Several predicted TC/TD interactions are shown to coincide with existing pathways involving Sgs1, Srs2 and Mus81. This reinforces the possibility of applying genetic interactions to predict pathways of protein complexes. Moreover, some experimentally testable gene interactions involving DNA repair are predicted.

Availability: Supplementary data and PARE software are available at http://www.stat.sinica.edu.tw/~gshieh/pare.htm.

Contact:  gshieh@stat.sinica.edu.tw
Tobacco Transcription Factors: Novel Insights into Transcriptional Regulation in the Solanaceae
Authors: Rushton Paul J. , Bokowiec Marta T. , Han Shengcheng , Zhang Hongbo , Brannock Jennifer F. , Chen Xianfeng , Laudeman Thomas W. , Timko Michael P.
Published: March 2008

Tobacco (Nicotiana tabacum) is a member of the Solanaceae, one of the agronomically most important groups of flowering plants. We have performed an in silico analysis of 1.15 million gene-space sequence reads from the tobacco nuclear genome and report the detailed analysis of more than 2,500 tobacco transcription factors (TFs). The tobacco genome contains at least one member of each of the 64 well-characterized TF families identified in sequenced vascular plant genomes, indicating that evolution of the Solanaceae was not associated with the gain or loss of TF families. However, we found notable differences between tobacco and non-Solanaceae species in TF family size and evidence for both tobacco- and Solanaceae-specific subfamily expansions. Compared with TF families from sequenced plant genomes, tobacco has a higher proportion of ERF/AP2, C2H2 zinc finger, homeodomain, GRF, TCP, zinc finger homeodomain, BES, and STERILE APETALA (SAP) genes and novel subfamilies of BES, C2H2 zinc finger, SAP, and NAC genes. The novel NAC subfamily, termed TNACS, appears restricted to the Solanaceae, as they are absent from currently sequenced plant genomes but present in tomato (Solanum lycopersicum), pepper (Capsicum annuum), and potato (Solanum tuberosum). They constitute approximately 25% of NAC genes in tobacco. Based on our phylogenetic studies, we predict that many of the more than 50 tobacco group IX ERF genes are involved in jasmonate responses. Consistent with this, over two-thirds of group IX ERF genes tested showed increased mRNA levels following jasmonate treatment. Our data are a major resource for the Solanaceae and fill a void in studies of TF families across the plant kingdom.
Surface morphology of sputtered Ta2O5thin films on Si substrates from X-ray reflectivity at a fixed angle
Authors: Lee Hsin-Yi , Huang Tzu-Wen , Lee Chih-Hao , Hsieh Yung-Wei
Published: March 2008

The temporal variation of the surface morphology of Ta2O5films on Si substrates has been measured using X-ray reflectivity at a fixed angle during radio-frequency magnetron sputtering. During an early stage of growth of polycrystalline Ta2O5, the variation of surface roughness revealed a morphology of island nucleation and island coalescence. For a thickness greater than 7 nm, the surface roughness increased, to more than 2 nm at a thickness of 80 nm. For crystalline Ta2O5films, the density of sputtered Ta2O5films increased and attained the bulk value for a film only at a thickness greater than 80 nm. For an amorphous sputtered film, the surface was less rough and the density was less than that for a crystalline film.
X-ray diffraction at constant penetration depth – a viable approach for characterizing steep residual stress gradients
Authors: Erbacher Thomas , Wanner Alexander , Beck Tilmann , Vöhringer Otmar
Published: March 2008

The experimental analysis of near-surface residual stresses by X-ray diffraction methods is based on measuring the spacings of lattice planes while the inclination ψ with respect to the surface plane is changed stepwise. A characteristic feature of conventional techniques is that the penetration depth of the X-rays is altered as inclination is varied. By simultaneously varying three different goniometer angles in a particular fashion, both the penetration depth and the measuring direction can be held constant while ψ is varied. Thus the normal and shear stresses can be derived from the sin2ψ plots by means of standard evaluation procedures developed for gradient-free stress states. The depth profile of residual stress is then obtainedviaLaplace transformation of the results from several stress measurements carried out at different penetration depths. In the present paper, the feasibility of this experimental approach for characterizing the strongly graded, non-equiaxed stress state existing at a machined surface is demonstrated. The results from constant-penetration-depth measurements on the ground surface of an engineering ceramic are compared with those from conventional sin2ψ measurements.
New measures of sharpness for symmetric powder diffraction peak profiles
Authors: Ida Takashi
Published: March 2008

New measures of sharpness for symmetric powder diffraction peak profiles are proposed. The sharpness parameter is defined through the \nuth-order moment of the Fourier transform of the profile function. Analytical expressions for the sharpness parameter for empirical model profile functions, namely the Gaussian, logistic distribution, hyperbolic secant, Lorentzian, Voigt, Pearson VII and pseudo-Voigt functions, and theoretical size-broadening profiles with statistical size distribution are presented. Theoretical diffraction profiles with complicated formulae can be approximated by empirical model functions assuming equivalent values of the sharpness parameter. The concept of the sharpness parameter provides a simple way to define an approximation for a theoretical diffraction peak profile with empirical model functions.
Molecular axes and planes as an Eigenvalue problem
Authors: Smilgies Detlef-M.
Published: March 2008

A statistical approach is used to define the long molecular axis and the main molecular plane. While the concept of molecular axis and plane is immediately useful for simple rod-like or planar molecules, it can be easily generalized to arbitrary molecules as well as molecular subgroups. From the molecular axes and planes, the orientation of the molecule with respect to the lattice as well as intermolecular orientations can be characterized. The method is applied for a comparison of pentacene andpara-quinquephenyl crystal structures.
Small-angle X-ray scattering study of intramuscular fish bone: collagen fibril superstructure determined from equidistant meridional reflections
Authors: Burger Christian , Zhou Hong-wen , Sicŝ Igors , Hsiao Benjamin S. , Chu Benjamin , Graham Lila , Glimcher Melvin J.
Published: March 2008

New insights into the bone collagen fibril superstructure have been obtained by novel small-angle X-ray scattering analysis. The analysis was carried out on the small-angle equidistant meridional reflections resulting from the periodic structure of collagen fibrils in their axial direction. Conventional two-dimensional analysis is difficult because of the large discrepancy of longitudinal and lateral length scales for individual fibrils, as well as their preferred orientation. The new approach represents an unapproximated analysis of the equidistant meridional reflections, which takes the exact separation of preferred orientation and fibril size effects into account. The analytical results (e.g.axial period, fibril diameteretc.) agree well with the parameters obtained from transmission electron microscopy.
Evaluation of the focusing performance of bent Laue crystals using wave-optical theory
Authors: Nesterets Ya. I. , Wilkins S. W.
Published: March 2008

Quantitative analysis of the focusing performance of bent Laue crystals is carried out using the rigorous wave-optical formalism.Vianumerical solution of the Takagi equations and the Fresnel integral, the influence of diffraction on the formation of the image of an X-ray source is analysed. The results are compared with those obtained using a formalism based on the geometrical optics approximation and significant differences are found. A formula for the geometrical aberration of a cylindrically bent crystal is derived. The effect of the aberration on image formation is analysed.
Quantitative characterization of the contrast mechanisms of ultra-small-angle X-ray scattering imaging
Authors: Zhang F. , Long G. G. , Levine L. E. , Ilavsky J. , Jemian P. R.
Published: March 2008

A general treatment of X-ray imaging contrast for ultra-small-angle X-ray scattering (USAXS) imaging is presented; this approach makes use of phase propagation and dynamical diffraction theory to account quantitatively for the intensity distribution at the detector plane. Simulated results from a model system of micrometre-sized spherical SiO2particles embedded in a polypropylene matrix show good agreement with experimental measurements. Simulations by means of a separate geometrical ray-tracing method also account for the features in the USAXS images and offer a complementary view of small-angle X-ray scattering as a contrast mechanism. The ray-tracing analysis indicates that refraction, in the form of Porod scattering, and, to a much lesser extent, X-ray reflection account for the USAXS imaging contrast.
Microcrystal screening with a novel design for beamline-mountable crystallization wells
Authors: Lunde Christopher S. , Rouhani Shahab , Remis Jonathan P. , Glaeser Robert M.
Published: March 2008

A simple and flexible system is described forin situscreening of microcrystals of membrane proteins that are grown within a connected-bilayer matrix formed by hydrated lipids. Using sheets of appropriate polymer materials to create a thin multiwell cassette, crystals can be evaluated by UV microscopy as well as by more conventional forms of light microscopy. Crystallization wells can be individually excised and mounted for diffraction screening on a synchrotron X-ray source. In addition, crystallization hit rates were significantly improved by employing a vapor diffusion approach rather than the batch crystallization method that is normally used with hydrated-lipid gels.
Evidence of stacking-fault distribution along an InAs nanowire using micro-focused coherent X-ray diffraction
Authors: Chamard Virginie , Stangl Julian , Labat Stephane , Mandl Bernhard , Lechner Rainer T. , Metzger Till H.
Published: March 2008

InAs nanowire samples grown by metal-organic chemical vapor deposition present a significant amount of wurtzite structure, while the zincblende lattice is known to be the stable crystal structure for the bulk material. The question of the wurtzite distribution in the sample is addressed using phase-sensitive coherent X-ray diffraction with a micro-focused beam at a synchrotron source. The simultaneous investigation of the wurtzite 10\bar{1}0, 20\bar{2}0 and 30\bar{3}0 reflections performed on a bunch of single wires shows unambiguously that the wurtzite contribution is a result of stacking faults distributed along the wire. Additional simulations lead to adjustments of the wire structural parameters, such as the wurtzite content, the strain distribution, the wire diameters and their respective orientations.
Ab initiostructure determination of a pharmaceutical compound, prednisolone succinate, from synchrotron powder data by combination of a genetic algorithm and the maximum entropy method
Authors: Nishibori Eiji , Ogura Tadakatsu , Aoyagi Shinobu , Sakata Makoto
Published: March 2008

The structure of a pharmaceutical compound, prednisolone succinate, has been determined by a newly developed analytical method forab initiostructure determination and refinements from X-ray powder data. It consists of a genetic algorithm (GA) for the structure determination process and the maximum entropy method (MEM), including its variations, for the structure refinement process. The crystal structure of prednisolone succinate has two molecules in the asymmetric unit and the total number of degrees of freedom is 25. In the structure refinement process, the various kinds of MEM analyses, such as difference MEM and omit MEM, in addition to ordinary MEM, play crucial roles in obtaining a better structural model. The data used in the present study were collected at BL02B2, SPring-8, which allowed the use of a wided-spacing range,d> 1.0 Å. The reliability factors,RwpandRI, of the final structure analysis by Rietveld refinement are less than 0.013 and 0.048, respectively. The structure determined in the present study gives noCHECKCIFalert relating to the fundamental structure, such as interatomic distances and bond angles, even in chemical bonds involving H atoms.
CAIROTEP:ORTEPIIIincorporatingCAIROfor better outputs
Authors: Lin Yun
Published: March 2008

CAIROTEPis a light-weight command-line utility for thermal ellipsoid plotting. It is based onORTEPIII(Version 1.03) and incorporates theCAIROgraphics rendering library as the plotting back-end. The current release ofCAIROTEPcan directly output molecular graphics in PNG, SVG, PDF and PostScript formats, and can potentially be extended to support a variety of output targets.CAIROTEPis mainly designed for integration into auto-processing projects to perform molecular graphics tasks (e.g.a Web publishing server for crystal data) and it is portable across all mainstream platforms.
Molecular envelopes derived from protein powder diffraction data
Authors: Wright Jonathan P. , Besnard Céline , Margiolaki Irene , Basso Sebastian , Camus Fabrice , Fitch Andrew N. , Fox Gavin C. , Pattison Philip , Schiltz Marc
Published: March 2008

The preparation of single crystals suitable for X-ray analysis is frequently the most difficult step in structural studies of proteins. With the aid of two examples, it is shown thatde novosolution of the crystallographic phase problem can be achieved at low resolution using microcrystalline powder samplesviathe single isomorphous replacement method. With synchrotron radiation and optimized instrumentation, high-quality powder patterns have been recorded, from which it was possible to generate phase information for structure factors up to 6 Å resolution. pH- and radiation-induced anisotropic lattice changes were exploited to reduce the problem of overlapping reflections, which is a major challenge in protein powder diffraction. The resulting data were of sufficient quality to compute molecular envelopes of the protein molecule and to map out the solvent channels in the crystals. The results show that protein powder diffraction can yield low-resolution data that are potentially useful for the characterization of microcrystalline proteins as novel micro- and mesoporous materials as well as for structural studies of biologically important macromolecules.
Modified design and use of a high-pressure environmental stage for laboratory X-ray powder diffractometers
Authors: Whitfield Pamela S. , Nawaby A. Victoria , Blak Brian , Ross James
Published: March 2008

The popularity of supercritical CO2for materials processing makes thein situstudy of pressures up to 10 MPa in the laboratory particularly interesting. This paper describes a modified design for a 12.4 MPa (1800 psi) variable-temperature pressure vessel based on an existing cell reported by Koster van Groos, Guggenheim & Cornell [Rev. Sci. Instrum.(2003),74, 273–275]. The modifications satisfied the demands of the American Society of Mechanical Engineers design code 31.3, leading to legal design registration, construction and subsequent hydrostatic test. The thinner windows that the finite element analysis indicated as sufficient allow for rapid data collection, even using a laboratory-based Mo source. This type of application is demonstrated with a time-resolved data set showing the crystallization of a polylactic acid–clay nanocomposite under 6.8 MPa CO2.
Convenient off-line error quantification and characterization of concentricity of two circles of rotation for diffractometer alignment
Authors: Cranswick L. M. D. , Donaberger R. , Swainson I. P. , Tun Z.
Published: March 2008

To ensure concentricity of the θ–2θ rotation stages, but with a very limited 2θ range of rotation, an alignment technique using two dial gauges mounted at right angles to each other (XandYaxes) is described. The deflections of the orthogonal dial gauges are measured as a function of 2θ, with their probes impinging on a cylindrical pin centred on the θ axis. TheXandYcorrections required to bring the two rotation stages into concentricity can then be found using a least-squares fittingviaa freestanding program orviathe `solver' optimization within the MicrosoftExcelspreadsheet software. The same dial gauges provide guidance for applying the required positional corrections. AnExcelspreadsheet for determining theXandYcorrectionsvialeast squares has been deposited.
Small-angle neutron scattering and the errors in protein structures that arise from uncorrected background and intermolecular interactions
Authors: Rubinson Kenneth A. , Stanley Christopher , Krueger Susan
Published: March 2008

Small-angle neutron scattering (SANS) provides a unique method to probe soft matter in the 10–100 nm length scale in solutions. In order to determine the shape and size of biological macromolecular structures correctly with SANS, a background-subtracted, undistorted scattering curve must be measured, and the required accuracy and precision is especially needed at the short-length-scale limit. A true scattering curve is also needed to discern whether intermolecular interactions are present, which also are probed in the SANS experiment. This article shows how to detect intermolecular interactions so that subsequent structure modeling can be performed using only data that do not contain such contributions. It is also shown how control of many factors can lead to an accurate baseline, or background, correction for scattering from proteins, especially to account for proton incoherent scattering. Failure to make this background correction properly from proteins, polymers, nucleic acids and lipids can result in incorrect values for the calculated shapes and sizes of the molecules as well as the derived magnitudes of the intermolecular interactions.
Patterns of species co‐occurrence and density compensation: a test for interspecific competition in bat ectoparasite infracommunities
Authors: Sebastián Tello J. , Stevens Richard D. , Dick Carl W.
Published: March 2008

Parasites constitute an ideal system with which to investigate patterns and mechanisms of community structure and dynamics. Nevertheless, despite their prevalence in natural systems, parasites have been examined less often than other organisms traditionally used for testing hypotheses of community assembly. In the present study, we investigate possible effects of competitive interactions on patterns of distribution (co‐occurrence) and density among a group of streblid bat flies parasitic on short‐tailed fruit bats, Carollia perspicillata. Using null model analyses of species co‐occurrence, we did not find evidence that competition affects the distribution of bat fly species across hosts. Moreover, when non‐infested hosts were included, analyses showed evidence for interspecific aggregation, rather than for the segregation predicted by competition theory. Partial Pearson correlations among bat fly species densities showed no evidence of negative covariation in two of three cases. In the species pair for which a significant negative correlation was found, a visual analysis of plotted covariation indicated a constraint line, suggesting that competition between these two species might become operational only in some infracommunities when abundances of bat flies approach a maximum set by one or more limiting resources. Moreover, when a community‐wide estimation of the significance of density compensation was calculated, the result was not significant. Overall, we find no evidence that competition influences the distribution of bat flies on their hosts, and mixed support for effects of competition on the densities of species. These results are consistent with the idea that competition plays a role in structuring natural communities, but in many systems its effects are context‐dependent and might not be important relative to other factors. Wider analyses across taxonomic and environmental gradients and a detailed consideration of the different hypothesized effects of competition are necessary to fully understand the importance of competition on natural communities.
Search and navigation in dynamic environments – from individual behaviors to population distributions
Authors: Mueller Thomas , Fagan William F.
Published: March 2008

Animal movement receives widespread attention within ecology and behavior. However, much research is restricted within isolated sub‐disciplines focusing on single phenomena such as navigation (e.g. homing behavior), search strategies (e.g. Levy flights) or theoretical considerations of optimal population dispersion (e.g. ideal free distribution). To help synthesize existing research, we outline a unifying conceptual framework that integrates individual‐level behaviors and population‐level spatial distributions with respect to spatio‐temporal resource dynamics. We distinguish among (1) non‐oriented movements based on diffusion and kinesis in response to proximate stimuli, (2) oriented movements utilizing perceptual cues of distant targets, and (3) memory mechanisms that assume prior knowledge of a target's location. Species’ use of these mechanisms depends on life‐history traits and resource dynamics, which together shape population‐level patterns. Resources with little spatial variability should facilitate sedentary ranges, whereas resources with predictable seasonal variation in spatial distributions should generate migratory patterns. A third pattern, ‘nomadism’, should emerge when resource distributions are unpredictable in both space and time. We summarize recent advances in analyses of animal trajectories and outline three major components on which future studies should focus: (1) integration across alternative movement mechanisms involving links between state variables and specific mechanisms, (2) consideration of dynamics in resource landscapes or environments that include resource gradients in predictability, variability, scale, and abundance, and finally (3) quantitative methods to distinguish among population distributions. We suggest that combining techniques such as evolutionary programming and pattern oriented modeling will help to build strong links between underlying movement mechanisms and broad‐scale population distributions.
Weighting against homoplasy improves phylogenetic analysis of morphological data sets
Authors: Goloboff Pablo A. , Carpenter James M. , Arias J. Salvador , Esquivel Daniel Rafael Miranda
Published: March 2008

The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are advanced. Characters that collectively determine few well‐supported groups may be highly reliable when taken individually (as shown by specific examples), so that inferring greater reliability for sets of characters that lead to an increase in jackknife frequencies may not always be warranted. But even if changes in jackknife frequencies can be used to infer reliability, we demonstrate that jackknife frequencies in large molecular data sets are actually improved when downweighting characters according to their homoplasy but using properly rescaled functions (instead of the very strong standard functions, or the extreme of inclusion/exclusion); this further weakens the argument that downweighting homoplastic characters is undesirable. Last, we show that downweighting characters according to their homoplasy (using standard homoplasy‐weighting methods) on 70 morphological data sets (with 50–170 taxa), produces clear increases in jackknife frequencies. The results obtained under homoplasy weighting also appear more stable than results under equal weights: adding either taxa or characters, when weighting against homoplasy, produced results more similar to original analyses (i.e., with larger numbers of groups that continue being supported after addition of taxa or characters), with similar or lower error rates (i.e., proportion of groups recovered that subsequently turn out to be incorrect). Therefore, the same argument that had been advanced against homoplasy weighting in the case of large molecular data sets is an argument in favor of such weighting in the case of morphological data sets.

© The Willi Hennig Society 2008.
Both CD4+ and CD8+ T cell epitopes fused to heat shock cognate protein 70 (hsc70) can function to eradicate tumors
Authors: Mizukami Shusaku , Kajiwara Chiaki , Ishikawa Hiroshi , Katayama Ichiro , Yui Katsuyuki , Udono Heiichiro
Published: March 2008

Vaccination with heat shock proteins (HSP) protects mice from challenge with the tumor from which the HSP were isolated. The antigenicity of HSP vaccination is thought to result from HSP‐associated endogenous major histocompatibility complex class I peptides or their precursors. The vaccination effect can be achieved in an adjuvant‐free manner and is mediated by CD8+ T cells, indicating that HSP can act as a natural adjuvant and cross‐prime T cells in vivo. We previously devised a recombinant vaccine composed of a CD8+ T cell epitope fused to the carboxyl‐terminus of hsc70 and demonstrated efficient generation of antigen‐specific cytotoxic T lymphocyte (CTL) after vaccination with a few micrograms of the hsc70‐CTL epitope fusion protein. The present study aimed to determine if the fusion protein vaccine could control tumor growth in vivo and whether simultaneous fusion of a CD4+ T cell epitope to the amino terminus of the hsc70‐CTL epitope would be a more potent vaccine compared to the CTL epitope alone. Ovalbumin (OVA)–derived 8 mer peptide, OVA257‐264, and 16mer peptide, OVA265‐280, were used as CD8+ and CD4+ T cell epitopes, respectively. Vaccination with hsc70‐OVA257‐264 generated peptide specific CTL more effectively than a peptide plus incomplete Freund's adjuvant combination, and suppressed growth of OVA expressing EL4 (E.G7) and B16 melanoma tumor cells. Addition of OVA265‐280 to the amino‐terminus of hsc70‐OVA257‐264 (OVA265‐280‐hsc70‐OVA257‐264) enhanced the generation of the OVA257‐264‐specific CTL population, leading to better eradication of MO5 lung metastasis compared to hsc70‐OVA257‐264. Our results suggest that fusion of both CD4+ and CD8+ T cell epitopes to hsc70 enhances tumor immunity beyond the effect of the CD8+ T cell epitope alone. (Cancer Sci 2008; 99: 1008–1015)
Alcohol outlet density and assault: a spatial analysis
Authors: Livingston Michael
Published: March 2008

Aims A large number of studies have found links between alcohol outlet densities and assault rates in local areas. This study tests a variety of specifications of this link, focusing in particular on the possibility of a non‐linear relationship.

Design Cross‐sectional data on police‐recorded assaults during high alcohol hours, liquor outlets and socio‐demographic characteristics were obtained for 223 postcodes in Melbourne, Australia. These data were used to construct a series of models testing the nature of the relationship between alcohol outlet density and assault, while controlling for socio‐demographic factors and spatial auto‐correlation. Four types of relationship were examined: a normal linear relationship between outlet density and assault, a non‐linear relationship with potential threshold or saturation densities, a relationship mediated by the socio‐economic status of the neighbourhood and a relationship which takes into account the effect of outlets in surrounding neighbourhoods.

Findings The model positing non‐linear relationships between outlet density and assaults was found to fit the data most effectively. An increasing accelerating effect for the density of hotel (pub) licences was found, suggesting a plausible upper limit for these licences in Melbourne postcodes.

Conclusions The study finds positive relationships between outlet density and assault rates and provides evidence that this relationship is non‐linear and thus has critical values at which licensing policy‐makers can impose density limits.