bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical characteristics and microstructure of ZnO quantum dots-SiO2 nanocomposite films prepared by sputtering methods
Authors: Peng Yu-Yun , Hsieh Tsung-Eong , Hsu Chia-Hung
Published: November 2006

ZnO quantum dots (QDs)-SiO2 nanocomposite films were prepared using the target-attached radio-frequency sputtering. The transmission electron microscopy revealed the uniform dispersion of ZnO QDs with diameters about 2–7nm in amorphous SiO2 matrix. The photoluminescence showed that small ZnO QDs are able to emit white light with luminescence spectra similar to those of the present GaN-based light emitting diode (LED). The calculated chromaticity coordinates of emitting light evidenced the feasibility of ZnO QDs-SiO2 nanocomposite films as the fluorescence material in optoelectronic devices.
Fast phase imaging in liquids using a rapid scan atomic force microscope
Authors: Uchihashi Takayuki , Ando Toshio , Yamashita Hayato
Published: November 2006

The authors report on fast phase imaging in liquids achieved by fast phase detection in rapid scan atomic force microscopy. The phase-shift images clearly revealed the compositional heterogeneities in styrene-butadiene-styrene block copolymer films even at an imaging rate of less than 100ms∕frame. They found that the contrast variations of the phase images depended on the phase-shift detection timing within a single oscillation cycle. The phase contrast increased as the tip approached the surface in each oscillation during imaging, while it decreased as the tip withdrew from the surface.
Nano- and microscale adhesion energy measurement for Au–Au contacts in microswitch structures
Authors: Zong Zong , Cao Yifang , Rahbar Nima , Soboyejo Wole
Published: November 2006

This paper presents a study of adhesion energies that are relevant to Au–Au microswitch contacts at the nano- and micronscales. Adhesion measurements are obtained from cantilevered Au microelectromechanical system (MEMS) microswitch structures with varying lengths. Scanning electron microscopy measurements of the microbeam profiles are combined with fracture mechanics model for the estimation of the adhesion energy. Adhesion contact and pull-off experiments are combined with theoretical models for the extraction of adhesion energies associated with Au-coated atomic force microscopy tips and Au microswitch substrates. Finite element method simulation was also performed to account for crack-tip shielding contributions from asperities in contact between Au–Au microscale cantilevered MEMS structure. The estimates of adhesion energies obtained for micron-scale contacts are shown to be in good agreement with those obtained for nanoscale contacts when appropriate “crack-tip shielding” corrections are used to account for the effects of the surface roughness of “crack-tip” shielding due to contact between micron-scale Au–Au surfaces.
Observation of enhanced efficiency in the excitation of ion-induced LiF:Mg,Ti thermoluminescent peaks
Authors: Massillon-JL G. , Gamboa-deBuen I. , Brandan M. E.
Published: November 2006

LiF:Mg,Ti thermoluminescent relative efficiency (RE), with respect to Co60 gammas, induced by H1, He3, C12, O16, and Ne20 has been measured as a function of linear energy transfer (LET) from 1.55to517keV∕μm. RE for high-temperature peaks are >1 (up to 20), displaying maxima at 20–300keV∕μm. RE for peaks 4 and 5 decreases monotonically from 1, with increasing LET. A correlation is observed between supralinearity in the gamma response and enhanced efficiency to ions. Katz track structure theory [J. J. Butts and R. Katz, Radiat. Res. 30, 865 (1967)] reproduces the main features of the ion data, though it overestimates RE for the lighter ions. The agreement of the model fits and the measurements does not permit the evaluation of “sensitive site” sizes. On the other hand, Horowitz modified track structure theory [J. Kalef-Ezra and Y. S. Horowitz, Int. J. Appl. Radiat. Isot. 33, 1085 (1982)] describes the global trends in the data, particularly the high efficiencies observed for the high temperature peaks if a Co60 supralinearity function is used in the model.
Enhancement factor distribution around a single surface-enhanced Raman scattering hot spot and its relation to single molecule detection
Authors: Le Ru E. C. , Etchegoin P. G. , Meyer M.
Published: November 2006

We provide the theoretical framework to understand the phenomenology and statistics of single molecule (SM) signals arising in surface enhanced Raman scattering (SERS) under the presence of so-called electromagnetic hot spots. We show that most characteristics of the SM-SERS phenomenon can be tracked down to the presence of a tail-like (power law) distribution of enhancements and we propose a specific model for it. We analyze, in the light of this, the phenomenology of SM-SERS and show how the different experimental manifestations of the effect reported in the literature can be analyzed and understood under a unified “universal” framework with a minimum set of parameters.
Infrared and Raman spectra of silica polymorphs from an ab initio parametrized polarizable force field
Authors: Liang Yunfeng , Miranda Caetano R. , Scandolo Sandro
Published: November 2006

The general aim of this study is to test the reliability of polarizable model potentials for the prediction of vibrational (infrared and Raman) spectra in highly anharmonic systems such as high temperature crystalline phases. By using an ab initio parametrized interatomic potential for SiO2 and molecular dynamics simulations, we calculate the infrared and Raman spectra for quartz, cristobalite, and stishovite at various thermodynamic conditions. The model is found to perform very well in the prediction of infrared spectra. Raman peak positions are also reproduced very well by the model; however, Raman intensities calculated by explicitly taking the derivative of the polarizability with respect to the atomic displacements are found to be in poorer agreement than intensities calculated using a parametrized “bond polarizability” model. Calculated spectra for the high temperature β phases, where the role of dynamical disorder and anharmonicities is predominant, are found to be in excellent agreement with experiments. For the octahedral phases, our simulations are able to reproduce changes in the Raman spectra across the rutile-to-CaCl2 transition around 50GPa, including the observed phonon softening.
Domainlike precursor clusters in the paraelectric phase of the uniaxial relaxor Sr0.61Ba0.39Nb2O6
Authors: Dec Jan , Shvartsman Vladimir V. , Kleemann Wolfgang
Published: November 2006

Dielectric spectra measured within 10−3Hz⩽f⩽104Hz in the paraelectric state of Sr0.61Ba0.39Nb2O6 (SBN61) at T>320K reveal a broadened Debye-type relaxation at f≈100Hz and a power-law low-f increase at f<10−1Hz. These anomalies are attributed to the dynamic modes wall segment relaxation and creep of the interfaces between polar nanoregions (PNRs) and paraelectric bulk. This structure is self-organized by the statistical distribution of quenched random fields due to the charge disorder of SBN61. The PNRs and their thermal evolution are visualized by piezoresponse microscopy.
Efficient surface plasmon field confinement in one-dimensional crystal line-defect waveguides
Authors: Weeber J.-C. , Baudrion A.-L. , Bouhelier A. , Bruyant A. , Colas des Francs G. , Zia R. , Dereux A.
Published: November 2006

The authors operate a near-field optical microscope to investigate surface plasmon polariton (SPP) propagation along linear waveguides opened into one-dimensional (1D) plasmonic crystals, i.e., crystals featuring a single lattice plane orientation. They show that efficient SPP field confinement can be achieved by this type of waveguide although no band gap exists in the direction perpendicular to the waveguide axis. From computed wave-vector diagrams, they show that 1D plasmonic crystals can open a wide range of prohibited propagation directions preventing from a significant coupling of the waveguide SPP modes with the crystal Bloch modes. Finally, the authors demonstrate that the field distributions of the guided SPP modes can be qualitatively understood from simple Ewald constructions.
Ferroelectric enhancement in heterostructured ZnO∕BiFeO3-PbTiO3 film
Authors: Yu Shengwen , Chen Rui , Zhang Guanjun , Cheng Jinrong , Meng Zhongyan
Published: November 2006

The authors have prepared heterostructured ZnO∕BiFeO3-PbTiO3 (BFO-PT) composite film and BFO-PT film on Pt∕Ti∕SiO2∕Si substrates by pulsed-laser deposition. The structure and morphologies of the films were characterized by x-ray diffraction (XRD) and scanning electron microscope. XRD results show that both films are perovskite structured last with different orientations. The leakage current density in the ZnO∕BFO-PT film was found to be nearly two orders of magnitude lower. This could be due to the introduced ZnO layer behaving as a Schottky barrier between the BFO-PT film and top electrodes. The dramatic ferroelectric enhancement in ZnO∕BFO-PT film is mostly ascribed to the improved insulation.
Non-Ohmic and dielectric properties of a Ca2Cu2Ti4O12 polycrystalline system
Authors: Ramírez M. A. , Bueno P. R. , Varela J. A. , Longo E.
Published: November 2006

An investigation was made into the non-Ohmic and dielectric properties of a Ca2Cu2Ti4O12 perovskite-type system. Compared to the traditional CaCu3Ti4O12-based composition, the imbalance between the Ca and Cu atoms caused the formation of a polycrystalline system presenting ∼33.3mol% of CaCu3Ti4O12 (traditional composition) and ∼66.7mol% of CaTiO3. As for non-Ohmic properties, the effect of this Ca and Cu atom imbalance was that a nonlinear electric behavior of ∼1500 was obtained. This high nonlinear electrical behavior emerged in detriment to the ultrahigh dielectric property frequently reported. The high non-Ohmic property was explained by the existence of Schottky-type barriers, whose formation mechanism may be similar to that proposed for traditional metal oxide non-Ohmic devices, according to similarities discussed herein.
Electron affinity of Li7
Authors: Pachucki Krzysztof , Komasa Jacek
Published: November 2006

Variationally optimized exponentially correlated Gaussian functions are employed to obtain nonrelativistic wave functions of the lithium atom and its negative ion. The energy levels are computed by means of the expansion in powers of the fine-structure constant α. The first term of this expansion corresponds to the nonrelativistic energy. The higher order terms represent the relativistic and radiative corrections and are determined by some effective Hamiltonians. Highly accurate expectation values of singular operators entering these Hamiltonians are computed using a set of expectation value identities. The resulting electron affinity of lithium atom 4984.96(18)cm−1 agrees very well with 4984.90(17)cm−1 of the latest measurements.
GaSb quantum-well-based “buffer-free” vertical light emitting diode monolithically embedded within a GaAs cavity incorporating interfacial misfit arrays
Authors: Mehta M. , Balakrishnan G. , Huang S. , Khoshakhlagh A. , Jallipalli A. , Patel P. , Kutty M. N. , Dawson L. R. , Huffaker D. L.
Published: November 2006

The authors demonstrate a monolithic, electrically injected, vertically emitting GaSb∕AlGaSb light emitting diode (LED) emitting at 1.6μm comprised of a hybrid GaAs∕GaSb-based structure. The LED is comprised of a GaSb∕AlGaSb quantum well/barrier active region embedded within high index contrast GaAs∕AlGaAs distributed Bragg reflectors (DBRs) using two interfacial misfit (IMF) arrays to relieve the strain induced from the high 8% lattice mismatch between the material systems. The first IMF is formed under compressive strain conditions to enable strain-free, defect-free deposition of GaSb active region directly on the lower GaAs∕AlAs DBRs without need for thick buffer. The second IMF is formed under tensile conditions to enable the upper GaAs∕AlAs DBRs on the GaSb active region. The device demonstrates a maximum output power of 3.5μW. Initial diode optical and electrical characteristics along with IMF band structure are discussed.
Molecular hydrogen formation in hydrogenated silicon nitride
Authors: Dekkers H. F. W. , Beaucarne G. , Hiller M. , Charifi H. , Slaoui A.
Published: November 2006

Hydrogen is released from hydrogenated silicon nitride (SiNx:H) during thermal treatments. The formation of molecular hydrogen (H2) in SiNx:H layers with low mass density is confirmed by Raman spectroscopy. However, no H2 is observed in layers with a high mass density despite clear evidence that hydrogen diffuses through those layers. Therefore hydrogen migrates in those layers in a different form. This is consistent with the observed improvement of the hydrogen passivation of silicon substrates using thermally treated high density SiNx:H antireflection coatings.
Percolation of polyatomic species with the presence of impurities
Authors: Cornette V. , Ramirez-Pastor A. J. , Nieto F.
Published: November 2006

In this paper, the percolation of (a) linear segments of size k and (b) k-mers of different structures and forms deposited on a square lattice contaminated with previously adsorbed impurities have been studied. The contaminated or diluted lattice is built by randomly selecting a fraction of the elements of the lattice (either bonds or sites) which are considered forbidden for deposition. Results are obtained by extensive use of finite size scaling theory. Thus, in order to test the universality of the phase transition occurring in the system, the numerical values of the critical exponents were determined. The characteristic parameters of the percolation problem are dependent not only on the form and structure of the k-mers but also on the properties of the lattice where they are deposited. A phase diagram separating a percolating from a nonpercolating region is determined as a function of the parameters of the problem. A comparison between random site and random bond percolation in the presence of impurities on the lattice is presented.
Low-Temperature Synthesis of Nearly Monodisperse ZnS Nanospheres Using a Facile Solution-Phase Approach
Authors: Wang Weizhi , Chen Liyong , Wang Shutao , Xi Baojuan , Xiong Shenglin , Qian Yitai , Zhang Zude
Published: November 2006

This paper describes a facile and controllable solution-phase process for the preparation of nearly monodisperse ZnS nanospheres, with an average diameter of 150 nm, at a low temperature (80°C). Thiourea is used both as a sulfur source and as a capping ligand which can direct initially formed ZnS particles to aggregate into nanospheres. The average diameter of ZnS nanospheres could be readily controlled by varying the reaction time. On the basis of the results of different reaction times and Fourier transform infrared (FT-IR) spectrum analysis, a possible aggregation mechanism to form ZnS nanospheres is proposed. The UV-vis absorption spectra of the obtained ZnS nanospheres exhibits an obvious blue shift due to the quantum confinement effect.
Dendritic compartmentalization of chloride cotransporters underlies directional responses of starburst amacrine cells in retina
Authors: Gavrikov Konstantin E. , Nilson James E. , Dmitriev Andrey V. , Zucker Charles L. , Mangel Stuart C.
Published: November 2006

The mechanisms in the retina that generate light responses selective for the direction of image motion remain unresolved. Recent evidence indicates that directionally selective light responses occur first in the retina in the dendrites of an interneuron, i.e., the starburst amacrine cell, and that these responses are highly sensitive to the activity of Na-K-2Cl (NKCC) and K-Cl (KCC), two types of chloride cotransporter that determine whether the neurotransmitter GABA depolarizes or hyperpolarizes neurons, respectively. We show here that selective blockade of the NKCC2 and KCC2 cotransporters located on starburst dendrites consistently hyperpolarized and depolarized the starburst cells, respectively, and greatly reduced or eliminated their directionally selective light responses. By mapping NKCC2 and KCC2 antibody staining on these dendrites, we further show that NKCC2 and KCC2 are preferentially located in the proximal and distal dendritic compartments, respectively. Finally, measurements of the GABA reversal potential in different starburst dendritic compartments indicate that the GABA reversal potential at the distal dendrite is more hyperpolarized than at the proximal dendrite due to KCC2 activity. These results thus demonstrate that the differential distribution of NKCC2 on the proximal dendrites and KCC2 on the distal dendrites of starburst cells results in a GABA-evoked depolarization and hyperpolarization at the NKCC2 and KCC2 compartments, respectively, and underlies the directionally selective light responses of the dendrites. The functional compartmentalization of interneuron dendrites may be an important means by which the nervous system encodes complex information at the subcellular level.
NMDA receptor surface mobility depends on NR2A-2B subunits
Authors: Groc Laurent , Heine Martin , Cousins Sarah L. , Stephenson F. Anne , Lounis Brahim , Cognet Laurent , Choquet Daniel
Published: November 2006

The NR2 subunit composition of NMDA receptors (NMDARs) varies during development, and this change is important in NMDAR-dependent signaling. In particular, synaptic NMDAR switch from containing mostly NR2B subunit to a mixture of NR2B and NR2A subunits. The pathways by which neurons differentially traffic NR2A- and NR2B-containing NMDARs are poorly understood. Using single-particle and -molecule approaches and specific antibodies directed against NR2A and NR2B extracellular epitopes, we investigated the surface mobility of native NR2A and NR2B subunits at the surface of cultured neurons. The surface mobility of NMDARs depends on the NR2 subunit subtype, with NR2A-containing NMDARs being more stable than NR2B-containing ones, and NR2A subunit overexpression stabilizes surface NR2B-containing NMDARs. The developmental change in the synaptic surface content of NR2A and NR2B subunits was correlated with a developmental change in the time spent by the subunits within synapses. This suggests that the switch in synaptic NMDAR subtypes depends on the regulation of the receptor surface trafficking.
Active retrotransposition by a synthetic L1 element in mice
Authors: An Wenfeng , Han Jeffrey S. , Wheelan Sarah J. , Davis Edward S. , Coombes Candice E. , Ye Ping , Triplett Christina , Boeke Jef D.
Published: November 2006

Long interspersed element type 1 (L1) retrotransposons are ubiquitous mammalian mobile elements and potential tools for
in vivo
mutagenesis; however, native L1 elements are relatively inactive in mice when introduced as transgenes. We have previously described a synthetic L1 element,
ORFeus
, containing two synonymously recoded ORFs relative to mouse L1. It is significantly more active for retrotransposition in cell culture than all native L1 elements tested. To study its activity
in vivo
, we developed a transgenic mouse model in which
ORFeus
expression was controlled by a constitutive heterologous promoter, and we established definitive evidence for
ORFeus
retrotransposition activity both in germ line and somatic tissues. Germ line retrotransposition frequencies resulting in 0.33 insertions per animal are seen among progeny of
ORFeus
donor element heterozygotes derived from a single founder, representing a >20-fold increase over native L1 elements. We observe somatic transposition events in 100% of the
ORFeus
donor-containing animals, and an average of 17 different insertions are easily recovered from each animal; modeling suggests that the number of somatic insertions per animal exceeds this number by perhaps several orders of magnitude. Nearly 200 insertions were precisely mapped, and their distribution in the mouse genome appears random relative to transcription units and guanine-cytosine content. The results suggest that
ORFeus
may be developed into useful tools for
in vivo
mutagenesis.
Crystal structure of π initiator protein–iteron complex of plasmid R6K: Implications for initiation of plasmid DNA replication
Authors: Swan Michael K. , Bastia Deepak , Davies Christopher
Published: November 2006

We have determined the crystal structure of a monomeric biologically active form of the π initiator protein of plasmid R6K as a complex with a single copy of its cognate DNA-binding site (iteron) at 3.1-Å resolution. The initiator belongs to the family of winged helix type of proteins. The structure reveals that the protein contacts the iteron DNA at two primary recognition helices, namely the C-terminal α4′ and the N-terminal α4 helices, that recognize the 5′ half and the 3′ half of the 22-bp iteron, respectively. The base-amino acid contacts are all located in α4′, whereas the α4 helix and its vicinity mainly contact the phosphate groups of the iteron. Mutational analyses show that the contacts of both recognition helices with DNA are necessary for iteron binding and replication initiation. Considerations of a large number of site-directed mutations reveal that two distinct regions, namely α2 and α5 and its vicinity, are required for DNA looping and initiator dimerization, respectively. Further analysis of mutant forms of π revealed the possible domain that interacts with the DnaB helicase. Thus, the structure–function analysis presented illuminates aspects of initiation mechanism of R6K and its control.
Epididymis-Specific Pathologic Disorders in Rats Exposed to Gossypol from Weaning Through Puberty
Authors: de Andrade Sérgio Faloni , Oliva Samara Urban , Klinefelter Gary Robert , De Grava Kempinas Wilma
Published: November 2006

Previous work in our laboratory revealed that the pubertal period of reproductive development in the male rat was particularly vulnerable to gossypol exposure, with a higher frequency of round structures in the lumen of the cauda epididymidis in the treated rats. Herein, we utilized hemicastration and electron microscopy to confirm that the epididymis is a definitive target of gossypol. Although exposure to gossypol from weaning through puberty caused a significant decrease in daily sperm production, as well as in the concentration of sperm in the epididymis, serum testosterone levels and reproductive organ weights were not altered. In gossypol treated rats, sperm morphology was compromised severely, but the epithelium in testis and epididymis appeared morphologically normal. Ultrastructural examination revealed that round structures, present only in gossypol exposed males, represented: (1) principal cells exfoliated from the epididymal epithelium; (2) epididymal epithelial cell cytoplasm containing degenerating sperm; and (3) degenerating epithelial cells, consisting of vesicles and particles of different sizes, forms and densities. Taken together, the data confirm that gossypol targets the epididymis, disturbing both the structure and function of this organ, and presumably disrupts sperm maturation.
Calpain Inhibition Attenuates iNOS Production and Midzonal Hepatic Necrosis in a Repeat Dose Model of Endotoxemia in Rats
Authors: Rose Robert , Banerjee Atrayee , Ramaiah Shashi K.
Published: November 2006

Systemic exposure to bacterial lipopolysaccharide (LPS, endotoxin) induces hypotension, disseminated intravascular coagulation and neutrophil infiltration in various organs including the lung, kidney and liver. A rat endotoxemic neutrophilic hepatitis model (repeat dose LPS, 10 mg/kg, i.v. 24 hours apart) was developed exhibiting hepatic neutrophil infiltration and mid-zonal hepatic necrosis. The goal of the study was to investigate the role of the intracellular enzyme calpain in the development of neutrophilic hepatitis with midzonal necrosis in this model. A second goal was to compare the observed protective effects of calpain inhibition with a relatively selective inducible nitric oxide synthase (iNOS) inhibitor aminoguanidine (AG) and an inhibitor of coagulation, heparin. When compared to rats administered LPS alone, administration of calpain 1 inhibitor prior to LPS significantly reduced hepatic iNOS expression, hepatic neutrophil infiltration and attenuated midzonal hepatic necrosis. Administration of AG or heparin prior to LPS also decreased liver iNOS expression, hepatic neutrophil infiltration and liver pathology comparable to calpain inhibition. Blood neutrophil activation, as measured by the neutrophil adhesion molecule CD11b integrin, was upregulated in all the LPS treated groups regardless of inhibitor administration. We conclude that amelioration of liver pathology via calpain inhibition is likely dependent on the down-regulation of iNOS expression in the rat model of LPS-mediated hepatitis.
Optimal Sampling of Rat Liver Tissue for Toxicogenomic Studies
Authors: Foley Julie F. , Collins Jennifer B. , Umbach David M. , Grissom Sherry , Boorman Gary A. , Heinloth Alexandra N.
Published: November 2006

Different degrees of a toxic response between and within the various lobes of the liver have been observed in rodents following treatment with acetaminophen. This study was designed to compare 2 sampling methods of the rat liver for gene-expression analysis. Ten male Fischer 344/N rats, 12–14 weeks of age, were treated with vehicle (0.5% aqueous ethyl cellulose) or acetaminophen (APAP, 1500 mg/kg) and sacrificed 24 hours following dose administration. Two representative sections were collected from the left liver lobe, stained with hematoxylin and eosin (H&E), and evaluated independently by 2 pathologists. The central core of the left lobe was cubed and frozen. Five random cubes were conserved, while the remaining left lobe core was pulverized. From each of the 10 animals, 2 random cubes and 2 samples from the homogeneous, pulverized samples were prepared for microarray analysis. Histopathologic evaluation revealed a variable response of centrilobular necrosis within the left lobe. Multiple methods used to analyze the microarray data indicated that sampling technique was not a major contributor to the variability observed in the gene expression data; however, only the powdered samples clustered for all animals, even those with disparate histopathologic results. Additionally, a powdered sample provided the advantages of a homogenous sample pool and the ability to use sample aliquots for other analyses to include proteomics, metabonomics, and other molecular techniques.
A framework for gene expression analysis
Authors: Schreiber Andreas W. , Baumann Ute
Published: November 2006

Motivation: Global gene expression measurements as obtained, for example, in microarray experiments can provide important clues to the underlying transcriptional control mechanisms and network structure of a biological cell. In the absence of a detailed understanding of this gene regulation, current attempts at classification of expression data rely on clustering and pattern recognition techniques employing ad-hoc similarity criteria. To improve this situation, a better understanding of the expected relationships between expression profiles of genes associated by biological function is required.

Results: It is shown that perturbation expansions familiar from biological systems theory make precise predictions for the types of relationships to be expected for expression profiles of biologically associated genes, even if the underlying biological factors responsible for this association are not known. Classification criteria are derived, most of which are not usually employed in clustering algorithms. The approach is illustrated by using the AtGenExpress Arabidopsis thaliana developmental expression map.

Contact:  andreas.schreiber@adelaide.edu.au

Supplementary information: Supplementary material is available at Bioinformatics online.
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
Authors: Emanuelsson Olof , Nagalakshmi Ugrappa , Zheng Deyou , Rozowsky Joel S. , Urban Alexander E. , Du Jiang , Lian Zheng , Stolc Viktor , Weissman Sherman , Snyder Michael , Gerstein Mark B.
Published: November 2006

Genomic tiling microarrays have become a popular tool for interrogating the transcriptional activity of large regions of the genome in an unbiased fashion. There are several key parameters associated with each tiling experiment (e.g., experimental protocols and genomic tiling density). Here, we assess the role of these parameters as they are manifest in different tiling-array platforms used for transcription mapping. First, we analyze how a number of published tiling-array experiments agree with established gene annotation on human chromosome 22. We observe that the transcription detected from high-density arrays correlates substantially better with annotation than that from other array types. Next, we analyze the transcription-mapping performance of the two main high-density oligonucleotide array platforms in the ENCODE regions of the human genome. We hybridize identical biological samples and develop several ways of scoring the arrays and segmenting the genome into transcribed and nontranscribed regions, with the aim of making the platforms most comparable to each other. Finally, we develop a platform comparison approach based on agreement with known annotation. Overall, we find that the performance improves with more data points per locus, coupled with statistical scoring approaches that properly take advantage of this, where this larger number of data points arises from higher genomic tiling density and the use of replicate arrays and mismatches. While we do find significant differences in the performance of the two high-density platforms, we also find that they complement each other to some extent. Finally, our experiments reveal a significant amount of novel transcription outside of known genes, and an appreciable sample of this was validated by independent experiments.
The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus
Authors: Takeda Hiroshi , Toyooka Takashi , Ikeuchi Yoshiho , Yokobori Shin‐ichi , Okadome Kan , Takano Fuyumi , Oshima Tairo , Suzuki Tsutomu , Endo Yaeta , Hori Hiroyuki
Published: November 2006

Transfer RNA (m1G37) methyltransferase (TrmD) catalyzes methyl‐transfer from S‐adenosyl‐L‐methionine to the N1 atom of G37 in tRNA. In Escherichia coli cells, TrmD methylates tRNA species possessing a G36G37 sequence. It was previously believed that G36 was the positive determinant of TrmD recognition. In the current study, we demonstrate that TrmD from Aquifex aeolicus methylates tRNA transcripts possessing an A36G37 sequence as well as tRNA transcripts possessing a G36G37 sequence. In contrast, tRNA transcripts possessing pyrimidine36G37 were not methylated at all. These substrate specificities were confirmed by an in vitro kinetic assay using 16 tRNA transcripts. The modified nucleoside and the position in yeast tRNAPhe transcript were confirmed by LC/MS. Furthermore, nine truncated tRNA molecules were tested to clarify the additional recognition site. Unexpectedly, A. aeolicus TrmD protein efficiently methylated the micro helix corresponding to the anti‐codon arm. Because the disruption of the anti‐codon stem caused the complete loss of the methyl group acceptance activity, the anti‐codon stem is essential for the recognition. Moreover, the existence of the D‐arm structure inhibited the activity. Recently, it was reported that E. coli TrmD methylates yeast tRNAPhe harboring a sequence A36G37. Thus, recognition of the purine36G37 sequence is probably common to eubacteria TrmD proteins.
Compomers in restorative therapy of children: a literature review
Authors: KRÄMER NORBERT , FRANKENBERGER ROLAND
Published: November 2006

Objective.  The restoration of carious primary teeth plays an underestimated role in paediatric dentistry. This is astonishing for many reasons, not least because many new materials have been introduced in recent years. New or modified techniques and materials, with better aesthetics and flexural properties, allow minimally invasive treatment. A transfer of techniques between different dentitions, however, may be problematic because of both micromorphological differences and compliance. Therefore, this paper deals with options for restoring primary teeth and the early stages of the mixed dentition using polyacid‐modified composites, the so‐called compomers.

Methods.  Medline and Embase were scanned from 1990 through 2006. Furthermore, a hand‐search of nonlisted but peer‐reviewed papers was performed. The search items were compomer*, dent*, primary* and deciduous*, which identified 109 relevant publications.

Conclusions.  Based on high clinical success rates, compomers are now an effective alternative to other materials for restorative therapy in the anterior and posterior primary teeth. A minimum amount of compliance is still mandatory in order to allow for a few minutes of adhesive pretreatment and layering without contamination. If this is not the case, compomers make no sense. Stainless steel crowns are still the most effective from of restoration for severely decayed primary molars.
Wildland fire effects on forest structure over an altitudinal gradient, Grand Canyon National Park, USA
Authors: FULÉ PETER Z. , LAUGHLIN DANIEL C.
Published: November 2006

Restoration of wildland fire to forests is a challenge when historical fire regimes have been altered. We studied four fires that burned over approximately 7865 ha on an altitudinal gradient in Grand Canyon National Park, USA, in 2003. The fires met criteria for the current USA policy allowing the restoration of fire's ecological role in forest landscapes: Wildland Fire Use for Resource Benefits.

After the fires burned out, we remeasured 82 permanent pre‐established monitoring plots burned by the fires plus 43 additional plots on unburned companion sites.

The maximum height of charring of tree boles and basal area mortality increased in mean value and variability with altitude. At a low‐altitudePinus–Quercussite, tree density declined significantly but basal area was unchanged. At a mid‐altitude mixed‐conifer site and a high‐altitudePicea/Abies/Populussite, both density and basal area declined.

The thinning effect of fire was concentrated on smaller, shorter, fire‐susceptible trees. Small‐diameter trees (< 20 cm diameter) made up 79–95% of all tree mortality. Shade‐tolerant conifers, particularly true firs and spruce, experienced disproportionate mortality (31–82% basal area decline), while fire‐resistant ponderosa pine and Douglas fir tended to survive (2–8% basal area decline). Delayed mortality between the first and second years following the fires accounted for only 4·2% of trees dying at the low‐altitude site but 15·6% and 11·2% at the mid‐ and high‐altitude sites, respectively. Regeneration density was highly variable but forest floor and woody debris declined in burned areas.

Synthesis and applications.This study shows that, even after an unusually long fire‐free period (1880–2003), at the mid‐ and high‐altitude burned sites fire effects were consistent with restoration of historical patterns, moving the ecosystems closer to historical reference conditions. Fires simultaneously reduced the living, dead and ladder fuels that made the forest vulnerable to uncharacteristically severe fire. These effects make the forests more resistant to the expected increases in fire size and severity under future climate conditions. Even at longer‐than‐historical fire intervals, the wildland fire use policy can benefit Grand Canyon forests.
Horn growth rate and longevity: implications for natural and artificial selection in thinhorn sheep (Ovis dalli)
Authors: LOEHR J. , CAREY J. , HOEFS M. , SUHONEN J. , YLÖNEN H.
Published: November 2006

We used horn measurements from natural and hunted mortalities of male thinhorn sheep Ovis dalli from Yukon Territory, Canada, to examine the relationship between rapid growth early in life and longevity. We found that rapid growth was associated with reduced longevity for sheep aged 5 years and older for both the hunted and natural mortality data sets. The negative relationship between growth rate and longevity in hunted sheep can at least partially be explained by morphologically biased hunting regulations. The same trend was evident from natural mortalities from populations that were not hunted or underwent very limited hunting, suggesting a naturally imposed mortality cost directly or indirectly associated with rapid growth. Age and growth rate were both positively associated with horn size at death for both data sets, however of the two growth rate appeared to be a better predictor. Large horn size can be achieved both by individuals that grow horns rapidly and by those that have greater longevity, and the trade‐off between growth rate and longevity could limit horn size evolution in this species. The similarity in the relationship between growth rate and longevity for hunted and natural mortalities suggests that horn growth rate should not respond to artificial selection. Our study highlights the need for the existence and study of protected populations to properly assess the impacts of selective harvesting.
Psoriasis in childhood and adolescence: evaluation of demographic and clinical features
Authors: SEYHAN MUAMMER , COŞKUN BAŞAK KANDI , SAĞLAM HÜLYA , ÖZCAN HAMDI , KARINCAOĞLU YELDA
Published: November 2006

Background: The present study was aimed to define the gender ratio, familial occurrence, age of onset, precipitating factors, clinical types, nail and joint involvement of psoriasis in childhood and adolescence in Turkey.

Methods: A total of 61 children with psoriasis under 18 years old were evaluated retrospectively, for age, gender, age of disease onset, family history, concomitant disease, the clinical type of psoriasis, clinical localization, nail and joint involvement and treatment modalities.

Results: Of the patients, 23 (37.70%) were boys and 38 (62.30%) were girls. Mean age was 9.28 ± 4.02 years in girls and 11.18 ± 3.85 years in boys (9.96 ± 4.03 years in all children). Mean age at the onset of the disease was 6.81 ± 4.11 years in girls and 7.03 ± 4.28 years in boys (6.89 ± 4.14 years in all patients). In 14 (23%) cases, a positive family history was detected. The most frequent probable triggering factors were upper respiratory tract infections (14.8%) and positive throat culture for A group ß‐hemolytic streptococcus (21.3%). Frequency of emotional stress and psychiatric morbidity were 54% and 9.8%, respectively. The most frequent localizations at onset were trunk (44.3%), extremities (54.0%), and scalp (36.0%). Three children (4.9%) had a history of dissemination from psoriatic diaper rash. In total, 51 (83.6%) patients presented with psoriasis vulgaris, eight (13.1%) with generalized pustular psoriasis, and the remaining two (3.3%) with erythrodermic psoriasis.

Conclusion: The incidence of psoriasis among dermatological patients in childhood and adolescence was 3.8%. The disease tends to appear earlier in girls than boys. The authors suggested that stress and upper respiratory infections are the most important triggering factors in childhood and adolescence psoriasis.
Prediction of transfusions in extremely low‐birthweight infants in the erythropoietin era
Authors: HOSONO SHIGEHARU , MUGISHIMA HIDEO , SHIMADA MASAMI , MINATO MICHIYOSHI , OKADA TOMO , TAKAHASHI SHIGERU , HARADA KENSUKE
Published: November 2006

Background: The purpose of the present paper was to detect the clinical factors most predictive of red blood cell (RBC) transfusion in extremely low‐birthweight (ELBW) infants in the recombinant human erythropoietin era.

Methods: Between 1995 and 2000, 66 ELBW infants were admitted to a level III neonatal intensive care unit. Fifty‐four of 66 infants were eligible for enrollment in the present study. Infants were treated with erythropoietin 200 IU/kg per dose s.c. twice a week with 4–6 mg/kg per day iron supplement.

Results: The mean gestational age and birthweight were 26.5 ± 2.1 weeks and 776 ± 134 g, respectively. Ten of 54 ELBW infants (18.5%) died during the first 21 days. Eight of 10 dead infants (80.0%) and 27 of 44 surviving infants (61.4%) received one or more RBC transfusions. The overall requirement for RBC transfusions in the surviving infants was 3.0 ± 3.2 per infant/hospital course (range: 0–9) . There were significant differences in gestational weeks, birthweight, initial hemoglobin value, 5 min Apgar score, phlebotomy loss, phlebotomy loss/birthweight, duration of mechanical ventilation, duration of oxygen supplement, and incidence of both intraventricular hemorrhage and chronic lung disease between the transfused and non‐transfused group. The predictive variables, initial hemoglobin level (odds ratio [OR] 2.61; 1 g/dL), birthweight (OR 3.00; 100 g), and gestational week (OR 1.89; 1 week), were found to be most predictive for transfusion on logistic regression analysis.

Conclusion: ELBW infants are still the population at greatest risk for repeated blood transfusions after introduction of erythropoietin treatment. If labor develops, it is often impossible to extend the pregnancy period, therefore efforts should be made to increase hemoglobin level at birth.
Sandifer Syndrome: A continuing problem of misdiagnosis
Authors: KABAKUŞ NIMET , KURT ABDULLAH
Published: November 2006

Background:Sandifer Syndrome is an uncommon clinical entity characterized by gastroesophageal reflux, irritability and abnormal movements of the body and contortions of the neck. The majority of paroxysmal cases, in particular, tend to show an association with epilepsy.

Methods:The clinical, laboratory and 6‐month observation results of the four patients (two boys, two girls) have been presented.

Results:The 6‐month prospective observation/treatment of four patients aged between 2 and 14 months (mean age, 6.5 ± 5.2 months) with a diagnosis of Sandifer Syndrome has been investigated. Due to paroxysmal extensor jerks, two of the patients were misdiagnosed with infantile spasm and they were treated accordingly. In the clinical observations of the patients, abnormal neurobehavioral attacks (irritability, crying, head/eye version, torticollis, extensor spasm and dystonic posture) 5–10 times daily were observed. In two of the patients, motor growth retardation was observed, in one patient, bronchospasm attacks were observed, and in all the patients iron deficiency anemia was observed. The electroencephalograms of the patients which were taken during the routine, sleepless and paroxysmal behaviors were normal; the gastroesophageal scintigraphies were positive in the manner of reflux. Management of the infant with gastroesophageal reflux disease, in addition to nonpharmacological interventions pharmacologic therapy, including metoclopramide HCl and Fe (6 mg/kg per day, oral) was useful for the patients, and their paroxysmal attacks decreased dramatically (0–2 attacks/day).

Conclusion:These findings suggest that infants or children with these atypical movements should be evaluated for Sandifer Syndrome. Expensive and comprehensive neurologic examination may be unnecessary. Early diagnosis permits prompt treatment and relief of the problem. Medical management is usually successful.
Second Meeting of the International Society for Phylogenetic Nomenclature: a Report
Authors: Laurin Michel , Cantino Philip D.
Published: November 2006

The Second Meeting of the International Society for Phylogenetic Nomenclature (ISPN) convened at Yale University in New Haven from June 28 to July 2, 2006. In addition to contributed talks, the conference included symposia on phylogenetic nomenclature of species, phyloinformatics, and implementing phylogenetic nomenclature. Other discussion focused on recent controversial additions to the draft PhyloCode concerning the choice of names for total clades, and the Committee on Phylogenetic Nomenclature (CPN) was encouraged to revisit this issue. A proposal to permit emendation of phylogenetic definitions without CPN approval under certain circumstances was well received, and there was wide support for a proposed mechanism to use Linnaean binomina in the context of phylogenetic nomenclature without extending the PhyloCode to govern species names. The ISPN Council voted to expand the CPN from 9 to 12 members.
We Value What Values Us: The Appeal of Identity‐Affirming Science
Authors: Morton Thomas A. , Haslam S. Alexander , Postmes Tom , Ryan Michelle K.
Published: November 2006

Members of the public (Study 1; n = 184) and university students (Study 2; n = 101) evaluated a piece of research and indicated their support for its continuation. The research findings were held constant, but the methods that revealed those findings were attributed to either neuroscience or social science, and the conclusions based on those findings were biased either in favor of men or in favor of women. Study 1 revealed that participants were more positive about research that affirmed their gender identity and that was based on neuroscience rather than social science. Study 2 found this pattern to be apparent in more specialist samples. Indeed, participants with some scientific training were more influenced by research that affirmed the reader's gender identity. Participants with less scientific training, in comparison, were more influenced by the type of science described when making judgments about the value of the research. Contrary to popular claims, this suggests that scientific knowledge alone is no protection against the effects of bias on research evaluation. Implications for the practice and popularization of science are discussed.
The Sense of Divine Control and Psychological Distress: Variations Across Race and Socioeconomic Status
Authors: SCHIEMAN SCOTT , PUDROVSKA TETYANA , PEARLIN LEONARD I. , ELLISON CHRISTOPHER G.
Published: November 2006

This study examines race and socioeconomic status (SES) differences in levels of the sense of divine control and its association with psychological distress. Using data from adults aged 65 and older in the District of Columbia and two adjoining counties in Maryland, we document that levels of the sense of divine control are highest among African Americans and individuals of low SES. Although the association between SES and perceived divine control is more negative among whites net of statistical adjustments for other indicators of religiosity and stressors, these conditions contribute modestly to the race × SES interaction effect. In addition, the sense of divine control is associated negatively with distress among low‐SES African Americans and positively with distress among low‐SES white elders. These patterns remain stable net of other forms of religiosity, an array of stressors, and the personal resources of the sense of mastery and self‐esteem. Our findings elaborate on social stratification differences in religiosity and their different associations with well‐being.
Whether to Adopt Statements on Homosexuality in Two Denominations: A Research Note
Authors: DJUPE PAUL A. , OLSON LAURA R. , GILBERT CHRISTOPHER P.
Published: November 2006

Some of the most contentious issues in American religion today concern homosexuality. In 1998, we asked 2,300 clergy in the Evangelical Lutheran Church in America (ELCA) and the Episcopal Church whether their denomination should adopt official statements on homosexuality. A year later, we asked the same question of 1,600 church members in 60 of those clergy's congregations. In this research note, we analyze the attitudes of clergy and church members about beginning the process to compose formal denominational statements on homosexuality. We find great differences between the two denominations, reflecting established conflict in the Episcopal Church and a lack thereof in the ELCA. The attitudes of both clergy and church members, shaped by denominational context, reflect their general attitudes toward gay rights and the public involvement of the denomination. Clergy exhibit particular concern about how a denominational statement might affect their own congregation, and church members take significant cues from their clergy.