bluuebunny/crossref_metadata_2025 huggingface dataset:
Manipulation of tunneling frequencies using magnetic fields for resonant tunneling effects of surface plasmons
Authors: Lan Yung-Chiang , Chang Yun-Chorng , Lee Peng-Hsiao
Published: April 2007

This work investigates the manipulation of terahertz surface plasmons (SPs) on a semiconductor surface by applying an external static magnetic field. The dispersion relations of the coupled surface magnetoplasmon under the Voigt configuration in the semiconductor-insulator-semiconductor structure are derived. For a TM-polarized wave that is normally incident onto a semiconductor film with periodic narrow grooves on both surfaces, the applied external static magnetic field with the Voigt configuration redshifts the frequencies of the SP-induced resonant tunneling. This phenomenon is attributable to the reduction in the effective plasma frequency by the applied magnetic field.
Detection of charge states in nanowire quantum dots using a quantum point contact
Authors: Wallin D. , Fuhrer A. , Fröberg L. E. , Samuelson L. , Xu H. Q. , Hofling S. , Forchel A.
Published: April 2007

The authors demonstrate operation of a charge readout scheme for quantum dots in a semiconductor nanowire using a quantum point contact defined in a GaAs∕AlGaAs two-dimensional electron gas beneath the nanowire. The quantum dots were fabricated by epitaxial growth of InP barriers along a n-type InAs nanowire. Applying negative voltages to two split-gate electrodes aligned to the nanowire induces a quantum point contact in the two-dimensional electron gas such that charging of quantum dots in the nanowire modulates the quantum point contact transmission, thus resulting in the desired detector response.
Single-frequency active Q-switched distributed fiber laser using acoustic waves
Authors: Delgado-Pinar Martina , Díez Antonio , Cruz José Luis , Andrés Miguel V.
Published: April 2007

This letter presents a single mode, actively Q-switched distributed feedback fiber laser. Acoustic pulses are launched into an erbium-doped fiber Bragg grating, resulting in the introduction of a traveling defect. Thus, a transmission peak appears in the reflection band while the pulse travels along the grating. This effect allows the laser to operate in a Q-switched regime, providing optical pulses which repetition rate was continuously tuned up to 10kHz. Pulses of 168mW of peak power and 73ns of temporal width were obtained at low repetition rate.
Phase transformation in BiNbO4 ceramics
Authors: Zhou Di , Wang Hong , Yao Xi , Wei Xiaoyong , Xiang Feng , Pang Lixia
Published: April 2007

Phase transformation from β-BiNbO4 to α-BiNbO4 in BiNbO4 bulk samples was studied. From x-ray diffraction patterns, the transformation from β to α phase of BiNbO4 could be observed by heating the bulk samples of β-BiNbO4 from low temperatures to 700–1030°C. Such a transformation did not occur in powder samples and in the cooling course. This phenomenon might be related with associated activation of stress and heat energy in the heating course. Differential thermal analysis, shrinkage, and dielectric properties as a function of temperature were carried out, and all the results confirmed the transformation from β to α phase of BiNbO4.
Nonlinear photoinduced anisotropy and modifiable optical image display in a bacteriorhodopsin/polymer composite film
Authors: Wei Lai , Luo Jia , Zhu Jiang , Lu Ming , Zhao You-yuan , Ma De-wang , Ding Jian-dong
Published: April 2007

The nonlinear photoinduced anisotropy with large birefringence in a bacteriorhodopsin/polymer composite (bR/PC) film was observed. The contrast ratio, a ratio of the maximum to the minimum intensity of transmitted probe light through the bR/PC film within the linear gray scale range could reach ∼350:1. An all-optical image display in different colors was performed. The intensity of the transmitted signal could be modulated by adjusting the multibeam polarization states and intensities. Therefore, the positive image, negative image, and image erasure in display were demonstrated.
Fast switching of polymer-stabilized liquid crystal pi cells
Authors: Huang Chi Yen , Fung Ri Xin , Lin Ying Ging , Hsieh Chia Ting
Published: April 2007

This work demonstrates a dual-frequency polymer-stabilized liquid crystal pi cell with zero bias and a short response time. The high curing voltage and low curing intensity give the cell a low dark state and a high bright state, such that the transmittance against the applied voltage curve is steep. The response time is under 1ms and is independent of monomer concentration because a strong electric torque is exerted on the liquid crystals. The cell is useful in field-sequential color systems, and the low operating voltage of ∼5V makes the cell compatible with conventional thin film transistor driving voltages.
Distributed Bragg reflector laser using buried SiO2 grating and self-aligned band gap tuning
Authors: Teng J. H. , Dong J. R. , Chua S. J. , Foo B. S. , Lai M. Y. , Wang Y. J. , Ang S. S. , Yin R.
Published: April 2007

The authors report a technology to make a distributed Bragg reflector laser with buried dielectric grating and band gap tuned reflector region. The Bragg reflector is constructed by high coupling coefficient gratings made of SiO2 and InP. The band gap of the reflector is blueshifted by self-aligned quantum well intermixing using the buried SiO2 grating itself. The photoluminescence peak wavelength can be shifted by ∼45meV for the quantum well sample covered by SiO2 grating compared to thermal shift only at annealing temperature of 800°C for 100s. The enhanced interdiffusion is caused by the P vacancies generated at SiO2 and InP interfaces as proved by secondary ion mass spectroscopy.
Transient optoelastography in optically diffusive media
Authors: Bossy Emmanuel , Funke Arik R. , Daoudi Khalid , Boccara Albert-Claude , Tanter Mickael , Fink Mathias
Published: April 2007

The authors present a camera-based optical detection scheme designed to detect the transient motion created by the acoustic radiation force in soft elastic media. An optically diffusive tissue-mimicking phantom was illuminated with coherent laser light, and a high speed camera (2kHz frame rate) was used to acquire and cross-correlate consecutive speckle patterns. Time-resolved transient decorrelation of the optical speckle was measured as the result of localized motion induced by the radiation force and the associated propagating shear waves. The proposed technique is sensitive only to the low frequency transient motion induced in the medium by the radiation force.
Synthesizing tungsten oxide nanowires by a thermal evaporation method
Authors: Hong Kunquan , Xie Maohai , Hu Rong , Wu Huasheng
Published: April 2007

Tungsten oxide W18O49 nanowires with diameters of 10–20nm were synthesized with high yield by thermal evaporation in a tube furnace. By heating tungsten trioxide powder at 900°C in vacuum (5×10−3torr), W18O49 nanowires with diameters of 10–20nm and lengths up to micrometers were produced with high yield on the Au-coated Si substrates located in the low temperature zone (550–600°C) of the furnace. The morphology, composition, and crystal structure of the nanowires were characterized by various methods. The conditions and the mechanism of W18O49 nanowire growth are discussed.
Role of atomic nitrogen during GaN growth by plasma-assisted molecular beam epitaxy revealed by appearance mass spectrometry
Authors: Osaka J. , Senthil Kumar M. , Toyoda H. , Ishijima T. , Sugai H. , Mizutani T.
Published: April 2007

To identify the species which contribute to GaN growth, the authors investigated the discharge parameter (0.3–4.8SCCM (SCCM denotes cubic centimeter per minute at STP), 150–400W) dependences of the atomic N flux by appearance mass spectrometry and of the incorporated nitrogen atoms into GaN layers grown by plasma-assisted molecular beam epitaxy (PAMBE) using the rf-plasma source. Ion fluxes were also evaluated by ion current measurements. A good correlation between the supplied atomic N flux and the incorporated nitrogen flux was obtained under a wide range of plasma conditions. It was clarified that the atomic N plays a dominant role in the growth of GaN by PAMBE.
3,5-Dinitrosalicylic Acid in Molecular Assembly. III. Proton-Transfer Compounds of 3,5-Dinitrosalicylic Acid with Polycyclic Aromatic and Heteroaromatic Amines, and Overall Series Structural Systematics
Authors: Smith Graham , Wermuth Urs D. , Healy Peter C. , White Jonathan M.
Published: April 2007

The crystal structures of the 1:1 proton-transfer compounds of 3,5-dinitrosalicylic acid (dnsa) with a series of common polycyclic aromatic and heteroaromatic amines (quinoline, 1-naphthylamine, 1,2,3,4-tetrahydroquinoline, quinaldic acid, benzimidazole, 1,10-phenanthroline, and 2,2′-bipyridine) have been determined and the hydrogen-bonding associations in each analyzed. The compounds are [(C9H8N)+(dnsa)–] 1, [(C10H10N)+(dnsa)–] 2, [(C9H12N)+(dnsa)–] 3, [(C10H8NO2)+(dnsa)–] 4, [(C7H7N2)+(dnsa)–] 5, [(C12H9N2)+(dnsa)–] 6, and [(C10H9N2)+(dnsa)–] 7. In all compounds, protonation of either the substituent amino group or the hetero-N of the Lewis base occurs, with subsequent hydrogen bonding via this and other hydrogen donors variously to the carboxylate, phenate, and nitro oxygen acceptors of the dnsa anions. The result is the formation of primary N+–H···O associations which with secondary peripheral interactions, which within this set of compounds includes an increased incidence of aromatic C–H···O associations, give framework polymer structures. In three of the compounds [1, 4, and 6], cation–anion π–π interactions are also found. The completion of this series of compounds has now allowed the categorization of the molecular assembly modes in the proton-transfer compounds of 3,5-dinitrosalicylic acid.
Electrooxidative Cyclization of Hydroquinolyl Alcohols, Hydroquinolylamines, and Dimethyl Aminomalonates
Authors: Okimoto Mitsuhiro , Yoshida Takashi , Hoshi Masayuki , Hattori Kazuyuki , Komata Masashi , Numata Kaori , Tomozawa Kenta
Published: April 2007

Several hydroquinolyl alcohols and amines were electrochemically oxidized in methanol in the presence of sodium methoxide and potassium iodide to afford the corresponding intramolecular cyclization products. Furthermore, several amino malonates were electrochemically oxidized to yield the corresponding heterocyclic compounds through an intramolecular carbon–carbon bond formation in the presence of sodium cyanide in methanol.
Two New Multi-Manganese-Substituted Polyoxometalates
Authors: Zhang Zhiming , Wang Enbo , Chen Weilin , Tan Huaqiao
Published: April 2007

Two new multi-manganese-substituted polyoxotungstates K3Na10H3[{MnII(H2O)}2MnIII4(SiW6O26)(SiW9O34)2]·26H2O 1 and K5Na3[MnIII4(H2O)2(GeW9O34)2]·18H2O 2 have been successfully synthesized by the reaction of [β-XW11O36]8– (X = Si, Ge) with MnCl2 in the presence of potassium persulfate. Compound 1 consisted of two [B-α-SiW9O34]10– units and a [B-SiW6O26] unit linked by two isolated tri-manganese clusters to construct a double-sandwich structure. Compound 2 consisted of two [B-α-GeW9O34]10– units linked by a tetra-manganese cluster that was composed of four Mn3+ ions.
A Facile and Efficient Synthesis of Functionalized γ-Butyrolactones from Baylis - Hillman Adducts of Isatin
Authors: Shanmugam Ponnusamy , Vaithiyanathan Vadivel , Viswambharan Baby
Published: April 2007

A facile and efficient stereoselective synthesis of functionalized substituted γ-butyrolactones in excellent yield from the Baylis–Hillman adducts of isatin derivatives by a reductive cyclization methodology is reported.
New fossil woods of Proteaceae from the Oligocene of southern Patagonia
Authors: Pujana Roberto R.
Published: April 2007

The scarce fossil wood record of Proteaceae is complemented with the addition of a new morphogenus with two new species from the Oligocene of Patagonia, Scalarixylon patagonicum, gen. nov., sp. nov., and S. grandiradiatum, gen. nov., sp. nov. They become the first two fossil species that have all the typical characteristics of Proteaceae wood anatomy: wide multiseriate rays, tangential bands of vessels with unilateral banded associated parenchyma and simple perforation plates. They seem to be related to extant species that inhabit the subantarctic forests of Patagonia.
Morphological re-assessment of the Boodlea composita - Phyllodictyon anastomosans species complex (Siphonocladales: Chlorophyta)
Authors: Leliaert Frederik , Coppejans Eric
Published: April 2007

Boodlea composita (Harvey) F. Brand and Phyllodictyon anastomosans (Harvey) Kraft & M.J. Wynne, two widespread tropical siphonocladalean green algae, have had a long and confusing history because of the vague taxonomic boundaries between the two species. Molecular phylogenetic studies on the basis of nuclear-encoded rDNA sequences have resolved these indistinct species boundaries and suggest these taxa are part of a species complex. Detailed morphological investigations in combination with field and culture observations show that the concept of traditionally recognised taxa in this species complex is clouded by an ecologically induced phenotypic plasticity and developmental variability. Examination of a large number of specimens of B. composita, P. anastomosans and morphologically allied taxa including Boodlea siamensis Reinbold, Boodlea montagnei (Harvey ex J.E. Gray) Egerod, Nereodictyon imitans Gerloff and Struveopsis siamensis (Egerod) P. C. Silva, worldwide, including types, shows a wide morphological variety. We recognise seven more or less distinct morphological entities based on differences in thallus architectures, branching systems, cell dimensions and tenacular cell types. Awaiting the recovery of the true nature of the defined entities in this species complex (different species or growth forms of the same species), they are referred to as morphotypes, i.e. making no assumptions as to which taxonomic level they best apply.
Protein-induced, previously unidentified twin form of calcite
Authors: Pokroy B. , Kapon M. , Marin F. , Adir N. , Zolotoyabko E.
Published: April 2007

Using single-crystal x-ray diffraction, we found a formerly unknown twin form in calcite crystals grown from solution to which a mollusc shell-derived 17-kDa protein, Caspartin, was added. This intracrystalline protein was extracted from the calcitic prisms of thePinna nobilisshells. The observed twin form is characterized by the twinning plane of the (108)-type, which is in addition to the known four twin laws of calcite identified during 150 years of investigations. The established twin forms in calcite have twinning planes of the (001)-, (012)-, (104)-, and (018)-types. Our discovery provides additional evidence on the crucial role of biological macromolecules in biomineralization.
Depth-mediated reversal of the effects of climate change on long-term growth rates of exploited marine fish
Authors: Thresher Ronald E. , Koslow J. A. , Morison A. K. , Smith D. C.
Published: April 2007

The oceanographic consequences of climate change are increasingly well documented, but the biological impacts of this change on marine species much less so, in large part because of few long-term data sets. Using otolith analysis, we reconstructed historical changes in annual growth rates for the juveniles of eight long-lived fish species in the southwest Pacific, from as early as 1861. Six of the eight species show significant changes in growth rates during the last century, with the pattern differing systematically with depth. Increasing temperatures near the ocean surface correlate with increasing growth rates by species found in depths <250 m, whereas growth rates of deep-water (>1,000 m) species have declined substantially during the last century, which correlates with evidence of long-term cooling at these depths. The observations suggest that global climate change has enhanced some elements of productivity of the shallow-water stocks but also has reduced the productivity, and possibly the resilience, of the already slow-growing deep-water species.
The tiny eukaryote
Ostreococcus
provides genomic insights into the paradox of plankton speciation
Authors: Palenik Brian , Grimwood Jane , Aerts Andrea , Rouzé Pierre , Salamov Asaf , Putnam Nicholas , Dupont Chris , Jorgensen Richard , Derelle Evelyne , Rombauts Stephane , Zhou Kemin , Otillar Robert , Merchant Sabeeha S. , Podell Sheila , Gaasterland Terry , Napoli Carolyn , Gendler Karla , Manuell Andrea , Tai Vera , Vallon Olivier , Piganeau Gwenael , Jancek Séverine , Heijde Marc , Jabbari Kamel , Bowler Chris , Lohr Martin , Robbens Steven , Werner Gregory , Dubchak Inna , Pazour Gregory J. , Ren Qinghu , Paulsen Ian , Delwiche Chuck , Schmutz Jeremy , Rokhsar Daniel , Van de Peer Yves , Moreau Hervé , Grigoriev Igor V.
Published: April 2007

The smallest known eukaryotes, at ≈1-μm diameter, are
Ostreococcus tauri
and related species of marine phytoplankton. The genome of
Ostreococcus lucimarinus
has been completed and compared with that of
O. tauri
. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of
O. lucimarinus
provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.
KSper, a pH-sensitive K
+
current that controls sperm membrane potential
Authors: Navarro Betsy , Kirichok Yuriy , Clapham David E.
Published: April 2007

Mature mammalian spermatozoa are quiescent in the male reproductive tract. Upon ejaculation and during their transit through the female reproductive tract, they undergo changes that enable them to fertilize the egg. During this process of capacitation, they acquire progressive motility, develop hyperactivated motility, and are readied for the acrosome reaction. All of these processes are regulated by intracellular pH. In the female reproductive tract, the spermatozoan cytoplasm alkalinizes, which in turn activates a Ca
2+
-selective current (
I
CatSper
) required for hyperactivated motility. Here, we show that alkalinization also has a dramatic effect on membrane potential, producing a rapid hyperpolarization. This hyperpolarization is primarily mediated by a weakly outwardly rectifying K
+
current (
I
KSper
) originating from the principal piece of the sperm flagellum. Alkalinization activates the pH
i
-sensitive
I
KSper
, setting the membrane potential to negative potentials where Ca
2+
entry via
I
CatSper
is maximized.
I
KSper
is one of two dominant ion currents of capacitated sperm cells.
Small-molecule synergist of the Wnt/β-catenin signaling pathway
Authors: Zhang Qisheng , Major Michael B. , Takanashi Shinichi , Camp Nathan D. , Nishiya Naoyuki , Peters Eric C. , Ginsberg Mark H. , Jian Xiaoying , Randazzo Paul A. , Schultz Peter G. , Moon Randall T. , Ding Sheng
Published: April 2007

The Wnt/β-catenin signaling pathway regulates cell fate and behavior during embryogenesis, adult tissue homeostasis, and regeneration. When inappropriately activated, the pathway has been linked to colorectal cancer and melanoma, and when attenuated it may contribute to Alzheimer's disease and osteoporosis. Small molecules that modulate Wnt signaling will likely provide new insights into the regulation of this key developmental pathway and ultimately provide pharmacological agents to control Wnt signaling
in vivo
. To this end, we screened a library of 100,000 small molecules for activity in a cell-based assay of Wnt/β-catenin signaling and discovered a purine derivative, QS11, that synergizes with Wnt-3a ligand in the activation of Wnt/β-catenin signal transduction. Through affinity chromatography and subsequent functional assays, we showed that QS11 binds and inhibits the GTPase activating protein of ADP-ribosylation factor 1 (ARFGAP1), suggesting that QS11 modulates Wnt/β-catenin signaling through an effect on protein trafficking. Consistent with its function as an ARFGAP inhibitor, QS11 inhibits migration of ARFGAP overexpressing breast cancer cells.
Dissection of the pathway required for generation of vitamin A and for Drosophila phototransduction
Authors: Wang Tao , Jiao Yuchen , Montell Craig
Published: April 2007

Dietary carotenoids are precursors for the production of retinoids, which participate in many essential processes, including the formation of the photopigment rhodopsin. Despite the importance of conversion of carotenoids to vitamin A (all-trans-retinol), many questions remain concerning the mechanisms that promote this process, including the uptake of carotenoids. We use the Drosophila visual system as a genetic model to study retinoid formation from β-carotene. In a screen for mutations that affect the biosynthesis of rhodopsin, we identified a class B scavenger receptor, SANTA MARIA. We demonstrate that SANTA MARIA functions upstream of vitamin A formation in neurons and glia, which are outside of the retina. The protein is coexpressed and functionally coupled with the β, β-carotene-15, 15′-monooxygenase, NINAB, which converts β-carotene to all-trans-retinal. Another class B scavenger receptor, NINAD, functions upstream of SANTA MARIA in the uptake of carotenoids, enabling us to propose a pathway involving multiple extraretinal cell types and proteins essential for the formation of rhodopsin.
The interaction between the ER membrane protein UNC93B and TLR3, 7, and 9 is crucial for TLR signaling
Authors: Brinkmann Melanie M. , Spooner Eric , Hoebe Kasper , Beutler Bruce , Ploegh Hidde L. , Kim You-Me
Published: April 2007

Toll-like receptors (TLRs) sense the presence of microbial and viral pathogens by signal transduction mechanisms that remain to be fully elucidated. A single point mutation (H412R) in the polytopic endoplasmic reticulum (ER)–resident membrane protein UNC93B abolishes signaling via TLR3, 7, and 9. We show that UNC93B specifically interacts with TLR3, 7, 9, and 13, whereas introduction of the point mutation H412R in UNC93B abolishes their interactions. We establish the physical interaction of the intracellular TLRs with UNC93B in splenocytes and bone marrow–derived dendritic cells. Further, by expressing chimeric TLRs, we show that TLR3 and 9 bind to UNC93B via their transmembrane domains. We propose that a physical association between UNC93B and TLRs in the ER is essential for proper TLR signaling.
Sequential and Distinct Roles of the Cadherin Domain-containing Protein Axl2p in Cell Polarization in Yeast Cell Cycle
Authors: Gao Xiang-Dong , Sperber Lauren M. , Kane Steven A. , Tong Zongtian , Tong Amy Hin Yan , Boone Charles , Bi Erfei
Published: April 2007

Polarization of cell growth along a defined axis is essential for the generation of cell and tissue polarity. In the budding yeast Saccharomyces cerevisiae, Axl2p plays an essential role in polarity-axis determination, or more specifically, axial budding in MATa or α cells. Axl2p is a type I membrane glycoprotein containing four cadherin-like motifs in its extracellular domain. However, it is not known when and how Axl2p functions together with other components of the axial landmark, such as Bud3p and Bud4p, to direct axial budding. Here, we show that the recruitment of Axl2p to the bud neck after S/G2 phase of the cell cycle depends on Bud3p and Bud4p. This recruitment is mediated via an interaction between Bud4p and the central region of the Axl2p cytoplasmic tail. This region of Axl2p, together with its N-terminal region and its transmembrane domain, is sufficient for axial budding. In addition, our work demonstrates a previously unappreciated role for Axl2p. Axl2p interacts with Cdc42p and other polarity-establishment proteins, and it regulates septin organization in late G1 independently of its role in polarity-axis determination. Together, these results suggest that Axl2p plays sequential and distinct roles in the regulation of cellular morphogenesis in yeast cell cycle.
A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays
Authors: Xiao Yuanyuan , Segal Mark R. , Yang Y.H. , Yeh Ru-Fang
Published: April 2007

Motivation: Modern strategies for mapping disease loci require efficient genotyping of a large number of known polymorphic sites in the genome. The sensitive and high-throughput nature of hybridization-based DNA microarray technology provides an ideal platform for such an application by interrogating up to hundreds of thousands of single nucleotide polymorphisms (SNPs) in a single assay. Similar to the development of expression arrays, these genotyping arrays pose many data analytic challenges that are often platform specific. Affymetrix SNP arrays, e.g. use multiple sets of short oligonucleotide probes for each known SNP, and require effective statistical methods to combine these probe intensities in order to generate reliable and accurate genotype calls.

Results: We developed an integrated multi-SNP, multi-array genotype calling algorithm for Affymetrix SNP arrays, MAMS, that combines single-array multi-SNP (SAMS) and multi-array, single-SNP (MASS) calls to improve the accuracy of genotype calls, without the need for training data or computation-intensive normalization procedures as in other multi-array methods. The algorithm uses resampling techniques and model-based clustering to derive single array based genotype calls, which are subsequently refined by competitive genotype calls based on (MASS) clustering. The resampling scheme caps computation for single-array analysis and hence is readily scalable, important in view of expanding numbers of SNPs per array. The MASS update is designed to improve calls for atypical SNPs, harboring allele-imbalanced binding affinities, that are difficult to genotype without information from other arrays. Using a publicly available data set of HapMap samples from Affymetrix, and independent calls by alternative genotyping methods from the HapMap project, we show that our approach performs competitively to existing methods.

Availability: R functions are available upon request from the authors.

Contact:  yxiao@itsa.ucsf.edu and rufang@biostat.ucsf.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Murlet: a practical multiple alignment tool for structural RNA sequences
Authors: Kiryu Hisanori , Tabei Yasuo , Kin Taishin , Asai Kiyoshi
Published: April 2007

Motivation: Structural RNA genes exhibit unique evolutionary patterns that are designed to conserve their secondary structures; these patterns should be taken into account while constructing accurate multiple alignments of RNA genes. The Sankoff algorithm is a natural alignment algorithm that includes the effect of base-pair covariation in the alignment model. However, the extremely high computational cost of the Sankoff algorithm precludes its application to most RNA sequences.

Results: We propose an efficient algorithm for the multiple alignment of structural RNA sequences. Our algorithm is a variant of the Sankoff algorithm, and it uses an efficient scoring system that reduces the time and space requirements considerably without compromising on the alignment quality. First, our algorithm computes the match probability matrix that measures the alignability of each position pair between sequences as well as the base pairing probability matrix for each sequence. These probabilities are then combined to score the alignment using the Sankoff algorithm. By itself, our algorithm does not predict the consensus secondary structure of the alignment but uses external programs for the prediction. We demonstrate that both the alignment quality and the accuracy of the consensus secondary structure prediction from our alignment are the highest among the other programs examined. We also demonstrate that our algorithm can align relatively long RNA sequences such as the eukaryotic-type signal recognition particle RNA that is ∼300 nt in length; multiple alignment of such sequences has not been possible by using other Sankoff-based algorithms. The algorithm is implemented in the software named ‘Murlet’.

Availability: The C++ source code of the Murlet software and the test dataset used in this study are available at http://www.ncrna.org/papers/Murlet/

Contact: kiryu-h@aist.go.jp

Supplementary information: Supplementary data are available at Bioinformatics online.
TFmodeller: comparative modelling of protein–DNA complexes
Authors: Contreras-Moreira Bruno , Branger Pierre-Alain , Collado-Vides Julio
Published: April 2007

Summary: Interactions between proteins and DNA molecules lie at the core of the fundamental cellular processes such as transcriptional regulation. Some of these interactions have been experimentally described at atomic scale, but the molecular details of many others remain to be discovered. TFmodeller exploits the current knowledge about protein–DNA interfaces contained in the Protein Data Bank and uses it to model similar interfaces related by homology. Results are emailed to the user and include an evolutionary contact matrix, a schematic representation of the putative binding interface and atomic coordinates of the modelled complex. The library of complexes used by TFmodeller is updated on a weekly basis and is available for download.

Availability: TFmodeller and its web service interface are free for academic users at http://www.ccg.unam.mx/tfmodeller

Contact: contrera@ccg.unam.mx
A Comparison of Epinephrine Only, Arginine Vasopressin Only, and Epinephrine Followed by Arginine Vasopressin on the Survival Rate in a Rat Model of Anaphylactic Shock
Authors: Dewachter Pascale , Raëth-Fries Isabelle , Jouan-Hureaux Valérie , Menu Patrick , Vigneron Claude , Longrois Dan , Mertes Paul Michel
Published: April 2007

Background

Epinephrine and more recently arginine vasopressin (AVP) alone or in combination have been proposed in patients with anaphylactic shock, but few experimental data exist. The authors investigated the effects of epinephrine only, AVP only, or epinephrine followed by AVP in a model of anaphylactic shock.

Methods

Ovalbumin-sensitized Brown Norway rats were anesthetized, intubated, and shock induced with ovalbumin. Rats (n = 6/group) were randomly allocated to receive 5 min after shock onset: (1) saline (no-treatment group); (2) two boluses of epinephrine followed by continuous infusion (epinephrine group); (3) AVP bolus followed by continuous infusion (AVP group); (4) epinephrine bolus followed by AVP continuous infusion (epinephrine + AVP group). Mean arterial pressure (MAP) and skeletal muscle oxygen pressure (PtiO2) were measured. Continuous infusion rates were titrated to reach MAP values of 60 mmHg. Survival was analyzed.

Results

Without treatment, MAP and PtiO2 decreased rapidly with 0% survival. In the epinephrine group, MAP and PtiO2 recovered after an initial decrease, with 84% survival. In the AVP group, MAP was partially restored and subsequently decreased; PtiO2 values decreased to values similar to those in the no-treatment group; survival was 0%. In the epinephrine + AVP group, MAP and PtiO2 values increased more slowly as compared with the epinephrine group; survival was 100%.

Conclusions

In this model of anaphylactic shock, early treatment with epinephrine followed by continuous epinephrine or vasopressin infusion resulted in an excellent survival rate, whereas vasopressin only resulted in a 100% death rate. These experimental results suggest that epinephrine must still be considered as the first-line drug to treat anaphylactic shock.
Oral Donepezil Reduces Hypersensitivity after Nerve Injury by a Spinal Muscarinic Receptor Mechanism
Authors: Clayton Bridgette A. , Hayashida Ken-ichiro , Childers Steven R. , Xiao Ruoyu , Eisenach James C.
Published: April 2007

Background

Cholinesterase inhibitors which reach the central nervous system produce pain relief but are poorly tolerated because of gastrointestinal side effects. Here, the authors tested whether donepezil, a central nervous system penetrant cholinesterase inhibitor with a low incidence of gastrointestinal side effects, would relieve hypersensitivity in an animal model of neuropathic pain.

Methods

Male rats were anesthetized, and the L5 and L6 spinal nerves were ligated unilaterally. Hypersensitivity was measured by withdrawal threshold to von Frey filament application to the hind paw after oral donepezil, and antagonists administered centrally and peripherally. Efficacy of chronic oral donepezil to relieve hypersensitivity was tested, and activation of G proteins by M(2) muscarinic receptors was determined by carbachol-stimulated [(35)S]guanosine triphosphate (gamma)S autoradiography in brain and spinal cord.

Results

Spinal nerve ligation resulted in hypersensitivity that was more severe ipsilateral than contralateral to surgery. Oral donepezil reduced hypersensitivity bilaterally in a dose-dependent manner for 2 h, and this effect was blocked by spinal but not supraspinal or peripheral muscarinic receptor antagonism. Oral donepezil maintained efficacy over 2 weeks of twice daily administration, and this treatment did not lead to desensitization of muscarinic receptor-coupled G proteins in brain or spinal cord.

Conclusions

Donepezil, a well-tolerated cholinesterase inhibitor used in the treatment of Alzheimer dementia, reduces hypersensitivity in this rat model of neuropathic pain by actions on muscarinic receptors in the spinal cord. Lack of tolerance to this effect, in contrast to rapid tolerance to direct receptor agonists, suggests that cholinesterase inhibition may be useful in the treatment of neuropathic pain.
Effects of Intermittent Femoral Nerve Injections of Bupivacaine, Levobupivacaine, and Ropivacaine on Mitochondrial Energy Metabolism and Intracellular Calcium Homeostasis in Rat Psoas Muscle
Authors: Nouette-Gaulain Karine , Sirvent Pascal , Canal-Raffin Mireille , Morau Didier , Malgat Monique , Molimard Mathieu , Mercier Jacques , Lacampagne Alain , Sztark François , Capdevila Xavier
Published: April 2007

Background

Long-acting local anesthetics cause muscle damage. Moreover, long-acting local anesthetics act as uncoupler of oxidative phosphorylation in isolated mitochondria and enhance sarcoplasmic reticulum Ca(2+) release. The aim of the study was to evaluate effects of perineural injections of local anesthetics on mitochondrial energetic metabolism and intracellular calcium homeostasis in vivo.

Methods

Femoral nerve block catheters were inserted in adult male Wistar rats. Rats were randomized and received seven injections (1 ml/kg) of bupivacaine, levobupivacaine, ropivacaine, or isotonic saline at 8-h intervals. Rats were killed 8 h after the last injection. Psoas muscle was quickly dissected from next to the femoral nerve. Local anesthetic concentrations in muscle were determined. Oxidative capacity was measured in saponin-skinned fibers. Oxygen consumption rates were measured, and mitochondrial adenosine triphosphate synthesis rate was determined. Enzymatic activities of mitochondrial respiratory chain complexes were evaluated. Local calcium release events (calcium sparks) were analyzed as well as sarcoplasmic reticulum calcium content in saponin-skinned fibers.

Results

Eight hours after the last injection, psoas muscle concentration of local anesthetics was less than 0.3 microg/g tissue. Adenosine triphosphate synthesis and adenosine triphosphate-to-oxygen ratio were significantly decreased in the muscle of rats treated with local anesthetics. A global decrease (around 50%) in all of the enzyme activities of the respiratory chain was observed. Levobupivacaine increased the amplitude and frequency of the calcium sparks, whereas lower sarcoplasmic reticulum calcium content was shown.

Conclusion

Bupivacaine, levobupivacaine, and ropivacaine injected via femoral nerve block catheters induce a deleterious effect in mitochondrial energy, whereas only levobupivacaine disturbs calcium homeostasis.
Patient-requested Neuraxial Analgesia for Labor
Authors: Marucci Massimo , Cinnella Gilda , Perchiazzi Gaetano , Brienza Nicola , Fiore Tommaso , Warltier David C.
Published: April 2007

A systematic review, including a meta-analysis, on the timing effects of neuraxial analgesia (NA) on cesarean and instrumental vaginal deliveries in nulliparous women was conducted. Of 20 articles identified, 9 met the inclusion quality criteria (3,320 participants). Cesarean delivery (odds ratio, 1.00; 95% confidence interval, 0.82-1.23) and instrumental vaginal delivery (odds ratio, 1.00; 95% confidence interval, 0.83-1.21) rates were similar in the early NA and control groups. Neonates of women with early NA had a higher umbilical artery pH and received less naloxone. In the early NA group, fewer women were not compliant with assigned treatment and crossed over to the control group. Women receiving early NA for pain relief are not at increased risk of operative delivery, whereas those receiving early parenteral opioid and late epidural analgesia present a higher risk of instrumental vaginal delivery for nonreassuring fetal status, worse indices of neonatal wellness, and a lower quality of maternal analgesia.
The Real Options Component of Firm Market Value: The Case of the Technological Corporation
Authors: De Andrés‐Alonso Pablo , Azofra‐Palenzuela Valentín , De La Fuente‐Herrero Gabriel
Published: April 2007

Abstract:  This paper tests whether stock prices reflect investor's expectations regarding the value of real options. The analysis is implemented based on a sample of 391 high‐tech companies listed on main OECD stock markets during the period December 1994 through December 2000. Results confirm the predicted relation between the fraction of a firm's market value not accounted for by its assets‐in‐place, and a series of variables that are assumed to disclose its real options value, variables such as research and development activity, risk and skewness of stock returns, and size. The results are robust even after controlling for valuation date, sub‐industry, country, and alternative measures of risk.
The Market Value of UK Dividends From Shares With Differing Entitlements
Authors: Armitage Seth , Hodgkinson Lynn , Partington Graham
Published: April 2007

Abstract:  This paper determines the market value of dividends in the UK during periods before and after 1997. Previous studies, which use the ex‐dividend day method, tend to provide noisy and potentially biased measures of dividend value. We estimate the value of dividends from the prices of shares that are identical except for their dividend entitlements, and are traded concurrently (within the same hour). We argue that our estimates of dividend value are the cleanest yet available for the UK. Our evidence suggests that ex‐dividend day estimates are biased downwards, but that this bias may be mitigated by the use of robust regression. Dividend values are heterogeneous and are not explained by the tax‐clientele hypothesis.
ADVANCED AND REFINED TECHNIQUE IN THE PETROGRAPHIC STUDY OF CRYSTALLINE REFRACTORIES*
Authors: McCormick R. B.
Published: April 2007

Abstract

The new technique for the determination of the refractive indices of minerals, as developed by R. C. Emmons of the University of Wisconsin, is described. The paper contains a discussion of immersion media and a description of the double‐variation apparatus, the modified universal stage, and the smithsonite refractometer. Application of the technique to crystalline refractories is considered.
RAW LEADLESS GLAZES FOR POTTERY AND TILE AT CONE 2*
Authors: Merritt C. W.
Published: April 2007

Abstract

A base glaze was developed, using colemanite as the principal flux. A series of colors was produced by blending ten glazes containing different coloring materials.
OPAL GLASS. II, SILICON, CALCIUM, SODIUM, ALUMINUM, OXYGEN, AND FLUORINE SERIES*
Authors: Blau Henry H. , Silverman Alexander , Hicks Victor
Published: April 2007

The influence of alumina on the behavior of simple fluoride glasses is investigated. Analytical melting studies indicate that the fluorine may be liberated by at least three typical mechanisms. X‐ray diffraction studies reveal influences of alumina on crystallization.
A GRAPHICAL METHOD OF CALCULATING HEAT LOSS THROUGH FURNACE WALLS*
Authors: Weinland Clarence E.
Published: April 2007

Abstract

When a wide range of temperatures is considered, difficulty is encountered in accurately representing the thermal conductivity of any material, the temperature‐conductivity function of which is not a straight‐line relation. This difficulty can be obviated by use of the “true” conductivity function as defined herein.

The use of the “true” conductivity function confers the additional advantage that it makes possible a graphical method for the calculation of heat transmission through compound structures, under conditions of equilibrium heat flow. Though this is still a trial‐and‐error process, from the theoretical viewpoint it is more sound and from the practical angle more easily usable than the arithmetical method generally employed heretofore. The new method is illustrated by the solution of a typical problem.
RAPID METHOD OF ANALYSIS OF GLASS SAND*
Authors: Vilensky Michel B.
Published: April 2007

Abstract

The classical method for the analysis of glass sand, based on fusion of the pulverized material with sodium carbonate, dehydration of the silica with HCl, and determination of the other components from the filtrate, while accurate, requires considerable time. The method outlined by the writer, using HNO3 and HF, gives satisfactory results and requires only about one‐fourth the time.
FURTHER DATA ON ENAMEL ADHERENCE*
Authors: Kautz Karl
Published: April 2007

Abstract

Experiments designed to test the theories of gripping and electrochemical displacement as factors in the adherence of enamels to metals were performed. Rough surfaces on chromium, the stainless steels, and nickel produced no better adherence than smooth surfaces. Rough and smooth surfaces on iron enameled in vacuo and in nitrogen gave extremely poor adherence. Gripping action apparently functions on enameled noble metals.

Poor adherence on chromium, a metal higher than cobalt in the electrochemical series, and good adherence on copper, a metal below cobalt in the series, tend to show that electrolytic reactions, if they do occur, are not the fundamental cause of adherence. Enamels fired on iron in vacuo or in nitrogen are given the most advantageous conditions for electrolytic reactions to take place, yet the adherence in these cases is extremely poor.

Gripping action or electrolytic reactions could not function properly on oxidizable alloys and metals due to oxide layers which formed under the glass layer in firing. The importance of oxygen in enameling metals is emphasized by these experiments.

A brief review of the work of Pfeil, Castro and Portevin, and Mathewson, Spire, and Milligan on the constitution of iron scale is given. It is shown that metallic iron particles may exist in ferrous‐oxide scale as true primary dendrites, as rounded grains of residual α‐iron from the base, and as minute specks or thin layers of secondary α‐iron.

Microscopic study of iron‐enamel contact zones showed no true dendrites of iron to be present. In underfired enamels was found the α‐iron phase from the initial scale, but in the scale underlying this enamel both residual α‐iron phase and secondary α‐iron were found. In normally fired enamels only detached surface iron produced by slow oxidation of the iron base surface was found. The iron surface and the detached surface iron particles after proper etching showed a film of ferrous phase approximately 3 × 10‐5 inch thick between the glass and metal. This film of ferrous phase is believed to be the medium which bonds the enamel and iron together.

Microscopic study also showed the effect of an increased diffusion of oxygen as the enamel became richer in iron oxide. Cobalt oxide in the enamel is believed to promote solution of ferrous phase and also to act as an oxygen carrier through the molten glass layer.

A description of the six stages in the complete firing of cobalt ground‐coat enamels on iron is given and also the reactions which occur in each stage.
THE FLOW OF CERAMIC BODIES AT ELEVATED TEMPERATURES*
Authors: Norton F. H.
Published: April 2007

Abstract

A study is made of the flow characteristics of a porcelain over a considerable range of stress and temperature. In the range of these tests, where the rate varied by a million to one, no lower limit was found to the flow. The flow always reached a steady rate, but this look as much as 400 hours in some cases. The relation of plastic flow‐to other types is discussed as well as the application of the flow diagram to the load test and the fusion point.
THE FLUXING EFFECT OF FELDSPAR IN WHITEWARE BODIES*
Authors: Schramm E. , Hall F. P.
Published: April 2007

Abstract

A review is given of literature dealing with the melting relations of the feldspars, the solubility of quartz and clay in feldspar, the use of feldspar in bodies, and the direct determination of viscosity. An experimental study is reported, based on the determination of vitrification curves and viscosity at high temperature for several types of bodies, employing different typical feldspars alone and in mixtures. Various potash feldspars give similar results when allowance is made for free quartz content. The action of several natural feldspars of intermediate soda content was duplicated with chemically identical blends of pure microcline and pure albite. The validity of chemical control is confirmed. The action of feldspar is best considered, not as a simple melting and solution process, but as providing a source of fluxing elements needed to bring about glass‐forming reactions.
QUARTZ AS A DEVITRIFICATION PRODUCT OF VITREOUS SILICA*
Authors: Trostel L. J.
Published: April 2007

Abstract

Quartz has been observed as a devitrification product of vitreous silica prepared from glass sand when heated for four hours at 1300°C. Another type of commercial vitreous silica did not devitrify under the same conditions. Examination of the various properties of the two samples of vitreous silica by means of the microscope, interferometer, and X‐ray did not disclose differences which would explain the cause of the devitrification. Several theories arc advanced to explain the phenomena observed.
DE‐AIRING SEWER PIPE*
Authors: Rankin J. E.
Published: April 2007

Abstract

The Steele method of de‐airing sewer pipe features an air‐tight, inclosed mud chamber, fed by an inclosed chute from the de‐airing unit, which is connected in a straight line with a 12‐foot pug mill. Tempering clay with two wet pans has been discontinued. The plasticity has been increased, the pipes emerge straighter from the press, dry straighter, and are stronger and tougher with a resultant decrease in waste in house and kilns. The outer surface is smoother with practically no lamination or visible blisters. The crushing strength is increased and the absorption decreased.
A CRITICAL ANALYSIS OF SOME STATEMENTS AND EXPERIMENTS ON THE ADHERENCE OF SHEET‐STEEL GROUND COATS*
Authors: Lord J. O.
Published: April 2007

Abstract

A review and discussion are presented of the developments in the study of enamel adherence, notably in the publications of Kautz, Staley, and King.
SIZE DISTRIBUTION OF CERAMIC POWDERS AS DETERMINED BY A PARTICLE‐SIZE AIR ANALYZER*
Authors: Roller Paul S.
Published: April 2007

The use of air as a fluid for analytical separation of microscopic‐size particles has been given a new impetus by the development of a system involving a dynamic relationship between the powder sample and the air jet. This relationship is such that the powder charge is caused to circulate automatically and at the same time to translate in a direction opposite to that of the incoming air. Particle‐size analysis embodying this principle is described with the samples consisting of ceramic materials. Advantages of the air‐separation method of analysis are discussed.