bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rhodopsin patterning in central photoreceptor cells of the blowflyCalliphora vicina: cloning and characterization ofCalliphorarhodopsins Rh3, Rh5 and Rh6
Authors: Schmitt Angelika , Vogt Andreas , Friedmann Katrin , Paulsen Reinhard , Huber Armin 
Published: March 2005

SUMMARYThe ommatidia that constitute the compound eyes of flies contain eight photoreceptor cells, which are divided into two classes: the peripheral photoreceptors, R1–6, and the central photoreceptors, R7 and R8. In the fruit fly, Drosophila, R1–6 express the same rhodopsin (Rh1),whilst the R7 and R8 of a given ommatidium express either Rh3 and Rh5, or Rh4 and Rh6, respectively. We have studied whether this expression pattern of rhodopsins is conserved in the blowfly Calliphora vicina. We have cloned three novel Calliphora rhodopsins, which are homologues of Drosophila Rh3, Rh5 and Rh6, with an amino acid sequence identity of 80.7%, 60.9% and 86.1%, respectively. Immunocytochemical studies with antibodies specific for Rh3, Rh5 and Rh6 revealed that Rh3 is expressed in a subset of R7 cells, while Rh5 and Rh6 are expressed in a non-overlapping subset of R8 cells. Rh3 and Rh5 are present in most cases in the same ommatidia, which account for approximately 27% of all ommatidia, and Rh6 is found in the complementary 73%. The similarity of the rhodopsin expression pattern of Calliphora with that of Drosophila suggests that the developmental mechanism regulating the terminal differentiation of R7 and R8 cells are highly conserved between these fly species.
Development of the acoustically evoked behavioral response in zebrafish to pure tones
Authors: Zeddies David G. , Fay Richard R. 
Published: March 2005

SUMMARY
Zebrafish (Danio rerio) were placed in small wells that could be driven vertically with a series of calibrated sinusoids. Video images of the fish were obtained and analyzed to determine the levels and frequencies at which the fish responded to the stimulus tones. It was found that fish 4 days post fertilization (dpf) did not respond to the stimulus tones, whereas fish 5 dpf to adult did respond. It was further found that the stimulus thresholds and frequency bandwidth to which the fish responded did not change from 5 dpf to adult; indicating that the otolithic organ adaptations for high-frequency hearing are already present in larval fish. Deflating the swimbladders in adult fish eliminated their response, which is consistent with sensing sound pressure. Deflating the swimbladder in larval fish did not affect their thresholds, which is consistent with sensing the particle motion of the fluid directly. Because adult fish with Weberian ossicles have a greater input to the inner ear for a given sound pressure level (SPL), the finding that the adult and larval fish respond at the same SPL with intact swimbladders suggests that the acoustic startle response threshold is adjusted as the fish develop in order to maintain appropriate reactions to relevant stimuli.
Preparation of Chiral Poly(dipyridylamine). Its Metal Complex-controlled Steric Structure, and Its Light Emitting Properties
Authors: Horie Masaki , Yamaguchi Isao , Tanimoto Akitoshi , Yamamoto Takakazu 
Published: March 2005

Abstract
A new type of polyaniline, poly(dipyridylamine), with a coordination site and a chiral side chain was prepared. The polymer formed polymer–metal complexes, and steric structure of the polymer–metal complex was controlled by the kind of the coordinating metal species, as revealed by remarkable changes of the CD spectrum caused by coordination with the metal.
Dye-sensitized Solar Cells with an Extremely Thin Liquid Film as the Redox Electron Mediator
Authors: Kumara G R Asoka , Kaneko Shoji , Konno Akinori , Okuya Masayuki , Tennakone Kirthi 
Published: March 2005

Abstract
Dye-sensitized photoelectrochemical and solid-state solar cells are well known. A possible third alternative is a hybrid of both types where an extremely thin film of liquid is interposed between the dye-coated nanocrystalline semiconductor surface and a solid hole collector. To illustrate the principle a model system is constructed with graphite as the hole collector.
Photochromic Cyan Dyes of Fulgide Derivatives in Polymer Film
Authors: Matsushima Ryoka , Ito Yoshiro , Yamashita Ken-ichi , Yamamoto Kanako , Kouno Yoshiumi 
Published: March 2005

Abstract
Photochromic polymer films doped with 3–4 wt % fulgide derivatives exhibit high thermal and photochemical fatigue resistances as well as good color property to serve as cyan dyes for rewritable color display and printing materials.
Aldol Condensation in Water Using Polyethylene Glycol 400
Authors: Tanemura Kiyoshi , Suzuki Tsuneo , Nishida Yoko , Horaguchi Takaaki 
Published: March 2005

Abstract
Efficient and environmentally friendly synthesis of chalcones and 2,6-bis(arylmethylidene)cycloalkanones was carried out by aldol condensation of ketones with aromatic aldehydes in water in the presence of polyethylene glycol 400.
Synthesis and Structure of a Molecular Metal Propeller with Three Leaves, a Tetranuclear Silver(I) Cluster Formed by 2-Mercaptobenzoate and Triphenylphosphine Ligands
Authors: Noguchi Ryusuke , Hara Akihiro , Sugie Akiyoshi , Tanabe Sawako , Nomiya Kenji 
Published: March 2005

Abstract
A tetranuclear silver(I) cluster, [Ag(2-Hmba)(PPh3)]4·0.5CHCl3·0.5C2H5OH 1 (2-H2mba = 2-mercaptobenzoic acid), was prepared using the silver(I)–oxygen bonding precursor [Ag2(R-Hpyrrld)(S-Hpyrrld)] (H2pyrrld = 2-pyrrolidone-5-carboxylic acid), PPh3 and 2-H2mba in an organic solvent. The crystal structure of 1 was composed of a racemic mixture of a propeller cluster having three “leaves” constructed with three Ag(μ3-S)(μ2-S)P units and one Ag(μ2-S)3P unit. The Hpyrrld− ligand in the precursor plays an important role in the formation of 1, although this ligand disappeared from the product.
Reaction of Dilithiosilane R2SiLi2 and Dilithiogermane R2GeLi2 (R = SiMetBu2) with MesBCl2 (Mes = 2,4,6-trimethylphenyl): Evidence for the Formation of Silaborene R2Si=BMes and Germaborene R2Ge=BMes
Authors: Nakata Norio , Izumi Rika , Lee Vladimir Ya , Ichinohe Masaaki , Sekiguchi Akira 
Published: March 2005

Abstract
1,1-Dilithiosilane and -germane, R2SiLi2 and R2GeLi2 (R = SiMetBu2) reacted with MesBCl2 to give the unexpected seven-membered ring products, [1,3,2]oxasila- and -germaborepanes, through the intermediate formation of &gt;Si=B– and &gt;Ge=B– doubly bonded species.
Lewis Base-catalyzed [2,3]-Wittig Rearrangement of Silyl Enolates Generated from α-Allyloxy Ketones
Authors: Sato Yoshinori , Fujisawa Hidehiko , Mukaiyama Teruaki 
Published: March 2005

Abstract
Silyl enolates generated from α-allyloxy ketones afforded the [2,3]-Wittig rearrangement products in good to high yields in the presence of a catalytic amount of Lewis base such as lithium 2-pyrrolidone, lithium acetamide, or lithium hexamethyldisilazide in DMF at room temperature.
Chlorotrimethylsilane as a Mild and Effective Source of Acid Catalyst in Reductive Benzylation
Authors: Izumi Minoru , Fukase Koichi 
Published: March 2005

Abstract
New reductive benzylation of hydroxy functions was effected by using the combination of benzaldehyde, TMSCl, and Et3SiH. TMSCl first reacts with alcohols to form HCl, which is probably the ultimate catalyst for this reaction system. TMSCl can also trap water and thus effectively promote dehydration reactions when more than stoichiometric amount of TMSCl is used. Although excess TMSCl was required for the foregoing reactions, TMSCl could be readily removed by simple evaporation.
Hydrothermal Synthesis and Structure of Zero-dimensional Organic–inorganic Perovskites
Authors: Takeoka Yuko , Asai Keisuke , Rikukawa Masahiro , Sanui Kohei 
Published: March 2005

Abstract
A low-dimensional organic–inorganic perovskite compound, (C4H8N2H4)2PbBr6·2H2O, was synthesized from cyclic amines and PbBr2 by using a hydrothermal reaction. The versatile optical properties caused by the quantum confinement structure were investigated.
Optically Transparent Thin Film of Layered Niobate (K4Nb6O17) Intercalated with Tris(2,2′-bipyridyl)ruthenium(II)
Authors: Tong Zhiwei , Takagi Shinsuke , Tachibana Hiroshi , Takagi Katsuhiko , Inoue Haruo 
Published: March 2005

Abstract
A unique guest–guest ion exchange method was developed for preparing a thin film of a nano-layered K4Nb6O17·3H2O that possesses both 1) optical transparency and 2) ion-exchangeability, the first example of such a material. An optically transparent Ru(bpy)32+–K4Nb6O17 hybrid thin film, a potential photo-responsive electrode, was successfully prepared by the guest–guest exchange method by use of the intercalation compound MV2+–K4Nb6O17 as a precursor.
Structural Control of Mesoporous Silica by a Bicontinuous Microemulsion-aided Process
Authors: Moriguchi Isamu , Shono Yuki , Tachikawa Hiromi , Yamada Hirotoshi , Kudo Tetsuichi , Teraoka Yasutake , Nishimi Taisei 
Published: March 2005

Abstract
Mesoporous silica was successfully synthesized via a sol–gel process in a bicontinuous microemulsion of tetradecane/didodecyldimethylammonium bromide/aq HCl ternary system. The surface area, pore size and pore volume of silica varied dependent on the composition of bicontinuous microemulsion.
Laboratory Evaluation of Pullout Capacity of Reinforced Silty Sands in Drained and Undrained Conditions
Authors: Lee H-S , Bobet A 
Published: March 2005

Abstract
This paper presents results of laboratory pullout tests performed to determine the drained and undrained pullout capacity of reinforced silty sands. The pullout tests were conducted for different soil types: clean sand and silty sand with 5, 10, 15, and 35 % silt, and overburden pressures: 30, 100, and 200 kPa. Pullout experiments were performed on a large pullout box with dimension 1.5 m long, 0.5 m high, and 0.4 m wide, where a single steel inclusion was placed inside a mass of homogeneous soil. Both drained and undrained pullout capacities depended on the silt content and increased with internal friction angle of the soil and with overburden pressure. Undrained conditions could significantly reduce the pullout capacity. The reduction was caused by the generation of excess pore pressures in the soil under rapid loading, which in turn decreased the effective normal stress at the soil-reinforcement interface.
Collapse Behavior of Compacted Coal Ash Fills
Authors: Pusadkar SS , Ramasamy G 
Published: March 2005

Abstract
Coal ash is widely used in construction of embankments and fills. Compacted coal ash fills are likely to undergo collapse on inundation due to rise of water table or infiltration of rainwater. This paper brings out various factors influencing collapse potential of coal ash. Single oedometer and double oedometer collapse tests and plate load collapse tests were carried out on compacted fly ash (FA), bottom ash (BA), and mixture of fly ash and bottom ash in equal proportion (FA50 + BA50). The results reveal that fly ash is susceptible to collapse, while bottom ash and FA50 + BA50 show negligible collapse. However, a plate load collapse test conducted on compacted ash bed of FA50 + BA50 shows large settlement of plate on inundation. This suggests that the use of the results of single oedometer collapse tests can help estimate only that component of settlement of footing or test plate that is due to compression of the test bed on inundation, and not the total settlement that is due to both collapse compression and shear deformation of the loaded bed.
Using the Velocity Graph Method to Interpret Rising-Head Permeability Tests after Dewatering the Screen
Authors: Chapuis RP 
Published: March 2005

AbstractThis paper examines rising-head permeability tests performed on monitoring wells after the water level has been lowered down to the screened zone. Frequently, the usual semi-log graph appears as a set of two or three linear portions, making it difficult to assess the mean field hydraulic conductivity around the filter pack. Three tests, one in an unconfined aquifer and two in aquitards, are used to show that the usual semi-log graph can be curved either downwards or upwards. The velocity graph, which is linked to the conservation equation, clarifies what happens during and after dewatering the screened zone and the filter pack. In an unconfined aquifer, when the screened zone is close to the water table and dewatering is obtained by pumping, the curvature is due to the lowering of the water table before testing. Thus, the hydraulic conductivity must be calculated using a piezometric level lower than the pre-test value. In an aquitard, the curvature may be due either to an initial slow infilling of the dewatered filter pack (when it is too coarse to retain water by capillarity), or to an erroneous estimate of the piezometric level. The latter is due to the long time lag of the monitoring well and the natural drift of the piezometric level during the several testing days. In all cases, plotting the velocity graph clarifies what happens during the rising-head test.
Deceleration and Acceleration of Crack Propagation after an Overload under Negative Baseline Stress Ratio
Authors: Makabe C , Purnowidodo A , Miyazaki T , McEvily AJ 
Published: March 2005

Abstract
In a previously reported study, it was found that the fatigue crack growth rate actually accelerated after a tensile overload under a negative value of baseline stress ratio R. This type of crack propagation behavior is related to the change in the compression residual stress to tensile residual stress distributed in the vicinity of the crack tip upon unloading to minimum load after an overload. In the present investigation, focused on the negative stress ratio, it was found that the deceleration and acceleration of crack propagation were associated with crack opening displacement at the overload point and the conditions of applied baseline cyclic stress. The fatigue crack growth rate decelerated after being overloaded at a positive R value. However, that rate accelerated rather than decelerated in some stress conditions at a negative R value. Therefore, the residual fatigue life after overloading became longer or shorter, depending on the overload level and baseline stress conditions.
Evaluation of Hydraulic Pressure Drop using Manganin Wire and a Wiper-Cam-Operated Directional Valve
Authors: Tsung T-T , Han L-L 
Published: March 2005

Abstract
In this paper, we have constructed equipment to be effective in generating a hydraulic pressure drop that can be employed as a step function, mainly by means of a cam mechanism that operates a spool-type directional control valve and measures the pressure with a manganin wire and a Wheatstone bridge system. The wiper cam is specially designed to operate a hydraulic piston with quick return and to generate a pressure drop in the testing chamber within an extremely short time. Results show the pressure drop from 250 bars to zero requires only 0.45 ms. Furthermore, we also compare the characteristics of pressure drop with various chamber volumes and spool valve overlaps. Results show the best pressure-drop rate when the chamber volume and overlap are 4 cm3 and 4 mm, respectively.
Stochastic Models for Horizontal Gene Transfer
Authors: Suchard Marc A 
Published: March 2005

AbstractHorizontal gene transfer (HGT) plays a critical role in evolution across all domains of life with important biological and medical implications. I propose a simple class of stochastic models to examine HGT using multiple orthologous gene alignments. The models function in a hierarchical phylogenetic framework. The top level of the hierarchy is based on a random walk process in “tree space” that allows for the development of a joint probabilistic distribution over multiple gene trees and an unknown, but estimable species tree. I consider two general forms of random walks. The first form is derived from the subtree prune and regraft (SPR) operator that mirrors the observed effects that HGT has on inferred trees. The second form is based on walks over complete graphs and offers numerically tractable solutions for an increasing number of taxa. The bottom level of the hierarchy utilizes standard phylogenetic models to reconstruct gene trees given multiple gene alignments conditional on the random walk process. I develop a well-mixing Markov chain Monte Carlo algorithm to fit the models in a Bayesian framework. I demonstrate the flexibility of these stochastic models to test competing ideas about HGT by examining the complexity hypothesis. Using 144 orthologous gene alignments from six prokaryotes previously collected and analyzed, Bayesian model selection finds support for (1) the SPR model over the alternative form, (2) the 16S rRNA reconstruction as the most likely species tree, and (3) increased HGT of operational genes compared to informational genes.
Improving Quantitative Trait Loci Mapping Resolution in Experimental Crosses by the Use of Genotypically Selected Samples
Authors: Xu Zongli , Zou Fei , Vision Todd J 
Published: March 2005

Abstract
One of the key factors contributing to the success of a quantitative trait locus (QTL) mapping experiment is the precision with which QTL positions can be estimated. We show, using simulations, that QTL mapping precision for an experimental cross can be increased by the use of a genotypically selected sample of individuals rather than an unselected sample of the same size. Selection is performed using a previously described method that optimizes the complementarity of the crossover sites within the sample. Although the increase in precision is accompanied by a decrease in QTL detection power at markers distant from QTL, only a modest increase in marker density is needed to obtain equivalent power over the whole map. Selected samples also show a slight reduction in the number of false-positive QTL. We find that two features of selected samples independently contribute to these effects: an increase in the number of crossover sites and increased evenness in crossover spacing. We provide an empirical formula for crossover enrichment in selected samples that is useful in experimental design and data analysis. For QTL studies in which the phenotyping is more of a limiting factor than the generation of individuals and the scoring of genotypes, selective sampling is an attractive strategy for increasing genome-wide QTL map resolution.
Quantitative Trait Loci That Control Dengue-2 Virus Dissemination in the Mosquito Aedes aegypti
Authors: Bennett Kristine E , Flick Don , Fleming Karen H , Jochim Ryan , Beaty Barry J , Black William C 
Published: March 2005

Abstract
The mosquito Aedes aegypti is the most important vector of yellow fever and dengue fever flaviviruses. Ae. aegypti eradication campaigns have not been sustainable and there are no effective vaccines for dengue viruses. Alternative control strategies may depend upon identification of mosquito genes that condition flavivirus susceptibility and may ultimately provide clues for interrupting transmission. Quantitative trait loci affecting the ability of Ae. aegypti to develop a dengue-2 infection in the midgut have been mapped previously. Herein we report on QTL that determine whether mosquitoes with a dengue-2-infected gut can then disseminate the virus to other tissues. A strain selected for high rates of dengue-2 dissemination was crossed to a strain selected for low dissemination rates. QTL were mapped in the F2 and again in an F5 advanced intercross line. QTL were detected at 31 cM on chromosome I, at 32 cM on chromosome II, and between 44 and 52 cM on chromosome III. Alleles at these QTL were additive or dominant in determining rates of dengue-2 dissemination and accounted for ∼45% of the phenotypic variance. The locations of dengue-2 midgut infection and dissemination QTL correspond to those found in earlier studies.
Origin and Evolution of a Chimeric Fusion Gene in Drosophila subobscura, D. madeirensis and D. guancheSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY874360, AY874361, AY874362, AY874363, AY874364, AY874365, AY874366, AY874367, AY874368, AY874369, AY874370, AY874371, AY874372, AY874373, AY874374, AY874375, AY874376, AY874377, AY874378.
Authors: Jones Corbin D , Custer Andrew W , Begun David J 
Published: March 2005

Abstract
An understanding of the mutational and evolutionary mechanisms underlying the emergence of novel genes is critical to studies of phenotypic and genomic evolution. Here we describe a new example of a recently formed chimeric fusion gene that occurs in Drosophila guanche, D. madeirensis, and D. subobscura. This new gene, which we name Adh-Twain, resulted from an Adh mRNA that retrotransposed into the Gapdh-like gene, CG9010. Adh-Twain is transcribed; its 5′ promoters and transcription patterns appear similar to those of CG9010. Population genetic and phylogenetic analyses suggest that the amino acid sequence of Adh-Twain evolved rapidly via directional selection shortly after it arose. Its more recent history, however, is characterized by slower evolution consistent with increasing functional constraints. We present a model for the origin of this new gene and discuss genetic and evolutionary factors affecting the evolution of new genes and functions.
A Unified Model of Codon Reassignment in Alternative Genetic Codes
Authors: Sengupta Supratim , Higgs Paul G 
Published: March 2005

Abstract
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a new framework for codon reassignment that incorporates two previously proposed mechanisms (codon disappearance and ambiguous intermediate) and introduces two further mechanisms (unassigned codon and compensatory change). Our theory is based on the observation that reassignment involves a gain and a loss. The loss could be the deletion or loss of function of a tRNA or release factor. The gain could be the gain of a new type of tRNA or the gain of function of an existing tRNA due to mutation or base modification. The four mechanisms are distinguished by whether the codon disappears from the genome during the reassignment and by the order of the gain and loss events. We present simulations of the gain-loss model showing that all four mechanisms can occur within the same framework as the parameters are varied. We investigate the way the frequencies of the mechanisms are influenced by selection strengths, the number of codons undergoing reassignment, directional mutation pressure, and selection for reduced genome size.