bluuebunny/crossref_metadata_2025_split huggingface dataset:
Legume Anchor Markers Link Syntenic Regions Between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis
Authors: Hougaard Birgit Kristine , Madsen Lene Heegaard , Sandal Niels , de Carvalho Moretzsohn Marcio , Fredslund Jakob , Schauser Leif , Nielsen Anna Marie , Rohde Trine , Sato Shusei , Tabata Satoshi , Bertioli David John , Stougaard Jens 
Published: August 2008

Abstract
We have previously described a bioinformatics pipeline identifying comparative anchor-tagged sequence (CATS) loci, combined with design of intron-spanning primers. The derived anchor markers defining the linkage position of homologous genes are essential for evaluating genome conservation among related species and facilitate transfer of genetic and genome information between species. Here we validate this global approach in the common bean and in the AA genome complement of the allotetraploid peanut. We present the successful conversion of ∼50% of the bioinformatics-defined primers into legume anchor markers in bean and diploid Arachis species. One hundred and four new loci representing single-copy genes were added to the existing bean map. These new legume anchor-marker loci enabled the alignment of genetic linkage maps through corresponding genes and provided an estimate of the extent of synteny and collinearity. Extensive macrosynteny between Lotus and bean was uncovered on 8 of the 11 bean chromosomes and large blocks of macrosynteny were also found between bean and Medicago. This suggests that anchor markers can facilitate a better understanding of the genes and genetics of important traits in crops with largely uncharacterized genomes using genetic and genome information from related model plants.
An Empirical Test for Branch-Specific Positive Selection
Authors: Nickel Gabrielle C , Tefft David L , Goglin Karrie , Adams Mark D 
Published: August 2008

AbstractThe use of phylogenetic analysis to predict positive selection specific to human genes is complicated by the very close evolutionary relationship with our nearest extant primate relatives, chimpanzees. To assess the power and limitations inherent in use of maximum-likelihood (ML) analysis of codon substitution patterns in such recently diverged species, a series of simulations was performed to assess the impact of several parameters of the evolutionary model on prediction of human-specific positive selection, including branch length and dN/dS ratio. Parameters were varied across a range of values observed in alignments of 175 transcription factor (TF) genes that were sequenced in 12 primate species. The ML method largely lacks the power to detect positive selection that has occurred since the most recent common ancestor between humans and chimpanzees. An alternative null model was developed on the basis of gene-specific evaluation of the empirical distribution of ML results, using simulated neutrally evolving sequences. This empirical test provides greater sensitivity to detect lineage-specific positive selection in the context of recent evolutionary divergence.
Urease activity in aged copper and zinc-spiked soils: Relationship to CaCl2-extractable metals and Cu2+ activity
Authors: Kim Bojeong , McBride Murray B , Hay Anthony G 
Published: August 2008

Abstract
In the present study, the utilization of dilute CaCl2 extraction and free metal ion activity was tested for its ability to predict urease activity in soils that was measured by a simple and rapid urease assay. Two soil series (an Arkport sandy loam and a Hudson silty clay loam) were spiked with Cu and Zn, both singly and in combination, and then field aged for over a year prior to use. For both the metal-spiked Arkport and Hudson soils, much of the inhibition in measured urease activity was explained by increased CaCl2-extractable Cu, with a lesser effect from increased Zn extractability. A positive but weak interaction between Cu and Zn suggested by regression analysis indicates the toxicity of Cu-Zn mixtures to soil urease is slightly less than additive (antagonistic). Copper extractability using CaCl2 was able to predict urease activity in only one of the tested soils. By contrast, measurements of Cu2+ activity were predictive of reduced urease activity in both soils (R2adj = 0.726, p &lt; 0.0001), indicating that Cu2+ activity is a more useful predictor of urease inhibition in soils than CaCl2-extractable Cu. The present study also highlighted the importance that clay mineral content had on controlling the availability of added metals in soils over time since a greater aging effect on Cu toxicity was found for the fine-textured Hudson than the coarse-textured Arkport soil.
Time-Dependent transcriptional profiles of genes of the hypothalamic-pituitary-gonadal axis in medaka (Oryzias latipes) exposed to fadrozole and 17β-trenbolone
Authors: Zhang Xiaowei , Hecker Markus , Park June-Woo , Tompsett Amber R , Jones Paul D , Newsted John , Au Doris W. T , Kong Richard , Wu Rudolf S. S , Giesy John P 
Published: August 2008

AbstractBoth the anabolic androgen 17β-trenbolone (TRB) and the aromatase inhibitor fadrozole (FAD) can cause decreased plasma concentrations of estrogen (E2) and reduce fecundity of fish. However, the underlying mechanisms and the molecular pathways involved are largely unknown. The present study was designed to assess time-dependent effects of FAD and TRB on the transcriptional responses of the hypothalamic-pituitary-gonadal (HPG) axis of Japanese medaka (Oryzias latipes). Fourteen-week-old Japanese medaka were exposed to 50 μg FAD/L or 2 μg TRB/L in a 7-d static renewal test, and the expression profiles of 36 HPG axis genes were measured by means of a medaka HPG real-time reverse-transcription polymerase chain reaction array after 8 h, 32 h, or 7 d of exposure. Exposure to TRB or FAD caused lesser fecundity of Japanese medaka and down-regulated transcription of vitellogenin and choriogenin (CHG) gene expression in the liver of females. Exposure to FAD for 8 h resulted in an 8-fold and 71-fold down-regulation of expression of estrogen receptor α and choriogenin L (CHG L), respectively, in female liver. 17β-Trenbolone caused similar down-regulation of these genes, but the effects were not observed until 32 h of exposure. These results support the hypothesis that FAD reduces plasma E2 more quickly by inhibiting aromatase enzyme activity than does TRB, which inhibits the production of the E2 precursor testosterone. Exposure to FAD and TRB resulted in rapid (after 8 h) down-regulation of luteinizing hormone receptor and low-density-lipoprotein receptor in the testis to compensate for excessive androgen levels. Overall, the molecular responses observed in the present study differentiate the mechanisms of the reduced fecundity by TRB and FAD.
Solid-state linear polarized IR-spectroscopy of croconic and rhodizonic acids
Authors: Kolev Tsonko , Koleva Bojidarka , Spiteller Michael 
Published: August 2008

Abstract
The applications of linear-polarized IR-spectroscopy to oriented colloid suspensions in a nematic host are demonstrated with croconic and rhodizonic acids. The experimental IR vibrational assignments of the solid-state of both neutral compounds are presented. Assignments are supported by theoretical quantum chemical calculations and vibrational analysis at the DFT level of theoretical approximation with the 6-311++G** basis set.
Nuclear magnetic resonance spectroscopic studies of the trihexyl (tetradecyl) phosphonium chloride ionic liquid mixtures with water
Authors: Dwan Jerrod , Durant Dan , Ghandi Khashayar 
Published: August 2008

Abstract
Tetra-alkyl Phosphonium ionic liquids are phosphonium salts with melting points near room temperature. We report the NMR studies of water-trihexyl (tetradecyl) phosphonium chloride ionic liquid mixtures. The proton chemical shifts were used to investigate the intermolecular interactions in mixtures of ionic liquids and water. The OH chemical shifts were found to decrease as the water concentration in the ionic liquid increased, and their rate of change with temperature decreased with water concentration. The CH2 and CH3 chemical shifts were found to move downfield with the increase in temperature, and moved further downfield as water concentration was decreased. The interface of experimental data and the results of quantum calculations suggest a significant binding of phosphonium cations to chloride anion and water molecules. As well, the analysis of the data suggests a possible transformation from cationchloride-water configuration at low water concentrations to cation-water-water at higher water concentrations.
Thermodynamic and kinetic properties of scandium (I) ion reacting with SCO in gas phase
Authors: Yin Ping , Qu Rongjun , Chen Hou , Tian Yuan , Yin Gui , Bao Chongrong 
Published: August 2008

Abstract
Theoretical studies on the thermodynamic and kinetic properties of the reactions of scandium (I) ion with the sulfur-transfer reagent SCO via the C-O bond activation pathway have been carried out over the temperature range of 200-1200 K using the DFT/B3LYP method, general statistical thermodynamics, and Eyring transition state theory with Wigner correction. The relevant reactions include reaction 1 1Sc+ + SCO → 1IM1 → 1TS1 → 1IM2 (Step 1) → 1TS2 → 1IM3 → 1ScO+ + 1CS (Step 2), and reaction 2 3Sc+ + SCO → 3IM1 → CP → 1IM2 → 1TS2 → 1IM3 → 1ScO+ +1CS in which the spin multiplicity changes from the triplet state to the singlet state in the crossing region. It was concluded that the order of the equilibrium constants (K) and the reaction rate constants (k) are consistent with that of their corresponding exoergic energies, ΔE, and reaction barriers, respectively. Step 2 of reaction 1 is both thermodynamically and kinetically favored over the whole temperature range. Moreover, both Reaction 1 and reaction 2 are exothermic and spontaneous processes in which their entropy increases, and the magnitudes of their thermodynamic values all decrease with increasing temperature.
Consequence of hydrogen atom abstraction from 5’-hydroxyl group of 2’-deoxyadenosine. Theoretical quantum mechanics study
Authors: Karwowski Bolesław 
Published: August 2008

Abstract
Reactive oxygen species (ROS) may generate different nucleoside/nucleotide radicals in a cell environment. In this study, the possibility of cyclic-2’-deoxyadenosines formation by a rearrangement of their free radicals was investigated. It seems that for cyclic-nucleosides formation, adoption of an O4’-exo conformation by the sugar moiety is necessary. However, this is the energetically unfavoured form of the 2-deoxyribose ring. Moreover, the creation of a O5’, C8 bond in purine deoxy-nucleosides/nucleotides leads to the termination of the DNA elongation process.
2-(benzimidazol-2-yl)-3-hydroxychromone derivatives: spectroscopic properties and a possibile alternative intramolecular proton phototransfer
Authors: Svechkarev D. , Karpushina G. , Lukatskaya L. , Doroshenko A. 
Published: August 2008

Abstract
Three 2-(benzimidazol-2-yl)-3-hydroxychromone derivatives were synthesized. Their spectroscopic and fluorescent properties, due to excited state intramolecular proton transfer (ESIPT) from OH to carbonyl, were studied. Theoretical possibility of an alternative intramolecular H-bonding and experimental evidence for such behavior are discussed.
Can N-heterocyclic germylenes behave as Lewis acids - is there another side to Meller germylenes?
Authors: Kühl Olaf 
Published: August 2008

Abstract
N-Heterocyclic germylenes are known to exist in two structurally different forms, the planar Meller germylenes and the monoimino germylenes that feature an envelope structure. This essay reviews recent reports dealing with radical and cationic Meller type germylenes featuring the monoimino germylene structure, discusses their transformations and relationships, and asks the question whether indeed N-heterocyclic germylenes can be turned into Lewis acids.
2-pyrrolidone - capped Mn3O4 nanocrystals
Authors: Özkaya Tevhide , Baykal Abdulhadi , Toprak Muhammet 
Published: August 2008

Abstract
Water-soluble Mn3O4 nanocrystals have been prepared through thermal decomposition in a high temperature boiling solvent, 2-pyrrolidone. The final product was characterized with XRD, SEM, TEM, FTIR and Zeta Potential measurements. Average crystallite size was calculated as ∼15 nm using XRD peak broadening. TEM analysis revealed spherical nanoparticles with an average diameter of 14±0.4 nm. FTIR analysis indicated that 2-pyrrolidone coordinates with the Mn3O4 nanocrystals only via O from the carbonyl group, thus confining their growth and protecting their surfaces from interaction with neighboring particles.
Palladium(0)-catalyzed amination of allylic natural terpenic functionalized olefins
Authors: Houssame Soufiane , Anane Hafid , Firdoussi Larbi , Karim Abdellah 
Published: August 2008

Abstract
The palladium(0) catalyzed amination of allylic acetates and carbonates derivatives from terpenic olefins was carried out under mild conditions. The reaction offers a very good method for the preparation of allylic amines and thus to provide a useful entry to new functionalized terpenic olefin products. The mechanism involving a formation of p-allyl-palladium intermediate complex is in good agreement with the results obtained with the optically active substrates, as well as via an analysis of the observed regio-and stereoselectivity.
Gas-phase synthesis of inorganic fullerene-like structures and inorganic nanotubes
Authors: Deepak F. , Tenne Reshef 
Published: August 2008

Abstract
Following the discovery of fullerenes (C60) and carbon nanotubes, it was shown that nanoparticles of inorganic layered compounds, like WS2 and MoS2, are unstable in the planar form and they form closed cage structures with polyhedral or nanotubular shapes. Although initially the method of synthesis for the formation of such closed caged structures and nanotubes involved starting from the respective oxides, it is now well established that the gas-phase synthetic route (using metal chlorides, carbonyls etc) provides an alternative which is suitable for the synthesis of very many closed caged structures and nanotubes hitherto unknown. Various issues with this method of synthesis, including its fundamentals, mechanism, and the properties of the inorganic fullerene-like structures produced are reviewed, together with some possible applications.
Synthesis of Xenbucin using Suzuki reaction catalyzed by Pd/C in water
Authors: Kuuloja Noora , Kylmälä Tuula , Xu Youjun , Franzén Robert 
Published: August 2008

Abstract
Xenbucin 1, an analgesic drug, was synthesized in 4 steps using two different routes. The biaryl fragment could successfully be produced via a Pd/C catalysed Suzuki coupling in water using sodium tetraphenylborate as a phenylation reagent. Overall yields of the routes were 36% and 59%, respectively.
Sol-gel preparation and characterization of non-substituted and Sr-substituted lanthanum cobaltates
Authors: Cizauskaite Sigute , Kareiva Aivaras 
Published: August 2008

Abstract
This paper reports on the results concerning the sol-gel preparation and characterization of Sr-substituted perovskite lanthanum cobaltates La1−xSrxCoO3−δ (x = 0.0, 0.25, 0.5 and 0.75). The metal ions, generated by dissolving starting materials in diluted acetic acid were complexed by 1,2-ethanediol to obtain the precursors for the non-substituted and Sr-substituted LaCoO3. The influence of the synthesis temperature, heating time and the amount of substituent on the phase purity of La1−xSrxCoO3−δ were investigated. The phase transformations, composition and micro-structural features in the gels and polycrystalline samples were studied by thermal analysis (TG/DTA), infrared spectroscopy (IR), powder X-ray diffraction analysis (XRD) and scanning electron microscopy (SEM).
Kinetic studies for the esterification of acetic acid with epichlorohydrin over an anion exchange resin catalyst
Authors: Muresan Emil , Oprea Spiridon , Hulea Vasile , Malutan Theodor , Vata Mihai 
Published: August 2008

Abstract
The kinetics of the esterification reaction between acetic acid and epichlorohydrin catalysed by Purolite A-520E strong basic anion exchange resin was studied. The effects of certain parameters such as stirring speed, particle diameter, temperature, catalyst amount and molar ratio between reactants were experimentally determined. It was found that the overall reaction rate is intrinsically kinetically controlled. The partial orders of reaction with respect to catalyst, acetic acid and epichlorohydrin were determined. A reaction mechanism is proposed. Based on chromatographic data and taking into account the partial orders of reaction, a more detailed kinetic model is suggested.
Preparation and characterization of alumina-zirconia composite material with different acid ratios by the sol-gel method
Authors: Ergu Ozgecan , Gürü Metin , Cabbar Canan 
Published: August 2008

Abstract
Alumina-zirconia composite materials were produced with different acid ratios by the sol-gel method using aluminum isopropoxide and zirconium chloride. The composites were produced by changing acid/alkoxside ratio in alumina. The composite materials were calcinated at 600°C, 900°C and 1300°C. The effects of acid concentration and calcination temperature on the surface area and pore radius were determined from the nitrogen adsorption isotherm at 77 K. The density of the composites was also measured. The minimum density of produced material was recorded as 1.35 g cm−3 at an acid/alkoxside ratio of 0.2. The highest specific surface area and pore diameter of the lightest material are 191.86 m2 g−1 and 18.4 Ǻ, respectively. Although pore diameter and specific surface area are not changed at any of the experimental temperatures which were tested by decreasing acid/alkoxside ratio, the density is slightly increased. However, it was observed that the calcination temperature significantly affects the surface area and density of the material.
Synthesis and structural peculiarities of gallium Complexes with novel paullone derivatives
Authors: Ginzinger Werner , Arion Vladimir , Giester Gerald , Galanski Markus , Keppler Bernhard 
Published: August 2008

Abstract
9-Bromo-7,12-dihydroindolo[3,2-d][1]benzazepin-6-ylhydrazine was reacted with 2-acetylpyridine to give a Schiff base as a potential tridentate ligand. The reaction of this ligand with gallium chloride afforded complexes of 1:1 and 2:1 stoichiometry. The results of X-ray diffraction studies of the ligand and both gallium complexes are reported and compared with the data for a related gallium complex with a Schiff base obtained from 9-bromo-7,12-dihydroindolo[3,2-d][1]benzazepin-6-ylhydrazine and 2-hydroxybenzaldehyde.
Combination of cloud point extraction and flame atomic absorption spectrometry for preconcentration and determination of trace iron in environmental and biological samples
Authors: Ghaedi Mehrorang , Shokrollahi Ardeshir , Mehrnoosh Raziyeh , Hossaini Omid , Soylak Mustafa 
Published: August 2008

Abstract
In the presented work, the conditions for cloud point extraction of iron from aqueous solutions using 7-iodo-8-hydroxyquinolin-5-sulphonic acid (Ferron) was investigated and optimized. The procedure is based on the separation of its ferron complex into the micellar media by adding the surfactant Triton X-114. After phase separation, the surfactant-rich phase was dissolved with 1.0 M HNO3 in methanol. Iron was determined by flame atomic absorption spectrometry. Optimization of the pH, ligand and surfactant quantities, incubation time, temperature, viscosity, sample volume, and interfering ions were investigated. The effects of the matrix ions were also examined. The detection limits for three times the standard deviations of the blank for iron was 0.4 ng m L-1, enrichment factor of 19.6 and preconcentration factor of 30 could be achieved. The validity of cloud point extraction was checked by employing real samples including soil, blood, spinach, milk, meat, liver and orange juice samples using the standard addition method, which gave satisfactory results.In the presented work, the conditions for cloud point extraction of iron from aqueous solutions using 7-iodo-8-hydroxyquinolin-5-sulphonic acid (Ferron) was investigated and optimized. The procedure is based on the separation of its ferron complex into the micellar media by adding the surfactant Triton X-114. After phase separation, the surfactant-rich phase was dissolved with 1.0 M HNO3 in methanol. Iron was determined by flame atomic absorption spectrometry. Optimization of the pH, ligand and surfactant quantities, incubation time, temperature, viscosity, sample volume, and interfering ions were investigated. The effects of the matrix ions were also examined. The detection limits for three times the standard deviations of the blank for iron was 0.4 ng m L−1, enrichment factor of 19.6 and preconcentration factor of 30 could be achieved. The validity of cloud point extraction was checked by employing real samples including soil, blood, spinach, milk, meat, liver and orange juice samples using the standard addition method, which gave satisfactory results.
Structural and dielectric studies of lead-free ceramics: Na1/2Y1/2TiO3
Authors: Barik Subrat , Choudhary Ram , Mahapatra Prasanta 
Published: August 2008

Abstract
The polycrystalline samples of Na1/2Y1/2TiO3 were prepared by the mixed-oxide method. A preliminary X-ray structural analysis was shown to exhibit the formation of a single-phase compound with an orthorhombic structure. Microstructural analysis by scanning electron microscopy (SEM) exhibits well defined grains distributed uniformly through out the sample suggesting the compactness and homogeneity of the sample. Detailed studies of dielectric properties of Na1/2Y1/2TiO3 in a wide frequency range (102–106 Hz) at different temperatures (31–500°C) show a dielectric anomaly at 105°C, which may be related to a ferroelectricparaelectric phase transition as suggested by hysteresis loop at room temperature. An ac conductivity (σ
ac) of the material is mainly governed by the polaron hopping mechanism, which is also influenced by both frequency and temperature. The activation energy was obtained from the plot of temperature with a.c. conductivity.
A symmetry based investigation of the band gap of SWCNTs
Authors: Pakkhesal Mehdi , Ghayour Rahim 
Published: August 2008

Abstract
In this paper we use symmetry of Single Walled Carbon Nanotubes (SWCNTs) to generate some types of virtual sub-bands that are lower in number than the real sub-bands obtained through conventional-TB. It is shown that the virtual sub-bands maintain the value of band gap. In obtaining the sub bands, the interactions of the nearest and the second and third-nearest neighbors are taken into account. As the consequence of lower number of sub-bands, a significant reduction in computational effort has occurred and made the approach useful.
A first-principles studies on TlX (X=P, As)
Authors: Ciftci Yasemin , Colakoglu Kemal , Deligoz Engin 
Published: August 2008

Abstract
We present an ab initio study of the structural, electronic and thermodynamic properties of TlX(X=P,As). The plane-wave pseudopotential approach to the density-functional theory within the LDA and GGA approximations implemented in VASP (Viena Ab-initio Simulation Package) is used. The calculated lattice parameter, elastic constants, and band structures are compared with other available theoretical results, and good agreement is obtained. In addition, we have calculated the transition pressure (P
t) from zinc-blende (ZB) to (rock-salt) NaCl structures, and have examined some thermodynamic properties.