bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vegetation and topographic influences on the connectivity of shallow groundwater between hillslopes and streams
Authors: Emanuel Ryan E. , Hazen Anna G. , McGlynn Brian L. , Jencso Kelsey G. 
Published: June 2013

ABSTRACTLittle is known about the combined effects of vegetation and topography on hillslope water table dynamics. In forested headwater catchments, complex terrain and vegetation intersect to impose large spatial and temporal variability in the vertical and lateral redistribution of water from hillslopes to streams. Here, we demonstrate, using empirical data from the Northern Rocky Mountains, that vegetation interacts with landscape topography to influence hillslope–riparian–stream hydrologic connectivity. We compared a measured relationship between hillslope contributing area and hydrologic connectivity during the growing season to LiDAR‐derived vegetation characteristics and found that two behavioural regimes emerged. Among some hillslopes, hydrologic connectivity decreased as vegetation density increased, demonstrating that growing season hydrologic connectivity is subject to the balance between evapotranspiration and lateral redistribution of soil water. Among other hillslopes, hydrologic connectivity increased as vegetation density increased. For the latter set of hillslopes, hydrologic connectivity cannot be explained by topography and vegetation alone. When we compared joint distributions of vegetation density and modelled solar irradiance between the two regimes as another indicator of evapotranspiration, we found that conditions were generally more favourable for higher transpiration on hillslopes where hydrologic connectivity decreased as vegetation density increased than on hillslopes where the opposite behaviour was observed. Our results demonstrate not only the importance of vegetation heterogeneity for hillslope–riparian–stream connectivity but also the importance of other spatially distributed variables such as energy availability when considering the influence of topography on hydrological processes. Copyright © 2013 John Wiley & Sons, Ltd.
Application of GaCp as a Ligand in Coordination Chemistry: Similarities and Differences to GaCp*
Authors: Naglav Dominik , Tobey Briac , Schnepf Andreas 
Published: June 2013

AbstractSolid “GaI” reacts with NaCp to give (η5‐cyclopentadienyl)gallium (GaCp). Further reaction of a solution of GaCp with [Cr(CO)5(coe)] (coe = cyclooctene) or Co2(CO)8 leads to CpGa–Cr(CO)5 (1) or (thf)GaCp{Co(CO)4}2 (4), respectively, which shows that GaCp can be used as a terminal ligand in coordination chemistry, but unlike its bulkier analogue GaCp* (Cp* = C5Me5), it also acts as a reducing agent.
On the Configurational Stability of Chiral Heteroatom‐Substituted [D1]Methylpalladium Complexes as Intermediates of Stille and Suzuki–Miyaura Cross‐Coupling Reactions
Authors: Malova Krizkova Petra , Hammerschmidt Friedrich 
Published: June 2013

AbstractEnantiomerically pure (S)‐tributylstannyl[D1]methanol and (R)‐ and (S)‐tributylstannyl[D1]methyl benzoates were Stille‐coupled with bromobenzene and benzoyl chloride in 1,4‐dioxane and toluene using [(Ph3P)4Pd] or [(Ph3P)2PdCl2] either alone or in combination with CuCN as cocatalyst at temperatures up to 80 °C. The products were found to be enantiomerically pure. (R)‐ and (S)‐N‐(tributylstannyl[D1]methyl)phthalimides gave enantiomerically pure products with benzoyl chloride, but with bromobenzene protected phenyl[D1]methylamines gave products of only 52–69 %eedepending on the solvent used. Tributyl(thio[D1]methyl)stannanes could not be Stille‐coupled with benzoyl chloride or with bromobenzene. Similarly, dimethyl phenyl[D1]methylboronate underwent a Suzuki–Miyaura coupling with bromobenzene to give phenyl[D1]methylsilane with 99 %ee. All couplings followed a retentive course and, except in one case, the intermediate [XCHDPdLn] complexes were found to be microscopically configurationally stable.
Investigating Reliability on Fuel Cell Model Identification. Part III: Behavior of Assessment Criteria and Limits in Identification
Authors: Tsikonis L. , Van herle J. , Favrat D. 
Published: June 2013

AbstractThe present paper is the third and last part of an investigation on what determines reliability in fuel cell model identification. In continuation to the effect of experimental design (Part I) and a process method for stochastic calculation of a model's parameters (Part II), this paper concentrates on the assessment of a model validation. Four criteria are examined. The fit of the model's output to experimental data, the determinant of the covariance matrix of the parameters, the determinant of their correlation matrix, and the product of their variances. As regards the fit to the data, results show that this is mainly a function of the number of measurement points. Repetitions do not seem to improve the average of the fit significantly, but it does improve its variation. For the other three criteria, which are also mathematically linked, results show a counterbalance between them, leading to the conclusion that they cannot be optimized simultaneously. This happens especially between the determinants of the covariance and the correlation matrices.
Spatial olfactory learning facilitates long‐term depression in the hippocampus
Authors: André Marion Agnès Emma , Manahan‐Vaughan Denise 
Published: June 2013

ABSTRACTRecently, it has emerged that visual spatial exploration facilitates synaptic plasticity at different synapses within the trisynaptic network. Particularly striking is the finding that visuospatial contexts facilitate hippocampal long‐term depression (LTD), raising the possibility that this form of plasticity may be important for memory formation. It is not known whether other sensory modalities elicit similar permissive effects on LTD. Here, we explored if spatial olfactory learning facilitates LTD in the hippocampus region of freely behaving rats. Patterned afferent stimulation of the Schaffer collaterals elicited short‐term depression (STD) (<1 h) of evoked responses in the Stratum radiatum of the CA1 region. Coupling of this protocol with novel exploration of a spatial constellation of olfactory cues facilitated short‐term depression into LTD that lasted for over 24 h. Facilitation of LTD did not occur when animals were re‐exposed 1 week later to the same odors in the same spatial constellation. Evaluation of learning behavior revealed that 1 week after the 1st odor exposure, the animals remembered the odors and their relative positions. These data support that the hippocampus can use nonvisuospatial resources, and specifically can use spatial olfactory information, to facilitate LTD and to generate spatial representations. The data also support that a tight relationship exists between the processing of spatial contextual information and the expression of LTD in the hippocampus. © 2013 Wiley Periodicals, Inc.
Dual‐Polarized Ultra Wideband CPW‐Fed Slot Antenna with Reconfigurable Circular Polarization Characteristic for Wimax and Wlan Applications
Authors: Pouyanfar Negin , Rezaeieh Sasan Ahdi 
Published: June 2013

ABSTRACTA simple yet efficient ultra wideband coplanar waveguide‐fed slot antenna with dual polarization is presented. Antenna has reconfigurable circular polarization (CP) for WIMAX and WLAN applications and a pure linear polarization for rest of the operating band. A total CP bandwidth larger than 20% can be attained simply by sequentially creating a crooked T‐shape and two bent slots around the patch. The CP for each band can be created upon desired application simply by on/off operation of three pin diodes, designed between patch and strips. Novel and simple design of the radiating patch, UWB operating bandwidth, reconfigurable 3‐dB axial ratio operating band, stable gain, and compact size of the antenna are of the great merits of this work. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2023–2026, 2013
Dual‐Band Ring Slot Antenna with Circular Polarization
Authors: Lin Chin‐Sung , Chen Li‐Ting , Chen Tsair‐Rong , Row Jeen‐Sheen 
Published: June 2013

ABSTRACTA design for dual‐band circularly polarized (CP) antennas is presented. The antenna is composed of two concentric shorted annular slots, and each slot can generate CP radiation at its one wavelength resonant mode or one‐and‐a‐half wavelength resonant mode by varying the position of the shorted section. When the one wavelength mode of the outer slot and the one‐and‐a‐half wavelength mode of the inner slot are simultaneously excited with a microstrip line, the antenna has two CP operating frequencies with a large frequency ratio (FR). A small FR can also be achieved when the outer and inner annular slots are operated at the one‐and‐a‐half wavelength mode and one wavelength mode, respectively. For the proposed design, two examples with the FRs of 1.05 and 1.9 are designed and implemented. Details of the experimental results are shown. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2077–2080, 2013
Effective Analysis of Terminated Lossless Planar Multilayer Periodic EBG Structures Using an Equivalent Transmission‐Line Model with Meta‐Smith Charts
Authors: Torrungrueng Danai , Sanphuang Varittha 
Published: June 2013

ABSTRACTLossless planar multilayer periodic electromagnetic bandgap (EBG) structures of dielectric media, illuminated by an oblique electromagnetic plane wave and terminated in a surface impedance with an arbitrary number of multilayers in a unit cell, can be effectively analyzed using an equivalent transmission‐line (TL) model based on conjugately characteristic‐impedance TLs (CCITLs). In this article, both characteristic impedances with nonnegative characteristic resistances (NNCRs) and negative characteristic resistances (NCRs) associated with CCITLs are considered. It is found that the equivalent CCITL model yields accurate results, and can simplify the analysis of these EBG structures with some physical insight. In addition, Meta‐Smith charts (MSCs) can be employed to further simplify the analysis. It is found that MSCs can provide clearer data set than the standard Smith chart with accurate results, and the bilinear transformation can be effectively used to transform dataset between MSCs and the Smith chart. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2222–2228, 2013
Compact Uwb Multilayer 3 Db Directional Coupler Design And Analysis on Coupler Performances
Authors: Abang Zaidel Dyg Norkhairunnisa , Abdul Rahim Sharul Kamal , Seman Norhudah , Adam Ashraf Abdulrahman , Rahman Tharek Abdul , Hall Peter S. 
Published: June 2013

ABSTRACTAn extended works of a diamond shaped 3 dB coupler design that is operating in ultra‐wideband frequency range is presented in this article. The proposed design is accomplished by using multilayer technology in which the structure is formed by three layers of conductors and interleaved by a layer of substrate between each one of the conductor layer. The proposed designed coupler simulation result shows that the design exhibits a coupling of 3 dB return loss and isolation better than 22 and 21 dB, respectively. Whereas, the phase difference performance is in the range of 90° ± 2° over the designated band. The coupler is fabricated and measured. Analysis studies on the parametric value are presented and discussed to observe the effect of the dimension of the patch to the performance of the coupler. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2214–2219, 2013
A Novel Modeling of Millimeter‐Wave Al0.27Ga0.73N/AlN/GaN Hemt Based on Artificial Neural Network
Authors: Cheng Zhi‐qun , Wang Xi , Zhang Qi‐qun 
Published: June 2013

ABSTRACTAn artificial neural network (ANN) was used for modeling millimeter‐wave Al0.27Ga0.73N/AlN/GaN high electron mobility transistor (HEMT) with multi‐biases in this article. Millimeter‐wave Al0.27Ga0.73N/AlN/GaN HEMT with gate width of 2 × 75 µm and gate length of 0.3 µm was designed and fabricated at first, and then its performance was measured for modeling. NeuroModelerPlus_V2.1E software was trained to learn the input‐output relationship from the data about DC and AC performances of proposed device. ANN DC model and AC model were set up and embedded in software of ADS together to form a model of millimeter‐wave Al0.27Ga0.73N/AlN/GaN HEMT, which can be used in circuit design. The results of the simulation of the model showed that it corresponded with the measurement results. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2124–2127, 2013
Discrete Green's Function Approach for The Analysis of A Dual Band‐Notched Uwb Antenna
Authors: Mirhadi Salma , Soleimani Mohammad , Abdolali Ali 
Published: June 2013

ABSTRACTA novel UWB monopole antenna with trident feeding and dual band‐notched characteristics is proposed. The antenna consists of two bottom corner notches for improvement of impedance matching and two U‐shaped slots for rejection of WLAN and WiMAX bands. Discrete Green's function approach has been utilized to numerically achieve time‐domain current distribution on the antenna. A good agreement between simulation and experimental results is observed. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:2168–2174, 2013
Synthesis of novel hyperbranched polymers featuring oxazoline linear units and their application in fast‐drying solvent‐borne coating formulations
Authors: Cheng Ge , Greenland Barnaby W. , Lampard Chris , Williams Neal , Bahra Malkit S. , Hayes Wayne 
Published: June 2013

ABSTRACTNovel acid‐terminated hyperbranched polymers (HBPs) containing adipic acid and oxazoline monomers derived from oleic and linoleic acid have been synthesized via a bulk polymerization procedure. Branching was achieved as a consequence of an acid‐catalyzed opening of the oxazoline ring to produce a trifunctional monomer in situ which delivered branching levels of >45% as determined by 1H and 13C NMR spectroscopy. The HBPs were soluble in common solvents, such as CHCl3, acetone, tetrahydrofuran, dimethylformamide, and dimethyl sulfoxide and were further functionalized by addition of citronellol to afford white‐spirit soluble materials that could be used in coating formulations. During end group modification, a reduction in branching levels of the HBPs (down to 12–24%) was observed, predominantly on account of oxazoline ring reformation and trans‐esterification processes under the reaction conditions used. In comparison to commercial alkyd resin paint coatings, formulations of the citronellol‐functionalized hyperbranched materials blended with a commercial alkyd resin exhibited dramatic decreases of the blend viscosity when the HBP content was increased. The curing characteristics of the HBP/alkyd blend formulations were studied by dynamic mechanical analysis which revealed that the new coatings cured more quickly and produced tougher materials than otherwise identical coatings prepared from only the commercial alkyd resins. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 3964–3974
Selective peptide inhibitors of bifunctional thymidylate synthase‐dihydrofolate reductase from Toxoplasma gondii provide insights into domain–domain communication and allosteric regulation
Authors: J. Landau Mark , Sharma Hitesh , Anderson Karen S. 
Published: June 2013

AbstractThe bifunctional enzyme thymidylate synthase–dihydrofolate reductase (TS–DHFR) plays an essential role in DNA synthesis and is unique to several species of pathogenic protozoans, including the parasite Toxoplasma gondii. Infection by T. gondii causes the prevalent disease toxoplasmosis, for which TS–DHFR is a major therapeutic target. Here, we design peptides that target the dimer interface between the TS domains of bifunctional T. gondii TS–DHFR by mimicking β‐strands at the interface, revealing a previously unknown allosteric target. The current study shows that these β‐strand mimetic peptides bind to the apo‐enzyme in a species‐selective manner to inhibit both the TS and distal DHFR. Fluorescence spectroscopy was used to monitor conformational switching of the TS domain and demonstrate that these peptides induce a conformational change in the enzyme. Using structure‐guided mutagenesis, nonconserved residues in the linker between TS and DHFR were identified that play a key role in domain–domain communication and in peptide inhibition of the DHFR domain. These studies validate allosteric inhibition of apo‐TS, specifically at the TS–TS interface, as a potential target for novel, species‐specific therapeutics for treating T. gondii parasitic infections and overcoming drug resistance.
Extension of metal oxide laser ionization mass spectrometry to analytes with varied chemical functionalities
Authors: McAlpin Casey R. , Voorhees Kent J. 
Published: June 2013

RATIONALEApplications of metal oxide laser ionization mass spectrometry (MOLI MS) have been limited to compounds that provide protons for ionization upon adsorption to a metal oxide surface. The addition of a small molecule, which can act as a proton source and extend MOLI MS applications to a wider variety of analytes, was investigated.METHODSMass spectrometric measurements were made with a PerSeptive Biosystems Voyager DE‐STR MALDI mass spectrometer, using NiO‐based MOLI to generate ions. NiO was pretreated in this study with a number of small molecules to act as proton sources during ionization. Peptides, monosaccharides, and a crude oil sample were analyzed with pretreated and untreated NiO.RESULTSCandidate small molecule proton donors were evaluated based on their effect on signal‐to‐noise ratio and peak intensity for tristearin. The best performing proton source was used for subsequent analyses. The analysis of monosaccharides, peptides and compounds in heavy crude oil was enhanced by the use of proton source treated NiO for MOLI MS. Proton/cation exchange following ionization was observed.CONCLUSIONSAddition of a proton source to NiO enhanced the MOLI MS response for peptides, carbohydrates, and compounds in a crude oil sample. Efficient ionization of these samples effectively extended applications of MOLI MS beyond lipid analytes containing esters. Copyright © 2013 John Wiley & Sons, Ltd.
On the Crystal Chemistry of Alkaline Earth‐ and Rare Earth‐Oxocobaltates
Authors: Müller‐Buschbaum Hanskarl 
Published: June 2013

AbstractA review on the crystal chemistry of oxocobaltates of alkaline earth and rare earth metals is presented according to the formula of the compounds, based on increasing metal and oxygen content. The well‐known structures of perowskites and K2NiF4‐type compounds and their higher homologues have been ignored and cross‐referred to older publications. Cobalt shows mainly the oxidation states Co2+ and Co3+. In many cases it exhibits integer valences like Co2.28+, Co2.5+, Co2.54+, Co2.8+, Co3.5, and Co3.6+, referred in the ICSD database. The dominant coordination polyhedra are CoO4‐tetrahedra and CoO6‐oktahedra. In two cases a trigonal prismatic CoO6‐coordination is observed. Composition, crystal structure, and oxidation state of cobalt often depend on the preparation conditions. In contrast to the alkaline oxides, the alkaline earth and rare earth oxides used for preparations are less reactive. Therefore the necessary reaction temperatures are much higher. In these cases single crystals for x‐ray investigation were prepared by plasma‐burner and CO2‐LASER techniques.
Complex between α-bungarotoxin and an α7 nicotinic receptor ligand-binding domain chimaera
Authors: Huang Sun , Li Shu-Xing , Bren Nina , Cheng Kevin , Gomoto Ryan , Chen Lin , Sine Steven M. 
Published: June 2013

To identify high-affinity interactions between long-chain α-neurotoxins and nicotinic receptors, we determined the crystal structure of the complex between α-btx (α-bungarotoxin) and a pentameric ligand-binding domain constructed from the human α7 AChR (acetylcholine receptor) and AChBP (acetylcholine-binding protein). The complex buries ~2000 Å2 (1 Å=0.1 nm) of surface area, within which Arg36 and Phe32 from finger II of α-btx form a π-cation stack that aligns edge-to-face with the conserved Tyr184 from loop-C of α7, while Asp30 of α-btx forms a hydrogen bond with the hydroxy group of Tyr184. These inter-residue interactions diverge from those in a 4.2 Å structure of α-ctx (α-cobratoxin) bound to AChBP, but are similar to those in a 1.94 Å structure of α-btx bound to the monomeric α1 extracellular domain, although compared with the monomer-bound complex, the α-btx backbone exhibits a large shift relative to the protein surface. Mutational analyses show that replacing Tyr184 with a threonine residue abolishes high-affinity α-btx binding, whereas replacing with a phenylalanine residue maintains high affinity. Comparison of the α-btx complex with that coupled to the agonist epibatidine reveals structural rearrangements within the binding pocket and throughout each subunit. The overall findings highlight structural principles by which α-neurotoxins interact with nicotinic receptors.
GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment
Authors: Zhang Zhaojun , Huang Shunping , Wang Jack , Zhang Xiang , Pardo Manuel de Villena Fernando , McMillan Leonard , Wang Wei 
Published: June 2013

Abstract
Motivation: RNA-seq techniques provide an unparalleled means for exploring a transcriptome with deep coverage and base pair level resolution. Various analysis tools have been developed to align and assemble RNA-seq data, such as the widely used TopHat/Cufflinks pipeline. A common observation is that a sizable fraction of the fragments/reads align to multiple locations of the genome. These multiple alignments pose substantial challenges to existing RNA-seq analysis tools. Inappropriate treatment may result in reporting spurious expressed genes (false positives) and missing the real expressed genes (false negatives). Such errors impact the subsequent analysis, such as differential expression analysis. In our study, we observe that ∼3.5% of transcripts reported by TopHat/Cufflinks pipeline correspond to annotated nonfunctional pseudogenes. Moreover, ∼10.0% of reported transcripts are not annotated in the Ensembl database. These genes could be either novel expressed genes or false discoveries.
Results: We examine the underlying genomic features that lead to multiple alignments and investigate how they generate systematic errors in RNA-seq analysis. We develop a general tool, GeneScissors, which exploits machine learning techniques guided by biological knowledge to detect and correct spurious transcriptome inference by existing RNA-seq analysis methods. In our simulated study, GeneScissors can predict spurious transcriptome calls owing to misalignment with an accuracy close to 90%. It provides substantial improvement over the widely used TopHat/Cufflinks or MapSplice/Cufflinks pipelines in both precision and F-measurement. On real data, GeneScissors reports 53.6% less pseudogenes and 0.97% more expressed and annotated transcripts, when compared with the TopHat/Cufflinks pipeline. In addition, among the 10.0% unannotated transcripts reported by TopHat/Cufflinks, GeneScissors finds that &gt;16.3% of them are false positives.
Availability: The software can be downloaded at http://csbio.unc.edu/genescissors/
Contact: weiwang@cs.ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics online.