bluuebunny/crossref_metadata_2025 huggingface dataset:
How to infer impacts of ITS services in different user cases
Authors: Kulmala Risto , Mans Dick , El‐Araby Khaled , Penttinen Merja
Published: September 2013

Despite the widely acknowledged potential of intelligent transport systems and services (ITS), the deployment of ITS has generally been scattered and slow. One of the main reasons for this is that people deciding on investments in the road and public transport sector often lack knowledge of the feasibility, cost‐effectiveness, impacts and user acceptance of ITS solutions to their own transport related problems. One solution is to build up an intelligent ITS toolkit, which would propose to the decision maker the most viable ITS solutions in relation to his problems in his context. The study describes how such a toolkit has been designed and developed, including the knowledge base and inference engine providing the intelligence to that toolkit. The study is focusing on how to infer the most likely impacts and benefit/cost matching the user input on the basis of existing ITS evaluations studies and the available assessment expertise in the specific user contexts.
Routing systems to extend the driving range of electric vehicles
Authors: Neaimeh Myriam , Hill Graeme A. , Hübner Yvonne , Blythe Phil T.
Published: September 2013

This study develops a more accurate range prediction for electric vehicles (EVs) resulting in a routing system that could extend the driving range of EVs through calculating the minimum energy route to a destination, based on topography and traffic conditions of the road network. Energy expenditure of EVs under different conditions is derived using high‐resolution real‐world data from the SwitchEV trial. The SwitchEV trial has recorded the second‐by‐second driving events of 44 all‐electric vehicles covering a distance of over 400 000 miles across the North East of England, between March 2010 and May 2013. Linear models are used to determine the energy expenditure equations and Dijkstra's graph search algorithm is used to find the route minimising energy consumption. The results from this study are being used to better inform the decisions of the smart navigation and eco‐driving assist systems in EVs, thus improving the intelligent transport systems provisions for EV drivers. The outputs of the research are twofold: providing more accurate estimations of available range and supporting drivers’ optimisation of energy consumption and as a result extending their driving range. Both outputs could help mitigate range anxiety and make EVs a more attractive proposition to potential customers.
Dual‐mode dual‐band bandpass filters design using open‐loop slotline resonators
Authors: Liu Haiwen , Shen Li , Shi Li Yun , Jiang Yang , Guan Xuehui , Wu Tiantian
Published: September 2013

A dual‐mode open‐loop slotline resonator with a centre‐loaded stub is proposed. The loaded stub is used to excite non‐degenerate modes, that is, the even and odd modes. Distinct characteristics of this dual‐mode resonator are investigated by using even–odd mode analysis. Also, equivalent circuit models for non‐degenerate modes are given to determine the resonance conditions and the location of transmission zero. Then, two novel approaches for designing dual‐mode dual‐band bandpass filters are presented. One approach consists of simple microstrip feedlines and two embedded open‐loop slotline resonators for single substrate configuration. The other is composed by using dual‐mode open‐loop resonators in the form of microstrip and slotline structures on a single substrate. A microstrip invert L‐shape feeding structure is employed to simultaneously feed the microstrip and slotline resonator on different layers for broadside coupling. Both of them provide sufficient degrees of freedom to control the centre frequencies and fractional bandwidths of both passbands independently. The two filters are designed, fabricated and measured. A good agreement between the simulation and measurement verifies the validity of this design methodology.
Resolving manifold ambiguities for direction‐of‐arrival estimation of sparse array using semi‐circular substrates
Authors: Liu Jiazhou , Zhao Zhiqin , He Ziyuan , Nie Zaiping , Liu Qing‐Huo
Published: September 2013

Sparse linear array has some advantages over uniform linear array in some applications. However, it is well known that sparse array always suffers from manifold ambiguity, which has significant influence on direction‐of‐arrival (DOA) estimation and resolution. In this study, a new method based on the multiple signal classification (MUSIC) for resolving manifold ambiguities of uncorrelated sources by using semi‐circular substrate is proposed for DOA estimation of sparse array. Spurious MUSIC peak spectrums are generated because of a linear combination of the steering vectors of true DOAs. The main idea of the proposed method is to setup one or several semi‐circular medium substrates at the front of some elements. The phases of these elements are changed through the refractive index and the radii of those semi‐circular substrates. This treatment breaks down the previous linearity of the steering vectors for the array without adding the substrates. Thus, true DOA peaks can be discriminated according to this feature. Simulation results show good performance of the proposed method. Trivial and non‐trivial ambiguities are efficiently resolved.
High‐selectivity wideband balanced bandpass filters using symmetrical multi‐mode resonators
Authors: Feng Wenjie , Che Wenquan , Gu Liming , Xue Quan
Published: September 2013

Two novel high‐selectivity wideband balanced bandpass filters using symmetrical multi‐mode resonators are presented. The proposed novel multi‐mode resonator is used to realise a six‐order wide passband in the differential mode. In addition, wide stopbands with insertion loss greater than 15 and 20 dB for the commode mode (0–18.5 GHz, 0–19 GHz) can also be achieved by the multi‐mode resonators. The even/odd‐modes of the symmetrical multi‐mode resonators can be adjusted by changing the characteristic impedance of the shorted/open stubs. Two planar wideband balanced filters with 3 dB fractional bandwidths of 67.6 and 63.7% are designed and fabricated. The theoretical and measured results are in good agreement and show good in‐band filtering performances and high selectivity.
Generation of arbitrary polarisation in any direction by cross dipole
Authors: Marhic Michel E. , Mehta Amit , Pal Arpan
Published: September 2013

The authors show that a wave with any desired polarisation state can generally be generated in any direction with respect to two crossed dipoles, and a closed‐form expression is provided for the complex ratio of the required drive voltages. The authors also provide a simple projection method for the polarisation ellipse in the case where the dipole centres coincide. For achieving the authors’ aim of exploiting closed‐form equations to generate circularly polarised (CP)/elliptically polarised (EP)/linearly polarised in any direction, two orthogonally placed dipoles resonating at 1 GHz each are designed. By selecting complex feed solutions, which are provided from the proposed closed‐form equations, it is realised precise polarisation states in a number of directions. Four separate such cases to generated CP and EP were investigated, and in all of them the numerical simulations and experiments validated the proposed theoretical predictions.
Propagation and stability characteristics of a 500-m-long laser-based fiducial line for high-precision alignment of long-distance linear accelerators
Authors: Suwada Tsuyoshi , Satoh Masanori , Telada Souichi , Minoshima Kaoru
Published: September 2013

A laser-based alignment system with a He-Ne laser has been newly developed in order to precisely align accelerator units at the KEKB injector linac. The laser beam was first implemented as a 500-m-long fiducial straight line for alignment measurements. We experimentally investigated the propagation and stability characteristics of the laser beam passing through laser pipes in vacuum. The pointing stability at the last fiducial point was successfully obtained with the transverse displacements of ±40 μm level in one standard deviation by applying a feedback control. This pointing stability corresponds to an angle of ±0.08 μrad. This report contains a detailed description of the experimental investigation for the propagation and stability characteristics of the laser beam in the laser-based alignment system for long-distance linear accelerators.
Optimal geometries and harmonic vibrational frequencies of the global minima of water clusters (H2O)n, n = 2–6, and several hexamer local minima at the CCSD(T) level of theory
Authors: Miliordos Evangelos , Aprà Edoardo , Xantheas Sotiris S.
Published: September 2013

We report the first optimum geometries and harmonic vibrational frequencies for the ring pentamer and several water hexamer (prism, cage, cyclic and two book) at the coupled-cluster including single, double, and full perturbative triple excitations (CCSD(T))/aug-cc-pVDZ level of theory. All five examined hexamer isomer minima previously reported by Møller-Plesset perturbation theory (MP2) are also minima on the CCSD(T) potential energy surface (PES). In addition, all CCSD(T) minimum energy structures for the n = 2–6 cluster isomers are quite close to the ones previously obtained by MP2 on the respective PESs, as confirmed by a modified Procrustes analysis that quantifies the difference between any two cluster geometries. The CCSD(T) results confirm the cooperative effect of the homodromic ring networks (systematic contraction of the nearest-neighbor (nn) intermolecular separations with cluster size) previously reported by MP2, albeit with O–O distances shorter by ∼0.02 Å, indicating that MP2 overcorrects this effect. The harmonic frequencies at the minimum geometries were obtained by the double differentiation of the CCSD(T) energy using an efficient scheme based on internal coordinates that reduces the number of required single point energy evaluations by ∼15% when compared to the corresponding double differentiation using Cartesian coordinates. Negligible differences between MP2 and CCSD(T) frequencies are found for the librational modes, while uniform increases of ∼15 and ∼25 cm−1 are observed for the bending and “free” OH harmonic frequencies. The largest differences between CCSD(T) and MP2 are observed for the harmonic hydrogen bonded frequencies, for which the former produces larger absolute values than the latter. Their CCSD(T) redshifts from the monomer values (Δω) are smaller than the MP2 ones, due to the fact that CCSD(T) produces shorter elongations (ΔR) of the respective hydrogen bonded OH lengths from the monomer value with respect to MP2. Both the MP2 and CCSD(T) results for the hydrogen bonded frequencies were found to closely follow the relation −Δω = s · ΔR, with a rate of s = 20.2 cm−1/0.001 Å for hydrogen bonded frequencies with IR intensities >400 km/mol. The CCSD(T) harmonic frequencies, when corrected using the MP2 anharmonicities obtained from second order vibrational perturbation theory, produce anharmonic CCSD(T) estimates that are within <60 cm−1 from the measured infrared (IR) active bands of the n = 2–6 clusters. Furthermore, the CCSD(T) harmonic redshifts (with respect to the monomer) trace the measured ones quite accurately. The energetic order between the various hexamer isomers on the PES (prism has the lowest energy) previously reported at MP2 was found to be preserved at the CCSD(T) level, whereas the inclusion of anharmonic corrections further stabilizes the cage among the hexamer isomers.
State to state photodissociation dynamics of D2O in the B band
Authors: Zhou Linsen , Lin Guang-Shuang-Mu , Xie Daiqian
Published: September 2013

State-to-state photodissociation dynamics of D2O in the B band has been investigated using the recently developed diabatic potential energy surfaces. Quantum dynamical calculations including the electronic $\tilde X$X̃ and $\tilde B$B̃ states were carried out using a Chebyshev real wave packet method. The nonadiabatic channel via the DOD conical intersection is facile, direct, and fast, which produces rotationally hot and vibrationally cold OD($\tilde X$X̃) product. On the other hand, the adiabatic channel on the excited state, leading to the OD($\tilde A$Ã) product, is dominated by long-lived resonances, which depend sensitively on the potential energy surface. The calculated absorption spectra, product state distributions, branching ratios, and angular distributions are in reasonably good agreement with the latest experimental results.
Kinetics of formation and coarsening of nanoporous α-titanium dealloyed with Mg melt
Authors: Tsuda Masashi , Wada Takeshi , Kato Hidemi
Published: September 2013

The transition behavior from a Ti–Cu alloy to nanoporous α-Ti, the kinetics of the dealloying reaction, and the coarsening of nanoporous α-Ti were studied, and the mechanism of dealloying with a metallic melt was investigated. When a Ti50Cu50 alloy disk was immersed in a Mg melt, the Cu content decreased from the surface of the disk, and transition layers of α-Ti and Ti2Cu were formed. The growth of the transition layers followed a parabolic law and the activation energy was close to those reported for the diffusion of solute atoms in liquids, suggesting that diffusion of Cu in the Mg melt mainly contributed to the rate-controlling process for the dealloying reaction. The temperature and time dependences of the ligament size followed a power law with an exponent of 4, suggesting that surface diffusion plays an important role in coarsening. All of these results are consistent with those reported for dealloying in aqueous solution, indicating that the underlying dealloying mechanism in a metallic melt is similar to that in aqueous solution.
Design and implementation of a novel portable atomic layer deposition/chemical vapor deposition hybrid reactor
Authors: Selvaraj Sathees Kannan , Jursich Gregory , Takoudis Christos G.
Published: September 2013

We report the development of a novel portable atomic layer deposition chemical vapor deposition (ALD/CVD) hybrid reactor setup. Unique feature of this reactor is the use of ALD/CVD mode in a single portable deposition system to fabricate multi-layer thin films over a broad range from “bulk-like” multi-micrometer to nanometer atomic dimensions. The precursor delivery system and control-architecture are designed so that continuous reactant flows for CVD and cyclic pulsating flows for ALD mode are facilitated. A custom-written LabVIEW program controls the valve sequencing to allow synthesis of different kinds of film structures under either ALD or CVD mode or both. The entire reactor setup weighs less than 40 lb and has a relatively small footprint of 8 × 9 in., making it compact and easy for transportation. The reactor is tested in the ALD mode with titanium oxide (TiO2) ALD using tetrakis(diethylamino)titanium and water vapor. The resulting growth rate of 0.04 nm/cycle and purity of the films are in good agreement with literature values. The ALD/CVD hybrid mode is demonstrated with ALD of TiO2 and CVD of tin oxide (SnOx). Transmission electron microscopy images of the resulting films confirm the formation of successive distinct TiO2-ALD and SnOx-CVD layers.
The nonlinear energy spectrum dependence of the optical conductivity in graphene
Authors: Yang C. H. , Luo Y. , Liu Z. S. , Jiang J. J.
Published: September 2013

In this article, we present a theoretical study of the optical spectrum induced by electron-electron interaction in graphene, which can be compared with the case in a conventional two-dimensional electron gas (2DEG). It is found that in sharp contrast to the conventional 2DEG, two intra- and inter-band transition channels for optical transition via absorption scattering can be observed. The optical conductivity depends on the electron density, the linearity of the energy spectrum, and the broadening width. The dependence of the optical spectrum on radiation frequency and broadening width is discussed. Analytical and numerical results showed that the inter-band transition contribution to optical conductivity has a turning point at two times the Fermi energy where the Fermi energy position can be tuned by the gate voltage. And the intra-band contribution depends on nonlinear energy dispersion and broadening width obviously.
Isolation of high quality graphene from Ru by solution phase intercalation
Authors: Koren E. , Sutter E. , Bliznakov S. , Ivars-Barcelo F. , Sutter P.
Published: September 2013

We introduce a method for isolating graphene grown on epitaxial Ru(0001)/α-Al2O3. The strong graphene/Ru(0001) coupling is weakened by electrochemically driven intercalation of hydrogen underpotentially deposited in aqueous KOH solution, which allows the penetration of water molecules at the graphene/Ru(0001) interface. Following these electrochemically driven processes, the graphene can be isolated by electrochemical hydrogen evolution and transferred to arbitrary supports. Raman and transport measurements demonstrate the high quality of the transferred graphene. Our results show that intercalation, typically carried out in vacuum, can be extended to solution environments for graphene processing under ambient conditions.
Determination of electron mobility in tris(8-hydroxy-quinolinato) aluminum by admittance spectroscopy
Authors: Wang Yanping , Chen Jiangshan , Dong Lisong , Ma Dongge
Published: September 2013

The electron mobilities of tris(8-hydroxy-quinolinato) aluminum (Alq3) thin films at various thicknesses (70–280 nm) have been determined by using admittance spectroscopy measurements. Our results show that the electric field dependence of electron mobilities exhibits different behaviors at different thicknesses of Alq3 films. Clearly, when the thickness of Alq3 film is less than 150 nm, the electron mobilities slightly decrease with increasing the electric field. For the thickness of Alq3 film more than 150 nm, however, the mobilities increase as the electric field increases. The phenomena are well discussed by energetic disorder. Using temperature dependent I–V characteristics, we further calculated the density of traps.
Multi-functional manipulations of microobjects based on electrolysis of water
Authors: Li Ning , Hu Junhui
Published: September 2013

The micromanipulation technology still faces some challenges. Direct rotary step-driving of a microobject has not been realized by physical means. The implementation of 3-D attitude adjustment of a microobject usually involves a complicated driving and controlling system. The capability and controllability of releasing sticky microobjects from a probe is still limited. In this paper, we demonstrate a strategy to use hydrogen bubbles generated by electrolysis of water to manipulate microobjects in water on a substrate surface. Manipulation functions implemented by this strategy include direct rotary step-driving and attitude adjustment of a single microparticle, and controlled release of a single sticky microparticle.
Exchange-stiffness constant of a Nd-Fe-B based nanocomposite determined by magnetic neutron scattering
Authors: Bick Jens-Peter , Suzuki Kiyonori , Gilbert Elliot P. , Forgan Edward M. , Schweins Ralf , Lindner Peter , Kübel Christian , Michels Andreas
Published: September 2013

We report magnetic-field-dependent small-angle neutron scattering (SANS) experiments on a Nd2Fe14B/Fe3B nanocomposite. For the two scattering geometries where the applied magnetic field is either perpendicular or parallel to the incoming neutron beam, we have independently analyzed the field-dependent SANS data in terms of micromagnetic theory, taking into account demagnetizing-field effects. The approach in reciprocal space is supported by an analysis of the data in real space and provides consistent results for the exchange-stiffness parameter and the mean magnetic anisotropy-field radius.
Influence of the channel electric field distribution on the polarization Coulomb field scattering in AlGaN/AlN/GaN heterostructure field-effect transistors
Authors: Yu Yingxia , Lin Zhaojun , Luan Chongbiao , Lv Yuanjie , Feng Zhihong , Yang Ming , Wang Yutang , Chen Hong
Published: September 2013

Using the Quasi-Two-Dimensional (quasi-2D) model, the current-voltage (I-V) characteristics of AlGaN/AlN/GaN heterostructure field-effect transistors (HFETs) with different gate length were simulated based on the measured capacitance-voltage (C-V) characteristics and I-V characteristics. By analyzing the simulation results, we found that the different polarization charge distribution generated by the different channel electric field distribution can result in different polarization Coulomb field scattering, and the difference of the electron mobility mostly caused by the polarization Coulomb field scattering can reach up to 1829.9 cm2/V·s for the prepared AlGaN/AlN/GaN HFET. In addition, it was also found that when the two-dimension electron gas (2DEG) sheet density is modulated by the drain-source bias, the electron mobility appears peak with the variation of the 2DEG sheet density, and the ratio of gate length to drain-source distance is smaller, the 2DEG sheet density corresponding to the peak point is higher.
Australian perennial shrub species add value to the feed base of grazing livestock in low- to medium-rainfall zones
Authors: Revell D. K. , Norman H. C. , Vercoe P. E. , Phillips N. , Toovey A. , Bickell S. , Hulm E. , Hughes S. , Emms J.
Published: September 2013

Australian native perennial shrubs that are adapted to drought and infertile soils contribute nutrients to grazing systems that would otherwise support limited ruminant productivity. In this study, we report the nutritive value of 39 Australian shrub species of the genera Atriplex, Rhagodia, Maireana, Chenopodium, Enchylaena, Acacia, Eremophila, and Kennedia. Edible foliage was sampled in winter and summer, and there was little difference in nutritive value between seasons. The in vitro organic matter digestibility of most shrub species was 40–70%. Most species contained medium to high levels of crude protein (12–22% of dry matter, DM) and high concentrations of sulfur (2–8 g/kg DM). In an 8-week grazing experiment in which Merino wethers grazed a ‘shrub system’ containing four shrub species and a sown inter-row of annual pasture, the sheep gained weight during autumn without supplementary feeding. By comparison, sheep fed senesced volunteer pasture and supplementary cereal grain only maintained weight. The forage shrubs provided up to 50% of the total DM intake of sheep grazing the ‘shrub system’ and made a modest contribution to the digestible energy intake of the animals and a large contribution to their crude protein and mineral intake. Considering the timely and predictable provision of limiting nutrients and benefits such as gut health and the provision of shade and shelter, we suggest that Australian shrub species can make a valuable addition to the feed base of low- to medium-rainfall zones in southern Australia.
N,N-Dialkyl-N′-Chlorosulfonyl Chloroformamidines in Heterocyclic Synthesis. Part X. The First Pyrazolo[1,5-b][1,2,4,6]thiatriazine Derivatives and their Unusual Reactions with Acylating Agents
Authors: Norman Rebecca E. , Perkins Michael V. , Liepa Andris J. , Francis Craig L.
Published: September 2013

N,N-dialkyl-N′-chlorosulfonyl chloroformamidines 1 underwent a regioselective reaction with 3-aminopyrazoles 2 to produce pyrazolo[1,5-b][1,2,4,6]thiatriazines 3, representatives of a new ring system. Attempted N-acylation of compounds 3 with acetic anhydride (or chloride) and benzoyl chloride in pyridine, only afforded 5-(pyridin-4-yl)-pyrazolo[1,5-b][1,2,4,6]thiatriazine derivatives 11. The analogous reaction with pyridazine led to the corresponding pyridazin-4-yl derivative.
Blind Man’s Bluff – Elaboration of Fragment Hits in the Absence of Structure for the Development
of Antitrypsin Deficiency Inhibitors
Authors: Headey Stephen J. , Pearce Mary C. , Scanlon Martin J. , Bottomley Stephen P.
Published: September 2013

The three pillars of rational drug design from a fragment library are an efficient screen, a robust assay, and atomic-resolution structures of the protein–ligand complexes. However, not all targets are amenable to structure determination by X-ray crystallography or NMR spectroscopy. In particular, targets involved in diseases of protein misfolding are inherently intractable. In the absence of structures, we are blind. However, the lack of structural information need not preclude the use of fragment-based approaches. The use of appropriate NMR techniques can enable us to detect the effects of protein binding on ligand resonances. In our efforts to identify compounds that affect the kinetics of α1-antitrypsin misfolding, we have used saturation transfer difference NMR spectroscopy to detect hits from mixtures of compounds in a fragment library. In the absence of structures, the initial challenge is three-fold: to (1) distinguish between binding sites; (2) evaluate the relative affinities of hits; and (3) advance them to the stage where activity can be detected in biological assays. We largely achieved these aims by the use of Carr–Purcell–Meiboom–Gill NMR competition experiments that detect differential relaxation of the ligand on protein binding.
Methoxy-Poly(ethylene glycol)-block-Poly(ε-caprolactone) Bearing Pendant Aldehyde Groups as pH-Responsive Drug Delivery Carrier
Authors: Ma Gejun , Li Deshan , Wang Ji , Zhang Xuefei , Tang Haoyu
Published: September 2013

A biodegradable amphiphilic block copolymer of methoxy poly(ethylene glycol)-block-poly(ϵ-caprolactone) bearing pendant aldehyde groups was synthesised by a combination of ring-opening polymerisation and thio-bromo ‘click’ chemistry. The free aldehyde groups on the copolymer were reacted with hydrophobic payloads (p-methoxylaniline as a model drug) by a benzoic–imine linker, which was responsive to pH change. NMR, FTIR, and gel permeation chromatography analysis confirmed the copolymer structures. In vitro release studies revealed that under acid stimulus, hydrolysis of the benzoic–imine bond resulted in a rapid drug release. This new amphiphilic block copolymer is expected to have promising applications in biodegradable controlled drug delivery systems.
Simple Metal-catalyst-free Production of Carbon Nanostructures
Authors: Ellis Thomas K. , Paras Christian , Hill Matthew R. , Stride John A.
Published: September 2013

We report the metal-catalyst-free production of multiwalled carbon nanotubes and nanobubbles, in a chemical reduction of hexachlorobenzene by metallic sodium, giving high yields (in excess of 80 %) and at temperatures as low as 190°C for multiwalled carbon nanotubes and 100°C for nanobubble formation. The carbon nanotube samples produced under solvothermal conditions were found to consist of large bundles of nanotubes (>50 µm) consistent with a facial growth from the surface of the molten metal. Meanwhile, the nanobubbles produced under ambient pressure were found to be small (≤1 µm), polydispersed (smallest ~50 nm), and the bulk to have a large microporous area. With the regulatory complexities and high environmental and economic costs of remediating waste containing highly hazardous halogenated aromatic chemicals, necessitating high-temperature incineration under strictly controlled conditions, this low-temperature, low-cost chemical degradation of hexachlorobenzene is of great potential as a scalable and workable remediation technology.
Synthesis of Anisotropic, Amphiphilic Grafted Multi-Star Polymers and Investigation of their Self-Assembling Characteristics
Authors: Blencowe Anton , Tan Jing Fung , Goh Tor Kit , Goldie Kenneth N. , Zhang Xuehua , Qiao Greg G.
Published: September 2013

Herein, we report the synthesis of amphiphilic multi-star architectures consisting of discrete poly(methacrylic acid)-based core cross-linked star polymers joined together by polystyrene-grafted linear connectors by a combination of atom transfer radical polymerisation of protected macroinitiator precursors and a copper-catalysed azide-alkyne cycloaddition grafting-to approach. The anisotropic multi-star architectures, which were obtained as individual di- and tri-star polymers with segregated hydrophobic and hydrophilic domains, undergo aggregation in apolar solvents resulting in the formation of large nanometre-scale vesicles. The self-assembling behaviour of these large amphiphilic multi-star polymers (Mw = 869–1097 kDa) was studied using dynamic light scattering, transmission electron microscopy, and atomic force microscopy.
pH sensing by FAK-His58 regulates focal adhesion remodeling
Authors: Choi Chang-Hoon , Webb Bradley A. , Chimenti Michael S. , Jacobson Matthew P. , Barber Diane L.
Published: September 2013

Intracellular pH (pHi) dynamics regulates diverse cellular processes, including remodeling of focal adhesions. We now report that focal adhesion kinase (FAK), a key regulator of focal adhesion remodeling, is a pH sensor responding to physiological changes in pH. The initial step in FAK activation is autophosphorylation of Tyr397, which increased with higher pHi. We used a genetically encoded biosensor to show increased pH at focal adhesions as they mature during cell spreading. We also show that cells with reduced pHi had attenuated FAK-pY397 as well as defective cell spreading and focal adhesions. Mutagenesis studies indicated FAK-His58 is critical for pH sensing and molecular dynamics simulations suggested a model in which His58 deprotonation drives conformational changes that may modulate accessibility of Tyr397 for autophosphorylation. Expression of FAK-H58A in fibroblasts was sufficient to restore defective autophosphorylation and cell spreading at low pHi. These data are relevant to understanding cancer metastasis, which is dependent on increased pHi and FAK activity.
Ero1-α and PDIs constitute a hierarchical electron transfer network of endoplasmic reticulum oxidoreductases
Authors: Araki Kazutaka , Iemura Shun-ichiro , Kamiya Yukiko , Ron David , Kato Koichi , Natsume Tohru , Nagata Kazuhiro
Published: September 2013

Ero1-α and endoplasmic reticulum (ER) oxidoreductases of the protein disulfide isomerase (PDI) family promote the efficient introduction of disulfide bonds into nascent polypeptides in the ER. However, the hierarchy of electron transfer among these oxidoreductases is poorly understood. In this paper, Ero1-α–associated oxidoreductases were identified by proteomic analysis and further confirmed by surface plasmon resonance. Ero1-α and PDI were found to constitute a regulatory hub, whereby PDI induced conformational flexibility in an Ero1-α shuttle cysteine (Cys99) facilitated intramolecular electron transfer to the active site. In isolation, Ero1-α also oxidized ERp46, ERp57, and P5; however, kinetic measurements and redox equilibrium analysis revealed that PDI preferentially oxidized other oxidoreductases. PDI accepted electrons from the other oxidoreductases via its a′ domain, bypassing the a domain, which serves as the electron acceptor from reduced glutathione. These observations provide an integrated picture of the hierarchy of cooperative redox interactions among ER oxidoreductases in mammalian cells.
Algebras whose Tits form accepts a maximal omnipresent root
Authors: de la Peña José , Skowroński Andrzej
Published: September 2013

Let

k
k

be an algebraically closed field and

A
A

be a finite-dimensional associative basic

k
k

-algebra of the form

A
=
k
Q

/

I

A=kQ/I

where

Q
Q

is a quiver without oriented cycles or double arrows and

I
I

is an admissible ideal of

k
Q

kQ

. We consider roots of the Tits form

q
A

q_A

, in particular in the case where

q
A

q_A

is weakly non-negative. We prove that for any maximal omnipresent root

v
v

of

q
A

q_A

, there exists an indecomposable

A
A

-module

X
X

such that v=dim X. Moreover, if

A
A

is strongly simply connected, the existence of a maximal omnipresent root of

q
A

q_A

implies that

A
A

is tame of tilted type.
Predator–prey population models of migrant insects with phase change
Authors: Cheke Robert A. , Tang Sanyi , Tratalos Jamie A.
Published: September 2013

Locusts and some noctuid moths exhibit polyphenism whereby they can change their “phase” from a solitary (“solitarious”) condition to a gregarious one. Gregarious phase insects are often migratory travelling from recession areas into larger invasion zones and, among locusts, occur in swarms. Difference equation models of the population dynamics of insects that take account of such changes between solitarious or gregarious phases in relation to predation, both with and without time delays, are described. Solutions of the models are non-linear. Chaotic solutions are obtainable under some circumstances even with very low values for the intrinsic rate of increase in the prey population, in contrast to previous conclusions from models without predation. Comparisons with the results obtained for single species with those obtained in this paper show that predation can reduce (i) the average density of the prey, (ii) durations of periods when the populations stay in the gregarious phase, and (iii) the frequency of their shifts from the solitarious state to the gregarious form. Similar results are obtained if a time delay is introduced to mimic a transient phase. With a wide range of parameter values, models including predation with or without random perturbation reveal several stable attractors for phase diagrams of the populations, which are biologically meaningful compared with empirical datasets and which were unobtainable without predation, suggesting that inclusion of predation and time delays improved the realism of the models. However, comparisons between autocorrelation analyses of locust time-series, but of swarms only, with those of model outputs suggest that inclusion of the time delay leads to less, not more, realism. The prediction of non-linearity in the dynamics of migrant insects with phase changes and its significance for forecasting to aid control is briefly discussed in relation to published data on the desert locust Schistocerca gregaria.
DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation
Authors: Lormand Justin D. , Buncher Noah , Murphy Connor T. , Kaur Parminder , Lee Marietta Y. , Burgers Peter , Wang Hong , Kunkel Thomas A. , Opresko Patricia L.
Published: September 2013

Previous evidence indicates that telomeres resemble common fragile sites and present a challenge for DNA replication. The precise impediments to replication fork progression at telomeric TTAGGG repeats are unknown, but are proposed to include G-quadruplexes (G4) on the G-rich strand. Here we examined DNA synthesis and progression by the replicative DNA polymerase δ/proliferating cell nuclear antigen/replication factor C complex on telomeric templates that mimic the leading C-rich and lagging G-rich strands. Increased polymerase stalling occurred on the G-rich template, compared with the C-rich and nontelomeric templates. Suppression of G4 formation by substituting Li+ for K+ as the cation, or by using templates with 7-deaza-G residues, did not alleviate Pol δ pause sites within the G residues. Furthermore, we provide evidence that G4 folding is less stable on single-stranded circular TTAGGG templates where ends are constrained, compared with linear oligonucleotides. Artificially stabilizing G4 structures on the circular templates with the G4 ligand BRACO-19 inhibited Pol δ progression into the G-rich repeats. Similar results were obtained for yeast and human Pol δ complexes. Our data indicate that G4 formation is not required for polymerase stalling on telomeric lagging strands and suggest that an alternative mechanism, in addition to stable G4s, contributes to replication stalling at telomeres.
A transient α-helical molecular recognition element in the disordered N-terminus of the Sgs1 helicase is critical for chromosome stability and binding of Top3/Rmi1
Authors: Kennedy Jessica A. , Daughdrill Gary W. , Schmidt Kristina H.
Published: September 2013

The RecQ-like DNA helicase family is essential for the maintenance of genome stability in all organisms. Sgs1, a member of this family in Saccharomyces cerevisiae, regulates early and late steps of double-strand break repair by homologous recombination. Using nuclear magnetic resonance spectroscopy, we show that the N-terminal 125 residues of Sgs1 are disordered and contain a transient α-helix that extends from residue 25 to 38. Based on the residue-specific knowledge of transient secondary structure, we designed proline mutations to disrupt this α-helix and observed hypersensitivity to DNA damaging agents and increased frequency of genome rearrangements. In vitro binding assays show that the defects of the proline mutants are the result of impaired binding of Top3 and Rmi1 to Sgs1. Extending mutagenesis N-terminally revealed a second functionally critical region that spans residues 9–17. Depending on the position of the proline substitution in the helix functional impairment of Sgs1 function varied, gradually increasing from the C- to the N-terminus. The multiscale approach we used to interrogate structure/function relationships in the long disordered N-terminal segment of Sgs1 allowed us to precisely define a functionally critical region and should be generally applicable to other disordered proteins.
Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features
Authors: Lv Jie , Liu Hongbo , Huang Zhijun , Su Jianzhong , He Hongjuan , Xiu Youcheng , Zhang Yan , Wu Qiong
Published: September 2013

In silico prediction of genomic long non-coding RNAs (lncRNAs) is prerequisite to the construction and elucidation of non-coding regulatory network. Chromatin modifications marked by chromatin regulators are important epigenetic features, which can be captured by prevailing high-throughput approaches such as ChIP sequencing. We demonstrate that the accuracy of lncRNA predictions can be greatly improved when incorporating high-throughput chromatin modifications over mouse embryonic stem differentiation toward adult Cerebellum by logistic regression with LASSO regularization. The discriminating features include H3K9me3, H3K27ac, H3K4me1, open reading frames and several repeat elements. Importantly, chromatin information is suggested to be complementary to genomic sequence information, highlighting the importance of an integrated model. Applying integrated model, we obtain a list of putative lncRNAs based on uncharacterized fragments from transcriptome assembly. We demonstrate that the putative lncRNAs have regulatory roles in vicinity of known gene loci by expression and Gene Ontology enrichment analysis. We also show that the lncRNA expression specificity can be efficiently modeled by the chromatin data with same developmental stage. The study not only supports the biological hypothesis that chromatin can regulate expression of tissue-specific or developmental stage-specific lncRNAs but also reveals the discriminating features between lncRNA and coding genes, which would guide further lncRNA identifications and characterizations.
Structural insights into Paf1 complex assembly and histone binding
Authors: Chu Xinlei , Qin Xiaohong , Xu Huisha , Li Lei , Wang Zheng , Li Fengzhi , Xie Xingqiao , Zhou Hao , Shen Yuequan , Long Jiafu
Published: September 2013

The highly conserved Paf1 complex (PAF1C) plays critical roles in RNA polymerase II transcription elongation and in the regulation of histone modifications. It has also been implicated in other diverse cellular activities, including posttranscriptional events, embryonic development and cell survival and maintenance of embryonic stem cell identity. Here, we report the structure of the human Paf1/Leo1 subcomplex within PAF1C. The overall structure reveals that the Paf1 and Leo1 subunits form a tightly associated heterodimer through antiparallel beta-sheet interactions. Detailed biochemical experiments indicate that Leo1 binds to PAF1C through Paf1 and that the Ctr9 subunit is the key scaffold protein in assembling PAF1C. Furthermore, we show that the Paf1/Leo1 heterodimer is necessary for its binding to histone H3, the histone octamer, and nucleosome in vitro. Our results shed light on the PAF1C assembly process and substrate recognition during various PAF1C-coordinated histone modifications.
Self-duplexing CUG repeats selectively inhibit mutant huntingtin expression
Authors: Fiszer Agnieszka , Olejniczak Marta , Galka-Marciniak Paulina , Mykowska Agnieszka , Krzyzosiak Wlodzimierz J.
Published: September 2013

Huntington’s disease (HD) is a neurodegenerative genetic disorder caused by the expansion of the CAG repeat in the translated sequence of the HTT gene. This expansion generates a mutant huntingtin protein that contains an abnormally elongated polyglutamine tract, which, together with mutant transcript, causes cellular dysfunction. Currently, there is no curative treatment available to patients suffering from HD; however, the selective inhibition of the mutant allele expression is a promising therapeutic option. In this study, we developed a new class of CAG repeat-targeting silencing reagents that consist of self-duplexing CUG repeats. Self-duplex formation was induced through one or several U-base substitutions. A number of self-duplexing guide-strand-only short interfering RNAs have been tested through transfection into cells derived from HD patients, showing distinct activity profiles. The best reagents were highly discriminatory between the normal and mutant HTT alleles (allele selectivity) and the HTT transcript and other transcripts containing shorter CAG repeats (gene selectivity). We also demonstrated that the self-duplexing CUG repeat short interfering RNAs use the RNA interference pathway to elicit silencing, and repeat-targeting reagents showed similar activity and selectivity when expressed from short hairpin RNA vectors to achieve more durable silencing effects.
On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs
Authors: Wu Chyuan-Chuan , Li Yi-Ching , Wang Ying-Ren , Li Tsai-Kun , Chan Nei-Li
Published: September 2013

Type II topoisomerases (Top2s) alter DNA topology via the formation of an enzyme–DNA adduct termed cleavage complex, which harbors a transient double-strand break in one DNA to allow the passage of another. Agents targeting human Top2s are clinically active anticancer drugs whose trapping of Top2-mediated DNA breakage effectively induces genome fragmentation and cell death. To understand the structural basis of this drug action, we previously determined the structure of human Top2 β-isoform forming a cleavage complex with the drug etoposide and DNA, and described the insertion of drug into DNA cleavage site and drug-induced decoupling of catalytic groups. By developing a post-crystallization drug replacement procedure that simplifies structural characterization of drug-stabilized cleavage complexes, we have extended the analysis toward other structurally distinct drugs, m-AMSA and mitoxantrone. Besides the expected drug intercalation, a switch in ribose puckering in the 3′-nucleotide of the cleavage site was robustly observed in the new structures, representing a new mechanism for trapping the Top2 cleavage complex. Analysis of drug-binding modes and the conformational landscapes of the drug-binding pockets provide rationalization of the drugs’ structural-activity relationships and explain why Top2 mutants exhibit differential effects toward each drug. Drug design guidelines were proposed to facilitate the development of isoform-specific Top2-targeting anticancer agents.
ATR kinase activation in G1 phase facilitates the repair of ionizing radiation-induced DNA damage
Authors: Gamper Armin M. , Rofougaran Reza , Watkins Simon C. , Greenberger Joel S. , Beumer Jan H. , Bakkenist Christopher J.
Published: September 2013

The kinase ATR is activated by RPA-coated single-stranded DNA generated at aberrant replicative structures and resected double strand breaks. While many hundred candidate ATR substrates have been identified, the essential role of ATR in the replicative stress response has impeded the study of ATR kinase-dependent signalling. Using recently developed selective drugs, we show that ATR inhibition has a significantly more potent effect than ATM inhibition on ionizing radiation (IR)-mediated cell killing. Transient ATR inhibition for a short interval after IR has long-term consequences that include an accumulation of RPA foci and a total abrogation of Chk1 S345 phosphorylation. We show that ATR kinase activity in G1 phase cells is important for survival after IR and that ATR colocalizes with RPA in the absence of detectable RPA S4/8 phosphorylation. Our data reveal that, unexpectedly, ATR kinase inhibitors may be more potent cellular radiosensitizers than ATM kinase inhibitors, and that this is associated with a novel role for ATR in G1 phase cells.
Spotted Wilt Disease Evaluation Among High-Oleic Peanut Cultivars
Authors: Branch W. D. , Culbreath A. K.
Published: September 2013

The release of high-oleic, United States runner and virginia market type peanut (Arachis hypogaea L.) cultivars has been steadily increasing during the past several years. Two planting dates were utilized for disease evaluation and agronomic performance among these newer high-oleic cultivars. The first planting date test was in mid-April to allow for increased incidence of spotted wilt disease caused by Tomato spotted wilt virus (TSWV). The second planting date test was in mid-May to allow for less TSWV and provide more of an optimum time by comparison. Significant differences (P ≤ 0.05) were found within each of the three (3-year) averages among cultivars for TSWV and total disease (TD) incidence, pod yield, and dollar values. Among the virginia-types, Georgia Hi-O/L, Georgia-05E, and Georgia-08V, and runner-types, Georgia-02C and Georgia-09B, consistently had the lowest TSWV and TD incidence and the highest pod yield and dollar values in both the mid-April and mid-May planting date tests. No significant differences were found between the mid-April and the mid-May planting dates when averaged across this 5-year study for TSWV and TD incidence, pod yield, and dollar values. This suggests that the high-level of TSWV-resistance among these newer high-oleic cultivars should have a greater influence than planting dates on agronomic performance.

Accepted for publication 8 June 2013. Published 12 August 2013.
Identification of the G143A Mutation in Cytochrome b Associated with QoI Resistance in Cercospora beticola Isolates from the Red River Valley
Authors: Bolton Melvin D. , Rivera-Varas Viviana , Secor Gary A. , Cattanach Allan W. , Metzger Michael S.
Published: September 2013

Cercospora leaf spot (CLS), caused by the fungal pathogen Cercospora beticola, is the most important foliar disease of sugarbeet. The disease is managed in part by timely applications of quinone outside inhibitor (QoI) fungicides. However, pathogen resistance to QoI fungicides is associated with the exchange of glycine to alanine at amino acid position 143 (G143A) in the C. beticola cytochrome b gene. To assess whether QoI resistance has developed in C. beticola in the Red River Valley (RRV) of Minnesota and North Dakota, a real-time PCR procedure was used to determine whether the G143A mutation could be identified in samples harvested from 922 fields across the RRV. In total, 12 fields located in diverse locations within the RRV contained the G143A mutation, suggesting that QoI resistance arose independently at each location and in several genetic backgrounds. This is the first report of QoI resistance in the RRV. Careful monitoring of the G143A mutation will be necessary to ensure that QoI fungicides remain efficacious for CLS management in the RRV region.

Accepted for publication 31 May 2013. Published 12 August 2013.
Identification of Poinsettia mosaic virus Associated with a Virus-like Mottle Symptom on Poinsettia in Ohio
Authors: Fisher John R. , Bell John
Published: September 2013

These results represent the first confirmed report of Poinsettia mosaic virus (PnMV) in poinsettia in Ohio. They also serve to increase awareness of the virus among poinsettia growers so they may more effectively scout nursery stock for infected plants.

Accepted for publication 22 May 2013. Published 13 August 2013.