bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of gamma-globulin at nanogram levels by its quenching effect on the fluorescence of a red emitting conjugated polymer
Authors: Zhang Ping , Zhuo Shujuan , Sun Lilin , Zhang Ping , Zhu Changqing
Published: March 2015

A novel red emitting fluorescence sensor has been constructed and used for the selective assay of gamma-globulin in the presence of serum albumin.
Influence of Mn incorporation on the supercapacitive properties of hybrid CuO/Cu(OH)2 electrodes
Authors: Shinde Surendra K. , Dubal Deepak P. , Ghodake Gajanan S. , Gomez-Romero Pedro , Kim Sungyeol , Fulari Vijay J.
Published: March 2015

Variation of specific capacitance of undoped and Mn doped CuO/Cu(OH)2 hybrid electrodes with corresponding SEM.
Poly(acrylic acid) functionalized magnetic graphene oxide nanocomposite for removal of methylene blue
Authors: Zhang Jiawen , Azam Md. Shafiul , Shi Chen , Huang Jun , Yan Bin , Liu Qingxia , Zeng Hongbo
Published: March 2015

A polyacrylic acid functionalized magnetic Fe3O4nanoparticle-graphene oxide nanocomposite shows high adsorption capacity of dye and excellent recyclability in water treatment.
Understanding the run-in tribological behavior of amorphous carbon films against Al2O3balls under high vacuum
Authors: Zhang Renhui , Lu Zhibin , Wang Liping
Published: March 2015

Run-in behavior of amorphous carbon films significantly affected their tribological properties.
Microwave-assisted C–N and C–S bond-forming reactions: an efficient three-component domino sequence for the synthesis of sulfoether-decorated imidazo[1,2-a]pyridines
Authors: Zhan Haiying , Cao Hua , Qiu Huifang , Li Naiying , Chen Longbin , Liu Jingyun , Cai Huiyin , Tan Jingwen
Published: March 2015

Microwave-assisted three-component domino reaction for the synthesis of sulfoether-decorated imidazo[1,2-a]pyridines.
Direct coupling of unactivated alkynes and C(sp3)–H bonds catalyzed by a Pt(ii, iv)-centered catalyst: a computational study
Authors: Li Zhi-Feng , Li Hui-Xue , Yang Xiao-Ping , Liu Xin-Wen , Zuo Guo-Fang , Zhao Cunyuan
Published: March 2015

Direct coupling of unactivated alkynes and C(sp3)–H bonds catalyzed by a Pt(ii, iv)-centered catalyst X (X = PtCl2, PtBr2, PtI2 and PtI4) (J. Am. Chem. Soc. 2009, 131, 16525) have been theoretically investigated with density functional theory (DFT).
Robust anti-reflective silica nanocoatings: abrasion resistance enhanced via capillary condensation of APTES
Authors: Cai Chao , Yang Xiaoli , Wang Zhen , Dong Haixia , Ma Hongwei , Zhao Ning , Xu Jian
Published: March 2015

Capillary condensation of APTES into silica anti-reflective coatings offers both excellent anti-reflective property and robust mechanical durability.
The first blue phase reactive monomers containing a bi-mesogenic core and their side-chain polymers
Authors: Wei Chong-Lun , Lin Yen-Ting , Chang Jin-Huai , Chiang I-Hung , Lin Hong-Cheu
Published: March 2015

Two blue phase reactive monomers with different spacer lengths are first reported to exhibit BPIII, which can be extended by copolymerization.
A fixed mass method for the Kramers-Moyal expansion—Application to time series with outliers
Authors: Petelczyc M. , Żebrowski J. J. , Orłowska-Baranowska E.
Published: March 2015

Extraction of stochastic and deterministic components from empirical data—necessary for the reconstruction of the dynamics of the system—is discussed. We determine both components using the Kramers-Moyal expansion. In our earlier papers, we obtained large fluctuations in the magnitude of both terms for rare or extreme valued events in the data. Calculations for such events are burdened by an unsatisfactory quality of the statistics. In general, the method is sensitive to the binning procedure applied for the construction of histograms. Instead of the commonly used constant width of bins, we use here a constant number of counts for each bin. This approach—the fixed mass method—allows to include in the calculation events, which do not yield satisfactory statistics in the fixed bin width method. The method developed is general. To demonstrate its properties, here, we present the modified Kramers-Moyal expansion method and discuss its properties by the application of the fixed mass method to four representative heart rate variability recordings with different numbers of ectopic beats. These beats may be rare events as well as outlying, i.e., very small or very large heart cycle lengths. The properties of ectopic beats are important not only for medical diagnostic purposes but the occurrence of ectopic beats is a general example of the kind of variability that occurs in a signal with outliers. To show that the method is general, we also present results for two examples of data from very different areas of science: daily temperatures at a large European city and recordings of traffics on a highway. Using the fixed mass method, to assess the dynamics leading to the outlying events we studied the occurrence of higher order terms of the Kramers-Moyal expansion in the recordings. We found that the higher order terms of the Kramers-Moyal expansion are negligible for heart rate variability. This finding opens the possibility of the application of the Langevin equation to the whole range of empirical signals containing rare or outlying events. Note, however, that the higher order terms are non-negligible for the other data studied here and for it the Langevin equation is not applicable as a model.
Nanomechanical and topographical imaging of living cells by atomic force microscopy with colloidal probes
Authors: Puricelli Luca , Galluzzi Massimiliano , Schulte Carsten , Podestà Alessandro , Milani Paolo
Published: March 2015

Atomic Force Microscopy (AFM) has a great potential as a tool to characterize mechanical and morphological properties of living cells; these properties have been shown to correlate with cells’ fate and patho-physiological state in view of the development of novel early-diagnostic strategies. Although several reports have described experimental and technical approaches for the characterization of cellular elasticity by means of AFM, a robust and commonly accepted methodology is still lacking. Here, we show that micrometric spherical probes (also known as colloidal probes) are well suited for performing a combined topographic and mechanical analysis of living cells, with spatial resolution suitable for a complete and accurate mapping of cell morphological and elastic properties, and superior reliability and accuracy in the mechanical measurements with respect to conventional and widely used sharp AFM tips. We address a number of issues concerning the nanomechanical analysis, including the applicability of contact mechanical models and the impact of a constrained contact geometry on the measured Young’s modulus (the finite-thickness effect). We have tested our protocol by imaging living PC12 and MDA-MB-231 cells, in order to demonstrate the importance of the correction of the finite-thickness effect and the change in Young’s modulus induced by the action of a cytoskeleton-targeting drug.
Next generation of the self-consistent and environment-dependent Hamiltonian: Applications to various boron allotropes from zero- to three-dimensional structures
Authors: Tandy P. , Yu Ming , Leahy C. , Jayanthi C. S. , Wu S. Y.
Published: March 2015

An upgrade of the previous self-consistent and environment-dependent linear combination of atomic orbitals Hamiltonian (referred as SCED-LCAO) has been developed. This improved version of the semi-empirical SCED-LCAO Hamiltonian, in addition to the inclusion of self-consistent determination of charge redistribution, multi-center interactions, and modeling of electron-electron correlation, has taken into account the effect excited on the orbitals due to the atomic aggregation. This important upgrade has been subjected to a stringent test, the construction of the SCED-LCAO Hamiltonian for boron. It was shown that the Hamiltonian for boron has successfully characterized the electron deficiency of boron and captured the complex chemical bonding in various boron allotropes, including the planar and quasi-planar, the convex, the ring, the icosahedral, and the fullerene-like clusters, the two-dimensional monolayer sheets, and the bulk alpha boron, demonstrating its transferability, robustness, reliability, and predictive power. The molecular dynamics simulation scheme based on the Hamiltonian has been applied to explore the existence and the energetics of ∼230 compact boron clusters BN with N in the range from ∼100 to 768, including the random, the rhombohedral, and the spherical icosahedral structures. It was found that, energetically, clusters containing whole icosahedral B12 units are more stable for boron clusters of larger size (N > 200). The ease with which the simulations both at 0 K and finite temperatures were completed is a demonstration of the efficiency of the SCED-LCAO Hamiltonian.
High average power, highly brilliant laser-produced plasma source for soft X-ray spectroscopy
Authors: Mantouvalou Ioanna , Witte Katharina , Grötzsch Daniel , Neitzel Michael , Günther Sabrina , Baumann Jonas , Jung Robert , Stiel Holger , Kanngießer Birgit , Sandner Wolfgang
Published: March 2015

In this work, a novel laser-produced plasma source is presented which delivers pulsed broadband soft X-radiation in the range between 100 and 1200 eV. The source was designed in view of long operating hours, high stability, and cost effectiveness. It relies on a rotating and translating metal target and achieves high stability through an on-line monitoring device using a four quadrant extreme ultraviolet diode in a pinhole camera arrangement. The source can be operated with three different laser pulse durations and various target materials and is equipped with two beamlines for simultaneous experiments. Characterization measurements are presented with special emphasis on the source position and emission stability of the source. As a first application, a near edge X-ray absorption fine structure measurement on a thin polyimide foil shows the potential of the source for soft X-ray spectroscopy.
The ReactorAFM: Non-contact atomic force microscope operating under high-pressure and high-temperature catalytic conditions
Authors: Roobol S. B. , Cañas-Ventura M. E. , Bergman M. , van Spronsen M. A. , Onderwaater W. G. , van der Tuijn P. C. , Koehler R. , Ofitserov A. , van Baarle G. J. C. , Frenken J. W. M.
Published: March 2015

An Atomic Force Microscope (AFM) has been integrated in a miniature high-pressure flow reactor for in-situ observations of heterogeneous catalytic reactions under conditions similar to those of industrial processes. The AFM can image model catalysts such as those consisting of metal nanoparticles on flat oxide supports in a gas atmosphere up to 6 bar and at a temperature up to 600 K, while the catalytic activity can be measured using mass spectrometry. The high-pressure reactor is placed inside an Ultrahigh Vacuum (UHV) system to supplement it with standard UHV sample preparation and characterization techniques. To demonstrate that this instrument successfully bridges both the pressure gap and the materials gap, images have been recorded of supported palladium nanoparticles catalyzing the oxidation of carbon monoxide under high-pressure, high-temperature conditions.
Invariant tori for a derivative nonlinear Schrödinger equation with quasi-periodic forcing
Authors: Liu Jie , Si Jianguo
Published: March 2015

This paper is concerned with a one dimensional derivative nonlinear Schrödinger equation with quasi-periodic forcing under periodic boundary conditions iut+uxx+ig(βt)(f(u2)u)x=0,x∈T≔R/2πZ, where g(βt) is real analytic and quasi-periodic on t with frequency vector β = (β1, β2, …, βm). f is real analytic in some neighborhood of the origin in ℂ, f(0) = 0 and f′(0) ≠ 0. We show that the above equation admits Cantor families of smooth quasi-periodic solutions of small amplitude. The proof is based on an abstract infinite dimensional Kolmogorov-Arnold-Moser theorem for unbounded perturbation vector fields and partial Birkhoff normal form.
A transformed framework for dynamic correlation in multireference problems
Authors: Sokolov Alexander Yu. , Chan Garnet Kin-Lic
Published: March 2015

We describe how multireference dynamic correlation theories can be naturally obtained as single-reference correlation theories in a canonically transformed frame. Such canonically transformed correlation theories are very simple and involve identical expressions to their single-reference counterparts. The corresponding excitations involve quasiparticles rather than the bare particles of the system. High-order density matrices (or their approximations) and the numerical metric instabilities common to multireference correlation theories do not appear. As an example, we formulate the Bogoliubov canonically transformed version of second-order Møller-Plesset perturbation theory and demonstrate its performance in H2, H2O, N2, and BeH2 bond dissociation.
Effect of external field on current-induced skyrmion dynamics in a nanowire
Authors: Lee Seung-Jae , Moon Jung-Hwan , Lee Kyung-Jin
Published: March 2015

We investigate the effect of external field on current-induced skyrmion dynamics in bilayer structures with interfacial Dzyaloshinskii-Moriya interaction. We find that the skyrmion velocity can be changed depending on the direction and magnitude of external magnetic field. Perpendicular magnetic field changes the velocity through the change in the skyrmion size. On the other hand, in-plane magnetic fields distort the magnetic skyrmion, which in turn affects the maximum skyrmion velocity obtained just before the annihilation of skyrmion at nanowire edges. Our results show that skyrmion velocity can be increased by applying magnetic fields along a proper direction.
The role of gas composition in plasma-dust structures in RF discharge
Authors: Maiorov S. A. , Kodanova S. K. , Dosbolayev M. K. , Ramazanov T. S. , Golyatina R. I. , Bastykova N. Kh. , Utegenov A. U.
Published: March 2015

The influence of a mixture of light and heavy gases, i.e., helium and argon, on plasma-dust structures in the radiofrequency discharge has been studied. The dust chains in the sheath of the radiofrequency discharge, the average distance between the dust particles and their chains, have been analyzed. A significant effect of small amounts of argon on the correlation characteristics of dust particles has been observed. The results of numerical simulation of ion and electron drift in the mixture of helium and argon are presented. It is shown that even 1% of argon admixture to helium produces such an effect that argon ions become the main components of the discharge, as they drift with lightweight helium forming a strongly anisotropic velocity distribution function.
Molecular dynamics simulations of soliton-like structures in a dusty plasma medium
Authors: Tiwari Sanat Kumar , Das Amita , Sen Abhijit , Kaw Predhiman
Published: March 2015

The existence and evolution of soliton-like structures in a dusty plasma medium are investigated in a first principles approach using molecular dynamic (MD) simulations of particles interacting via a Yukawa potential. These localized structures are found to exist in both weakly and strongly coupled regimes with their structures becoming sharper as the correlation effects between the dust particles get stronger. A surprising result, compared to fluid simulations, is the existence of rarefactive soliton-like structures in our non-dissipative system, a feature that arises from the charge conjugation symmetry property of the Yukawa fluid. Our simulation findings closely resemble many diverse experimental results reported in the past.
Determination of some basic physical parameters of SnO based on SnO/Si pn heterojunctions
Authors: Li Xiuxia , Liang Lingyan , Cao Hongtao , Qin Ruifeng , Zhang Hongliang , Gao Junhua , Zhuge Fei
Published: March 2015

P-SnO/n-Si heterojunctions were constructed by using e-beam evaporation in combination with ultra-violet lithography technique. The current-voltage and capacitance-voltage characteristics of the pn heterojunctions were systematically investigated, through which the diode parameters, such as the turn-on voltage, forward-to-reverse current ratio, series resistance, ideality factor, and build-in voltage, were also determined. In particular, the pn heterojunctions presented a relatively good electrical rectifying behavior, with a forward-to-reverse current ratio up to 58 ± 5 at ±2.0 V. The relative permittivity and work function of the SnO films were measured to be 18.8 ± 1.7 and 4.3 eV, respectively. The energy band diagram of the heterojunctions was depicted in detail, which can interpret the rectifying behavior very well.
Band gaps of wurtzite ScxGa1−xN alloys
Authors: Tsui H. C. L. , Goff L. E. , Rhode S. K. , Pereira S. , Beere H. E. , Farrer I. , Nicoll C. A. , Ritchie D. A. , Moram M. A.
Published: March 2015

Optical transmittance measurements on epitaxial, phase-pure, wurtzite-structure ScxGa1−xN films with 0 ≤ x ≤ 0.26 showed that their direct optical band gaps increased from 3.33 eV to 3.89 eV with increasing x, in agreement with theory. These films contained I1- and I2-type stacking faults. However, the direct optical band gaps decreased from 3.37 eV to 3.26 eV for ScxGa1−xN films, which additionally contained nanoscale lamellar inclusions of the zinc-blende phase, as revealed by aberration-corrected scanning transmission electron microscopy. Therefore, we conclude that the apparent reduction in ScxGa1−xN band gaps with increasing x is an artefact resulting from the presence of nanoscale zinc-blende inclusions.
Effects of graphene defect on electronic structures of its interface with organic semiconductor
Authors: Yang Qing-Dan , Dou Wei-Dong , Wang Chundong , Mo Hin-Wai , Lo Ming-Fai , Yuen Muk Fung , Ng Tsz-Wai , Zhang Wen-Jun , Tsang Sai-Wing , Lee Chun-Sing
Published: March 2015

Electronic structures of copper hexadecafluorophthalocyanine (F16CuPc)/graphene with different defect density were studied with ultra-violet photoelectron spectroscopy. We showed that the charge transfer interaction and charge flow direction can be interestingly tuned by controlling the defect density of graphene through time-controlled H2 plasma treatment. By increasing the treatment time of H2 plasma from 30 s to 5 min, both the interface surface dipole and the electron transporting barrier at F16CuPc/graphene interface are significantly reduced from 0.86 to 0.56 eV and 0.71 to 0.29 eV, respectively. These results suggested that graphene's defect control is a simple approach for tuning electronic properties of organic/graphene interfaces.
The renaissance of black phosphorus
Authors: Ling Xi , Wang Han , Huang Shengxi , Xia Fengnian , Dresselhaus Mildred S.
Published: March 2015

One hundred years after its first successful synthesis in the bulk form in 1914, black phosphorus (black P) was recently rediscovered from the perspective of a 2D layered material, attracting tremendous interest from condensed matter physicists, chemists, semiconductor device engineers, and material scientists. Similar to graphite and transition metal dichalcogenides (TMDs), black P has a layered structure but with a unique puckered single-layer geometry. Because the direct electronic band gap of thin film black P can be varied from 0.3 eV to around 2 eV, depending on its film thickness, and because of its high carrier mobility and anisotropic in-plane properties, black P is promising for novel applications in nanoelectronics and nanophotonics different from graphene and TMDs. Black P as a nanomaterial has already attracted much attention from researchers within the past year. Here, we offer our opinions on this emerging material with the goal of motivating and inspiring fellow researchers in the 2D materials community and the broad readership of PNAS to discuss and contribute to this exciting new field. We also give our perspectives on future 2D and thin film black P research directions, aiming to assist researchers coming from a variety of disciplines who are desirous of working in this exciting research field.
Human IL-32 expression protects mice against a hypervirulent strain of
Mycobacterium tuberculosis
Authors: Bai Xiyuan , Shang Shaobin , Henao-Tamayo Marcela , Basaraba Randall J. , Ovrutsky Alida R. , Matsuda Jennifer L. , Takeda Katsuyuki , Chan Mallory M. , Dakhama Azzeddine , Kinney William H. , Trostel Jessica , Bai An , Honda Jennifer R. , Achcar Rosane , Hartney John , Joosten Leo A. B. , Kim Soo-Hyun , Orme Ian , Dinarello Charles A. , Ordway Diane J. , Chan Edward D.
Published: March 2015

Significance

Interleukin-32 (IL-32) is induced by IL-1β, Toll-like receptor agonists, and nucleotide oligomerization domain as well as by
Mycobacterium tuberculosis
(
MTB
). Expression of human IL-32γ in the lungs of mice reduced the burden of
MTB
in both the lungs but also in the spleen and was associated with increased survival. Mechanistically, increased numbers of host-protective innate and adaptive immune cells were present in the IL-32 transgenic mice. Alveolar macrophages from the transgenic mice were also better able to control
MTB
infection and had increased colocalization of
MTB
with lysosomes. IL-32 expression was increased in the surgically resected lungs of tuberculosis patients, particularly in macrophages, airway epithelial cells, B cells, and T cells. Thus, IL-32 enhances host immunity against
MTB
.
Phonological elements and Diasystematic Construction Grammar
Authors: Höder Steffen
Published: March 2015

Usage-based CxG approaches share the central assumption that any grammar has to be acquired and organised through input-based abstraction and categorisation. Diasystematic Construction Grammar (DCxG) is based on the idea that these processes are not sensitive to language boundaries. Multilingual input thus results in multilingual grammars which are conceived of as constructicons containing language-specific as well as language-unspecific constructions. Within such systems, phonological structures play an important part in the identification of schematic constructions. However, the status of phonology in DCxG, as in CxG in general, yet remains unclear. This paper presents some arguments for including phonological elements systematically in the construction-based analysis of (multilingual) constructional systems.
Clause combining across grammars
Authors: Nir Bracha
Published: March 2015

The goal of the present study is to examine whether clause-combining rhetorical preferences that differentiate between Hebrew and English are maintained across grammars, specifically, in the context of text production in a non-native language. It examines the usage of various bi-clausal constructions marking different levels of event integration in texts written by advanced speakers of English, all native monolingual Hebrew speakers. The data analyzed consist of personal experience narratives that were collected from high-school and university-level students. These texts are compared to narratives that were collected from native speakers of both languages following the same design of study. Quantitative and qualitative analyses show differences and similarities between the three populations in terms of clause-combining strategies. They reveal that not only the constraints of the L1 but mainly those of the L2 guide non-native speakers in their choice of bi-clausal constructions, as devices expressing event integration. Results further show that event integration is reflected by constructions at different levels of the grammatical system, and that constraints on bi-clausal constructions at the more local, morpho-syntactic level are echoed by constraints at the level of discourse itself as a construction.
Words in action
Authors: de Nooijer Jacqueline A. , van Gog Tamara , Paas Fred , Zwaan Rolf A.
Published: March 2015

Research on embodied cognition has shown that action and language are closely intertwined. The present study seeks to exploit this relationship, by systematically investigating whether motor activation would improve eight-to-nine year old children’s learning of vocabulary in their first language. In a within-subjects paradigm, 49 children learned novel object manipulation, locomotion and abstract verbs via a verbal definition alone and in combination with gesture observation, imitation, or generation (i.e., enactment). Results showed that learning of locomotion verbs significantly improved through gesture observation compared to verbal definitions only. For learning object-manipulation verbs, children with good language skills seemed to benefit from imitation and enactment, while this appeared to hinder children with poor language skills. Learning of abstract verbs was not differentially affected by instructional condition. This study suggests that the effectiveness of observing and generating gestures for vocabulary learning may differ depending on verb type and language proficiency.
Sounding gay and sounding straight
Authors: Russell Eric
Published: March 2015

This paper presents a performance-based approach to the study of the phonetic encoding of sexual identity in Italian. Six male speakers were recruited after being controlled for familiarity, interaction, and comfort with members of both hetero- and homosexual communities. They were recorded reading introductory, scientific, and narrative paragraphs with the goals of conveying straight and gay identities, respectively, as well as in an unmarked style. Analysis focused on segmental (vowels, /s/, liquids), suprasegmental, and pragmatic components of performances, the results of which suggest that speakers use a combination of phonetic features to instantiate socially salient identities.
Acquisition of L2 Mandarin Chinese tones with learner-created tone visualizations
Authors: Chun Dorothy M. , Jiang Yan , Meyr Justine , Yang Rong
Published: March 2015

This paper reports on a study of 35 Mandarin Chinese learners who (1) created pitch curves of their spoken word tones and (2) compared their pitch curves with those of native speakers while practicing pronunciation. Following a pretest, the learners received training for 20–25 minutes weekly over nine weeks and took a posttest. Two types of data analyses were performed. First, native speakers of Mandarin auditorily rated the pretests and posttests. The ratings revealed that learners’ pronunciation of tones improved between pretest and posttest. Second, acoustic analyses of the learners’ recordings were conducted, and the learners’ production was compared with that of native speakers. Results indicated that students’ pronunciation of some tones improved in the posttest. The postsurveys indicated that two-thirds of the participants found viewing pitch curves helpful. This study confirms previous research but suggests that acoustic analyses complement auditory analyses with more precise indications of L2 learners’ tonal difficulties.
Translanguaging aspects of modality
Authors: Sidiropoulou Maria
Published: March 2015

This article explores aspects of modal marker use in English and Greek and suggests that parallel data may significantly contribute to raising learners’ intercultural sensitivity in the FL classroom, as an instance of TOLC (Translation in Other Language Contexts). Parallel data seem to assume a dynamic potential (privileging learner autonomy and developing self-study skills), which other traditional approaches to the use of the modal system lack, leaving important aspects of cross-cultural variation out of the perspective of the learner. The study focuses on two aspects of intercultural variation in the use of the modal systems of English and Greek, namely shifting degrees of possibility-certainty and the shift across epistemic-deontic, as manifested through a 2013–2014 sample of parallel data from newspapers. It offers a set of sample exercises highlighting the potential of translation to contribute valuable insights to L2/additional language learning (ALL) and syllabus design, assuming an ecological ethic in acknowledging the primacy of context, including L1, especially if L1 is a less widely spoken language.
CCM2–CCM3 interaction stabilizes their protein expression and permits endothelial network formation
Authors: Draheim Kyle M. , Li Xiaofeng , Zhang Rong , Fisher Oriana S. , Villari Giulia , Boggon Titus J. , Calderwood David A.
Published: March 2015

Mutations in the essential adaptor proteins CCM2 or CCM3 lead to cerebral cavernous malformations (CCM), vascular lesions that most frequently occur in the brain and are strongly associated with hemorrhagic stroke, seizures, and other neurological disorders. CCM2 binds CCM3, but the molecular basis of this interaction, and its functional significance, have not been elucidated. Here, we used x-ray crystallography and structure-guided mutagenesis to show that an α-helical LD-like motif within CCM2 binds the highly conserved “HP1” pocket of the CCM3 focal adhesion targeting (FAT) homology domain. By knocking down CCM2 or CCM3 and rescuing with binding-deficient mutants, we establish that CCM2–CCM3 interactions protect CCM2 and CCM3 proteins from proteasomal degradation and show that both CCM2 and CCM3 are required for normal endothelial cell network formation. However, CCM3 expression in the absence of CCM2 is sufficient to support normal cell growth, revealing complex-independent roles for CCM3.
Depression of voltage-activated Ca2+ release in skeletal muscle by activation of a voltage-sensing phosphatase
Authors: Berthier Christine , Kutchukian Candice , Bouvard Clément , Okamura Yasushi , Jacquemond Vincent
Published: March 2015

Phosphoinositides act as signaling molecules in numerous cellular transduction processes, and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) regulates the function of several types of plasma membrane ion channels. We investigated the potential role of PtdIns(4,5)P2 in Ca2+ homeostasis and excitation–contraction (E-C) coupling of mouse muscle fibers using in vivo expression of the voltage-sensing phosphatases (VSPs) Ciona intestinalis VSP (Ci-VSP) or Danio rerio VSP (Dr-VSP). Confocal images of enhanced green fluorescent protein–tagged Dr-VSP revealed a banded pattern consistent with VSP localization within the transverse tubule membrane. Rhod-2 Ca2+ transients generated by 0.5-s-long voltage-clamp depolarizing pulses sufficient to elicit Ca2+ release from the sarcoplasmic reticulum (SR) but below the range at which VSPs are activated were unaffected by the presence of the VSPs. However, in Ci-VSP–expressing fibers challenged by 5-s-long depolarizing pulses, the Ca2+ level late in the pulse (3 s after initiation) was significantly lower at 120 mV than at 20 mV. Furthermore, Ci-VSP–expressing fibers showed a reversible depression of Ca2+ release during trains, with the peak Ca2+ transient being reduced by ∼30% after the application of 10 200-ms-long pulses to 100 mV. A similar depression was observed in Dr-VSP–expressing fibers. Cav1.1 Ca2+ channel–mediated current was unaffected by Ci-VSP activation. In fibers expressing Ci-VSP and a pleckstrin homology domain fused with monomeric red fluorescent protein (PLCδ1PH-mRFP), depolarizing pulses elicited transient changes in mRFP fluorescence consistent with release of transverse tubule–bound PLCδ1PH domain into the cytosol; the voltage sensitivity of these changes was consistent with that of Ci-VSP activation, and recovery occurred with a time constant in the 10-s range. Our results indicate that the PtdIns(4,5)P2 level is tightly maintained in the transverse tubule membrane of the muscle fibers, and that VSP-induced depletion of PtdIns(4,5)P2 impairs voltage-activated Ca2+ release from the SR. Because Ca2+ release is thought to be independent from InsP3 signaling, the effect likely results from an interaction between PtdIns(4,5)P2 and a protein partner of the E-C coupling machinery.
Cysteine accessibility probes timing and extent of NBD separation along the dimer interface in gating CFTR channels
Authors: Chaves Luiz A. Poletto , Gadsby David C.
Published: March 2015

Cystic fibrosis transmembrane conductance regulator (CFTR) channel opening and closing are driven by cycles of adenosine triphosphate (ATP) binding–induced formation and hydrolysis-triggered disruption of a heterodimer of its cytoplasmic nucleotide-binding domains (NBDs). Although both composite sites enclosed within the heterodimer interface contain ATP in an open CFTR channel, ATP hydrolysis in the sole catalytically competent site causes channel closure. Opening of the NBD interface at that site then allows ADP–ATP exchange. But how frequently, and how far, the NBD surfaces separate at the other, inactive composite site remains unclear. We assessed separation at each composite site by monitoring access of nucleotide-sized hydrophilic, thiol-specific methanothiosulfonate (MTS) reagents to interfacial target cysteines introduced into either LSGGQ-like ATP-binding cassette signature sequence (replacing equivalent conserved serines: S549 and S1347). Covalent MTS-dependent modification of either cysteine while channels were kept closed by the absence of ATP impaired subsequent opening upon ATP readdition. Modification while channels were opening and closing in the presence of ATP caused macroscopic CFTR current to decline at the same speed as when the unmodified channels shut upon sudden ATP withdrawal. These results suggest that the target cysteines can be modified only in closed channels; that after modification the attached MTS adduct interferes with ATP-mediated opening; and that modification in the presence of ATP occurs rapidly once channels close, before they can reopen. This interpretation was corroborated by the finding that, for either cysteine target, the addition of the hydrolysis-impairing mutation K1250R (catalytic site Walker A Lys) similarly slowed, by an order of magnitude, channel closing on ATP removal and the speed of modification by MTS reagent in ATP. We conclude that, in every CFTR channel gating cycle, the NBD dimer interface separates simultaneously at both composite sites sufficiently to allow MTS reagents to access both signature-sequence serines. Relatively rapid modification of S1347C channels by larger reagents—MTS-glucose, MTS-biotin, and MTS-rhodamine—demonstrates that, at the noncatalytic composite site, this separation must exceed 8 Å.
Outlier detection at the transcriptome-proteome interface
Authors: Gunawardana Yawwani , Fujiwara Shuhei , Takeda Akiko , Woo Jeongmin , Woelk Christopher , Niranjan Mahesan
Published: March 2015

Background: In high-throughput experimental biology, it is widely acknowledged that while expression levels measured at the levels of transcriptome and the corresponding proteome do not, in general, correlate well, messenger RNA levels are used as convenient proxies for protein levels. Our interest is in developing data-driven computational models that can bridge the gap between these two levels of measurement at which different mechanisms of regulation may act on different molecular species causing any observed lack of correlations. To this end, we build data-driven predictors of protein levels using mRNA levels and known proxies of translation efficiencies as covariates. Previous work showed that in such a setting, outliers with respect to the model are reliable candidates for post-translational regulation.

Results: Here, we present and compare two novel formulations of deriving a protein concentration predictor from which outliers may be extracted in a systematic manner. The first approach, outlier rejecting regression, allows explicit specification of a certain fraction of the data as outliers. In a regression setting, this is a non-convex optimization problem which we solve by deriving a difference of convex functions algorithm (DCA). With post-translationally regulated proteins, one expects their concentrations to be affected primarily by disruption of protein stability. Our second algorithm exploits this observation by minimizing an asymmetric loss using quantile regression and extracts outlier proteins whose measured concentrations are lower than what a genome-wide regression would predict. We validate the two approaches on a dataset of yeast transcriptome and proteome. Functional annotation check on detected outliers demonstrate that the methods are able to identify post-translationally regulated genes with high statistical confidence.

Contact:  mn@ecs.soton.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Maize Lethal Necrosis (MLN), an Emerging Threat to Maize-Based Food Security in Sub-Saharan Africa
Authors: Mahuku George , Lockhart Benham E. , Wanjala Bramwel , Jones Mark W. , Kimunye Janet Njeri , Stewart Lucy R. , Cassone Bryan J. , Sevgan Subramanian , Nyasani Johnson O. , Kusia Elizabeth , Kumar P. Lava , Niblett C. L. , Kiggundu Andrew , Asea Godfrey , Pappu Hanu R. , Wangai Anne , Prasanna Boddupalli M. , Redinbaugh Margaret G.
Published: March 2015

In sub-Saharan Africa, maize is a staple food and key determinant of food security for smallholder farming communities. Pest and disease outbreaks are key constraints to maize productivity. In September 2011, a serious disease outbreak, later diagnosed as maize lethal necrosis (MLN), was reported on maize in Kenya. The disease has since been confirmed in Rwanda and the Democratic Republic of Congo, and similar symptoms have been reported in Tanzania, Uganda, South Sudan, and Ethiopia. In 2012, yield losses of up to 90% resulted in an estimated grain loss of 126,000 metric tons valued at $52 million in Kenya alone. In eastern Africa, MLN was found to result from coinfection of maize with Maize chlorotic mottle virus (MCMV) and Sugarcane mosaic virus (SCMV), although MCMV alone appears to cause significant crop losses. We summarize here the results of collaborative research undertaken to understand the biology and epidemiology of MLN in East Africa and to develop disease management strategies, including identification of MLN-tolerant maize germplasm. We discuss recent progress, identify major issues requiring further research, and discuss the possible next steps for effective management of MLN.
Biological, Serological, and Molecular Characterization of a Highly Divergent Strain ofGrapevine leafroll-associated virus 4Causing Grapevine Leafroll Disease
Authors: Reynard Jean-Sébastien , Schneeberger Pierre H. H. , Frey Jürg Ernst , Schaerer Santiago
Published: March 2015

The complete genome sequence of a highly divergent strain of Grapevine leafroll-associated virus 4 (GLRaV-4) was determined using 454 pyrosequencing technology. This virus, designated GLRaV-4 Ob, was detected in Vitis vinifera ‘Otcha bala’ from our grapevine virus collection at Agroscope. The GLRaV-4 Ob genome length and organization share similarities with members of subgroup II in the genus Ampelovirus (family Closteroviridae). Otcha bala was graft-inoculated onto indicator plants of cultivar Gamay to evaluate the biological properties of this new strain, and typical leafroll symptoms were induced. A monoclonal antibody for the rapid detection of GLRaV-4 Ob by enzyme-linked immunosorbent assay is available, thus facilitating large-scale diagnostics of this virus. Based on the relatively small size of the coat protein, the reduced amino acid identity and the distinct serological properties, our study clearly shows that GLRaV-4 Ob is a divergent strain of GLRaV-4. Furthermore, molecular and serological data revealed that the AA42 accession from which GLRaV-7 was originally reported is in fact co-infected with GLRaV-4 Ob and GLRaV-7. This finding challenges the idea that GLRaV-7 is a leafroll-causing agent.
Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?
Authors: Trucchi Emiliano , Facon Benoit , Gratton Paolo , Mori Emiliano , Stenseth Nils Chr. , Jentoft Sissel
Published: March 2015

Studying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of theH. cristatainvasive populations and compare their genetic diversity with that of native African populations of bothH. cristataand its sister species,H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from Sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity ofH. cristatainvasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.
Using heterogeneity in the population structure of U.S. swine farms to compare transmission models for porcine epidemic diarrhoea
Authors: O’Dea Eamon B. , Snelson Harry , Bansal Shweta
Published: March 2015

In 2013, U.S. swine producers were confronted with the disruptive emergence of porcine epidemic diarrhoea (PED). Movement of animals among farms is hypothesised to have played a role in the spread of PED among farms. Via this or other mechanisms, the rate of spread may also depend on the geographic density of farms and climate. To evaluate such effects on a large scale, we analyse state-level counts of outbreaks with variables describing the distribution of farm sizes and types, aggregate flows of animals among farms, and an index of climate. Our first main finding is that it is possible for a correlation analysis to be sensitive to transmission model parameters. This finding is based on a global sensitivity analysis of correlations on simulated data that included a biased and noisy observation model based on the available PED data. Our second main finding is that flows are significantly associated with the reports of PED outbreaks. This finding is based on correlations of pairwise relationships and regression modeling of total and weekly outbreak counts. These findings illustrate how variation in population structure may be employed along with observational data to improve understanding of disease spread.
Using targeted re-sequencing for identification of candidate genes and SNPs for a QTL affecting the pH value of chicken meat
Authors: Li Xidan , Liu Xiaodong , Nadaf Javad , Le Bihan-Duval Elisabeth , Berri Cécile , Dunn Ian C. , Talbot Richard , de Koning Dirk-Jan
Published: March 2015

Using targeted genetical genomics, a QTL affecting the initial post-mortem pH value of chicken breast muscle (Pectoralis major) on chromosome 1 (GGA1) was recently fine-mapped. Thirteen genes were present in the QTL region of about 1 Mb.

In this study, ten birds that were inferred to be homozygous for either the high (QQ) or low (qq) QTL allele were selected for re-sequencing. After enrichment for 1 Mb around the QTL region, > 200 x coverage for the QTL region in each of the ten birds was obtained. We used custom tools to identify putative causal mutations in the mapped QTL region from next generation sequence data. Four non-synonymous SNPs differentiating the two QTL genotype groups were identified within four local genes (PRDX4, EIF2S3, PCYT1B and E1BTD2). These were defined to be most likely candidate SNPs to explain the QTL effect. Moreover, 29 consensus SNPs were detected within gene-related regions (UTR regions and splicing sites) for the QQ birds and 26 for the qq birds. These could also play a role explaining the observed QTL effect.

The results provide an important step for prioritizing among a large amount of candidate mutations and significantly contribute to the understanding of the genetic mechanisms affecting the initial post-mortem pH value of chicken muscle.
Regional and global production networks: the case of China
Authors: Fung K.C.
Published: March 2015

Purpose

– The purpose of this paper is to examine various aspects of regional and global production networks, with a special focus on China.

Design/methodology/approach

– The author studies four different approaches to measure production networks and discuss their strengths and weaknesses. The author presents some of the results associated with some of these measurements.

Findings

– The author finds that using trade data alone is simple but incomplete. Bringing in input–output tables is useful but much more data would be needed. In addition, for the case of China, electronic goods and telecommunication goods tend to have a higher foreign value added.

Research limitations/implications

– Data with good quality can be a problem. The authors also have difficulty getting input–output tables for many years.

Practical implications

– The results can guide policymakers as to which industries can create more domestic value added. The results can also lead to betting of an understanding of trade balances measured in the value added.

Social implications

– The results can generate further understanding among citizens of many different countries, including China, about the importance of different sectors in generating the value added.

Originality/value

– The value of this paper is to focus on alternative ways to measure the value added in exports from China. The paper is the first to discuss the strengths and weaknesses of different approaches and present some of these results.
The usefulness of derivative disclosures for investment decision-making
Authors: Huang Zhen , Gao Simon
Published: March 2015

Purpose

– The purpose of this study is to examine the usefulness of derivative disclosures from the perspective of Chinese institutional investors in relation to their investment decision-making.

Design/methodology/approach

– This study uses semi-structured interviews with 21 institutional investors based in China including 10 funds managers and 11 professional analysts.

Findings

– This study finds that the information on the use of derivatives disclosed by listed companies in China is generally perceived to be useful to Chinese institutional investors (e.g. funds managers and professional analysts) in facilitating their investment decisions, although such information is generally thought to be less significant compared to other fundamental financial information such as assets, liabilities and profits/losses. It also finds that the current provisions of derivatives-related information by Chinese listed companies are largely unsatisfied primarily because of insufficient information and the lack of timely disclosures. Furthermore, it finds that the accounting and reporting policies currently imposed in China appear to be little understood by Chinese investors.

Research limitations/implications

– This study has its own limitations due to the approach of interviews with a relatively small sample from only two investment firms in China.

Practical implications

– The findings from the study provide a number of policy implications for derivatives regulators and accounting standards setters.

Originality/value

– This study is the first study of its kind to investigate the perceptions of Chinese institutional investors on the usefulness of derivatives reporting and disclosures with the use of interview research method.