bluuebunny/crossref_metadata_2025 huggingface dataset:
Association and liquid structure of pyridine–acetic acid mixtures determined from neutron scattering using a ‘free proton’ EPSR simulation model
Authors: McCune Jade A. , Turner Adam H. , Coleman Fergal , White Caithlin M. , Callear Samantha K. , Youngs Tristan G. A. , Swadźba-Kwaśny Małgorzata , Holbrey John D.
Published: February 2015

Hydrogen-bonded molecular acetic acid chains are observed in acid–base mixtures from small angle neutron diffraction.
A detailed study on the working mechanism of a heteropoly acid modified TiO2 photoanode for efficient dye-sensitized solar cells
Authors: Jiang Yanxia , Yang Yulin , Qiang Liangsheng , Fan Ruiqing , Li Liang , Ye Tengling , Na Yong , Shi Yan , Luan Tianzhu
Published: February 2015

The use of SiW11Ni as a photoanode in a DSSC results in the photocurrent of 7.82%, 31% higher than that of pristine P25 DSSCs.
Gut feedback mechanisms and food intake: a physiological approach to slow carbohydrate bioavailability
Authors: Zhang Genyi , Hasek Like Y. , Lee Byung-Hoo , Hamaker Bruce R.
Published: February 2015

Slow glucose bioavailability through neurohormonal feedback activated by location-specific nutrient deposition.
GC-on-chip: integrated column and photoionization detector
Authors: Akbar M. , Shakeel H. , Agah M.
Published: February 2015

We present a GC-on-chip module capable of providing highly efficient separation and ultra-sensitive detection of volatile organic compounds on a single platform.
A preliminary investigation of the mechanism of hexavalent chromium removal by corn-bran residue and derived chars
Authors: Zhang Jishi , Zheng Pengwei
Published: February 2015

Biochars were prepared from corn-bran residue (CBR) at 300–600 °C, which were utilized to removal Cr(vi) from aqueous solutions. The Cr(vi) removal capacity of CBR and CBR600 was attributed to the predominance of either reduction or adsorption.
High gas-sensor and supercapacitor performance of porous Co3O4 ultrathin nanosheets
Authors: Wang Xiuhua , Yao Shangwu , Wu Xiaoxiu , Shi Zhijie , Sun Hongxia , Que Ronghui
Published: February 2015

Porous Co3O4 ultrathin nanosheets exhibited good sensitivity and low concentration selectivity to ethanol.
Functional tuning of organic dyes containing 2,7-carbazole and other electron-rich segments in the conjugation pathway
Authors: Venkateswararao A. , Justin Thomas K. R. , Li Chun-Ting , Ho Kuo-Chuan
Published: February 2015

Organic dyes containing a triarylamine donor, a cyanoacrylic acid acceptor and a conjugation pathway composed of 2,7-carbazole, thiophene and fluorene have been synthesized and characterized as sensitizers for TiO2-based dye-sensitized solar cells.
Isoindoline-derived ligands and applications
Authors: Csonka Róbert , Speier Gábor , Kaizer József
Published: February 2015

During the past decade isoindoline-based ligands became the subject of growing interest due to their modular set-up.
Sol–gel-assisted, fast and low-temperature synthesis of La-doped Li3V2(PO4)3/C cathode materials for lithium-ion batteries
Authors: Yang Zhenyu , Hu Jinhuo , Chen Zhengyu , Zhong Jing , Gu Ningyu , Zhang Ning
Published: February 2015

La-doped Li3V2(PO4)3/C cathode materials are synthesized by a sol–gel-assisted, low-temperature sintering process. The resulting cathode has a stable specific capacity of 160 mA h g−1at 0.2 C, and retained a stable capacity of up to 116 mA h g−1at 5 C.
Activation of giant silicalite-1 monocrystals combining rapid thermal processing and ozone calcination
Authors: Navarro Marta , Mateo Ester , Diosdado Beatriz , Tsapatsis Michael , Coronas Joaquín
Published: February 2015

A rapid thermal processing (RTP) technique combined with ozone/oxygen calcination was applied to activate and heal a 1.1 mm2section of a silicalite-1 giant monocrystal.
Antibacterial wound dressing: plasma treatment effect on chitosan impregnation and in situ synthesis of silver chloride on cellulose surface
Authors: Vosmanská Vladimíra , Kolářová Kateřina , Rimpelová Silvie , Kolská Zdeňka , Švorčík Václav
Published: February 2015

Three-step modification of cellulose for production of wound dressing with antibacterial properties.
Ag-doped manganese oxide prepared by electrochemical deposition on carbon fiber for supercapacitors
Authors: Zeng Zifan , Sun Ping , Zhu Jiliang , Zhu Xiaohong
Published: February 2015

An Ag-doped MnOx electrode with high specific capacitance of 825 F g−1 has been fabricated by a cathodic deposition method for supercapacitors.
Dialkoxybenzo[j]fluoranthenes: synthesis, structures, photophysical properties, and optical waveguide application
Authors: Li Xiao-Jun , Li Meng , Yao Wei , Lu Hai-Yan , Zhao YongSheng , Chen Chuan-Feng
Published: February 2015

Dialkoxybenzo[j]fluoranthenes were readily synthesized, and showed strong fluorescence in solution and solid state, and exhibited excellent optical waveguide behavior.
Phenalenyl-fused porphyrins with different ground states
Authors: Zeng Wangdong , Lee Sangsu , Son Minjung , Ishida Masatoshi , Furukawa Ko , Hu Pan , Sun Zhe , Kim Dongho , Wu Jishan
Published: February 2015

Fusion of one or two phenalenyl units onto the porphyrin core led to biradicaloids with different ground state, physical property and chemical reactivity.
Synthesis and photocatalytic properties of metastable β-Bi2O3stabilized by surface-coordination effects
Authors: Jiang Hai-Ying , Li Peng , liu Guigao , Ye Jinhua , Lin Jun
Published: February 2015

A metastable semiconductor, β-Bi2O3, was successfully synthesized with the precursor Bi2O2CO3in this study, which showed much higher photocatalytic activity in the photooxidation of isopropyl alcohol (IPA) than thermally stable α-Bi2O3.
Graphene as a prominent antioxidant for diolefin elastomers
Authors: Tang Maozhu , Xing Wang , Wu Jinrong , Huang Guangsu , Xiang Kewei , Guo Lili , Li Guangxuan
Published: February 2015

Graphene is a promising antioxidant for diolefin elastomers, due to its free-radical scavenging and gas barrier abilities.
Fluorene co-polymers with high efficiency deep-blue electroluminescence
Authors: Santos José , Cook Javan H. , Al-Attar Hameed A. , Monkman Andrew P. , Bryce Martin R.
Published: February 2015

New deep blue emitting co-polymers are reported. In simple PLED architectures efficiency values as high as ηext,max 3.9% and Lmax 274 cd m−2 with CIE (0.17, 0.07) are obtained.
Water-soluble dopamine-based polymers for photoacoustic imaging
Authors: Repenko Tatjana , Fokong Stanley , De Laporte Laura , Go Dennis , Kiessling Fabian , Lammers Twan , Kuehne Alexander J. C.
Published: February 2015

Here we present a facile synthetic method yielding a linear form of polydopamineviaKumada-coupling, which can be converted into water-soluble melanin, generating high contrast in photoacoustic imaging.
Influence of the number and substitution position of phenyl groups on the aggregation-enhanced emission of benzene-cored luminogens
Authors: Li Lingzhi , Chen Ming , Zhang Haoke , Nie Han , Sun Jing Zhi , Qin Anjun , Tang Ben Zhong
Published: February 2015

The influence of the number and substitution position of phenyl groups on the emission of benzene-cored AIEgens is unambiguously revealed.
Hydrogenation of succinic acid over supported rhenium catalysts prepared by the microwave-assisted thermolytic method
Authors: Di Xin , Shao Zhengfeng , Li Chuang , Li Wenzhen , Liang Changhai
Published: February 2015

The Re/C catalysts prepared by the microwave-assisted thermolytic method exhibited good catalytic activity in the aqueous phase hydrogenation of succinic acid.
BF3-promoted electrochemical properties of quinoxaline in propylene carbonate
Authors: Carino Emily V. , Diesendruck Charles E. , Moore Jeffrey S. , Curtiss Larry A. , Assary Rajeev S. , Brushett Fikile R.
Published: February 2015

Electrochemical and density functional studies demonstrate that coordination of electrolyte constituents to quinoxalines modulates their electrochemical properties.
Synthesis of some novel steroidal 1,2,4,5-tetraoxanes
Authors: Das Archana M. , Hazarika Manash P.
Published: February 2015

A facile synthesis of A-ring manipulated C-20 methyl carboxylate steroid derivative with unsymmetrical dispiro 1,2,4,5-tetraoxanes has been focused herein via acid catalyzed cyclocondensation of bis-epidioxy ketone.
Preparation of plasmonic magnetic nanoparticles and their light scattering properties
Authors: Lee Minwoo , Kang Yoo-Lee , Rho Won-Yeop , Kyeong San , Jeong Sinyoung , Jeong Cheolhwan , Chung Woo-Jae , Kim Hyung-Mo , Kang Homan , Lee Yoon-Sik , Jeong DaeHong , Jun Bong-Hyun
Published: February 2015

Fe3O4@SiO2@Au nanoparticles (NPs) that have plasmonic and magnetic properties were prepared by simple immobilization method of Au NPs to silica coated magnetic NPs.
Pyruvate dehydrogenase complex and nicotinamide nucleotide transhydrogenase constitute an energy-consuming redox circuit
Authors: Fisher-Wellman Kelsey H. , Lin Chien-Te , Ryan Terence E. , Reese Lauren R. , Gilliam Laura A.A. , Cathey Brook L. , Lark Daniel S. , Smith Cody D. , Muoio Deborah M. , Neufer P. Darrell
Published: February 2015

Mitochondria generate and maintain a redox or “electrical” charge that is distributed throughout cells. The current work identifies a redox mechanism by which energy balance is continuously sensed and coupled to compensatory changes in energy expenditure.
Teaching Children Who Use Augmentative and Alternative Communication to Ask Inverted Yes/No Questions Using Aided Modeling
Authors: Kent-Walsh Jennifer , Binger Cathy , Buchanan Carolyn
Published: February 2015

Purpose

This study investigated the effects of a direct intervention program involving aided modeling and the presentation of contrastive targets on the aided production of inverted yes/no questions and possible generalization to other sentence types by children using augmentative and alternative communication (AAC).

Method

A single-case, multiple-probe, experimental design across participants was used to evaluate the effects of the instructional program with 3 children who had motor speech disorders and used AAC (ages 4;10 [years;months], 6;2, and 4;9). The treatment involved aided modeling of treatment and contrastive targets through concentrated modeling and interactive play activities. Direct treatment outcomes were examined by measuring the accuracy of producing inverted yes/no questions and
to be
declaratives through probes.

Results

All 3 participants showed a direct treatment effect, producing a greater number of inverted yes/no questions and
to be
declaratives within the probes following treatment compared with before treatment. All 3 participants evidenced some generalization to novel sentences.

Conclusions

Results provide initial evidence that instruction involving aided modeling with contrastive targets holds promise in targeting specific linguistic rules with children using AAC. Patterns of generalization may depend on participants' specific language deficits and acquisition patterns during intervention.
The Role of Sentence Position, Allomorph, and Morpheme Type on Accurate Use of s-Related Morphemes by Children Who Are Hard of Hearing
Authors: Koehlinger Keegan , Van Horne Amanda Owen , Oleson Jacob , McCreery Ryan , Moeller Mary Pat
Published: February 2015

Purpose

Production accuracy of s-related morphemes was examined in 3-year-olds with mild-to-severe hearing loss, focusing on perceptibility, articulation, and input frequency.

Method

Morphemes with /s/, /z/, and /ɪz/ as allomorphs (plural, possessive, third-person singular –s, and auxiliary and copula “is”) were analyzed from language samples gathered from 51 children (ages: 2;10 [years;months] to 3;8) who are hard of hearing (HH), all of whom used amplification. Articulation was assessed via the Goldman-Fristoe Test of Articulation–Second Edition, and monomorphemic word final /s/ and /z/ production. Hearing was measured via better ear pure tone average, unaided Speech Intelligibility Index, and aided sensation level of speech at 4 kHz.

Results

Unlike results reported for children with normal hearing, the group of children who are HH correctly produced the /ɪz/ allomorph more than /s/ and /z/ allomorphs. Relative accuracy levels for morphemes and sentence positions paralleled those of children with normal hearing. The 4-kHz sensation level scores (but not the better ear pure tone average or Speech Intelligibility Index), the Goldman-Fristoe Test of Articulation–Second Edition, and word final s/z use all predicted accuracy.

Conclusions

Both better hearing and higher articulation scores are associated with improved morpheme production, and better aided audibility in the high frequencies and word final production of s/z are particularly critical for morpheme acquisition in children who are HH.
Domain wall oscillations induced by spin torque in magnetic nanowires
Authors: Sbiaa R. , Chantrell R. W.
Published: February 2015

Using micromagnetic simulations, the effects of the non-adiabatic spin torque (β) and the geometry of nanowires on domain wall (DW) dynamics are investigated. For the case of in-plane anisotropy nanowire, it is observed that the type of DW and its dynamics depends on its dimension. For a fixed length, the critical switching current decreases almost exponentially with the width W, while the DW speed becomes faster for larger W. For the case of perpendicular anisotropy nanowire, it was observed that DW dynamics depends strongly on β. For small values of β, oscillations of DW around the center of nanowire were revealed even after the current is switched off. In addition to nanowire geometry and intrinsic material properties, β could provide a way to control DW dynamics.
Radial distribution of charged particles in a magnetic field
Authors: Sjue S. K. L. , Broussard L. J. , Makela M. , McGaughey P. L. , Young A. R. , Zeck B. A.
Published: February 2015

The radial spread of charged particles emitted from a point source in a magnetic field is a potential source of systematic error for any experiment where magnetic fields guide charged particles to detectors with finite size. Assuming uniform probability as a function of the phase along the particle’s helical trajectory, an analytic solution for the radial probability distribution function follows which applies to experiments in which particles are generated throughout a volume that spans a sufficient length along the axis of a homogeneous magnetic field. This approach leads to the same result as a different derivation given by Dubbers et al., Nucl. Instrum. Methods Phys. Res., Sect. A 763, 112–119 (2014). But the constant phase approximation does not strictly apply to finite source volumes or fixed positions, which lead to local maxima in the radial distribution of emitted particles at the plane of the detector. A simple method is given to calculate such distributions, then the effect is demonstrated with data from a 207Bi electron-conversion source in the superconducting solenoid magnet spectrometer of the Ultracold Neutron facility at the Los Alamos Neutron Science Center. Implications for neutron beta decay spectroscopy are discussed.
Limitations of electron cyclotron resonance ion source performances set by kinetic plasma instabilities
Authors: Tarvainen O. , Laulainen J. , Komppula J. , Kronholm R. , Kalvas T. , Koivisto H. , Izotov I. , Mansfeld D. , Skalyga V.
Published: February 2015

Electron cyclotron resonance ion source (ECRIS) plasmas are prone to kinetic instabilities due to anisotropy of the electron energy distribution function stemming from the resonant nature of the electron heating process. Electron cyclotron plasma instabilities are related to non-linear interaction between plasma waves and energetic electrons resulting to strong microwave emission and a burst of energetic electrons escaping the plasma, and explain the periodic oscillations of the extracted beam currents observed in several laboratories. It is demonstrated with a minimum-B 14 GHz ECRIS operating on helium, oxygen, and argon plasmas that kinetic instabilities restrict the parameter space available for the optimization of high charge state ion currents. The most critical parameter in terms of plasma stability is the strength of the solenoid magnetic field. It is demonstrated that due to the instabilities the optimum Bmin-field in single frequency heating mode is often ≤0.8BECR, which is the value suggested by the semiempirical scaling laws guiding the design of modern ECRISs. It is argued that the effect can be attributed not only to the absolute magnitude of the magnetic field but also to the variation of the average magnetic field gradient on the resonance surface.
How much time is needed to form a kinetically stable glass? AC calorimetric study of vapor-deposited glasses of ethylcyclohexane
Authors: Chua Y. Z. , Ahrenberg M. , Tylinski M. , Ediger M. D. , Schick C.
Published: February 2015

Glasses of ethylcyclohexane produced by physical vapor deposition have been characterized by in situ alternating current chip nanocalorimetry. Consistent with previous work on other organic molecules, we observe that glasses of high kinetic stability are formed at substrate temperatures around 0.85 Tg, where Tg is the conventional glass transition temperature. Ethylcyclohexane is the least fragile organic glass-former for which stable glass formation has been established. The isothermal transformation of the vapor-deposited glasses into the supercooled liquid state was also measured. At seven substrate temperatures, the transformation time was measured for glasses prepared with deposition rates across a range of four orders of magnitude. At low substrate temperatures, the transformation time is strongly dependent upon deposition rate, while the dependence weakens as Tg is approached from below. These data provide an estimate for the surface equilibration time required to maximize kinetic stability at each substrate temperature. This surface equilibration time is much smaller than the bulk α-relaxation time and within two orders of magnitude of the β-relaxation time of the ordinary glass. Kinetically stable glasses are formed even for substrate temperatures below the Vogel and the Kauzmann temperatures. Surprisingly, glasses formed in the limit of slow deposition at the lowest substrate temperatures are not as kinetically stable as those formed near 0.85 Tg.
Experimental platform for solidification and in-situ magnetization measurement of undercooled melt under strong magnetic field
Authors: Wang Jun , He Yixuan , Li Jinshan , Hu Rui , Kou Hongchao , Beaugnon Eric
Published: February 2015

An experimental platform for solidification of undercooled melt and synchronous measurement of magnetization under strong magnetic field is reported. The facility can be used for in-situ measurement of the magnetization of the undercooled melts and to studying the non-equilibrium solidification from deeply undercooled metals and alloys in magnetic field. The key advantages of this apparatus are first, we can obtain large undercooling in high fields by glass fluxing technique in combination with cyclical superheating and supercooling method, which is comparable to the maximum undercooling obtained by traditional method without magnetic field. Second, we can have a controlled thermal history with linear heating and cooling speed with high accuracy. Third, the temperature and magnetization measurement system are fast and on-line, which is very suitable for the investigation of both the structure transitions in the liquid in a wide temperature range (overheated and undercooled state) and the solid state phase transformations.
Physisorbed H2@Cu(100) surface: Potential and spectroscopy
Authors: Bernard Eddy , Houriez Céline , Mitrushchenkov Alexander O. , Guitou Marie , Chambaud Gilberte
Published: February 2015

Using an embedding approach, a 2-D potential energy function has been calculated to describe the physisorption interaction of H2 with a Cu(100) surface. For this purpose, a cluster model of the system calculated with highly correlated wavefunctions is combined with a periodic Density-Functional-Theory method using van der Waals-DF2 functional. Rotational and vibrational energy levels of physisorbed H2, as well as D2 and HD, are calculated using the 2D embedding corrected potential energy function. The calculated transitions are in a very good agreement with Electron-Energy-Loss-Spectroscopy observations.
In situ formation and characterisation of singly ionised atomic europium in rare gas matrices—Luminescence spectroscopy and MP2 calculations
Authors: Byrne Owen , Davis Barry , McCaffrey John G.
Published: February 2015

Irradiation of atomic europium isolated in the solid rare gases, with low intensity laser excitation of the y8P←a8S resonance transition at ca. 465 nm, is found to produce singly charged europium cations (Eu+) in large amounts in xenon and in smaller amounts in argon. Confirmation of the formation of matrix-isolated Eu+ is obtained from characteristic absorption bands in the UV and in the visible spectral regions. The luminescence produced with excitation of the cation bands is presented in greatest detail for Eu/Xe and assigned. Excitation of the 4f7(8S7/2)6p3/2 absorption bands of Eu+ between 390 and 410 nm produces emission which is quite distinct from that resulting from excitation of the 4f7(8S7/2)6p1/2 absorption (430 to 450 nm) features. The latter consists of narrow, resolved emission bands with Stokes shifts ten times smaller than the former. The observed spectral differences are discussed in relation to the different spatial symmetries of the p3/2 and p1/2 orbitals in these j-j coupled (7/2, 3/2)J and the (7/2, 1/2)J levels. Møller-Plesset calculations are conducted to obtain the molecular parameters of the neutral Eu-RG and cationic Eu+-RG diatomics (RG = Ar, Kr, Xe). From the short bond lengths and the strong binding energies obtained for the Eu+-RG species, these values suggest the isolation of the ion in small, possibly interstitial sites especially in xenon. In contrast, but consistent with previous work [O. Byrne and J. G. McCaffrey, J. Chem. Phys. 134, 124501 (2011)], the interaction potentials calculated herein for the Eu-RG diatomics suggest that the neutral Eu atom occupies tetra-vacancy (tv) and hexa-vacancy (hv) sites in the solid rare gas hosts. Possible reasons for the facile production of Eu+ in the solid rare gases are discussed. The mechanism proposed is that atomic europium is also acting as an electron acceptor, providing a temporary trap for the ionised electron in the matrices.
Spin Hall effect-controlled magnetization dynamics in NiMnSb
Authors: Dürrenfeld P. , Gerhard F. , Ranjbar M. , Gould C. , Molenkamp L. W. , Åkerman J.
Published: February 2015

We investigate the influence of a spin current generated from a platinum layer on the ferromagnetic resonance (FMR) properties of an adjacent ferromagnetic layer composed of the halfmetallic half-Heusler material NiMnSb. Spin Hall nano-oscillator devices are fabricated, and the technique of spin torque FMR is used to locally study the magnetic properties as in-plane anisotropies and resonance fields. A change in the FMR linewidth, in accordance with the additional spin torque produced by the spin Hall effect, is present for an applied dc current. For sufficiently large currents, this should yield auto-oscillations, which however are not achievable in the present device geometry.
Micromagnetic study of spin transfer switching with a spin polarization tilted out of the free layer plane
Authors: Chaves-O'Flynn Gabriel D. , Wolf Georg , Pinna Daniele , Kent Andrew D.
Published: February 2015

We present the results of zero temperature macrospin and micromagnetic simulations of spin transfer switching of thin film nanomagnets in the shape of an ellipse with a spin-polarization tilted out of the layer plane. The perpendicular component of the spin-polarization is shown to increase the reversal speed, leading to a lower current for switching in a given time. However, for tilt angles larger than a critical angle, the layer magnetization starts to precess about an out-of-plane axis, which leads to a final magnetization state that is very sensitive to simulation conditions. As the ellipse lateral size increases, this out-of-plane precession is suppressed, due to the excitation of spatially non-uniform magnetization modes.
Controlling the photoconductivity: Graphene oxide and polyaniline self assembled intercalation
Authors: Vempati Sesha , Ozcan Sefika , Uyar Tamer
Published: February 2015

We report on controlling the optoelectronic properties of self-assembled intercalating compound of graphene oxide (GO) and HCl doped polyaniline (PANI). Optical emission and X-ray diffraction studies revealed a secondary doping phenomenon of PANI with –OH and –COOH groups of GO, which essentially arbitrate the intercalation. A control on the polarity and the magnitude of the photoresponse (PR) is harnessed by manipulating the weight ratios of PANI to GO (viz., 1:1.5 and 1:2.2 are abbreviated as PG1.5 and PG2.2, respectively), where ±PR = 100(RDark – RUV-Vis)/RDark and R corresponds to the resistance of the device in dark or UV-Vis illumination. To be precise, the PR from GO, PANI, PG1.5, and PG2.2 are +34%, −111%, −51%, and +58%, respectively.
The plastic yield and flow behavior in metallic glasses
Authors: Thamburaja Prakash , Klusemann Benjamin , Adibi Sara , Bargmann Swantje
Published: February 2015

Metallic glasses have vast potential applications as components in microelectronics- and nanoelectronics-type devices. The design of such components through computer simulations requires the input of a faithful set of continuum-based constitutive equations. However, one long-standing controversial issue in modeling the plastic behavior of metallic glasses at the continuum level is the use of the most appropriate plastic yield criterion and flow rule. Guided by a series of molecular dynamics simulations conducted at low-homologous temperatures under homogeneous deformations, we quantitatively prove that the continuum plastic behavior in metallic glasses is most accurately described by a von Mises-type plastic yield criterion and flow rule.
Spin Hall magnetoresistance at high temperatures
Authors: Uchida Ken-ichi , Qiu Zhiyong , Kikkawa Takashi , Iguchi Ryo , Saitoh Eiji
Published: February 2015

The temperature dependence of spin Hall magnetoresistance (SMR) in Pt/Y3Fe5O12 (YIG) bilayer films has been investigated in a high temperature range from room temperature to near the Curie temperature of YIG. The experimental results show that the magnitude of the magnetoresistance ratio induced by the SMR monotonically decreases with increasing the temperature and almost disappears near the Curie temperature. We found that, near the Curie temperature, the temperature dependence of the SMR in the Pt/YIG film is steeper than that of a magnetization curve of the YIG; the critical exponent of the magnetoresistance ratio is estimated to be 0.9. This critical behavior of the SMR is attributed mainly to the temperature dependence of the spin-mixing conductance at the Pt/YIG interface.
The temperature dependence of atomic incorporation characteristics in growing GaInNAs films
Authors: Li Jingling , Zhang Shuguang , Gao Fangliang , Wen Lei , Zhou Shizhong , Li Guoqiang
Published: February 2015

We have systematically studied the temperature dependence of incorporation characteristics of nitrogen (N) and indium (In) in growing GaInNAs films. With the implementation of Monte-Carlo simulation, the low N adsorption energy (−0.10 eV) is demonstrated. To understand the atomic incorporation mechanism, temperature dependence of interactions between Group-III and V elements are subsequently discussed. We find that the In incorporation behaviors rather than that of N are more sensitive to the Tg, which can be experimentally verified by exploring the compositional modulation and structural changes of the GaInNAs films by means of high-resolution X-ray diffraction, X-ray photoelectron spectroscopy, scanning electron microscope, and secondary ion mass spectroscopy.
Effect of viscoelastic and dielectric relaxing matrix on ferroelastic behaviour of 1-3 piezocomposites
Authors: Jayendiran R. , Arockiarajan A.
Published: February 2015

This work focuses on evaluating the time-dependent non-linear ferroelastic behaviour of 1-3 piezocomposites under pure uni-axial compressive stress loading condition. An experimental setup is developed to study the influence of high-stress levels on the stress-strain and stress-polarization behaviour of 1-3 piezocomposites. The electro-elastic effective properties of 1-3 piezocomposites are measured experimentally based on IEEE standard and compared with the proposed numerical model using finite-element software ABAQUS. The time-dependent effective properties are evaluated using viscoelastic model and it is incorporated into a 3D micromechanical model to predict the viscoelastic behaviour of 1-3 piezocomposites under mechanical loading. The simulated results are compared with the viscoelastic behaviour of 1-3 piezocomposites obtained from experiments.
Does the telemetry technology matter? Comparing estimates of aquatic animal space-use generated from GPS-based and passive acoustic tracking
Authors: Dwyer Ross G. , Campbell Hamish A. , Irwin Terri R. , Franklin Craig E.
Published: February 2015

Underwater passive acoustic (PA) telemetry is becoming the preferred technology for investigating animal movement in aquatic systems; however, much of the current statistical tools for telemetry data were established from global positioning system (GPS)-based data. To understand the appropriateness of these tools for PA telemetry, we dual-tagged free-ranging aquatic animals that exist at the air-water interface (Crocodylus porosus, n=14). The location of each animal was simultaneously recorded over a 3-month period by fixed acoustic receivers and satellite positioning. Estimates of minimum travel distance and home range (HR) were then calculated from the PA and GPS datasets. The study revealed significant disparity between telemetry technologies in estimates of minimum travel distance and HR size. Of the five HR measures investigated, the linear distance measure produced the most comparable estimates of HR size and overlap. The kernel utilisation distribution with a reference smoothing parameter function and ad hoc function, however, produced comparable estimates when raw acoustic detections were grouped into periods when animals were within and between receiver detection fields. The study offers guidelines on how to improve the accuracy and precision of space-use estimates from PA telemetry, even in receiver arrangements with large areas of non-detection.
Tunable control of antibody immobilization using electric field
Authors: Emaminejad Sam , Javanmard Mehdi , Gupta Chaitanya , Chang Shuai , Davis Ronald W. , Howe Roger T.
Published: February 2015

Significance

We introduce a novel method for controlling orientation of proteins during immobilization on solid-state surfaces using electric fields. Atomic force microscopy measurements and fluorescence-based readout are used to confirm this phenomenon. This method of immobilization has broad implications for improvement in performance of both affinity-based protein assays and probe-free detection assays.
Noninvasive mapping of pancreatic inflammation in recent-onset type-1 diabetes patients
Authors: Gaglia Jason L. , Harisinghani Mukesh , Aganj Iman , Wojtkiewicz Gregory R. , Hedgire Sandeep , Benoist Christophe , Mathis Diane , Weissleder Ralph
Published: February 2015

Significance

We describe a readily exportable method for noninvasive imaging of the pancreatic inflammation underlying type-1 diabetes (T1D), based on MRI of the clinically approved magnetic nanoparticle ferumoxytol. This approach, which reflects nanoparticle uptake by macrophages in the inflamed pancreatic lesion, has been validated rigorously in mouse T1D models. Methodological advances reported here include extensive optimization of image acquisition and improved MRI registration and visualization technologies. A proof-of-principle study revealed a clear difference in whole-pancreas nanoparticle accumulation in patients with recent-onset T1D versus healthy controls and pronounced intra- and interpancreatic signal heterogeneity in patients. Noninvasive generation of 3D, high-resolution maps of pancreatic inflammation should prove invaluable in assessing T1D progression and as an indicator of response to therapy.
Anxieties of influence
Authors: Koskinen Kaisa , Paloposki Outi
Published: February 2015

A defining feature of retranslation is that a previous translation exists, and this earlier text has a first translator. In this article we argue that the figure of the first translator exerts an influence in the retranslation process, and all retranslators are forced to develop a stance towards the predecessor. Taking Harold Bloom’s notion of anxiety of influence in poetry as a starting point, we look at two cases of retranslation that share the same famous first translator, Pentti Saarikoski, analysing how and where the voice of this first translation can be heard in the retranslations. According to Bloom’s taxonomy, there are six modes available to poets. Applying the same taxonomy to our two retranslators, we find that they have resorted to different modes. What remains constant is that the figure of the first translator is an unavoidable function of the retranslation process and needs to be taken into account both by the retranslator and by researchers studying retranslations.
The evolution of the modern revolutionary tradition: a phenomenological reading of Hannah Arendt's On revolution
Authors: Fine Robert
Published: February 2015

This paper offers a reading of Hannah Arendt's On revolution through a phenomenological lens. It treats Arendt's text as a study of the evolution of the modern revolutionary tradition and the experiences of acute conflict and contradiction to which it has given rise. First, I address difficulties in conceiving of On revolution exclusively as political theory and affirm the helpfulness of bringing it into relation to sociology. Second, I draw attention to the triadic structure of Arendt's work in this case, its organisation in terms of the French, American, and ‘lost treasure’ moments of the modern revolutionary tradition. Third, I discuss Arendt's conceptual analysis of the modern idea of revolution, its differences from traditional ideas of revolution and the tensions involved in holding together its manifold and conflicted determinations. Fourth, I explore the different moments of the revolutionary tradition Arendt identifies, the experience of contradiction that arises at every stage, and the sense of normative evolution that comes from exploring the tradition as a whole. Finally, I propose that On revolution contains echoes of the idea of ‘rebellion as moderation’ earlier put forward by Albert Camus in The Rebel and that there is much to be gained from reading Arendt's text in this light. Overall, the paper argues for a reading of Arendt's text both as a substantive contribution to our understanding of the modern revolutionary tradition and as a methodological contribution to our ways of understanding modern political life.
Factor graph analysis of live cell–imaging data reveals mechanisms of cell fate decisions
Authors: Niederberger Theresa , Failmezger Henrik , Uskat Diana , Poron Don , Glauche Ingmar , Scherf Nico , Roeder Ingo , Schroeder Timm , Tresch Achim
Published: February 2015

Motivation : Cell fate decisions have a strong stochastic component. The identification of the underlying mechanisms therefore requires a rigorous statistical analysis of large ensembles of single cells that were tracked and phenotyped over time.

Results : We introduce a probabilistic framework for testing elementary hypotheses on dynamic cell behavior using time-lapse cell-imaging data. Factor graphs, probabilistic graphical models, are used to properly account for cell lineage and cell phenotype information. Our model is applied to time-lapse movies of murine granulocyte-macrophage progenitor (GMP) cells. It decides between competing hypotheses on the mechanisms of their differentiation. Our results theoretically substantiate previous experimental observations that lineage instruction, not selection is the cause for the differentiation of GMP cells into mature monocytes or neutrophil granulocytes.

Availability and implementation : The Matlab source code is available at http://treschgroup.de/Genealogies.html

Contact : failmezger@mpipz.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
mFASD: a structure-based algorithm for discriminating different types of metal-binding sites
Authors: He Wei , Liang Zhi , Teng Maikun , Niu Liwen
Published: February 2015

Motivation: A large number of proteins contain metal ions that are essential for their stability and biological activity. Identifying and characterizing metal-binding sites through computational methods is necessary when experimental clues are lacking. Almost all published computational methods are designed to distinguish metal-binding sites from non-metal-binding sites. However, discrimination between different types of metal-binding sites is also needed to make more accurate predictions.

Results: In this work, we proposed a novel algorithm called mFASD, which could discriminate different types of metal-binding sites effectively based on 3D structure data and is useful for accurate metal-binding site prediction. mFASD captures the characteristics of a metal-binding site by investigating the local chemical environment of a set of functional atoms that are considered to be in contact with the bound metal. Then a distance measure defined on functional atom sets enables the comparison between different metal-binding sites. The algorithm could discriminate most types of metal-binding sites from each other with high sensitivity and accuracy. We showed that cascading our method with existing ones could achieve a substantial improvement of the accuracy for metal-binding site prediction.

Availability and implementation: Source code and data used are freely available from http://staff.ustc.edu.cn/∼liangzhi/mfasd/

Contact:  liangzhi@ustc.edu.cn or hwkobe@mail.ustc.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Analysis of nanopore data using hidden Markov models
Authors: Schreiber Jacob , Karplus Kevin
Published: February 2015

Motivation: Nanopore-based sequencing techniques can reconstruct properties of biosequences by analyzing the sequence-dependent ionic current steps produced as biomolecules pass through a pore. Typically this involves alignment of new data to a reference, where both reference construction and alignment have been performed by hand.

Results: We propose an automated method for aligning nanopore data to a reference through the use of hidden Markov models. Several features that arise from prior processing steps and from the class of enzyme used can be simply incorporated into the model. Previously, the M2MspA nanopore was shown to be sensitive enough to distinguish between cytosine, methylcytosine and hydroxymethylcytosine. We validated our automated methodology on a subset of that data by automatically calculating an error rate for the distinction between the three cytosine variants and show that the automated methodology produces a 2–3% error rate, lower than the 10% error rate from previous manual segmentation and alignment.

Availability and implementation: The data, output, scripts and tutorials replicating the analysis are available at https://github.com/UCSCNanopore/Data/tree/master/Automation.

Contact:  karplus@soe.ucsc.edu or jmschreiber91@gmail.com

Supplementary information:  Supplementary data are available from Bioinformatics online.
KAPPA, a simple algorithm for discovery and clustering of proteins defined by a key amino acid pattern: a case study of the cysteine-rich proteins
Authors: Joly Valentin , Matton Daniel P.
Published: February 2015

Motivation: Proteins defined by a key amino acid pattern are key players in the exchange of signals between bacteria, animals and plants, as well as important mediators for cell–cell communication within a single organism. Their description and characterization open the way to a better knowledge of molecular signalling in a broad range of organisms, and to possible application in medical and agricultural research. The contrasted pattern of evolution in these proteins makes it difficult to detect and cluster them with classical sequence-based search tools. Here, we introduce Key Aminoacid Pattern-based Protein Analyzer (KAPPA), a new multi-platform program to detect them in a given set of proteins, analyze their pattern and cluster them by comparison to reference patterns ( ab initio search) or internal pairwise comparison ( de novo search).

Results: In this study, we use the concrete example of cysteine-rich proteins (CRPs) to show that the similarity of two cysteine patterns can be precisely and efficiently assessed by a quantitative tool created for KAPPA: the κ -score. We also demonstrate the clear advantage of KAPPA over other classical sequence search tools for ab initio search of new CRPs. Eventually, we present de novo clustering and subclustering functionalities that allow to rapidly generate consistent groups of CRPs without a seed reference.

Availability and implementation: KAPPA executables are available for Linux, Windows and Mac OS at http://kappa-sequence-search.sourceforge.net .

Contact:  dp.matton@umontreal.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Methods for the detection and assembly of novel sequence in high-throughput sequencing data
Authors: Holtgrewe Manuel , Kuchenbecker Leon , Reinert Knut
Published: February 2015

Motivation: Large insertions of novel sequence are an important type of structural variants. Previous studies used traditional de novo assemblers for assembling non-mapping high-throughput sequencing (HTS) or capillary reads and then tried to anchor them in the reference using paired read information.

Results: We present approaches for detecting insertion breakpoints and targeted assembly of large insertions from HTS paired data: BASIL and ANISE. On near identity repeats that are hard for assemblers, ANISE employs a repeat resolution step. This results in far better reconstructions than obtained by the compared methods. On simulated data, we found our insert assembler to be competitive with the de novo assemblers ABYSS and SGA while yielding already anchored inserted sequence as opposed to unanchored contigs as from ABYSS/SGA. On real-world data, we detected novel sequence in a human individual and thoroughly validated the assembled sequence. ANISE was found to be superior to the competing tool MindTheGap on both simulated and real-world data.

Availability and implementation: ANISE and BASIL are available for download at http://www.seqan.de/projects/herbarium under a permissive open source license.

Contact: manuel.holtgrewe@fu-berlin.de or knut.reinert@fu-berlin.de

Supplementary information: Supplementary data are available at Bioinformatics online.
TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples
Authors: He Liye , Wennerberg Krister , Aittokallio Tero , Tang Jing
Published: February 2015

Summary: Network pharmacology-based prediction of multi-targeted drug combinations is becoming a promising strategy to improve anticancer efficacy and safety. We developed a logic-based network algorithm, called Target Inhibition Interaction using Maximization and Minimization Averaging (TIMMA), which predicts the effects of drug combinations based on their binary drug-target interactions and single-drug sensitivity profiles in a given cancer sample. Here, we report the R implementation of the algorithm (TIMMA-R), which is much faster than the original MATLAB code. The major extensions include modeling of multiclass drug-target profiles and network visualization. We also show that the TIMMA-R predictions are robust to the intrinsic noise in the experimental data, thus making it a promising high-throughput tool to prioritize drug combinations in various cancer types for follow-up experimentation or clinical applications.

Availability and implementation: TIMMA-R source code is freely available at http://cran.r-project.org/web/packages/timma/ .

Contact:  jing.tang@helsinki.fi

Supplementary information:  Supplementary data are available at Bioinformatics online.
Into a rhythm: diel activity patterns and behaviour in Mediterranean slipper lobsters, Scyllarides latus
Authors: Goldstein Jason S. , Dubofsky Elizabeth A. , Spanier Ehud
Published: February 2015

Although the natural history for Mediterranean slipper lobsters (Scyllarides latus) is well established, there exists a disproportionate lack of important biological and physiological data to verify many key traits, including to what extent endogenous rhythms modulate aspects of their behaviour. Although Scyllarids appear nocturnally active, few studies exist that quantify this tendency. Our overall objective was to test the hypothesis that adult slipper lobsters are nocturnal and to determine if their diel activity rhythms are under the influence of an endogenous circadian clock. In the laboratory, we exposed a total of 16 animals (CLavg = 92.6 ± 6.6 mm; CL, carapace length) to a 12 : 12 light : dark (LD) cycle for 7–10 d, followed by ***constant dark (DD) for 15–20 d. Activity was assessed using a combination of time-lapse video and accelerometers. Of a total of 16 lobsters, we analysed data from 15 (one mortality). All 15 lobsters were evaluated using video. Thirteen of these lobsters were also evaluated using accelerometers. All lobsters were more active during night-time than during daytime and synchronized their activity to the LD cycle, expressing a diel activity pattern (τ = 24.04 ± 0.13 h). In DD, lobsters maintained a circadian rhythm with a τ of 23.87 ± 0.07 h. These findings may provide insight into the behaviour of these animals in their natural habitat and help explain their ability to anticipate dawn and dusk.
Cell-SELEX-based aptamer-conjugated nanomaterials for cancer diagnosis and therapy
Authors: Meng Hong-Min , Fu Ting , Zhang Xiao-Bing , Tan Weihong
Published: February 2015

Nucleic acid aptamers, which are generated by a novel technique called SELEX (systematic evolution of ligands by exponential enrichment), have recently attracted significant attention in the field of early detection and treatment of cancer based on their numerous merits, such as high affinity, high specificity, small size, little immunogenicity, stable structures, and ease of chemical modification. Furthermore, aptamers can gain more flexibility as cancer cell targeting tools when conjugated to nanomaterials, including metallic nanoparticles, carbon nanomaterials, DNA nanodevices, and polymeric nanoparticles. We discuss the progress achieved in cancer diagnosis and therapy through the conjugation of cell-SELEX-based aptamers with different nanomaterials.
Freedom of Choice of Hospital for Psychiatric Admissions
Authors: Virtzberg-Rofe' Dahlia , Rofe' Tzviel
Published: February 2015

The right to choose one’s health care setting is not upheld in some jurisdictions and for some populations. A case in point is Israel, where people with mental illnesses are not allowed to choose a hospital for their psychiatric admission when that is needed, but are only admitted to a hospital in their residential catchment area. This is in contrast to Israelis with other illnesses, who can access a variety of hospitals. The authors have contested this governmental practice in public and in court, and are lobbying for legislative change to this discriminative practice. Such human rights advocacy is relevant and applicable to many jurisdictions, and lessons learned from the Israeli process are shared in this chapter and will be shared in the future elsewhere based on progress with these legal procedures.