bluuebunny/crossref_metadata_2025 huggingface dataset:
Introduction
Authors: True Jacqui
Published: February 2013

What is feminist about feminist evolutionary theory, and how valid is the feminist evolutionary analytic approach for understanding violence against women globally? What has evolutionary analysis got to do with legal enclaves, pluralism, and inequitable family law, and how do they cause violence? And, moreover, is legal change, specifically adopting and diffusing similar liberal family status laws worldwide, the best strategy for ending pervasive and egregious violence against women? Valerie M. Hudson, Donna Lee Bowen, and Perpetua Lynne Nielsen's article, “What Is the Relationship between Inequity in Family Law and Violence against Women? Approaching the Issue of Legal Enclaves” (Politics & Gender. 2011. 7 (4): 453–92) raises theoretical, empirical, and praxeological questions for feminist scholars of politics and international relations that this Critical Perspectives section takes up with essays from six contributors selected from an open call for papers.
Religion and Ethnic Minority Attitudes in Britain toward the War in Afghanistan
Authors: Clements Ben
Published: February 2013

Public opinion research has demonstrated that minority religious and ethnic groups hold distinctive preferences on foreign policy issues, including military interventions in the Cold War and post-Cold War eras. There has been little scholarly research in Britain into the attitudes of minority groups on foreign policy issues. This article uses a nationally-representative survey of the ethnic minority population in Britain to examine the sources of public opinion towards the war in Afghanistan. Using multivariate analysis, it finds strong effects for religious affiliation, religiosity and political alienation. There is also evidence of a “gender gap” and age-related differences. The paper contributes to the literature on the impact of religion on public opinion and foreign policy and to analysis of the political attitudes of minority groups in Britain.
Arizona Twin Project: A Focus on Early Resilience
Authors: Lemery-Chalfant Kathryn , Clifford Sierra , McDonald Kristy , O'Brien T. Caitlin , Valiente Carlos
Published: February 2013

The Arizona Twin Project is an ongoing longitudinal study designed to elucidate the genetic and environmental influences underlying the development of early competence and resilience to common mental and physical health problems during infancy and childhood. Participants are a sample of 600 twins (25% Hispanic) recruited from birth records in the state of Arizona, United States. Primary caregivers were interviewed on twins’ development and early social environments when twins were 12 and 30 months of age. Measures include indices of prenatal and obstetrical risk coded from hospital medical records, as well as primary caregiver-report questionnaires assessing multiple indicators of environmental risk and resilience (e.g., parental warmth and control, family and social support), twins’ developmental maturity, temperament, health, behavior problems, and competencies. Preliminary findings highlight the importance of the early environment for infant and toddler health and well-being, both directly and as a moderator of genetic influences. Future directions include a third longitudinal assessment in middle childhood examining daily bidirectional relations between sleep, health behaviors, stress, and mood.
The Southern California Twin Register at the University of Southern California: III
Authors: Baker Laura A. , Tuvblad Catherine , Wang Pan , Gomez Karina , Bezdjian Serena , Niv Sharon , Raine Adrian
Published: February 2013

The Southern California Twin Register at the University of Southern California (USC) was initiated in 1984 and continues to provide an important resource for studies investigating genetic and environmental influences on human behavior. This article provides an update on the current register and its potential for future twin studies using recruitment through school district databases and voter records. An overview is also provided for an ongoing longitudinal twin study investigating the development of externalizing psychopathology from childhood to young adulthood, the USC Study of Risk Factors for Antisocial Behavior. Characteristics of the twins and their families are presented, including recruitment and participation rates, as well as attrition analyses and a summary of key findings to date.
Two Cohort and Three Independent Anonymous Twin Projects at the Keio Twin Research Center (KoTReC)
Authors: Ando Juko , Fujisawa Keiko K. , Shikishima Chizuru , Hiraishi Kai , Nozaki Mari , Yamagata Shinji , Takahashi Yusuke , Ozaki Koken , Suzuki Kunitake , Deno Minako , Sasaki Shoko , Toda Tatsushi , Kobayashi Kazuhiro , Sugimoto Yutaro , Okada Mitsuhiro , Kijima Nobuhiko , Ono Yutaka , Yoshimura Kimio , Kakihana Shinichiro , Maekawa Hiroko , Kamakura Toshimitsu , Nonaka Koichi , Kato Noriko , Ooki Syuichi
Published: February 2013

The Keio Twin Research Center has conducted two longitudinal twin cohort projects and has collected three independent and anonymous twin data sets for studies of phenotypes related to psychological, socio-economic, and mental health factors. The Keio Twin Study has examined adolescent and adult cohorts, with a total of over 2,400 pairs of twins and their parents. DNA samples are available for approximately 600 of these twin pairs. The Tokyo Twin Cohort Project has followed a total of 1,600 twin pairs from infancy to early childhood. The large-scale cross-sectional twin study (CROSS) has collected data from over 4,000 twin pairs, from 3 to 26 years of age, and from two high school twin cohorts containing a total of 1,000 pairs of twins. These data sets of anonymous twin studies have mainly targeted academic performance, attitude, and social environment. The present article introduces the research designs and major findings of our center, such as genetic structures of cognitive abilities, personality traits, and academic performances, developmental effects of genes and environment on attitude, socio-cognitive ability and parenting, genes x environment interaction on attitude and conduct problem, and statistical methodological challenges and so on. We discuss the challenges in conducting twin research in Japan.
Twin Studies of Multiple Myeloma / Research Reviews and News: Critique of Twin Research; Opposite-Sex Twins and Sexual Attraction; Twinning Rates and Assisted Reproductive Technology; Family History of Multiple Implantation / Human Interest: Book Party: Born Together — Reared Apart; Morning Sickness and Twins; Sexuality in Conjoined Twins; Kofi Annan: Opposite-Sex Twin; Switched at Birth
Authors: Segal Nancy L.
Published: February 2013

A foundation for studying multiple myeloma, launched by a monozygotic twin, is described. Twin studies of that disease are also examined. A summary of selected research studies and news events follows, with specific reference to a new critique of twin research, sexual attraction in separated opposite-sex twins, twinning rates following assisted reproductive technology and family histories of multiple implantation. Human interest topics cover a gathering of researchers from the Minnesota Study of Twins Reared Apart, morning sickness and twin pregnancy, sexuality in conjoined twins, a famous hidden twin, and a film about switched at birth babies.
The Vocabulary and Overclaiming Test (VOC-T)
Authors: Ziegler Matthias , Kemper Christoph , Rammstedt Beatrice
Published: February 2013

The present research aimed at constructing a questionnaire measuring overclaiming tendencies (VOC-T-bias) as an indicator of self-enhancement. An approach was used which also allows estimation of a score for vocabulary knowledge, the accuracy index (VOC-T-accuracy), using signal detection theory. For construction purposes, an online study was conducted with N = 1,176 participants. The resulting questionnaire, named Vocabulary and Overclaiming – Test (VOC-T) was investigated with regard to its psychometric properties in two further studies. Study 2 used data from a population representative sample (N = 527), and Study 3 was another online survey (N = 933). Results show that reliability estimates were satisfactory for the VOC-T-bias index and the VOC-T-accuracy index. Overclaiming did not correlate with knowledge, but it was sensitive to self-enhancement supporting the construct validity of the test scores. The VOC-T-accuracy index in turn covaried with general knowledge and even more so with verbal knowledge, which also supports construct validity. Moreover, the VOC-T-accuracy index had a meaningful correlation with age in both validation studies. All in all, the psychometric properties can be regarded as sufficient to recommend the VOC-T for research purposes.
Theoretical study of phenyl-substituted indacenodithiophene copolymers for high performance organic photovoltaics
Authors: Chochos Christos L. , Avgeropoulos Apostolos , Lidorikis Elefterios
Published: February 2013

The theoretical estimation of energy levels and energy gaps of conjugated polymers for organic photovoltaics (OPVs) represents in principle a useful tool for the prescreening of new donor systems as a suitable pair for the fullerene derivative [6,6]-phenyl-C61-butyric acid methyl ester (PC61BM). In this study, ten tetraphenyl-substituted indacenodithiophene (IDT) copolymers (eight in the form of donor-acceptor), whose energy gaps vary in the range of 1.48–2.11 eV have been selected and their highest occupied molecular orbitals (HOMOs), lowest unoccupied molecular orbitals (LUMOs), and gap energies have been calculated by applying density functional theory (DFT) and/or time-dependent density functional theory (TD-DFT) methods. In spite of the examined molecular structure variety, nice correlations (theoretical models) between experimental and theoretical electronic parameters were found. It is shown that the theoretical band gap estimated by the TD-DFT using dimer model compounds and DFT using tetramer model compounds provide in good agreement the optical band gap of these polymers. Finally, the optimum theoretical limits of the LUMO offset between the fullerene and the IDT tetramer model compounds, for which high performance OPVs (efficiency > 6%) are obtained, is presented for the first time.
Lowest triplet (n, π*) electronic state of acrolein: Determination of structural parameters by cavity ringdown spectroscopy and quantum-chemical methods
Authors: Hlavacek Nikolaus C. , McAnally Michael O. , Drucker Stephen
Published: February 2013

The cavity ringdown absorption spectrum of acrolein (propenal, CH2=CH—CH=O) was recorded near 412 nm, under bulk-gas conditions at room temperature and in a free-jet expansion. The measured spectral region includes the \documentclass[12pt]{minimal}\begin{document}$0^0_0$\end{document}000 band of the T1(n, π*) ← S0 system. We analyzed the \documentclass[12pt]{minimal}\begin{document}$0^0_0$\end{document}000 rotational contour by using the STROTA computer program [R. H. Judge et al., J. Chem. Phys. 103, 5343 (1995)]10.1063/1.470569, which incorporates an asymmetric rotor Hamiltonian for simulating and fitting singlet-triplet spectra. We used the program to fit T1(n, π*) inertial constants to the room-temperature contour. The determined values (cm−1), with 2σ confidence intervals, are A = 1.662 ± 0.003, B = 0.1485 ± 0.0006, C = 0.1363 ± 0.0004. Linewidth analysis of the jet-cooled spectrum yielded a value of 14 ± 2 ps for the lifetime of isolated acrolein molecules in the T1(n, π*), v = 0 state. We discuss the observed lifetime in the context of previous computational work on acrolein photochemistry. The spectroscopically derived inertial constants for the T1(n, π*) state were used to benchmark a variety of computational methods. One focus was on complete active space methods, such as complete active space self-consistent field (CASSCF) and second-order perturbation theory with a CASSCF reference function (CASPT2), which are applicable to excited states. We also examined the equation-of-motion coupled-cluster and time-dependent density function theory excited-state methods, and finally unrestricted ground-state techniques, including unrestricted density functional theory and unrestricted coupled-cluster theory with single and double and perturbative triple excitations. For each of the above methods, we or others [O. S. Bokareva et al., Int. J. Quantum Chem. 108, 2719 (2008)]10.1002/qua.21803 used a triple zeta-quality basis set to optimize the T1(n, π*) geometry of acrolein. We find that the multiconfigurational methods provide the best agreement with fitted inertial constants, while the economical unrestricted Perdew-Burke-Ernzerhof exchange-correlation hybrid functional (UPBE0) technique performs nearly as well.
Diffusion tensor imaging using a high-temperature superconducting resonator in a 3 T magnetic resonance imaging for a spontaneous rat brain tumor
Authors: Lin In-Tsang , Yang Hong-Chang , Chen Jyh-Horng
Published: February 2013

This study investigates the peri-tumor signal abnormalities of a spontaneous brain tumor in a rat by using a 4 cm high-temperature superconducting (HTS) surface resonator. Fractional anisotropy (FA) values derived from diffusion tensor imaging reflect the interstitial characteristic of the peri-lesional tissues of brain tumors. Low FA indicates interstitial tumor infiltration and tissue injury, while high FA indicates better tissue integrity. Better delineation of tissue contents obtained by the HTS surface resonator at 77 K may facilitate therapeutic strategy and improve clinical outcomes.
Shear modulus of simulated glass-forming model systems: Effects of boundary condition, temperature, and sampling time
Authors: Wittmer J. P. , Xu H. , Polińska P. , Weysser F. , Baschnagel J.
Published: February 2013

The shear modulus G of two glass-forming colloidal model systems in d = 3 and d = 2 dimensions is investigated by means of, respectively, molecular dynamics and Monte Carlo simulations. Comparing ensembles where either the shear strain γ or the conjugated (mean) shear stress τ are imposed, we compute G from the respective stress and strain fluctuations as a function of temperature T while keeping a constant normal pressure P. The choice of the ensemble is seen to be highly relevant for the shear stress fluctuations μF(T) which at constant τ decay monotonously with T following the affine shear elasticity μA(T), i.e., a simple two-point correlation function. At variance, non-monotonous behavior with a maximum at the glass transition temperature Tg is demonstrated for μF(T) at constant γ. The increase of G below Tg is reasonably fitted for both models by a continuous cusp singularity, G(T)∝(1 − T/Tg)1/2, in qualitative agreement with recent theoretical predictions. It is argued, however, that longer sampling times may lead to a sharper transition.
Zero-field splitting in nickel(II) complexes: A comparison of DFT and multi-configurational wavefunction calculations
Authors: Kubica A. , Kowalewski J. , Kruk D. , Odelius M.
Published: February 2013

The zero-field splitting (ZFS) is an important quantity in the electron spin Hamiltonian for S = 1 or higher. We report calculations of the ZFS in some six- and five-coordinated nickel(II) complexes (S = 1), using different levels of theory within the framework of the ORCA program package [F. Neese, Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2, 73 (2012)]10.1002/wcms.81. We compare the high-end ab initio calculations (complete active space self-consistent field and n-electron valence state perturbation theory), making use of both the second-order perturbation theory and the quasi-degenerate perturbation approach, with density functional theory (DFT) methods using different functionals. The pattern of results obtained at the ab initio levels is quite consistent and in reasonable agreement with experimental data. The DFT methods used to calculate the ZFS give very strongly functional-dependent results and do not seem to function well for our systems.
Dielectric function of Cu(In, Ga)Se2-based polycrystalline materials
Authors: Minoura Shota , Kodera Keita , Maekawa Takuji , Miyazaki Kenichi , Niki Shigeru , Fujiwara Hiroyuki
Published: February 2013

The dielectric functions of Cu(In, Ga)Se2(CIGS)-based polycrystalline layers with different Ga and Cu compositions have been determined by applying spectroscopic ellipsometry (SE) in a wide energy range of 0.7–6.5 eV. To suppress SE analysis errors induced by rough surface and compositional fluctuation, quite thin CIGS layers (<60 nm) with high uniformity toward the growth direction have been characterized using a self-consistent SE analysis method. We find that the optical model used in many previous studies is oversimplified particularly for the roughness/overlayer contribution, and all the artifacts arising from the simplified analysis have been removed almost completely in our approach. The CIGS dielectric functions with the variation of the Ga composition [x = Ga/(In + Ga)] revealed that (i) the whole CIGS dielectric function shifts toward higher energies with x, (ii) the band gap increases linearly with x without the band-gap bowing effect, and (iii) the overall absorption coefficients are significantly smaller than those reported earlier. Furthermore, the reduction of the Cu composition [y = Cu/(In + Ga)] leads to (i) the linear increase in the band-edge transition energy and (ii) the decrease in the absorption coefficient, due to the smaller interaction of the Cu 3d orbitals near the valence band maximum in the Cu-deficient layers. When y > 1, on the other hand, the free-carrier absorption increases drastically due to the formation of a semi-metallic CuxSe phase with a constant band gap in the CIGS component. In this study, by using a standard critical-point line-shape analysis, the critical point energies of the CIGS-based layers with different Ga and Cu compositions have been determined. Based on these results, we will discuss the optical transitions in CIGS-based polycrystalline materials.
The impact of substrate miscut on the morphology of InGaN epitaxial layers subjected to a growth interruption
Authors: Jouvet Nicolas , Kappers Menno J. , Humphreys Colin J. , Oliver Rachel A.
Published: February 2013

To investigate the formation of gross well width fluctuations in InGaN quantum wells subjected to a growth interruption or temperature ramp, the impact of substrate miscut on the morphology of thin InGaN epitaxial layers grown on GaN pseudo-substrates has been studied. Following a growth interruption, the InGaN layer morphology consists of interlinking strips of InGaN separated by elongated troughs. The troughs tend to align along the same direction as the step edges in the underlying GaN pseudo-substrate and the spacing of the troughs varies in direct proportion to the step edge spacing. However, the troughs are on average more widely spaced than the terrace edges, and analysis of the distribution of trough spacings and step edge spacings suggests that it may be double-monolayer steps which most influence the trough formation. A mechanism for trough formation is proposed in which indium is preferentially incorporated at double-monolayer step edges and that the resulting indium-rich regions decompose during the growth interruption, forming a trough.
Polarization-independent rapidly responding phase grating based on hybrid blue phase liquid crystal
Authors: Lin Yi-Ting , Jau Hung-Chang , Lin Tsung-Hsien
Published: February 2013

This work demonstrates a polymer-stabilized blue phase (PSBP) liquid crystal phase grating, which is made of hybrid PSBPs with two different Kerr constants. The Kerr constant of a PSBP is related to the morphology of the polymer network which can be controlled by the phase separation temperature. Owing to the non-patterned electrode and the optical isotropy of the PSBP, the diffraction effect can be completely switched off when the voltage is absent. The diffraction intensity increases when a uniform applied electrical field induces the phase difference in the hybrid PSBP. The phase grating is completely independent of the polarization of the incident light. Furthermore, the response time to switching is in the sub-millisecond range.
Thermocouple error correction for measuring the flame temperature with determination of emissivity and heat transfer coefficient
Authors: Hindasageri V. , Vedula R. P. , Prabhu S. V.
Published: February 2013

Temperature measurement by thermocouples is prone to errors due to conduction and radiation losses and therefore has to be corrected for precise measurement. The temperature dependent emissivity of the thermocouple wires is measured by the use of thermal infrared camera. The measured emissivities are found to be 20%–40% lower than the theoretical values predicted from theory of electromagnetism. A transient technique is employed for finding the heat transfer coefficients for the lead wire and the bead of the thermocouple. This method does not require the data of thermal properties and velocity of the burnt gases. The heat transfer coefficients obtained from the present method have an average deviation of 20% from the available heat transfer correlations in literature for non-reacting convective flow over cylinders and spheres. The parametric study of thermocouple error using the numerical code confirmed the existence of a minimum wire length beyond which the conduction loss is a constant minimal. Temperature of premixed methane-air flames stabilised on 16 mm diameter tube burner is measured by three B-type thermocouples of wire diameters: 0.15 mm, 0.30 mm, and 0.60 mm. The measurements are made at three distances from the burner tip (thermocouple tip to burner tip/burner diameter = 2, 4, and 6) at an equivalence ratio of 1 for the tube Reynolds number varying from 1000 to 2200. These measured flame temperatures are corrected by the present numerical procedure, the multi-element method, and the extrapolation method. The flame temperatures estimated by the two-element method and extrapolation method deviate from numerical results within 2.5% and 4%, respectively.
Diagonal control design for atomic force microscope piezoelectric tube nanopositioners
Authors: Bhikkaji B. , Yong Y. K. , Mahmood I. A. , Moheimani S. O. R.
Published: February 2013

Atomic Force Microscopes (AFM) are used for generating surface topography of samples at micro to atomic resolutions. Many commercial AFMs use piezoelectric tube nanopositioners for scanning. Scanning rates of these microscopes are hampered by the presence of low frequency resonant modes. When inadvertently excited, these modes lead to high amplitude mechanical vibrations causing the loss of accuracy, while scanning, and eventually to break down of the tube. Feedback control has been used to damp these resonant modes. Thereby, enabling higher scanning rates. Here, a multivariable controller is designed to damp the first resonant mode along both the x and y axis. Exploiting the inherent symmetry in the piezoelectric tube, the multivariable control design problem is recast as independent single-input single-output (SISO) designs. This in conjunction with integral resonant control is used for damping the first resonant mode.
Ion-acoustic K-dV and mK-dV solitons in a degenerate electron-ion dense plasma
Authors: Nahar L. , Zobaer M. S. , Roy N. , Mamun A. A.
Published: February 2013

A theoretical investigation has been made of the nonlinear propagation of ion-acoustic waves associated with a dense plasma system consisting degenerate electron and ion fluids. This fluid model, which is valid for both the non-relativistic and ultra-relativistic limits, has been employed with the reductive perturbation method. The K-dV and modified K-dV (mK-dV) equations have been derived and numerically analyzed. The basic features of solitons have been observed. It has been shown that the plasma system under consideration supports the propagation of solitons (electrostatic solitary structures) obtained from the solutions of K-dV and mK-dV equations. The implications of our results obtained from this investigation in compact astrophysical objects have been briefly discussed.
Hole doping of graphene supported on Ir(111) by AlBr3
Authors: Vinogradov N. A. , Simonov K. A. , Zakharov A. A. , Wells J. W. , Generalov A. V. , Vinogradov A. S. , Mårtensson N. , Preobrajenski A. B.
Published: February 2013

In this letter, we report an easy and tenable way to tune the type of charge carriers in graphene, using a buried layer of AlBr3 and its derivatives on the graphene/Ir(111) interface. Upon the deposition of AlBr3 on graphene/Ir(111) and subsequent temperature-assisted intercalation of graphene/Ir(111) with atomic Br and AlBr3, pronounced hole doping of graphene is observed. The evolution of the graphene/Br-AlBr3/Ir(111) system at different stages of intercalation has been investigated by means of microbeam low-energy electron microscopy/electron diffraction, core-level photoelectron spectroscopy, and angle-resolved photoelectron spectroscopy.
Comment on “On the theoretical determination of the Prigogine-Defay ratio in glass transition” [J. Chem. Phys. 136, 124502 (2012)]
Authors: Garden Jean-Luc , Guillou Hervé , Richard Jacques
Published: February 2013

Generally, experimentally determined values of the Prigogine-Defay (PD) ratio are different from unity. This can be explained if one considers that more than one single order parameter are involved in the thermodynamics of the glass transition process. Against the consensual view, Tropin et al. demonstrated that PD ratios can be different from unity even if one single order parameter is involved. This “Comment” aims to discuss fundamental mistakes leading to this conclusion in the recent article “On the theoretical determination of the Prigogine-Defay ratio in glass transition” [J. Chem. Phys. 136, 124502 (2012)] by Tropin et al.10.1063/1.3694531
Note: A simple experimental arrangement to generate optical vortex beams
Authors: Kumar Dhirendra , Das Abhijit , Boruah Bosanta R.
Published: February 2013

In this Note, we present a simple experimental arrangement to generate optical vortex beams. We have demonstrated how by taking print of an interferogram on a transparent sheet, vortex beams with various topological charges can be generated. Experimental results show that the vortex beam indeed carries the topological charge that is used to compute the interferograms. In addition to being simple and inexpensive, one major advantage of the arrangement is that it makes it possible to generate different vortex beams quickly, unlike using the photographic process to create the holograms.
Origin of the different multiferroism in BiFeO3 and GaFeO3
Authors: Bahoosh S. G. , Wesselinowa J. M.
Published: February 2013

We have proposed microscopic models for describing the multiferroic properties of BiFeO3 and GaFeO3. It is shown that the mechanisms of the multiferroism are different. In BiFeO3, the magnetoelectric coupling is biquadratic, whereas in GaFeO3 it is linear. The site disorder between Ga and Fe is a primary source of the net magnetic moment in GaFeO3. The temperature and magnetic field dependence of the polarization is calculated in order to show that the proposed models for these two multiferroics are correct. Near the magnetic phase transition temperature TN we obtain a kink in the electric properties.
Thermoacoustic resonance effect and circuit modelling of biological tissue
Authors: Gao Fei , Zheng Yuanjin , Feng Xiaohua , Ohl Claus-Dieter
Published: February 2013

In this letter, thermoacoustic resonance effect is predicted from theoretical analysis with series resistor-inductor-capacitor resonance circuit model and then observed experimentally using muscle tissue illuminated by multi-pulse microwave source. Through model fitting, the circuit parameters are extracted to characterize quantitatively the resonant response of the tissue. Coherent demodulation is applied to obtain the enhanced signal-to-noise ratio and spatial information by treating tissue as a communication channel. This physical phenomenon shows significantly higher sensitivity than conventional single microwave pulse induced thermoacoustic effect, enabling the potential design of low-power thermoacoustic imaging device for portable and on-site diagnosis.
Improved chemical and electrical stability of gold silicon contacts via epitaxial electrodeposition
Authors: Akhtari-Zavareh Azadeh , Li Wenjie , Maroun Fouad , Allongue Philippe , Kavanagh Karen L.
Published: February 2013

The ballistic transport and junction stability of epitaxial Au, grown on Si (111) and (001) substrates via electrodeposition, have been investigated as a function of Au thickness (6.7–14.1 nm). Scanning tunneling microscopy (STM) with ballistic emission electron microscopy (BEEM) showed hot electron transmission for diodes with Au thicknesses greater than 7 nm, whereas for thinner samples surface or interfacial oxidation meant that macroscopic current-voltage characteristics gave high barrier heights (0.8 eV) but no detectable BEEM transport at room temperature. Diodes that remained electrically stable for several months after exposure to air also show an atomically abrupt and epitaxial Au/Si interface via cross-sectional transmission electron microscopy. Degradation in rectifying diode properties through surface or interfacial reactions is indicated by poorer STM images and decreasing or no BEEM transmission, correlated with the formation of a continuous interfacial layer.
Al-doped ZnO thin-film transistor embedded micro-cantilever as a piezoresistive sensor
Authors: Ray Prasenjit , Ramgopal Rao V.
Published: February 2013

In this work, an aluminium-doped zinc oxide (AZO) thin film transistor, embedded in a polymer micro-cantilever, is demonstrated for nano-mechanical sensing applications. This device senses the surface stress due to a change in the carrier mobility of the semi-conducting layer. Due to the low Young's modulus and high strain sensitivity of the AZO layer, this micro-cantilever shows a deflection sensitivity of 116 ppm per nanometer of deflection. Also, mechanical characterization of these devices shows that the resonance frequency is in the range of a few tens of kilohertz which is suitable for sensor applications.
Oxyhalogen–Sulfur Chemistry: Oxidation of a Thiourea Dimer, Formamidine Disulfide, by Chlorine Dioxide
Authors: Martincigh Bice S. , Mhike Morgen , Morakinyo Kayode , Adigun Risikat Ajibola , Simoyi Reuben H.
Published: February 2013

The oxidation of formamidine disulfide, FDS, the dimer of thiourea, by aqueous chlorine dioxide has been studied in highly acidic and mildly acidic media. FDS is one of the possible oxidation intermediates formed in the oxidation of thiourea by oxyhalogens to urea and sulfate. The reaction is exceedingly slow, giving urea and sulfate with a stoichiometric ratio of 5 : 14 FDS to chlorine dioxide after an incubation period of up to 72 h and only in highly acidic media which discourages the disproportionation of chlorine dioxide to the oxidatively inert chlorate. Mass spectrometric data suggest that the oxidative pathway proceeds predominantly through the sulfinic acid, proceeding next to the products sulfate and urea, while by-passing the sulfonic acid. Transient formation of the unstable sulfenic acid was also not observed.
Revisiting an important component of plant genomes: microsatellites
Authors: Gao Caihua , Ren Xiaodong , Mason Annaliese S. , Li Jiana , Wang Wei , Xiao Meili , Fu Donghui
Published: February 2013

Microsatellites are some of the most highly variable repetitive DNA tracts in genomes. Few studies focus on whether the characteristic instability of microsatellites is linked to phenotypic effects in plants. We summarise recent data to investigate how microsatellite variations affect gene expression and hence phenotype. We discuss how the basic characteristics of microsatellites may contribute to phenotypic effects. In summary, microsatellites in plants are universal and highly mutable, they coexist and coevolve with transposable elements, and are under selective pressure. The number of motif nucleotides, the type of motif and transposon activity all contribute to the nonrandom generation and decay of microsatellites, and to conservation and distribution biases. Although microsatellites are generated by accident, they mature through responses to environmental change before final decay. This process is mediated by organism adjustment mechanisms, which maintain a balance between birth versus death and growth versus decay in microsatellites. Close relationships also exist between the physical structure, variation and functionality of microsatellites: in most plant species, sequences containing microsatellites are associated with catalytic activity and binding functions, are expressed in the membrane and organelles, and participate in the developmental and metabolic processes. Microsatellites contribute to genome structure and functional plasticity, and may be considered to promote species evolution in plants in response to environmental changes. In conclusion, the generation, loss, functionality and evolution of microsatellites can be related to plant gene expression and functional alterations. The effect of microsatellites on phenotypic variation may be as significant in plants as it is in animals.
Critique and complexity: presenting a more effective way to conceptualise the knowledge adoption process
Authors: Brown Chris
Published: February 2013

The process of 'knowledge adoption' is defined as the means through which policy-makers digest, accept then 'take on board' research findings. It is argued in Brown, however, that current models designed to explain knowledge adoption activity fail to fully account for the complexities
that affect its operation. Within this paper, existing frameworks are explored and critiqued, and an alternative approach is presented. It is argued that this alternative conceptualisation provides a more effective explanation of the knowledge adoption process and significantly improves on
extant work in this area.
RNA-eXpress annotates novel transcript features in RNA-seq data
Authors: Forster Samuel C. , Finkel Alexander M. , Gould Jodee A. , Hertzog Paul J.
Published: February 2013

Summary: Next-generation sequencing is rapidly becoming the approach of choice for transcriptional analysis experiments. Substantial advances have been achieved in computational approaches to support these technologies. These approaches typically rely on existing transcript annotations, introducing a bias towards known genes, require specific experimental design and computational resources, or focus only on identification of splice variants (ignoring other biologically relevant transcribed features contained within the data that may be important for downstream analysis). Biologically relevant transcribed features also include large and small non-coding RNA, new transcription start sites, alternative promoters, RNA editing and processing of coding transcripts. Also, many existing solutions lack accessible interfaces required for wide scale adoption. We present a user-friendly, rapid and computation-efficient feature annotation framework (RNA-eXpress) that enables identification of transcripts and other genomic and transcriptional features independently of current annotations. RNA-eXpress accepts mapped reads in the standard binary alignment (BAM) format and produces a study-specific feature annotation in GTF format, comparison statistics, sequence extraction and feature counts. The framework is designed to be easily accessible while allowing advanced users to integrate new feature-identification algorithms through simple class extension, thus facilitating expansion to novel feature types or identification of study-specific feature types.

Availability and implementation: RNA-eXpress software, source code, user manuals, supporting tutorials, developer guides and example data are available at http://www.rnaexpress.org.

Contact:  paul.hertzog@monash.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information
Authors: Anderson James W. J. , Haas Pierre A. , Mathieson Leigh-Anne , Volynkin Vladimir , Lyngsø Rune , Tataru Paula , Hein Jotun
Published: February 2013

Motivation: Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current implementation considers both evolutionary information and folding kinetics, thus losing information that, when considered, might lead to better predictions.

Results: We present an iterative algorithm, Oxfold, in the framework of stochastic context-free grammars, that emulates the kinetics of RNA folding in a simplified way, in combination with a molecular evolution model. This method improves considerably on existing grammatical models that do not consider folding kinetics. Additionally, the model compares favourably to non-kinetic thermodynamic models.

Availability: http://www.stats.ox.ac.uk/∼anderson.

Contact: anderson@stats.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Quantifying spatial relationships from whole retinal images
Authors: Ruttenberg Brian E. , Luna Gabriel , Lewis Geoffrey P. , Fisher Steven K. , Singh Ambuj K.
Published: February 2013

Motivation: Microscopy advances have enabled the acquisition of large-scale biological images that capture whole tissues in situ. This in turn has fostered the study of spatial relationships between cells and various biological structures, which has proved enormously beneficial toward understanding organ and organism function. However, the unique nature of biological images and tissues precludes the application of many existing spatial mining and quantification methods necessary to make inferences about the data. Especially difficult is attempting to quantify the spatial correlation between heterogeneous structures and point objects, which often occurs in many biological tissues.

Results: We develop a method to quantify the spatial correlation between a continuous structure and point data in large (17 500 × 17 500 pixel) biological images. We use this method to study the spatial relationship between the vasculature and a type of cell in the retina called astrocytes. We use a geodesic feature space based on vascular structures and embed astrocytes into the space by spatial sampling. We then propose a quantification method in this feature space that enables us to empirically demonstrate that the spatial distribution of astrocytes is often correlated with vascular structure. Additionally, these patterns are conserved in the retina after injury. These results prove the long-assumed patterns of astrocyte spatial distribution and provide a novel methodology for conducting other spatial studies of similar tissue and structures.

Availability: The Matlab code for the method described in this article can be found at http://www.cs.ucsb.edu/∼dbl/software.php.

Contact:  bruttenberg@cra.com or ambuj@cs.ucsb.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction
Authors: Pires Douglas E. V. , de Melo-Minardi Raquel C. , da Silveira Carlos H. , Campos Frederico F. , Meira Wagner
Published: February 2013

Motivation: Receptor-ligand interactions are a central phenomenon in most biological systems. They are characterized by molecular recognition, a complex process mainly driven by physicochemical and structural properties of both receptor and ligand. Understanding and predicting these interactions are major steps towards protein ligand prediction, target identification, lead discovery and drug design.

Results: We propose a novel graph-based–binding pocket signature called aCSM, which proved to be efficient and effective in handling large-scale protein ligand prediction tasks. We compare our results with those described in the literature and demonstrate that our algorithm overcomes the competitor’s techniques. Finally, we predict novel ligands for proteins from Trypanosoma cruzi, the parasite responsible for Chagas disease, and validate them in silico via a docking protocol, showing the applicability of the method in suggesting ligands for pockets in a real-world scenario.

Availability and implementation: Datasets and the source code are available at http://www.dcc.ufmg.br/∼dpires/acsm.

Contact:  dpires@dcc.ufmg.br or raquelcm@dcc.ufmg.br

Supplementary information:  Supplementary data are available at Bioinformatics online.
displayHTS: a R package for displaying data and results from high-throughput screening experiments
Authors: Zhang Xiaohua Douglas , Zhang Zhaozhi
Published: February 2013

Summary: The R package displayHTS implements recently developed methods and figures for displaying data and hit selection results in high-throughput screening (HTS) experiments. It generates not only certain useful distinctive graphics such as the plate-well series plot, plate image and dual-flashlight plot but also other commonly used figures such as volcano plot and plate correlation plot. These figures are critical for visualizing the data and displaying important features of HTS data and hit selection results.

Availability and implementation: The package is freely available from CRAN: http://cran.r-project.org/mirrors.html, being distributed under the GNU General Public License.

Contact:  xiaohua_zhang@merck.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships
Authors: Kosinski Jan , Barbato Alessandro , Tramontano Anna
Published: February 2013

Summary: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure.

MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model.

Availability and implementation: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported.

Contact:  anna.tramontano@uniroma1.it

Supplementary information:  Supplementary data are available at Bioinformatics online
Phylogenomic clustering for selecting non-redundant genomes for comparative genomics
Authors: Moreno-Hagelsieb Gabriel , Wang Zilin , Walsh Stephanie , ElSherbiny Aisha
Published: February 2013

Motivation: Analyses in comparative genomics often require non-redundant genome datasets. Eliminating redundancy is not as simple as keeping one strain for each named species because genomes might be redundant at a higher taxonomic level than that of species for some analyses; some strains with different species names can be as similar as most strains sharing a species name, whereas some strains sharing a species name can be so different that they should be put into different groups; and some genomes lack a species name.

Results: We have implemented a method and Web server that clusters a genome dataset into groups of redundant genomes at different thresholds based on a few phylogenomic distance measures.

Availability: The Web interface, similarity and distance data and R-scripts can be accessed at http://microbiome.wlu.ca/research/redundancy/.

Contact:  gmoreno@wlu.ca
The Soviet Enterprise: What Have We Learned from the Archives?
Authors: Kragh Martin
Published: February 2013

Business historians have hitherto paid only scant attention to the Soviet experience. This article is an attempt to summarize the knowledge we have gained in the two decades following the collapse of the Soviet economy, and draws on published research, document volumes, and previously unexplored archival sources. In the conclusion, I make the case that the Soviet experience can provide relevant comparative examples for the field of business history.
The acoustic multifrequency classification of two sympatric euphausiid species (Meganyctiphanes norvegica and Thysanoessa raschii), with empirical and SDWBA model validation
Authors: McQuinn Ian H. , Dion Maxime , St. Pierre Jean-François
Published: February 2013

McQuinn, I. H., Dion, M., and St. Pierre, J.-F. 2013. The acoustic multifrequency classification of two sympatric euphausiid species (Meganyctiphanes norvegica and Thysanoessa raschii), with empirical and SDWBA model validation. – ICES Journal of Marine Science, 70: 636–649. The ecosystem approach to fishery management requires monitoring capabilities at all trophic levels, including pelagic organisms. However, the usefulness of active acoustics for ecosystem monitoring has been limited by ambiguities in the identification of scattering layers. Increasingly, multifrequency acoustic methods are being developed for the classification of scattering layers into species or species groups. We describe a method for distinguishing between sympatric northern and Arctic krill (Meganyctiphanes norvegica and Thysanoessa raschii) using sv amplitude ratios from 38, 120, and 200 kHz data which were pre-processed through a self-noise removal algorithm. Acoustic frequency responses of both euphausiid species were predicted from species-specific parameterizations of a SDWBA physical model using specific body forms (shape, volume, and length) for Arctic and northern krill. Classification and model validation were achieved using macrozooplankton samples collected from multiple-sampler (BIONESS) and ringnet (JackNet) hauls, both equipped with a strobe light to reduce avoidance by euphausiids. SDWBA frequency responses were calculated for a range of orientations (± 45°) and compared with observed frequency responses, solving for orientation by least squares. A tilt angle distribution of N[9°,4°] and N[12°,6°] for T. raschii and M. norvegica, respectively resulted in best fits. The models also provided species-specific TS–length relationships.