bluuebunny/crossref_metadata_2025 huggingface dataset:
Synchronization and equitable partitions in weighted networks
Authors: Aguiar Manuela A. D. , Dias Ana Paula S.
Published: July 2018

The work presented in this paper has two purposes. One is to expose that the coupled cell network formalism of Golubitsky, Stewart, and collaborators accommodates in a natural way the weighted networks, that is, graphs where the connections have associated weights that can be any real number. Recall that, in the former setup, the network connections have associated nonnegative integer values. Here, some of the central concepts and results in the former formalism are present and applied to the weighted setup. These results are strongly associated with the existence of synchrony subspaces and balanced relations. This work also makes the correspondence between the concepts of synchrony subspace and balanced relation with those of cluster of synchrony and equitable partition, respectively, which are used in the other strand of literature. This correspondence implies that the results of these two strands of literature are linked. In particular, we remark that the results stated here for weighted coupled cell networks apply in that other strand of literature, and examples are given to illustrate that.
Real-time implementation of inverse synthetic aperture radar imaging using field programmable gate array and digital signal processors
Authors: Zhang Rui , Quan Yinghui , Qian Cheng , Yang Lei , Li Yachao , Xing Mengdao
Published: July 2018

Inverse synthetic aperture radar (ISAR) imaging plays an important role in modern radar systems. It is a powerful tool to surveil the air and space targets under all-weather and day-and-night conditions. With increasing demands for space surveillance and target recognition, real-time ISAR imaging is of great urgency. Based on field programmable gate arrays and digital signal processors, a new design of real-time processing of ISAR imaging is presented in this paper. First, a thorough description of the imaging algorithm is presented. The algorithm includes pulse compression, envelope alignment, phase adjustment, and cross range focusing. For the pulse compression, two different methods are adopted to process the “Dechirp” data and the directly sampled wideband data, respectively. Second, a hardware design of real-time imaging processing is given. Each step of the algorithm is mapped onto the hardware, and the computing resources and latency are analyzed. Finally, the realization is verified by both the simulated and measured data, and the quality of imaging result is evaluated qualitatively.
Rank ordered beta distributions of nonlinear map symbolic dynamics families with a first-order transition between dynamical regimes
Authors: Alvarez-Martinez Roberto , Cocho Germinal , Martinez-Mekler Gustavo
Published: July 2018

Rank-ordered distributions have been a matter of intense study. Often Zipf type invariant scaling is invoked; however, in the last decade the ubiquity of a Discrete Generalized Beta Distribution, DGBD, with two scaling exponents has been established. This distribution incorporates deviations from the power law at the extremes. A proper understanding of the meaning of these exponents is still lacking. Here, using two families of unimodal maps on the [0,1] interval, we construct binary sequences via standard symbolic dynamics. In both cases, the tent map, which is at the convex-concave border of the mapping families, separates intermittent regimes from chaotic dynamics. We show that the frequencies of n-tuples of the generated symbolic sequences are remarkably well fitted by the DGBD. We argue that in the underlying dynamics an order-disorder competition takes place and that one of the exponents is related to multiple range correlations, while the other is sensitive to disorder. In our study, we implement thermodynamic formalisms with which we can readily calculate n-tuple frequencies, in some particular cases, analytically. We show that for the convex mappings there is a first-order thermodynamic phase transition, while concave mappings have smooth free energy densities. Within our DGBD study, the transition between these two regimes coincides with a zero value for both exponents; in this sense, they may even be considered as indicators of the transition. An analysis of the difference between the exponents reinforces the interpretation we have assigned to them. Furthermore, the two regimes can be identified by the sign of such a difference. We also show that divergences in the invariant densities are responsible for the first order phase transitions observed in a range of the rank-frequency distributions. Our findings give further support to previous studies based on expansion-modification algorithms, birth-death processes, and random variable subtraction dynamics.
Vibrational spectroscopy via stimulated Raman induced Kerr lensing
Authors: Raanan Dekel , Lüttig Julian , Silberberg Yaron , Oron Dan
Published: July 2018

We present a new method for the measurement of the stimulated Raman spectrum based on time-dependent spatial modulation of a laser beam as it passes through a Raman active medium. This effect is similar to the instantaneous Kerr lensing and Kerr deflection yet involves resonant vibrations which result in a time-dependent refractive index change. We use sub-nanojoule pulses together with a sensitive pump-probe measurement apparatus to excite and detect the fine (10−5–10−4) temporal and spatial variations in intensity resulting from the Raman-induced Kerr effect. We demonstrate the effect by changing the spatial overlap between the pump and probe at the sample and measuring the time-dependent deformation of the probe beam’s cross section. This method is particularly useful for detection of low-frequency Raman lines, as we demonstrate by measuring the Raman spectrum of neat liquids in a cuvette.
k-space optical microscopy of nanoparticle arrays: Opportunities and artifacts
Authors: Bryche Jean-François , Barbillon Grégory , Bartenlian Bernard , Dujardin Gérald , Boer-Duchemin Elizabeth , Le Moal Eric
Published: July 2018

We report on the performance and inherent artifacts of k-space optical microscopy for the study of periodic arrays of nanoparticles under the various illumination configurations available on an inverted optical microscope. We focus on the origin of these artifacts and the ways to overcome or even benefit from them. In particular, a recently reported artifact, called the “condenser effect,” is demonstrated here in a new way. The consequences of this artifact (which is due to spurious reflections in the objective) on Fourier-space imaging and spectroscopic measurements are analyzed in detail. The advantages of using k-space optical microscopy to determine the optical band structure of plasmonic arrays and to perform surface plasmon resonance experiments are demonstrated. Potential applications of k-space imaging for the accurate lateral and axial positioning of the sample in optical microscopy are investigated.
Strain rate and temperature dependence of the mechanical properties of polymers: A universal time-temperature superposition principle
Authors: Tao Wei , Shen Jianxiang , Chen Yulong , Liu Jun , Gao Yangyang , Wu Youping , Zhang Liqun , Tsige Mesfin
Published: July 2018

Establishing the Time-Temperature and Frequency-Temperature Superposition Principles (TTSP and FTSP) to describe the mechanical behavior of polymeric materials is always of paramount significance. In this work, by adopting the classic coarse-grained model, we investigate the validity of these superposition principles for a series of networks, such as the pure polymer network, interpenetrating polymer networks composed of stiff and flexible networks (IPNs-SF), interpenetrating polymer networks composed of different cross-linking networks (IPNs-DC), polymer nanocomposites (PNCs), and surface grafted modified PNCs. The study focuses on the three critical mechanical properties such as the stress relaxation, the storage modulus versus the frequency obtained from the dynamic periodic shear deformation, and the uniaxial tensile stress-strain. The glass transition temperature (Tg) is about 0.47 for the simulated polymer network (CL400), and a smooth master curve is obtained for the stress relaxation process by setting the reference temperature Tref = 0.6 via the horizontal shifting process, indicating the validity of TTSP. Furthermore, similar smooth master curves are also achieved for both dynamic periodic shear and uniaxial tensile deformation, which exhibit similar trends and share the identical linear viscoelastic regime in the temperature interval above Tg: 0.55<T<1.0. Importantly, the Williams-Landel-Ferry and Vogel-Fulcher-Tammann equations are both adopted to quantitatively analyze non-linear TTSP behavior when the temperature approaches Tg. For the three mechanical properties, we emphasize that the master curve from TTSP or FTSP is independent of the reference temperature if it is higher than Tg, and based on the linear relation of the shift factor versus the inverse of the temperature higher than Tg, we propose a universal framework for the description of the TTSP or FTSP on the various mechanical properties. Then, we verify that the TTSP seems to be valid for the IPNs-DC system, while it does not hold for both PNCs and IPNs-SF systems because of their structural and dynamic heterogeneity. Furthermore, for PNCs filled with NPs grafted with polymer chains, the TTSP recovers back to be valid because of the enhanced compatibility between polymer and NPs attributed to the grafted polymer chains.
Separation of variables for linear Lax algebras and classical r-matrices
Authors: Dubrovin B. , Skrypnyk T.
Published: July 2018

We consider the problem of separation of variables for the algebraically integrable Hamiltonian systems possessing gl(n)-valued Lax matrices depending on a spectral parameter that satisfy linear Poisson brackets with some gl(n) ⊗ gl(n)-valued classical r-matrices. We formulate, in terms of the corresponding r-matrices, a sufficient condition that guarantees that the “separating polynomials” of Sklyanin [Commun. Math. Phys. 150, 181 (1992)], Scott [J. Math. Phys. 35, 5831 (1994)], Gekhtman [Commun. Math. Phys. 167, 593 (1995)], and Diener and Dubrovin (Algebraic-geometrical Darboux coordinates in R-matrix formalism, SISSA, Preprint Report No. 88-94-FM, 1994) produce a system of canonical variables. We consider two examples of classical r-matrices and separating polynomials. One of these examples, namely, the n-parametric family of non-skew-symmetric non-dynamical classical r-matrices of Skrypnyk [Phys. Lett. A 334, 390 (2005); 347, 266 (2005)] and the corresponding separating polynomials is new. We show that the separating polynomials of Diener and Dubrovin produce in this case a complete set of separated variables for the corresponding generalized Gaudin models with or without external magnetic field.
Effects of electrode size on the voltage of a tree-based energy generator
Authors: Hao Zhibin , Liu Kai , Li Wenbin , Zhang Junguo , Kan Jiangming , Hao Xiaomie
Published: July 2018

A standing tree and its surrounding soil form a sustainable energy generator, which is expected to decrease the need for in-the-field battery changes of low-power sensors used in forests, thereby enhancing forest monitoring technologies. Although various tree-powered circuits and sensors have already been invented, the low voltage of such a generator still causes great difficulty in energy harvesting and utilization. Hence, a key issue that must be addressed is the increasing voltage level. A larger electrode may generate a higher voltage level. However, the relationship between the electrode size and voltage remains unclear. Moreover, larger electrodes will incur higher costs and worsen portability. Therefore, this study aims to preliminarily ascertain the effect of the electrode size on voltage and to provide a reference for optimally using such a generator. Six plate-shaped ground electrodes of different side lengths were used to measure the tree-soil voltage. The measured data show that voltage has a logarithmic relationship with the effective surface area of the ground electrode. With the increasing area of the electrode, the voltage rises by at least 57% relative to the initial value; however, its growth rate declines markedly. Therefore, a larger electrode size is not always better for a generator when considering efficiency, cost, and portability. In this study, an electrode size of 10 cm × 10 cm × 0.3 cm was found to be optimal.
Protein escape at the ribosomal exit tunnel: Effects of native interactions, tunnel length, and macromolecular crowding
Authors: Bui Phuong Thuy , Hoang Trinh Xuan
Published: July 2018

How fast a post-translational nascent protein escapes from the ribosomal exit tunnel is relevant to its folding and protection against aggregation. Here, by using Langevin molecular dynamics, we show that non-local native interactions help decrease the escape time, and foldable proteins generally escape much faster than same-length, self-repulsive homopolymers at low temperatures. The escape process, however, is slowed down by the local interactions that stabilize the α-helices. The escape time is found to increase with both the tunnel length and the concentration of macromolecular crowders outside the tunnel. We show that a simple diffusion model described by the Smoluchowski equation with an effective linear potential can be used to map out the escape time distribution for various tunnel lengths and various crowder concentrations. The consistency between the simulation data and the diffusion model, however, is found only for the tunnel length smaller than a crossover length of 90 Å–110 Å, above which the escape time increases much faster with the tunnel length. It is suggested that the length of ribosomal exit tunnel has been selected by evolution to facilitate both the efficient folding and the efficient escape of single-domain proteins. We show that macromolecular crowders lead to an increase in the escape time, and attractive crowders are unfavorable for the folding of nascent polypeptide.
Fractional powers and singular perturbations of quantum differential Hamiltonians
Authors: Michelangeli A. , Ottolini A. , Scandone R.
Published: July 2018

We consider the fractional powers of singular (point-like) perturbations of the Laplacian and the singular perturbations of fractional powers of the Laplacian, and we compare two such constructions focusing on their perturbative structure for resolvents and on the local singularity structure of their domains. In application to the linear and non-linear Schrödinger equations for the corresponding operators, we outline a programme of relevant questions that deserve being investigated.
Pulse inversion enhances the passive mapping of microbubble-based ultrasound therapy
Authors: Pouliopoulos Antonios N. , Burgess Mark T. , Konofagou Elisa E.
Published: July 2018

Therapeutic ultrasound combined with preformed circulating microbubbles has enabled non-invasive and targeted drug delivery into the brain, tumors, and blood clots. Monitoring the microbubble activity is essential for the success of such therapies; however, skull and tissues limit our ability to detect low acoustic signals. Here, we show that by emitting consecutive therapeutic pulses of inverse polarity, the sensitivity in the detection of weak bubble acoustic signals during blood-brain barrier opening is enhanced compared to therapeutic pulses of the same polarity. Synchronous passive mapping of the cavitation activity was conducted using delay-and-sum beamforming with absolute time delays, which offers superior spatial resolution compared to the existing asynchronous passive imaging techniques. Sonication with pulse inversion allowed filter-free suppression of the tissue signals by up to 8 dB in a tissue-mimicking phantom and by 7 dB in vivo, compared to exposure without pulse inversion, enabling enhanced passive mapping of microbubble activity. Both therapeutic schemes resulted in similar free-field microbubble activation in vitro and efficient blood-brain barrier opening in vivo.
Mutual neutralization of H+ and D+ with the atomic halide anions Cl−,Br−, and I−
Authors: Sawyer Jordan C. , Miller Thomas M. , Sweeny Brendan C. , Ard Shaun G. , Viggiano Albert A. , Shuman Nicholas S.
Published: July 2018

Mutual neutralization (MN) rate constants kMN for the reactions of H+ and D+ with the atomic halide anions Cl−, Br−, and I− were measured using the variable electron and neutral density attachment mass spectrometry technique in a flowing afterglow Langmuir probe apparatus. At 300 K, the rate constants for each reaction studied are on the order of 10−8 cm3 s−1. A trend for the rate constants of the systems in this work, kMNCl−<kMNBr−<kMN(I−), is consistent with prior studies of rare gas cation with atomic halide anion MN. A recent theoretical study involving ab initio quantum mechanical treatment of the H++Cl− and D++Cl− reactions reported rate constants significantly lower than the rates reported here. A previously proposed empirical model that predicts atom-atom kMN as a simple function of the total reaction exothermicity shows good agreement with the newly measured rate constants.
Electron emission from carbon velvet due to incident xenon ions
Authors: Patino M. I. , Wirz R. E.
Published: July 2018

We present measurements of the ion-induced electron emission from carbon velvet. The results from carbon velvet with high aspect ratio vertical fibers (6.8 μm diameter and 2.6 mm length) show a more than 60% reduction in ion-induced electron emission for normal incident xenon ions over the entire ion incident energy investigated (i.e., 500–2000 eV) when compared to graphite. This is important for plasma-facing surfaces that are exposed to large fluxes of energetic ions, such as beam dumps and chamber walls used to control facility effects in plasma-thruster ground tests.
Hierarchical and decentralized optimization method based on multi-agent system for multiple AC/DC hybrid microgrids
Authors: Wang Shouxiang , Li Lingxiao , Huang Bibin , Jiang Liping
Published: July 2018

AC/DC hybrid microgrids (MGs) have been developed rapidly in recent years due to their efficient integration and management of large-scale distributed energy resources. How to achieve the optimal operation and coordinated control of AC/DC hybrid MGs has become crucial. A multi-agent system (MAS) based hierarchical and decentralized method for coordination operation of multiple AC/DC hybrid MGs is proposed. First, a structure of AC/DC hybrid MGs including wind turbines, photovoltaics, micro-hydro, and biogas generators is designed, which aims at reducing the power conversion loss. Second, a three-level MAS including distribution network (DN) level, MG level, and distributed generation (DG) level is presented. At the DG level, the DG agents obtain the optimal results from the MG agent. At the MG level, the independent optimization is implemented based on the mixed integer linear programming, and the consensus algorithm is utilized to realize the coordination of MG with adjacent MGs through the communication among MG agents when there is imbalance power. At the DN level, the DN agent performs power exchange with AC/DC hybrid MGs to balance the load demand when needed. Finally, the distributed energy management platform is developed by the Java Agent Development Framework platform to simulate the optimal operation of AC/DC hybrid MGs. The results show the rationality and availability of the proposed optimization method.
Selective activation of localized mechanical resonators via a phonon waveguide
Authors: Hatanaka D. , Gourmelon A. , Mahboob I. , Yamaguchi H.
Published: July 2018

An electromechanical phonon waveguide that is weakly connected to three localized mechanical resonators is developed. A nonlinear elastic effect induced by intense piezoelectric excitation enables acoustic waves in the waveguide to be transferred to the spatially distinct resonators. Adjusting the frequency of the nonlinear modulation enables a target resonator to be selectively driven by switching the acoustic wave from the waveguide to it. The ability to remotely control multiple mechanical resonators via the phonon waveguide opens up the possibility of a phonon network in which acoustic waves can be guided to distributed sub-systems.
Magnetoelectricity in La2NiMnO6 and its PVDF impregnated derivative
Authors: Tiwary Sweta , Kuila S. , Sahoo M. R. , Barik A. , Babu P. D. , Vishwakarma P. N.
Published: July 2018

La2NiMnO6 is prepared for two different sintering time durations: 4 hour (4H) and 24 hour (24H). The magnetization data suggest a double ferromagnetic (FM) transition for 24H, whereas a single FM transition for 4H sample. The 4H sample was found to possess several microscopic pores compared with the 24H sample, and thus, these pores are vacuum impregnated with polyvinylidene fluoride (PVDF). The PVDF in the impregnated sample is found to crystallize in beta phase. The first and second order magnetoelectric coefficients are extracted from the measured data and plotted as a function of temperature. The room temperature region is found to be dominated by the magnetoconductivity/magnetoloss and thus resulting low ME voltage. With lowering of temperature, the situation improves, and for T < 200 K, the loss component becomes negligible so that the true magnetoelectricity is observed. A comparative study on all the three samples (4H, 24H, and 4H + PVDF) shows a significant enhancement in the magnetoelectricity in the 4H + PVDF sample. The highlight of this report is the unique way to arrest the porosity by PVDF impregnation into the pores of La2NiMnO6 so that leakage is minimized.
The hydration structure of methylthiolate from QM/MM molecular dynamics
Authors: Awoonor-Williams Ernest , Rowley Christopher N.
Published: July 2018

Thiols are widely present in biological systems, most notably as the side chain of cysteine amino acids in proteins. Thiols can be deprotonated to form a thiolate which affords a diverse range of enzymatic activity and modes for chemical modification of proteins. Parameters for modeling thiolates using molecular mechanical force fields have not yet been validated, in part due to the lack of structural data on thiolate solvation. Here, the CHARMM36 and Amber models for thiolates in aqueous solutions are assessed using free energy perturbation and hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. The hydration structure of methylthiolate was calculated from 1 ns of QM/MM MD (PBE0-D3/def2-TZVP//TIP3P), which shows that the water–S− distances are approximately 2 Å with a coordination number near 6. The CHARMM thiolate parameters predict a thiolate S radius close to the QM/MM value and predict a hydration Gibbs energy of −329.2 kJ/mol, close to the experimental value of −318 kJ/mol. The cysteine thiolate model in the Amber force field underestimates the thiolate radius by 0.2 Å and overestimates the thiolate hydration energy by 119 kJ/mol because it uses the same Lennard-Jones parameters for thiolates as for thiols. A recent Drude polarizable model for methylthiolate with optimized thiolate parameters also performs well. SAPT2+ [Symmetry Adapted Perturbation Theory (SAPT)] analysis indicates that exchange repulsion is larger for the methylthiolate, consistent with it having a more diffuse electron density distribution in comparison with the parent thiol. These data demonstrate that it is important to define distinct non-bonded parameters for the protonated/deprotonated states of amino acid side chains in molecular mechanical force fields.
Amplitude demodulation for electrical capacitance tomography based on singular value decomposition
Authors: Hao Zhenhua , Cui Ziqiang , Yue Shihong , Wang Huaxiang
Published: July 2018

Amplitude demodulation is essential in image reconstruction for electrical capacitance tomography (ECT). In this paper, an amplitude demodulation method is proposed based on singular value decomposition (SVD), which can substitute the role of phase-sensitive demodulation in ECT. First, an M × N Hankel matrix is constructed based on a set of discrete samples. Then, SVD operation is performed on the matrix. Finally, the mathematical expression between the sinusoid amplitude and effective singular values is given; i.e., the first two singular values are used to estimate the amplitude information of the acquired signal. The proposed method has the following advantages: (1) since no reference signals are needed, the synchronization between the acquired and reference signals is not necessary; (2) this method can obtain the amplitude information of the acquired signal with a high signal-to-noise ratio (SNR), even in the case of non-integrity period sampling; and (3) SVD itself can also implement the filtering function; thus, no additional low-pass filters are required in the signal conditioning module. The demodulation accuracy and feasibility of the proposed method were verified by numerical simulations and experiments, indicating that it can provide amplitude demodulation with excellent SNR and robust performances.
A review on applications of Cu2ZnSnS4 as alternative counter electrodes in dye-sensitized solar cells
Authors: Roy Anurag , Sujatha Devi Parukuttaymma , Karazhanov Smagul , Mamedov D. , Mallick Tapas Kumar , Sundaram Senthilarasu
Published: July 2018

A contribution of counter electrode (CE) emphasis a great impact towards enhancement of a dye-sensitized solar cell's (DSSC) performance and Pt based CE sets a significant benchmark in this field. Owing to cost effective noble metal, less abundance and industrial large scale application purpose, an effective replacement for Pt is highly demanded. There are several approaches to improve the performance of a CE for enhancing the power conversion efficiency with a less costly and facile device. To address this issue, reasonable efforts execute to find out suitable replacement of Pt is becoming a challenge by keeping the same electrochemical properties of Pt in a cheaper and eco-friendlier manner. With this, cheaper element based quaternary chalcogenide, Cu2ZnSnS4 (CZTS) becomes a prominent alternative to Pt and used as a successful CE in DSSC also. This review presents brief discussion about the basic properties of CZTS including its synthesis strategy, physicochemical properties and morphology execution and ultimate application as an alternative Pt free CE for a low cost based enhanced DSSC device. It is therefore, imperative for engineering of CZTS material and optimization of the fabrication method for the improvement of DSSC performance.
Giant negative thermal expansion in Fe-Mn-Ga magnetic shape memory alloys
Authors: Sun X. M. , Cong D. Y. , Ren Y. , Brown D. E. , Li R. G. , Li S. H. , Yang Z. , Xiong W. X. , Nie Z. H. , Wang L. , Wang Y. D.
Published: July 2018

Fe-Mn-Ga magnetic shape memory alloys can undergo martensitic transformation (MT) from a paramagnetic cubic phase to a ferromagnetic tetragonal phase. The MT is accompanied by a large volume change; yet, these alloys have never been explored for technological applications as negative thermal expansion (NTE) materials. Here, by careful chemical modification, tunable NTE characteristics including wide operating temperature windows (ΔT) and large negative linear coefficients of thermal expansion (αl) have been achieved in Fe44−xMn28Ga28+x (x = 1, 2, and 2.5) alloys. Typically, a giant NTE ΔT of 81 K and αl = −50.2 × 10−6 K−1 were realized in the Fe43Mn28Ga29 alloy upon cooling from 290 K. The relationships between the NTE features, the MT, and the substitution of Ga for Fe were discussed. Furthermore, the Fe-Mn-Ga alloys possess excellent mechanical properties, high electrical conductivity and high thermal conductivity. With these advantages, the Fe-Mn-Ga magnetic shape memory alloys show promising prospects for use as advanced NTE materials.
Electrostatic fields control grain boundary structure in SrTiO3
Authors: Hughes L. A. , Marple M. , van Benthem K.
Published: July 2018

Functional properties of oxide ceramics are often controlled by the addition of dopant elements and the resulting alteration of oxygen vacancy concentrations within grain boundary core structures. A challenge in designing nanoscale ceramic microstructures is forming stable grain boundary networks, while minimizing unwanted impurity concentrations. In this study, it was discovered that the application of electrostatic fields during diffusion bonding of undoped SrTiO3 bicrystals leads to modifications of grain boundary core structures while misorientation angles remained unchanged. The applied electric field not only changes atomic and electronic interface structures, but also causes modifications of ensuing dielectric properties by altering local oxygen vacancy concentrations. The observations for this model system demonstrate the potential to control and modify the microscopic degrees of freedom of grain boundaries in the absence of dopant elements. Field-assisted modifications of grain boundary networks may become a disruptive technology in designing oxide microstructures for a wide range of applications.
Effect of morphology on optical and efficiently enhanced electrical properties of W-ZnS for UV sensor applications
Authors: Prasad Neena , Balasubramanian Karthikeyan
Published: July 2018

The influence of the morphology on the electron transport properties of ZnS nanostructures has been assessed by the electrical measurements on different ZnS nanostructures. High-quality poly(vinylpyrrolidone) capped wurtzite-ZnS micro- and nanostructures have been prepared by one step hydrothermal methods at low temperatures. Detailed structural investigation based on X-ray diffraction results and morphological analyses have been carried out using field emission scanning electron microscopy, transmission electron microscopy, selected area diffraction pattern, and high-resolution transmission electron microscopy techniques. In order to examine the formation of compound ZnS, the atomic ratio of Zn to S has been found from Energy Dispersion Spectroscopy. The bandgap of the samples has been calculated from the UV-visible absorption spectra in the reflectance mode at room temperature. The dependence of size and shape on excitonic and trap-state emission features of the nanostructures has been studied from the photoluminescence (PL) studies, and the enhancement of PL intensity in 1D nanostructures has also been discussed. High yield and highly crystalline long nanorods and nanowires have been found to be best suited for advanced optoelectronic systems because they have better photoconductivity than microparticles and nanoparticles.
Ferroelectric polymer nanostructure with enhanced flexoelectric response for force-induced memory
Authors: Liu Jia-Hao , Chen Xin , Li Yang , Guo Xu , Ge Hai-Xiong , Shen Qun-Dong
Published: July 2018

Through utilizing individual nanodots, as smallest memory units, to convert stress into readable electronic information, we report force-induced high-density data storage in the periodic nanostructure of ferroelectric polymer fabricated by nanoimprinting lithography. The nanostructure is ideal for the stress concentration and increasing the non-uniformity of strains, thus leading to strain gradients inversely proportional to the feature size. A force as low as 400 nN is applied to generate the internal electric field in response to strain gradients and switch polarization state of each memory unit. It can achieve storage density theoretically up to TB/inch2 with the up-to-date nanofabrication technology to miniaturize the unit size.
Abnormal temperature effects on the dynamic yield stress of alpha-brass
Authors: Zaretsky E. B. , Kanel G. I.
Published: July 2018

The evolution of elastic-plastic wave in 70Cu-30Zn brass was measured so as to obtain information about its dynamic strength properties at normal and elevated temperatures. The different propagation velocities of plastic shock recorded in as-rolled and annealed brass can be explained in terms of a strong work-hardening. Measuring the decay of an elastic precursor wave revealed a transition from high-rate to low-rate mechanisms of plastic deformation. Unexpectedly, the flow stresses grow with increasing the temperature in both regimes. While at high strain rates this effect can be explained by phonon drag mechanisms, abnormal thermal hardening at a lower strain rate is apparently associated with different levels of short range order in the alloy at normal and elevated temperatures.
Singlet oxygen modification abolishes voltage-dependent inactivation of the sea urchin spHCN channel
Authors: Idikuda Vinay , Gao Weihua , Grant Khade , Su Zhuocheng , Liu Qinglian , Zhou Lei
Published: July 2018

Photochemically or metabolically generated singlet oxygen (1O2) reacts broadly with macromolecules in the cell. Because of its short lifetime and working distance, 1O2 holds potential as an effective and precise nanoscale tool for basic research and clinical practice. Here we investigate the modification of the spHCN channel that results from photochemically and chemically generated 1O2. The spHCN channel shows strong voltage-dependent inactivation in the absence of cAMP. In the presence of photosensitizers, short laser pulses transform the gating properties of spHCN by abolishing inactivation and increasing the macroscopic current amplitude. Alanine replacement of a histidine residue near the activation gate within the channel’s pore abolishes key modification effects. Application of a variety of chemicals including 1O2 scavengers and 1O2 generators supports the involvement of 1O2 and excludes other reactive oxygen species. This study provides new understanding about the photodynamic modification of ion channels by 1O2 at the molecular level.
There is no haecceitic Euthyphro problem
Authors: Skiles Alexander
Published: July 2018

Jason Bowers and Meg Wallace (‘The Haecceitic Euthyphro Problem’, Analysis, 2018) have recently argued that those who hold that every individual instantiates a ‘haecceity’ (or ‘individual essence’) are caught up in a Euthyphro-style dilemma when confronted with familiar cases of fission and fusion. Key to Bowers and Wallace’s dilemma are certain assumptions about the nature of metaphysical explanation and the explanatory commitments of belief in haecceities. However, I argue that the dilemma only arises due to a failure to distinguish between providing a metaphysical explanation of why a fact holds vs. a metaphysical explanation of what it is for a fact to hold. In the process, I also shed light on the explanatory commitments of belief in haecceities.
zfRegeneration: a database for gene expression profiling during regeneration
Authors: Nieto-Arellano Rocío , Sánchez-Iranzo Héctor
Published: July 2018

Motivation

Zebrafish is a model organism with the ability to regenerate many different organs. Although RNA-Seq has been used extensively to study this process, there are no databases that allow easy access to data.

Results

Here we develop the first regeneration database that provides easy access to a large number of RNA-Seq datasets through custom-made plots of expression levels, differential expression analyses, correlations of genes and comparisons of the different datasets. zfRegeneration has a user-friendly web interface designed to enhance regeneration studies and to overcome the barriers between different research groups that study the regeneration of distinct organs. Using several case studies, we demonstrate that zfRegeneration provides a unique platform to analyse and understand gene expression during regeneration.

Availability and implementation

zfRegeneration is freely available at www.zfregeneration.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
Quantifying the notions of canalizing and master genes in a gene regulatory network—a Boolean network modeling perspective
Authors: Kim Eunji , Ivanov Ivan , Dougherty Edward R
Published: July 2018

Motivation

Canalizing genes enforce broad corrective actions on cellular processes for the purpose of biological robustness maintaining a constant phenotype to remain unchanged in spite of genetic mutations or environmental perturbations. Despite their central role in biological systems, the observation/detection of canalizing genes is often impeded because the behavior of affected genes is highly varied relative to the inactive canalizer. Therefore, the activity of canalizing genes is difficult to predict to any significant degree by their subject genes under normal cell conditions.

Results

We investigate this question and present a quantitative framework that allows for the estimation of the power of canalizing genes in the context of Boolean Networks (BNs) with perturbation. This framework borrows tools from the Pattern Recognition theory and uses the coefficient of determination (CoD) to capture the capacity of the canalizing genes. The canalizing power (CP) of a gene is quantitatively characterized by two terms: regulation power (RP) and incapacitating power (IP). We base this assumption on the idea that canalizing power of a gene should be quantified by the extent of its regulation on the overall network and the extent of control that the gene takes over from other master genes when it is activated, which is equivalent to reduction of the control of other master genes upon its activation. Following this, the CP concept is illustrated with examples in which the goal is to provide preliminary evidence that CP can be used to characterize the ability of canalizing genes.

Availability and implementation

A library of functions written in MATLAB for computing CP is available at http://github.com/eunjikim-angie/CanalizingPower.
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution
Authors: Xia Li Charlie , Ai Dongmei , Lee Hojoon , Andor Noemi , Li Chao , Zhang Nancy R , Ji Hanlee P
Published: July 2018

Background

Simulating genome sequence data with variant features facilitates the development and benchmarking of structural variant analysis programs. However, there are only a few data simulators that provide structural variants in silico and even fewer that provide variants with different allelic fraction and haplotypes.

Findings

We developed SVEngine, an open-source tool to address this need. SVEngine simulates next-generation sequencing data with embedded structural variations. As input, SVEngine takes template haploid sequences (FASTA) and an external variant file, a variant distribution file, and/or a clonal phylogeny tree file (NEWICK) as input. Subsequently, it simulates and outputs sequence contigs (FASTAs), sequence reads (FASTQs), and/or post-alignment files (BAMs). All of the files contain the desired variants, along with BED files containing the ground truth. SVEngine's flexible design process enables one to specify size, position, and allelic fraction for deletions, insertions, duplications, inversions, and translocations. Finally, SVEngine simulates sequence data that replicate the characteristics of a sequencing library with mixed sizes of DNA insert molecules. To improve the compute speed, SVEngine is highly parallelized to reduce the simulation time.

Conclusions

We demonstrated the versatile features of SVEngine and its improved runtime comparisons with other available simulators. SVEngine's features include the simulation of locus-specific variant frequency designed to mimic the phylogeny of cancer clonal evolution. We validated SVEngine's accuracy by simulating genome-wide structural variants of NA12878 and a heterogeneous cancer genome. Our evaluation included checking various sequencing mapping features such as coverage change, read clipping, insert size shift, and neighboring hanging read pairs for representative variant types. Structural variant callers Lumpy and Manta and tumor heterogeneity estimator THetA2 were able to perform realistically on the simulated data. SVEngine is implemented as a standard Python package and is freely available for academic use .
Evolution, Diversification, and Biogeography of Grasshoppers (Orthoptera: Acrididae)
Authors: Song Hojun , Mariño-Pérez Ricardo , Woller Derek A , Cigliano Maria Marta
Published: July 2018

The grasshopper family Acrididae is one of the most diverse lineages within Orthoptera, including more than 6,700 valid species distributed worldwide. Grasshoppers are dominant herbivores, which have diversified into grassland, desert, semi-aquatic, alpine, and tropical forest habitats, and exhibit a wide array of morphological, ecological, and behavioral diversity. Nevertheless, the phylogeny of Acrididae as a whole has never been proposed. In this study, we present the first comprehensive phylogeny of Acrididae based on mitochondrial genomes and nuclear genes to test monophyly of the family and different subfamilies as well as to understand the evolutionary relationships among them. We recovered the monophyletic Acrididae and identified four major clades as well as several well-characterized subfamilies, but we also found that paraphyly is rampant across many subfamilies, highlighting the need for a taxonomic revision of the family. We found that Acrididae originated in the Paleocene of the Cenozoic period (59.3 million years ago) and, because the separation of South America and Africa predates the origin of the family, we hypothesize that the current cosmopolitan distribution of Acrididae was largely achieved by dispersal. We also inferred that the common ancestor of modern grasshoppers originated in South America, contrary to a popular belief that they originated in Africa, based on a biogeographical analysis. We estimate that there have been a number of colonization and recolonization events between the New World and the Old World throughout the diversification of Acrididae, and, thus, the current diversity in any given region is a reflection of this complex history.
Weak lensing by voids in weak lensing maps
Authors: Davies Christopher T , Cautun Marius , Li Baojiu
Published: July 2018

Cosmic voids are an important probe of large-scale structure that can constrain cosmological parameters and test cosmological models. We present a new paradigm for void studies: void detection in weak lensing convergence maps. This approach identifies objects that relate directly to our theoretical understanding of voids as underdensities in the total matter field and presents several advantages compared to the customary method of finding voids in the galaxy distribution. We exemplify this approach by identifying voids using the weak lensing peaks as tracers of the large-scale structure. We find self-similarity in the void abundance across a range of peak signal-to-noise selection thresholds. The voids obtained via this approach give a tangential shear signal up to ∼40 times larger than voids identified in the galaxy distribution.
Smoking-Related Stigma: A Public Health Tool or a Damaging Force?
Authors: Lozano Paula , Thrasher James F , Forthofer Melinda , Hardin James , Shigematsu Luz Myriam Reynales , Arillo Santillán Edna , Fleischer Nancy L
Published: July 2018

Background

Tobacco control policies and other denormalization strategies may reduce tobacco use by stigmatizing smoking. This raises an important question: Does perceived smoking-related stigma contribute to a smoker’s decision to quit? The aim of this study was to evaluate if perceived smoking-related stigma was associated with smoking cessation outcomes among smokers in Mexico and Uruguay.

Methods

We analyzed prospective data from a panel of adult smokers who participated in the 2008–2012 administrations of the International Tobacco Control Policy Evaluation Surveys in Mexico and Uruguay. We defined two analytic samples of participants: the quit behavior sample (n = 3896 Mexico; n = 1525 Uruguay) and the relapse sample (n = 596 Mexico). Generalized estimating equations were used to evaluate if different aspects of perceived stigma (ie, discomfort, marginalization, and negative stereotype) at baseline were associated with smoking cessation outcomes at follow-up.

Results

We found that perceived smoking-related stigma was associated with a higher likelihood of making a quit attempt in Uruguay but with a lower likelihood of successful quitting in Mexico.

Conclusions

This study suggests that perceived smoking-related stigma may be associated with more quit attempts, but less successful quitting among smokers. It is possible that once stigma is internalized by smokers, it may function as a damaging force. Future studies should evaluate the influence of internalized stigma on smoking behavior.

Implications

Although perceived smoking-related stigma may prompt smokers to quit smoking, smoking stigma may also serve as a damaging force for some individuals, making quitting more difficult. This study found that perceived smoking-related stigma was associated with a higher likelihood of making a quit attempt in Uruguay but with a lower likelihood of successful quitting in Mexico.
Lucilius
Authors: Chahoud Anna
Published: July 2018

Gaius Lucilius (fl. c. 130 bce–103/2 bce) was the inventor of Roman satire as we know it. Born of an equestrian family from Suessa Aurunca in Campania, he was an affluent landowner, the great uncle of Pompey the Great, and as such intended for a senatorial career, which he proudly turned down to undertake a career unprecedented for a Roman citizen: Lucilius was the first non-professional poet in Rome. He was a prominent figure in the Middle Republic, a personal friend of Laelius and Scipio Aemilianus, under whom he served in the Numantine War in 134/3 bce, and enjoyed such renown that he was awarded a public funeral, in Naples in 103/2 bce. He had an extensive Greek education and contacts with Greek intellectuals of his time; the skeptic philosopher Clitomachus, Head of the Academy (c. 127/6–110–109 bce), dedicated a work on problems of cognitive theory to him. Variety of themes, independence, and freedom of speech characterize his poetry, which he called sermones, “conversations,” apparently never using the term satura that his predecessor Ennius had given his experiments with miscellaneous verse. Personal poetry at Rome truly begins with Lucilius, whose pronounced subjectivity and unrestrained aggressiveness would become synonymous with satire itself for every subsequent writer in the genre, from Horace to Persius to Juvenal. Of Lucilius’s thirty books of verse satires––initially written in the iambo-trochaic meter of comic dialogue, before he settled on the hexameter––approximately thirteen hundred lines survive through the quotations of later writers from the late Republic through Late Antiquity.