bluuebunny/crossref_metadata_2025 huggingface dataset:
Study of the time-domain electromagnetic pulse standard field generation setup and its application
Authors: Yan Youjie , Jiang Tingyong , Chen Jin , Liu Xiaolong , Meng Lin , Cheng Zhenbo , Liu Zhen
Published: July 2018

In this paper, a time-domain electromagnetic pulse standard field generation setup was designed and manufactured for transient electromagnetic pulse sensor calibration. The calibration setup is based on the mono-cone structure. It can produce a calculated electromagnetic pulse field with the electric field intensity from 100 V/m to 600 V/m. The quantity of the electric field intensity is traced to the national primary standard of the pulse parameter, the S parameter, and the length quantity. The standard uncertainty of the produced electric field is 2.4%. The waveform and field distribution of the standard field were verified by experiment. Based on this facility, the calibration methods and uncertainty evaluation methods for two types of electromagnetic pulse sensors (TEM horn and D-dot sensor) were proposed. Finally, we obtained the calibration results of the sensors. The standard uncertainties of the calibration are 3.6% for the TEM horn and 3.0% for the D-dot sensor.
Nonlinear convection of binary liquids in a porous medium
Authors: Rameshwar Y. , Anuradha V. , Srinivas G. , Pérez L. M. , Laroze D. , Pleiner H.
Published: July 2018

Thermal convection of binary mixtures in a porous medium is studied with stress-free boundary conditions. The linear stability analysis is studied by using the normal mode method. The effects of the material parameters have been studied at the onset of convection. Using a multiple scale analysis near the onset of the stationary convection, a cubic-quintic amplitude equation is derived. The influence of the Lewis number and the separation ratio on the supercritical-subcritical transition is discussed. Stationary front solutions and localized states are analyzed at the Maxwell point. Near the threshold of the oscillatory convection, a set of two coupled complex cubic-quintic Ginzburg-Landau type amplitude equations is derived, and implicit analytical expressions for the coefficients are given.
Swelling of individual nanodomains in hydrated block copolymer electrolyte membranes
Authors: Chen X. Chelsea , Jiang Xi , Balsara Nitash P.
Published: July 2018

In this work, we examine the swelling of nanostructured block copolymer electrolytes immersed in liquid water. A series of sulfonated polystyrene-b-polyethylene-b-polystyrene (S-SES) membranes having the same nominal chemical composition but two different morphologies are prepared by systematic changes in processing. We start with a membrane comprising a mixture of homopolymer polystyrene (hPS) and a polystyrene-b-polyethylene-b-polystyrene (SES) copolymer. hPS is subsequently selectively removed from the membrane and the polystyrene domains are sulfonated to give S-SES membranes. The morphology of the membranes is controlled by controlling ϕv, the volume fraction of hPS in the blended membrane. The morphology of the membranes was studied by small angle X-ray scattering (SAXS), cryogenic scanning transmission electron microscopy (cryo-STEM), and cryogenic electron tomography. The overall domain swelling measured by SAXS decreases slightly at ϕv = 0.29; a crossover from lamellar to bicontinuous morphology is obtained at the same value of ϕv. The bicontinuous morphologies absorb more water than the lamellar morphologies. By contrast, the nanodomain swelling of the bicontinuous membrane (120%) is slightly less than that of the lamellar membrane (150%). Quantitative analysis of the STEM images and electron tomography was used to determine the swelling on the hydrophilic and hydrophobic domains due to exposure to water. The hydrophilic sulfonated polystyrene-rich domain spacing increases while the hydrophobic polyethylene domain spacing decreases when the membranes are hydrated. The extent of increase and decrease is not a strong function of ϕv.
Laser shock compression induced crystallization of Ce3Al metallic glass
Authors: Bryant Alex W. , Scripka David , Alamgir Faisal M. , Thadhani Naresh N.
Published: July 2018

Laser shock compression studies on Ce3Al metallic glass performed using a 3 J Nd:YAG laser indicate shock-induced crystallization, evidenced by the presence of a two-wave/stepped particle velocity profile and structural changes observed via X-ray Diffraction (XRD) analysis of recovered material. A direct shock-compression setup was designed with 25 μm thick Ni driver foil, 40 μm thick Ce3Al metallic glass ribbon, and 3 mm thick poly(methyl methacrylate) (PMMA) backer window for use with input laser energies varying from 100 to 2000 mJ and corresponding estimated peak pressures of 1.4 to 4.1 GPa in Ce3Al. At shock pressures below ∼1.8 GPa (300 mJ laser input energy), samples were recovered showing no obvious deformation or structural changes evidenced via XRD analysis. At higher laser energies and shock pressures above the elastic limit, samples were recovered showing visible deformation and crystallization evidenced by Rietveld analysis of diffraction patterns. The corresponding velocity profiles also showed a stepped wave structure, increasing in magnitude with energy. The overall results reveal possible densification of the glass due to delocalization of 4f electrons in Ce at lower laser shock pressures and increased crystallization with preferred orientation and distortion of the nanocrystals at higher shock compression conditions.
Influence of an integrated quasi-reference electrode on the stability of all-solid-state AlGaN/GaN based pH sensors
Authors: Xing Jieying , Huang Dejia , Dai Yaqiong , Liu Yuebo , Ren Yuan , Han Xiaobiao , Yang Hang , Hou Yaqian , Wu Zhisheng , Liu Yang , Zhang Baijun
Published: July 2018

An all-solid-state AlGaN/GaN based ion-sensitive heterostructure field effect transistor (ISHFET) pH sensor was fabricated by integrating a noble metal (Au) quasi-reference electrode to improve the device stability when measuring the pH value of a small aqueous volume. In this paper, the influence of the size of the quasi-reference electrode against the stability of the pH readings was investigated. Through optimizing the size of the integrated quasi-reference electrode, the all-solid-state ISHFET pH sensor can sustain stable pH measurements for aqueous solutions of micro-litre size. A sensitivity of 55 mV/pH was achieved by the pH sensor at room temperature. Thus, the device may have potential uses in biomedical applications which require small volume pH measurements.
Non-inductive vertical position measurements by Faraday-effect polarimetry on EAST tokamak
Authors: Ding W. X. , Liu H. Q. , Qian J. P. , Brower D. L. , Xiao B. J. , Chen J. , Zou Z. Y. , Jie Y. X. , Luo Z. P. , Gong X. Z. , Hu L. Q. , Wan B. N.
Published: July 2018

Vertical instability control in an elongated plasma is highly desirable for a tokamak reactor. A multi-channel 694 GHz far-infrared laser-based polarimeter-interferometer system has been used to provide a non-inductive vertical position measurement in the long-pulse EAST tokamak. A detailed comparison of vertical position measurements by polarimetry and external inductive flux loops has been used to validate Faraday-effect polarimetry as an accurate high-time response vertical position sensor.
A morphology phase unwrapping method with one code grating
Authors: Ma Mengchao , Yao Pengcheng , Deng Ji , Deng Huaxia , Zhang Jin , Zhong Xiang
Published: July 2018

This paper presents a fast and robust phase unwrapping method with only one code grating, named the morphology phase unwrapping (MPU) method. Using mathematical morphology operations, more than 36 fringe orders can be obtained accurately from only one code grating rather than at least three code gratings. Comparison experiments demonstrate that MPU has the highest robustness with a high quality factor (Q > 99.9%) under different conditions. Fast-changing facial expressions are reconstructed, indicating potential applications in the fields of augmented reality and virtual reality.
Integration of ferroelectric Pb(Zr0.52Ti0.48)O3 thin films on conducting nanocrystalline diamond for high performance device applications
Authors: Rath Martando , Kumar Dinesh , Rao M. S. Ramachandra
Published: July 2018

We report on the direct integration of a Pb(Zr0.52Ti0.48)O3 (PZT) thin film on a hot filament chemical vapor deposition grown conducting boron doped nanocrystalline diamond (B-NCD) film. A conducting B-NCD thin film with a grain size less than 100 nm and surface roughness close to 8 nm is used as a metallic bottom electrode. X-ray diffraction and Raman spectroscopy revealed the single phase perovskite ferroelectric nature of the pulsed laser deposited grown PZT thin film directly on the conducting B-NCD substrate with an electrical resistivity of 10 mΩ-cm. The PZT thin film grown on the B-NCD/Si substrate showed the high remanent polarization (2Pr) of 68 μC/cm2 and high dielectric constant of ∼1300 with a low leakage current density of ∼10−5 A/cm2. Macroscopic and nanoscale polarization switching experiments are performed to confirm the ferroelectric nature of the PZT/B-NCD capacitor. A very small degradation of remanent polarization of 10% even after 1010 switching cycles of the sample demonstrates the excellent ferroelectric performance of the multilayer.
A spin-1 representation for dual-funnel energy landscapes
Authors: Elenewski Justin E. , Velizhanin Kirill A. , Zwolak Michael
Published: July 2018

The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. We explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model—left, right, and unstructured—can account for most key intermediates during chiral interconversion. Competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 kBT to 0.3 kBT along the left-to-right interconversion pathway.
Design of InGaN-ZnSnN2 quantum wells for high-efficiency amber light emitting diodes
Authors: Karim Md Rezaul , Zhao Hongping
Published: July 2018

InGaN-ZnSnN2 based quantum wells (QWs) structure is proposed and studied as an active region for high efficiency amber (λ ∼ 600 nm) light emitting diodes (LEDs), which remains a great challenge in pure InGaN based LEDs. In the proposed InGaN-ZnSnN2 QW heterostructure, the thin ZnSnN2 layer serves as a confinement layer for the hole wavefunction utilizing the large band offset at the InGaN-ZnSnN2 interface in the valence band. The barrier layer is composed of GaN or AlGaN/GaN in which the thin AlGaN layer is used for a better confinement of the electron wavefunction in the conduction band. Utilizing the properties of band offsets between ZnSnN2 and InGaN, the design of InGaN-ZnSnN2 QW allows us to use much lower In-content (∼10%) to reach peak emission wavelength at 600 nm, which is unachievable in conventional InGaN QW LEDs. Furthermore, the electron-hole wavefunction overlap (Γe-h) for the InGaN-ZnSnN2 QW design is significantly increased to 60% vs. 8% from that of the conventional InGaN QW emitting at the same wavelength. The tremendous enhancement in electron-hole wavefunction overlap results in ∼225× increase in the spontaneous emission radiative recombination rate of the proposed QW as compared to that of the conventional one using much higher In-content. The InGaN-ZnSnN2 QW structure design provides a promising route to achieve high efficiency amber LEDs.
Driving useful morphological changes in magnetic nanoparticle structures through the application of acoustic waves and magnetic fields
Authors: Huang An , Miansari Morteza , Friend James
Published: July 2018

The growing interest in acoustic manipulation of particles in micro to nanofluidics using surface acoustic waves, together with the many applications of magnetic nanoparticles—whether individual or in arrays—underpins our discovery of how these forces can be used to rapidly, easily, and irreversibly form 1D chains and 2D films. These films and chains are difficult to produce by other methods yet offer many advantages over suspensions of individual nanoparticles by making use of the scale of the structures formed, 10−9 to 10−5 m, and by taking a balance of the relevant external and interparticle forces, the underlying mechanisms responsible for the phenomena become apparent. For loosely connected 1D chains, the magnetic field alone is sufficient, though applying an acoustic field drives a topology change to interconnected loops of ∼10–100 particles. Increasing the acoustic field intensity drives a transition from these looped structures to dense 2D arrays via interparticle Bjerknes forces. Inter-particle drainage of the surrounding fluid leaves these structures intact after removal of the externally applied forces. The self-evident morphology transitions depend solely upon the relative amplitudes of the Brownian, Bjerknes, and magnetic forces.
Slip at the interface of a two-fluid swirling flow
Authors: Naumov Igor V. , Herrada Miguel A. , Sharifullin Bulat R. , Shtern Vladimir N.
Published: July 2018

This experimental and numerical study of a two-fluid swirling flow reveals a discontinuity of the radial velocity at the interface. The motion is driven by the rotating lid in a sealed vertical cylindrical container. The upper fluid radially diverges near the lid, goes downward near the sidewall, converges to the axis near the interface, and rises near the axis. This centrifugal circulation drives a bulk counter-circulation of the lower fluid at a slow rotation. As the rotation intensifies, a new circulation cell emerges in the lower fluid. The numerical simulations, performed under the continuity condition for all velocity and stress components, predict that the new cell emerges near the bottom and expands upward. In contrast, the new cell emerges near the interface and expands downward in the experiment. A slip condition is proposed for the radial velocity at the interface. The slip occurs due to the centrifugal force and difference in the fluid densities. The numerical simulations, performed with the slip condition, agree with the experiment.
Design, capabilities, and first results of the new laser blow-off system on Wendelstein 7-X
Authors: Wegner Th. , Geiger B. , Kunkel F. , Burhenn R. , Schröder T. , Biedermann C. , Buttenschön B. , Cseh G. , Drews P. , Grulke O. , Hollfeld K. , Killer C. , Kocsis G. , Krings T. , Langenberg A. , Marchuk O. , Neuner U. , Nicolai D. , Offermanns G. , Pablant N. A. , Rahbarnia K. , Satheeswaran G. , Schilling J. , Schweer B. , Szepesi T. , Thomsen H. ,   W7-X Team
Published: July 2018

We present a detailed overview and first results of the new laser blow-off system on the stellarator Wendelstein 7-X. The system allows impurity transport studies by the repetitive and controlled injection of different tracer ions into the plasma edge. A Nd:YAG laser is used to ablate a thin metal film, coated on a glass plate, with a repetition rate of up to 20 Hz. A remote-controlled adjustable optical system allows the variation of the laser spot diameter and enables the spot positioning to non-ablated areas on the target between laser pulses. During first experiments, clear spectral lines from higher ionization stages of the tracer ions have been observed in the X-ray to the extreme ultraviolet spectral range. The temporal behavior of the measured emission allows the estimate of transport properties, e.g., impurity transport times in the order of 100 ms. Although the strong injection of impurities is well detectable, the global plasma parameters are barely changed.
Calibrating torsional eigenmodes of micro-cantilevers for dynamic measurement of frictional forces
Authors: Thorén Per-Anders , Borgani Riccardo , Forchheimer Daniel , Haviland David B.
Published: July 2018

Non-invasive thermal noise calibration of both torsional and flexural eigenmodes is performed on numerous cantilevers of 10 different types. We show that for all tipless and short-tipped cantilevers, the ratio of torsional to flexural mode stiffness is given by the ratio of their resonant frequency times a constant, unique to that cantilever type. By determining this constant, we enable a calibration of the torsional eigenmode, starting from a calibration of the flexural eigenmode. Our results are well motivated from beam theory, and we verify them with finite element simulation.
Potential of mean force for two nanocrystals: Core geometry and size, hydrocarbon unsaturation, and universality with respect to the force field
Authors: Waltmann Curt , Horst Nathan , Travesset Alex
Published: July 2018

We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We analyze large cores (up to 10 nm in diameter) and ligands with unsaturated carbon bonds (oleic acid) and we investigate the accuracy of the computed potential of mean force by comparing different force fields. We also analyze the vortices that determine the bonding, including the case of asymmetric nanocrystals, and discuss effects related to the intrinsic anisotropy of the core. Overall our results are in agreement with the predictions of the recently proposed orbifold topological model.
Note: A data acquisition system for a high phase contrast medical computed tomography prototype
Authors: Sun Rongqi , Chen Lian , Wei Wenbin , Jin Ge
Published: July 2018

A Data Acquisition (DAQ) system is designed for a high phase contrast medical computed tomography prototype, which is based on the three-grating interferometry technology. The DAQ system contains 43 detector boards including 16 512 channels, 3 data collection boards, and one data transmission board (DTB). All digitized data from 43 detector board are collected and transmitted to the DTB through a slip ring. The communication between the DTB and Personal Computer is based on gigabit Ethernet. The efficient resolution of readout electronics is up to 14.6 bit. For all channels, the integral nonlinearity is no more than 0.1%. An air scan algorithm is employed to calibrate the channel gain non-uniformity.
Perspective: Superhard metal borides: A look forward
Authors: Akopov Georgiy , Pangilinan Lisa E. , Mohammadi Reza , Kaner Richard B.
Published: July 2018

Previous efforts toward the synthesis of materials with superior mechanical properties (e.g., superhardness, high bulk modulus, and high shear modulus) have focused on binary metal boride structures with short covalent bonds. In this paper, we discuss the methods for enhancing the intrinsic and extrinsic hardening factors commonly used to achieve these properties. As the realm of binary metal borides has all but been exhausted, there is a need to move to ternary and higher borides as well as to achieve greater morphological control at the nanoscale. The use of ternary and higher borides as starting materials provides a multitude of diverse compositional and structural combinations. These compounds merit further investigation as they offer the potential for the optimization of mechanical properties.
Excitation energies from diffusion Monte Carlo using selected configuration interaction nodes
Authors: Scemama Anthony , Benali Anouar , Jacquemin Denis , Caffarel Michel , Loos Pierre-François
Published: July 2018

Quantum Monte Carlo (QMC) is a stochastic method that has been particularly successful for ground-state electronic structure calculations but mostly unexplored for the computation of excited-state energies. Here, we show that within a Jastrow-free QMC protocol relying on a deterministic and systematic construction of nodal surfaces using selected configuration interaction (sCI) expansions, one is able to obtain accurate excitation energies at the fixed-node diffusion Monte Carlo (FN-DMC) level. This evidences that the fixed-node errors in the ground and excited states obtained with sCI wave functions cancel out to a large extent. Our procedure is tested on two small organic molecules (water and formaldehyde) for which we report all-electron FN-DMC calculations. For both the singlet and triplet manifolds, accurate vertical excitation energies are obtained with relatively compact multideterminant expansions built with small (typically double-ζ) basis sets.
Communication: Infrared photodissociation spectroscopy of the H6+ cation in the gas phase
Authors: McDonald David C. , Wagner J. Philipp , Duncan Michael A.
Published: July 2018

The H6+ cation was generated in a pulsed-discharge supersonic expansion of hydrogen and mass-selected in a time-of-flight spectrometer. Its vibrational spectrum was measured in the region of 2050–4550 cm−1 using infrared photodissociation with a tunable OPO/OPA laser system. The H6+ photodissociates, producing H5+, H4+, and H3+ fragments; each of these fragment channels has a different spectrum. Computational studies identify two low-lying isomers described in previous work, whose energies were evaluated at the CCSD(T)/cc-pVTZ//MP2/cc-pVTZ level of theory. A D2d species having an H2+ cation bridging between two perpendicular H2 molecules is the global minimum structure. A Cs structure with an H3+ core ion bound to both H2 and an H atom lies 4.0 kcal mol−1 higher in energy. Anharmonic vibrational spectra were computed for each of these isomers with second-order vibrational perturbation theory (VPT2) in combination with density functional theory at the B2PLYP/cc-pVTZ level. The comparison between experimental and predicted spectra confirms the presence of both the D2d and Cs structures and explains the spectra in different fragmentation channels. Although we find reasonable agreement between the experiment and the spectra predicted by VPT2 computations, a more sophisticated computational approach is needed to better understand this complex system.
An infinite dimensional KAM theorem with application to two dimensional completely resonant beam equation
Authors: Geng Jiansheng , Zhou Shidi
Published: July 2018

In this paper, we consider the two dimensional completely resonant beam equation with cubic nonlinearity on T2. We prove the existence of the quasi-periodic solutions, which lie in a special subspace of L2(T2). After some transformations, we write the Hamiltonian of the equation as an angle-dependent block-diagonal normal form plus a small perturbation with some regularity. By establishing an abstract KAM (Kolmogorov-Arnold-Moser) theorem, we prove the existence of a class of invariant tori, which implies the existence of a class of small-amplitude quasi-periodic solutions. In each step of the KAM iteration, the measure estimate could be fulfilled by making use of the regularity of the nonlinearity.
First reliable recipe developed for hydrodynamical simulations in biomembranes
Authors: Johnson-Groh Mara
Published: July 2018

A new mathematical framework allows for simulating hydrodynamical interactions between objects in viscous sheets, providing a useful tool for modeling movement across biomembranes.
Linguistic history and historical linguistics
Authors: van Driem George
Published: July 2018

This invited response to a piece by LaPolla, published in issue 39/2 ofLTBA, addresses both LaPolla’s misrepresentations of the history of linguistics and his flawed understanding of historical linguistics. The history of linguistic thought with regard to the Tibeto-Burman or Trans-Himalayan language family vs. the Indo-Chinese or “Sino-Tibetan” family tree model is elucidated and juxtaposed against the remarkable robustness of certain ahistorical myths and the persistence of unscientific argumentation by vocal proponents of the Sino-Tibetanist paradigm, such as LaPolla.
Long-distance binding of French reflexive soi
Authors: Charnavel Isabelle
Published: July 2018

This paper aims at showing that long-distance binding can be reduced to logophoric exemption from Condition A based on the case study of French soi. Soi is usually treated as a long-distance anaphor similar to Icelandic sig. But once the relevant factors are disentangled, it turns out that soi is a standard anaphor that must be locally bound unless the relevant logophoric conditions are met, which exempt soi from binding requirements. First, soi is a first-person oriented generic, expressing a generalization based on the discourse participants’ identification with the antecedent. Second, this determines its logophoric conditions of exemption (speaker-orientedness): soi is exempt from Condition A when its antecedent includes the speaker and is the perspective center of its clause.
Morphological doublets in Brazilian Portuguese wh-constructions
Authors: Kato Mary Aizawa
Published: July 2018

This chapter contains an overview of diachronic and synchronic studies on Brazilian Portuguese wh-questions, and discusses the intriguing problem of apparent syntactic doublets, or optionality, in this domain. However, a careful examination of the diachronic order in which these patterns appear, and the variation exhibited in contemporary written and spoken corpora lead us to conclude that the co-occurring patterns do not constitute syntactic “doublets.”
Against control by implicit passive agents
Authors: Reed Lisa A.
Published: July 2018

Landau (2010, 2013) and van Urk (2011, 2013) argue that the understood agent of a passive verb is syntactically projected as a weak implicit argument. As such, it participates actively in Agree and predication, the mechanisms they assume are responsible for antecedent determination in control structures. This article examines French data involving control and passivization and proposes an alternative explanation for the facts, one that makes the diametrically opposed assumptions that the implicit agent of a passive verb is syntactically unprojected and that the reference of PRO is determined post-syntactically.
Romance evaluative que/che/să sentences as inverted optatives
Authors: Sánchez López Cristina
Published: July 2018

Romance exclamative sentences introduced by the conjunctions que (Spanish, French, Portuguese) and che (Italian) ‘that’ and the Romanian particle să plus a subjunctive verb can receive an evaluative meaning and express the speaker’s displeasure or discontent about the propositional content. This paper describes and analyzes their properties. I propose that Romance que/che/să evaluative sentences are expressive sentences that express the speaker’s emotion about a proposition. The proposition is compared with other salient alternative propositions according to an inverted bouletic scale, so that the proposition is the less desirable for the speaker. The main formal properties (mood and tense restrictions) and semantic properties (presupposition of factivity and negative evaluation of the proposition) of the sentences naturally follow from the analysis.
“Permissive” subjects and the decline of adverbial linking in the history of English
Authors: Los Bettelou
Published: July 2018

Earlier work by Los and Dreschler (2012) and Komen et al. (2014) offered quantitative evidence of a decline in clause-initial adverbials as discourse linkers in the history of English, and argued that subjects have taken over much of the function of discourse linking that was earlier performed by adverbials. The greater functional load of the subject called for more flexibility in which types of thematic roles could be expressed by subjects, and for more strategies to create subjects, such as crosslinguistically rare passives. The present paper draws attention to another mechanism that facilitates “permissive subjects” in Present-day English: causative/ergative valency alternations of the type Amazon shipped the order/The order has shipped. I present the morphosyntactic origin of the alternation and report in more detail on the workings of discourse linking in Old English texts, explaining why “permissive subjects” were not required at that stage.
MR4Cancer: a web server prioritizing master regulators for cancer
Authors: Ru Beibei , Tong Yin , Zhang Jiangwen
Published: July 2018

Motivation

During cancer stage transition, a master regulator (MR) refers to the key gene controlling cancer initiation and progression by orchestrating the associated target genes (termed as its regulon). Due to their inherent importance, MRs can serve as critical biomarkers for cancer diagnosis and prognosis, and therapeutic targets. However, it is challenging to infer key MRs that might explain gene expression profile changes between two groups due to lack of context-specific regulons, whose expression level can collectively reflect the activity of likely MRs. There is also a need to design an easy-to-use tool of MR identification for research community.

Results

First, we generated cancer-specific regulons for 26 cancer types by analyzing high-throughput omics data from TCGA, and extracted noncancer-specific regulons from public databases. We subsequently developed a web server MR4Cancer, integrating the regulons with statistical inference to identify and prioritize MRs driving a phenotypic divergence of interest. Based on the input gene list (e.g. differentially expressed genes) or expression profile with two groups, MR4Cancer outputs ranked MRs by enrichment testing against the predefined regulons. Gene Ontology and canonical pathway analyses are also conducted to elucidate the function of likely MRs. Moreover, MR4Cancer provides dynamic network visualization for MR-target relations, and users can interactively interrogate the network to produce new hypotheses and high-quality figures for publication. Finally, the presented case studies highlighted the performance of MR4Cancer. We expect this user-friendly and powerful web tool will provide researchers novel insights into tumorigenesis and therapeutic intervention.

Availability and implementation

http://cis.hku.hk/MR4Cancer

Supplementary information

Supplementary data are available at Bioinformatics online.
LipidIMMS Analyzer: integrating multi-dimensional information to support lipid identification in ion mobility—mass spectrometry based lipidomics
Authors: Zhou Zhiwei , Shen Xiaotao , Chen Xi , Tu Jia , Xiong Xin , Zhu Zheng-Jiang
Published: July 2018

Ion mobility—mass spectrometry (IM-MS) has showed great application potential for lipidomics. However, IM-MS based lipidomics is significantly restricted by the available software for lipid structural identification. Here, we developed a software tool, namely, LipidIMMS Analyzer, to support the accurate identification of lipids in IM-MS. For the first time, the software incorporates a large-scale database covering over 260 000 lipids and four-dimensional structural information for each lipid [i.e. m/z, retention time (RT), collision cross-section (CCS) and MS/MS spectra]. Therefore, multi-dimensional information can be readily integrated to support lipid identifications, and significantly improve the coverage and confidence of identification. Currently, the software supports different IM-MS instruments and data acquisition approaches.

Availability and implementation

The software is freely available at: http://imms.zhulab.cn/LipidIMMS/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements
Authors: Stedtfeld Robert D , Guo Xueping , Stedtfeld Tiffany M , Sheng Hongjie , Williams Maggie R , Hauschild Kristin , Gunturu Santosh , Tift Leo , Wang Fang , Howe Adina , Chai Benli , Yin Daqiang , Cole James R , Tiedje James M , Hashsham Syed A
Published: July 2018

The high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic elements to be targeted. Results of validating the updated array with a mock community of strains resulted in over 98% of tested instances incurring true positive/negative calls. Common queries related to sensitivity, quantification and conventional data analysis (e.g. Ct cutoff value, and estimated genomic copies without standard curves) were also explored. A combined list of new and previously used primer sets is provided with a recommended set based on redesign of primer sets and results of validation.
Maternal reproductive history: trends and inequalities in four population-based birth cohorts in Pelotas, Brazil, 1982–2015
Authors: Matijasevich Alicia , Victora Cesar G , Silveira Mariangela F , Wehrmeister Fernando C , Horta Bernardo L , Barros Fernando C ,   Pelotas Cohorts Study Group, Menezes Ana M B , Barros Aluisio J D , Bertoldi Andrea Dâmaso , Bassani Diego G , Gonçalves Helen , Santos Iná S , Murray Joseph , Tovo-Rodrigues Luciana , Assunção Maria Cecilia F , Domingues Marlos Rodrigues , Hallal Pedro R C
Published: July 2018

Background

Brazil experienced important progress in maternal and child health in recent decades. We aimed at describing secular trends as well as socioeconomic and ethnic inequalities in reproductive history indicators (birth spacing, previous adverse perinatal outcome, parity and multiple births) over a 33-year span.

Methods

Four population-based birth cohort studies included all hospital births in 1982, 1993, 2004 and 2015 in Pelotas, Southern Brazil. Information on reproductive history was collected through interviews. Indicators were stratified by family income quintiles and skin colour. Absolute and relative measures of inequality were calculated.

Results

From 1982 to 2015, the proportion of primiparae increased from 39.2% to 49.6%, and median birth interval increased by 23.2 months. Poor women were more likely to report short intervals and higher parity, although reductions were observed in all income and ethnic groups. History of previous low birthweight was inversely related to income and increased by 7.7% points (pp) over time—more rapidly in the richest (12.1 pp) than in the poorest quintile (0.4 pp). Multiple births increased from 1.7% to 2.7%, with the highest increase observed among the richest quintile and for white women (220% and 70% increase, respectively). Absolute and relative income and ethnic-related inequalities for short birth intervals increased, whereas inequalities for previous low birthweight decreased over time.

Conclusions

In this 33-year period there were increases in birth intervals, multiple births and reports of previous low-birthweight infants. These trends may be explained by increased family planning coverage, assisted reproduction and a rise in preterm births, respectively. Our results show that socioeconomic and ethnic inequalities in health are dynamic and vary over time, within the same location.
Nef Line Bundles on Calabi–Yau Threefolds, I
Authors: Lazić Vladimir , Oguiso Keiji , Peternell Thomas
Published: July 2018

We prove that a nef line bundle ${\mathcal{L}}$ with $c_1({\mathcal{L}})^2 \ne 0$ on a Calabi–Yau threefold $X$ with Picard number $2$ and with $c_3(X) \ne 0$ is semiample, that is, some multiple of $\mathcal L$ is generated by global sections.
Congress of Neurological Surgeons Systematic Review and Evidence-Based Guidelines on the Evaluation and Treatment of Patients With Thoracolumbar Spine Trauma: Classification of Injury
Authors: Dailey Andrew T , Arnold Paul M , Anderson Paul A , Chi John H , Dhall Sanjay S , Eichholz Kurt M , Harrop James S , Hoh Daniel J , Qureshi Sheeraz , Rabb Craig H , Raksin P B , Kaiser Michael G , O’Toole John E
Published: July 2018

QUESTION 1

Are there classification systems for fractures of the thoracolumbar spine that have been shown to be internally valid and reliable (ie, do these instruments provide consistent information between different care providers)?

RECOMMENDATION 1

A classification scheme that uses readily available clinical data (eg, computed tomography scans with or without magnetic resonance imaging) to convey injury morphology, such as Thoracolumbar Injury Classification and Severity Scale or the AO Spine Thoracolumbar Spine Injury Classification System, should be used to improve characterization of traumatic thoracolumbar injuries and communication among treating physicians.

Strength of Recommendation: Grade B

QUESTION 2

In treating patients with thoracolumbar fractures, does employing a formally tested classification system for treatment decision-making affect clinical outcomes?

RECOMMENDATION 2

There is insufficient evidence to recommend a universal classification system or severity score that will readily guide treatment of all injury types and thereby affect outcomes.

Strength of Recommendation: Grade Insufficient

The full version of the guideline can be reviewed at: https://www.cns.org/guideline-chapters/congress-neurological-surgeons-systematic-review-evidence-based-guidelines/chapter_2.
Is Length of Stay Influenced by the Weekday On Which Lumbar Surgery is Performed?
Authors: Sivaganesan Ahilan , Devin Clinton J , Khan Inamullah , Kerezoudis Panagiotis , Nian Hui , Harrell Frank E , Bydon Mohamad , Asher Anthony L
Published: July 2018

BACKGROUND

Reducing length of stay (LOS) in a safe manner has the potential to save significant costs for the care of patients undergoing elective lumbar spine surgery. Due to the relative absence on weekends of staff required for discharging patients to rehabilitation or nursing facilities, we hypothesize that patients undergoing lumbar surgery later in the week have a longer LOS than their counterparts.

OBJECTIVE

To analyze the effect of day of the week for lumbar surgery on LOS.

METHODS

Patients undergoing surgery for lumbar degenerative disease were prospectively enrolled in the multicenter quality and outcomes database registry. A multivariable proportional odds regression model was built with LOS as the outcome of interest and patient and surgical variables as covariates.

RESULTS

A total of 11 897 patients were analyzed. Among those discharged home, the regression analysis demonstrated significantly higher odds of longer LOS for patients undergoing surgery on Friday as compared to Monday (P < .001). Among those discharged to a facility, there were significantly higher odds of longer LOS for patients undergoing surgery on Wednesday (P < .001), Thursday (P < .001), and Friday (P = .002) as compared to Monday.

CONCLUSION

The findings of this study suggest that lumbar patients undergoing fusions and those discharged to a facility have longer LOS when surgery is later in the week. Scheduling these patients for surgery earlier in the week and ensuring adequate resources for patient disposition on weekends may lead to LOS reduction and cost savings for hospitals, payers, and patients alike.
Relationships of Long-Term Smoking and Moist Snuff Consumption With a DNA Methylation Age Relevant Smoking Index: An Analysis in Buccal Cells
Authors: Nwanaji-Enwerem Jamaji C , Cardenas Andres , Chai Peter R , Weisskopf Marc G , Baccarelli Andrea A , Boyer Edward W
Published: July 2018

Introduction

Currently, there is no widely accepted, non-self-report measure that simultaneously reflects smoking behaviors and is molecularly informative of general disease processes. Recently, researchers developed a smoking index (SI) using nucleated blood cells and a multi-tissue DNA methylation–based predictor of chronological age and disease (DNA methylation age [DNAm-age]). To better understand the utility of this novel SI in readily accessible cell types, we used buccal cell DNA methylation to examine SI relationships with long-term tobacco smoking and moist snuff consumption.

Methods

We used a publicly available dataset composed of buccal cell DNA methylation values from 120 middle-aged men (40 long-term smokers, 40 moist snuff consumers, and 40 nonsmokers). DNAm-age (353-CpGs) and SI (66-CpGs) were calculated using CpG sites measured using the Illumina HumanMethylation450 BeadChip. We estimated associations of tobacco consumption habits with both SI and DNAm-age using linear regression models adjusted for chronological age, race, and methylation technical covariates.

Results

In fully adjusted models with nonsmokers as the reference, smoking (β = 1.08, 95% CI = 0.82 to 1.33, p < .0001) but not snuff consumption (β = .06, 95% CI = −0.19 to 0.32, p = .63) was significantly associated with SI. SI was an excellent predictor of smoking versus nonsmoking (area under the curve = 0.92, 95% CI = 0.85 to 0.98). Four DNAm-age CpGs were differentially methylated between smokers and nonsmokers including cg14992253 [EIF3I], which has been previously shown to be differentially methylated with exposure to long-term fine-particle air pollution (PM2.5).

Conclusions

The 66-CpG SI appears to be a useful tool for measuring smoking-specific behaviors in buccal cells. Still, further research is needed to broadly confirm our findings and SI relationships with DNAm-age.

Implications

Our findings demonstrate that this 66-CpG blood-derived SI can reflect long-term tobacco smoking, but not long-term snuff consumption, in buccal cells. This evidence will be useful as the field works to identify an accurate non-self-report smoking biomarker that can be measured in an easily accessible tissue. Future research efforts should focus on (1) optimizing the relationship of the SI with DNAm-age so that the metric can maximize its utility as a tool for understanding general disease processes, and (2) determining normal values for the SI CpGs so that the measure is not as study sample specific.
Urban Nostalgia in the Music of Požoň sentimentál
Authors: Lange Barbara Rose
Published: July 2018

Chapter 5 discusses nostalgia and avant-garde art in Bratislava with a case study of the musical group Požoň sentimentál. This chapter argues that although nostalgia is a feature of the postcommunist urban scene, Bratislava residents and many other Central Europeans are not nostalgic. Drawing on the ideas of Eve Kosofsky Sedgwick, the chapter proposes that Bratislava avant-gardists make postmodern reparative readings. The chapter details how during the 1990s and early 2000s, Požoň sentimentál dramatized the city as it had existed a century earlier; alongside older writers and performers such as Egon Bondy, Požoň sentimentál explored forgotten motifs of the city’s history. The chapter describes how the group’s humorous enactments provoked controversy around the artistic canon, played with the city’s sonic environment, and prompted discussion over representations of the city’s former ethnic and confessional groups, especially the Jewish population decimated by the Holocaust.
Slovak Folk Song, Romani Pop, and Outer Space in the Music of Hudba z Marsu
Authors: Lange Barbara Rose
Published: July 2018

With a case study of the Slovak punk band Hudba z Marsu, Chapter 6 illustrates discrepancies that became sources of creative energy in the 1990s and 2000s. It details how Hudba z Marsu incorporated popular motifs from the mid-twentieth-century space race, old Slovak folk recordings, and live folkloric singing. The chapter describes how Hudba z Marsu established connections with local Romani (Gypsy) musicians; the West European world-music industry highlights such collaborations, but this chapter argues that Hudba z Marsu and Romani performers treated their interactions as an everyday matter. The chapter explains how live audiences physically enjoyed Hudba z Marsu’s juxtaposition of eras, identities, and genres. A discussion of musical criticism details how some listeners rejected Hudba z Marsu’s music as a rough effort, while others heard a sophisticated reflection on Slovak identity.
Recuperating the Alpine Image in Austrian Music
Authors: Lange Barbara Rose
Published: July 2018

Chapter 7 discusses the identity politics of alpine music in Austria; alongside art music, it defined the nation until the turn of the millennium. The chapter describes how past and present adherents of the far right claimed the alpine as German-speaking rather than multiethnic, and as traditional in its gender roles. The chapter then explores how intellectuals and artists proposed new concepts of the nation. Neue Volksmusik (new folk music) was one expression, while other musicians such as Hubert von Goisern were explicit in their criticisms especially by the early 2000s, when far-right political parties joined Austria’s national governing coalition. The chapter discusses musicians of the 2000s who added female and multiethnic dimensions to the alpine while they fostered audience participation. Hotel Palindrone blended Celtic and alpine sounds, Netnakisum reversed assumptions about gender, and singer Agnes Palmisano recalled earlier times when female yodelers performed in Vienna salons.
Persia 1700–1800
Authors: Rota Giorgio
Published: July 2018

The article offers brief descriptions and analyses of five virtually unknown 18th-century European sources on Persia written in different languages and spanning a period from the reign of Shah Soltan Hoseyn Safavi to the very first years of the reign of Fath-Ali Shah Qajar. It also presents the commented text of a sixth source, of unknown author, entitled Varij ragionamenti sopra lo stato presente, e la Crisi, in cui la Persia si trova, and advances the hypothesis that it could have been written by the famous Ragusan diplomat in Russian service, Florio Beneveni. Taken together, the six sources not only provide interesting information on a rather ‘obscure’ phase of Persian history, but also show that the interest for Persia at the European courts may have been decreased as compared to the Safavid period but was still considerable.
The Discovery of Sex
Authors: Taiz Lincoln , Taiz Lee
Published: July 2018

“The Discovery of Sex,” discusses the discovery of the role of the male in reproduction and the association of women with plants in the Ice Age. In the Upper Paleolithic many barriers could have combined to obscure the connection between sexual intercourse and childbirth. Examples include pre-puberty sexual activity, prolonged breast-feeding, and the alignment of cycles in the birthrate with periods of relative leisure and abundance. Numeracy is also relevant, as explored in relation to the Gravettian sculpture, the “Lady of Laussel.” The early association of plants and women is suggested by the discovery that clothing worn by some of the Paleolithic “Venus” figurines was composed of plant-based textiles. This association is consistent with roles of women as described in ethnographic studies of modern hunter-gatherer societies, and has implications for the status of women in Paleolithic society. Sexual symbolism in parietal art is examined, including the Magdalenian transition in iconography.