bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-growth-templating synthesis of 3D N,P,Co-doped mesoporous carbon frameworks for efficient bifunctional oxygen and carbon dioxide electroreduction
Authors: Pan Fuping , Liang Aimin , Duan Youxin , Liu Qiao , Zhang Junyan , Li Ying
Published: May 2017

3D N,P,Co-doped mesoporous carbon frameworks synthesizedviaa new self-growth-templating approach enable efficient bifunctional electrocatalysis in the ORR and CO2RR.
Water splitting in near-neutral media: using an Mn–Co-based nanowire array as a complementary electrocatalyst
Authors: Hao Shuai , Yang Yingchun
Published: May 2017

A Mn–Co–borate nanowire array on carbon cloth (Mn–Co–Bi/CC) acts as an efficient electrocatalyst for water oxidation with an overpotential of 366 mV to drive 10 mA cm−2 in 0.5 M K-Bi. The two-electrode electrolyser using Mn–Co–Bi/CC as the anode and MnCo2O4/CC as the cathode drives 10 mA cm−2 at 1.97 V.
BCN network-encapsulated multiple phases of molybdenum carbide for efficient hydrogen evolution reactions in acidic and alkaline media
Authors: Anjum Mohsin Ali Raza , Lee Min Hee , Lee Jae Sung
Published: May 2017

Five phases of molybdenum carbide encapsulated by a boron–carbon–nitrogen (BCN) network are synthesized by decomposition of a Mo–imidazole-borate organometallic complex with slight variations in the imidazole-borate ligand structure.
A new in situ strategy to eliminate partial internal short circuit in Ce0.8Sm0.2O1.9-based solid oxide fuel cells
Authors: Gong Zheng , Sun Wenping , Cao Jiafeng , Wu Yusen , Miao Lina , Liu Wei
Published: May 2017

A SrCeO3-based electron-blocking layer was formed via an in situ reaction when a Sr-containing Ni-SrCe0.95Yb0.05O3−δ anode was employed for a Ce0.8Sm0.2O1.9-based SOFC.
Ti2CO2MXene: a highly active and selective photocatalyst for CO2reduction
Authors: Zhang Xu , Zhang Zihe , Li Jielan , Zhao Xudong , Wu Dihua , Zhou Zhen
Published: May 2017

We investigated the reduction of CO2at the oxygen vacancy on MXene monolayers and Ti2CO2exhibited the best catalytic performance. Moreover, we proposed that CO and H2can introduce sufficient oxygen vacancies on O-terminated MXene.
High performance carbon-based printed perovskite solar cells with humidity assisted thermal treatment
Authors: Hashmi Syed Ghufran , Martineau David , Dar M. Ibrahim , Myllymäki Teemu T. T. , Sarikka Teemu , Ulla Vainio , Zakeeruddin Shaik Mohammed , Grätzel Michael
Published: May 2017

We report humidity assisted thermal exposure (HTE) as a post-treatment method for carbon based printed perovskite solar cells (CPSCs).
Unraveling factors leading to efficient norbornadiene–quadricyclane molecular solar-thermal energy storage systems
Authors: Jorner Kjell , Dreos Ambra , Emanuelsson Rikard , El Bakouri Ouissam , Fdez. Galván Ignacio , Börjesson Karl , Feixas Ferran , Lindh Roland , Zietz Burkhard , Moth-Poulsen Kasper , Ottosson Henrik
Published: May 2017

Increased steric bulk in norbornadienes with application in solar energy storage leads to higher quantum yields, red-shifted absorption and higher thermal stability.
Multi-arm star-branched polymer as an efficient contrast agent for tumor-targeted magnetic resonance imaging
Authors: Zu Guangyue , Kuang Ye , Dong Jingjin , Cao Yi , Wang Kewei , Liu Min , Luo Liqiang , Pei Renjun
Published: May 2017

Contrast agents with high efficiency and safety are excellent candidates as magnetic resonance imaging probes.
Layer-controlled two-dimensional perovskites: synthesis and optoelectronics
Authors: Jagielski Jakub , Kumar Sudhir , Yu Wen-Yueh , Shih Chih-Jen
Published: May 2017

Solution-processed layered-controlled 2D metal halide perovskites are emerging as one of the most promising candidates for low-cost photovoltaics and optoelectronics.
Raman spectroscopy and microscopy of electrochemically and chemically doped high-mobility semiconducting polymers
Authors: Francis C. , Fazzi D. , Grimm S. B. , Paulus F. , Beck S. , Hillebrandt S. , Pucci A. , Zaumseil J.
Published: May 2017

Raman spectra and DFT calculations show that p-doping of two semiconducting polymers affects mostly their electron-rich thienothiophene units.
Enhanced electromagnetic interference shielding behavior of Graphene Nanoplatelet/Ni/Wax nanocomposites
Authors: Im Hye Ji , Jun Gwang Hoon , Lee Dong Ju , Ryu Ho Jin , Hong Soon Hyung
Published: May 2017

GNP/Ni/Wax nanocomposites fabricated by a molecular-level mixing process show enhanced shielding effectiveness due to homogeneously decorated Ni nanoparticles on GNP with strong interfacial bonding.
Sky-blue aggregation-induced emission molecules for non-doped organic light-emitting diodes
Authors: Lo Dain , Chang Chih-Hao , Krucaite Gintare , Volyniuk Dmytro , Grazulevicius Juozas V. , Grigalevicius Saulius
Published: May 2017

Triphenylethene moieties decorated with different carbazole-based substitutions were synthesized to realize molecules harvesting strong blue aggregation-induced emission (AIE).
A risk-sensitive maximum principle for a Markov regime-switching jump-diffusion system and applications
Authors: Sun Zhongyang , Kemajou-Brown Isabelle , Menoukeu-Pamen Olivier
Published: May 2017

In this paper, we derive a general stochastic maximum principle for a risk-sensitive type optimal control problem of Markov regime-switching jump-diffusion model. The results are obtainedviaa logarithmic transformation and the relationship between adjoint variables and the value function. We apply the results to study both a linear-quadratic optimal control problem and a risk-sensitive benchmarked asset management problem for Markov regime-switching models. In the latter case, the optimal control is of feedback form and is given in terms of solutions to a Markov regime-switching Riccatti equation and an ordinary Markov regime-switching differential equation.
An improved 2D fem model for straight track corrugation using the mass redistribution method
Authors: Duan Fangfang , Pozzolini Cedric , Saulot Aurelien , Berthier Yves
Published: May 2017

In railway networks, rail corrugation remains a major problem which increases due to heavy traffic under urban conditions: various frictions, train dynamics, etc. But it is difficult to identify the real influence of each factor on both the onset and evolution of such defects on the strength of experiments alone. Thus it is very important to use numerical models to analyze corrugation defects. In this paper, we present an improvement of the finite element model to reproduce more realistically both the onset and evolution of straight track corrugation under transient conditions with the passage of multiple wheels. Furthermore, the application of finite element modeling to the rail-wheel contact problem is optimized by taking the mass redistribution method into account.
Nonlinear reconnecting edge localized modes in current-carrying plasmas
Authors: Ebrahimi F.
Published: May 2017

Nonlinear edge localized modes in a tokamak are examined using global three-dimensional resistive magnetohydrodynamics simulations. Coherent current-carrying filament (ribbon-like) structures wrapped around the torus are nonlinearly formed due to nonaxisymmetric reconnecting current sheet instabilities, the so-called peeling-like edge localized modes. These fast growing modes saturate by breaking axisymmetric current layers isolated near the plasma edge and go through repetitive relaxation cycles by expelling current radially outward and relaxing it back. The local bi-directional fluctuation-induced electromotive force (emf) from the edge localized modes, the dynamo action, relaxes the axisymmetric current density and forms current holes near the edge. The three-dimensional coherent current-carrying filament structures (sometimes referred to as 3-D plasmoids) observed here should also have strong implications for solar and astrophysical reconnection.
First-principle simulations of electronic structure in semicrystalline polyethylene
Authors: Moyassari A. , Unge M. , Hedenqvist M. S. , Gedde U. W. , Nilsson F.
Published: May 2017

In order to increase our fundamental knowledge about high-voltage cable insulation materials, realistic polyethylene (PE) structures, generated with a novel molecular modeling strategy, have been analyzed using first principle electronic structure simulations. The PE structures were constructed by first generating atomistic PE configurations with an off-lattice Monte Carlo method and then equilibrating the structures at the desired temperature and pressure using molecular dynamics simulations. Semicrystalline, fully crystalline and fully amorphous PE, in some cases including crosslinks and short-chain branches, were analyzed. The modeled PE had a structure in agreement with established experimental data. Linear-scaling density functional theory (LS-DFT) was used to examine the electronic structure (e.g., spatial distribution of molecular orbitals, bandgaps and mobility edges) on all the materials, whereas conventional DFT was used to validate the LS-DFT results on small systems. When hybrid functionals were used, the simulated bandgaps were close to the experimental values. The localization of valence and conduction band states was demonstrated. The localized states in the conduction band were primarily found in the free volume (result of gauche conformations) present in the amorphous regions. For branched and crosslinked structures, the localized electronic states closest to the valence band edge were positioned at branches and crosslinks, respectively. At 0 K, the activation energy for transport was lower for holes than for electrons. However, at room temperature, the effective activation energy was very low (∼0.1 eV) for both holes and electrons, which indicates that the mobility will be relatively high even below the mobility edges and suggests that charge carriers can be hot carriers above the mobility edges in the presence of a high electrical field.
Anomalous barrier escape: The roles of noise distribution and correlation
Authors: Hu Meng , Zhang Jia-Ming , Bao Jing-Dong
Published: May 2017

We study numerically and analytically the barrier escape dynamics of a particle driven by an underlying correlated Lévy noise for a smooth metastable potential. A “quasi-monochrome-color” Lévy noise, i.e., the first-order derivative variable of a linear second-order differential equation subjected to a symmetric α-stable white Lévy noise, also called the harmonic velocity Lévy noise, is proposed. Note that the time-integral of the noise Green function of this kind is equal to zero. This leads to the existence of underlying negative time correlation and implies that a step in one direction is likely followed by a step in the other direction. By using the noise of this kind as a driving source, we discuss the competition between long flights and underlying negative correlations in the metastable dynamics. The quite rich behaviors in the parameter space including an optimum α for the stationary escape rate have been found. Remarkably, slow diffusion does not decrease the stationary rate while a negative correlation increases net escape. An approximate expression for the Lévy-Kramers rate is obtained to support the numerically observed dependencies.
Asymmetric osmotic water permeation through a vesicle membrane
Authors: Su Jiaye , Zhao Yunzhen , Fang Chang , Shi Yue
Published: May 2017

Understanding the water permeation through a cell membrane is of primary importance for biological activities and a key step to capture its shape transformation in salt solution. In this work, we reveal the dynamical behaviors of osmotically driven transport of water molecules across a vesicle membrane by molecular dynamics simulations. Of particular interest is that the water transport in and out of vesicles is highly distinguishable given the osmotic force are the same, suggesting an asymmetric osmotic transportation. This asymmetric phenomenon exists in a broad range of parameter space such as the salt concentration, temperature, and vesicle size and can be ascribed to the similar asymmetric potential energy of lipid-ion, lipid-water, lipid-solution, lipid-lipid, and the lipid-lipid energy fluctuation. Specifically, the water flux has a linear increase with the salt concentration, similar to the prediction by Nernst-Planck equation or Fick’s first law. Furthermore, due to the Arrhenius relation between the membrane permeability and temperature, the water flux also exhibits excellent Arrhenius dependence on the temperature. Meanwhile, the water flux shows a linear increase with the vesicle surface area since the flux amount across a unit membrane area should be a constant. Finally, we also present the anonymous diffusion behaviors for the vesicle itself, where transitions from normal diffusion at short times to subdiffusion at long times are identified. Our results provide significant new physical insights for the osmotic water permeation through a vesicle membrane and are helpful for future experimental studies.
Uncertainty principles for Kac algebras
Authors: Liu Zhengwei , Wu Jinsong
Published: May 2017

In this paper, we introduce the notation of bi-shift of biprojections in subfactor theory to unimodular Kac algebras. We characterize the minimizers of the Hirschman-Beckner uncertainty principle and the Donoho-Stark uncertainty principle for unimodular Kac algebras with biprojections and prove Hardy’s uncertainty principle in terms of the minimizers.
Uniqueness theorem and uniqueness of inverse problems for lossy anisotropic inhomogeneous structures with diagonal material tensors
Authors: Dehbashi Reza , Bialkowski Konstanty S. , Abbosh Amin M.
Published: May 2017

The uniqueness theorem for lossy anisotropic inhomogeneous structures with diagonal material tensors is proven. For these materials, we prove that all the elements of the constitutive tensors must be lossy. Materials like cloaks and lenses designed based on transformation-optics (TO) could be examples of such materials. The uniqueness theorem is about the uniqueness of Maxwell's equations solutions for particular sets of boundary conditions. We prove the uniqueness theorem for three cases: Single medium, media composed of two lossy anisotropic inhomogeneous materials with diagonal constitutive parameters, and media composed of two materials, where a material with diagonal material tensors is surrounded by an isotropic material. The latter case can be considered for the TO-based materials like invisibility cloaks or hyper-lenses that usually have diagonal anisotropic inhomogeneous constitutive parameters and also because cloaks or hyper-lenses are usually surrounded by free space and the sources are usually outside. For the sake of our argument in the uniqueness theorem that loss is the main condition for the validity of this theory, for cloaks as an example case of our analysis, it is analytically and numerically proven that the ideal invisibility phenomenon is possible for a simple lossy structure. We also examine the uniqueness of the inverse problem for such structures. We prove that all these materials have the same surface field distribution on a surface enclosing the area of interest, while solutions to Maxwell's equations inside them are different. The uniqueness of the inverse problem suggests that within the surface, the same medium should exactly be present. However, for lossy anisotropic inhomogeneous structures with diagonal constitutive parameters, this paper illustrates that this might not be true, despite the result of a previous study that shows that uniqueness could be true for some anisotropic inhomogeneous structures. For the analysis, the transverse electric Z-polarization is used. The simulation results are obtained by using a commercial Finite-Element based simulator.
31-mode piezoelectric micromachined ultrasonic transducer with PZT thick film by granule spraying in vacuum process
Authors: Jung Joontaek , Annapureddy Venkateswarlu , Hwang Geon-Tae , Song Youngsup , Lee Wonjun , Kang Woojin , Ryu Jungho , Choi Hongsoo
Published: May 2017

A piezoelectric micromachined ultrasonic transducer (pMUT) is an ideal device for portable medical diagnosis systems, intravascular ultrasound systems, and ultrasonic cameras because of its favorable characteristics including small size, acoustic impedance matching with the body, low power consumption, and simple integration with the systems. Despite these advantages, practical applications are limited because of insufficient acoustic pressure of the pMUT caused by the thin active piezoelectric layer. Here, we report the fabrication of a thick piezoelectric Pb(Zr,Ti)O3 (PZT) film-based pMUT device having high deflection at low driving voltage using the granule spraying in vacuum (GSV) process. Pre-patterned high-density thick (exceeding 8 μm) PZT films were grown on 6-inch-diameter Si/SiO2/Ti/Pt silicon-on-insulator wafers at room temperature at a high deposition rate of ∼5 μm min−1. The fabrication process using the proposed GSV process was simple and fast, and the deflection of the pMUT exhibited a high value of 0.8 μm.
In situ control of synchronous germanide/silicide reactions with Ge/Si core/shell nanowires to monitor formation and strain evolution in abrupt 2.7 nm channel length
Authors: Chen Renjie , Nguyen Binh-Minh , Tang Wei , Liu Yang , Yoo Jinkyoung , Dayeh Shadi A.
Published: May 2017

The metal-semiconductor interface in self-aligned contact formation can determine the overall performance of nanoscale devices. This interfacial morphology is predicted and well researched in homogenous semiconductor nanowires (NWs) but was not pursued in heterostructured core/shell nanowires. We found here that the solid-state reactions between Ni and Ge/Si core/shell nanowires resulted in a protruded and a leading NiSiy segment into the channel. A single Ni2Ge/NiSiy to Ge/Si core/shell interface was achieved by the selective shell removal near the Ni source/drain contact areas. Using in situ transmission electron microscopy, we measured the growth rate and anisotropic strain evolution in ultra-short channels. We found elevated compressive strains near the interface between the compound contact and the NW and relatively lower strains near the center of the channel which increased exponentially below the 10 nm channel length to exceed 10% strain at ∼3 nm lengths. These compressive strains are expected to result in a non-homogeneous energy band structure in Ge/Si core/shell NWs below 10 nm and potentially benefit their transistor performance.
Electrical resonance of Amphotericin B channel activity in lipidic membranes
Authors: Récamier Karla S. , Ortega-Blake Iván , Parmananda P.
Published: May 2017

In our previous work [J. Membrane Biol. 237, 31 (2010)], we showed the dependence of the time average conductance of Nystatin channels as a function of the applied potential. Specifically, it was observed that greater potential induced enhanced channel activity. This indicates that the supramolecular structure could be stabilized by a large field, possibly by giving a preferential orientation to the monomers. In the present work, we entertain the notion that the process of pore formation in the lipidic membranes has an underlying deterministic component. To verify this hypothesis, experiments were performed under potentio-dynamic conditions, i.e., a square train of pulses of different frequencies (0.05–2 Hz) were applied to a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine membrane having 30 mol. % cholesterol and the presence of 35 μM Amphotericin B. An emergence of a resonant frequency, in the present experiments, is tantamount to observing fingerprints of determinism in the activity of these channels in lipidic membranes.
The groupoid of bifractional transformations
Authors: Agyo S. , Lei C. , Vourdas A.
Published: May 2017

Bifractional transformations which lead to quantities that interpolate between other known quantities are considered. They do not form a group, and groupoids are used to describe their mathematical structure. Bifractional coherent states and bifractional Wigner functions are also defined. The properties of the bifractional coherent states are studied. The bifractional Wigner functions are used in generalizations of the Moyal star formalism. A generalized Berezin formalism in this context is also studied.
Martensitic transformation in NiMnGa/Si bimorph nanoactuators with ultra-low hysteresis
Authors: Lambrecht F. , Sagardiluz N. , Gueltig M. , Aseguinolaza I. R. , Chernenko V. A. , Kohl M.
Published: May 2017

We report on the fabrication and in-situ characterization of temperature-dependent electrical resistance and deflection characteristics of free-standing NiMnGa/Si bimorph cantilevers with a NiMnGa layer thickness of 200 nm and a minimum lateral width of 50 nm. The martensitic transformation in the initial NiMnGa/Si bimorph films and nanomachined NiMnGa/Si bimorph cantilevers proceeds in a wide temperature range with a hardly detectable temperature hysteresis width below 1 K. This remarkable behavior is ascribed to the internal stress in the bimorph system that exceeds the stress limit of the critical point terminating the stress-temperature phase diagram as it is known for ferromagnetic shape memory alloys. Temperature-dependent deflection characteristics reveal a competition between the bimorph effect and the shape memory effect, causing beam deflection in opposite directions. The observation of the shape memory effect strongly depends on the NiMnGa/Si thickness ratio, causing a maximum deflection change per beam length of 3% in agreement with finite element simulations.
Black silicon morphologies using conventional RIE processing
Authors: Chowdhury Zahidur R. , Loh Joel Y. Y. , Pishon Md. Nishanto Nahid , Kherani Nazir P.
Published: May 2017

We report on the use of conventional non-Bosch, non-cryogenic Reactive Ion Etching (RIE) processing to produce a range of low optical reflection morphologies on <100> silicon wafer. Tapered structures and nano dendritic-pillars are patterned into silicon over a pressure range of 550 - 700 mTorr at various run times. Low pressure RIE conditions yield tapered profiles while at higher pressures nano-pillars are produced. The optimized condition of 650 mTorr for 20-30 minutes yields uniform distribution of nano dendritic pillars resulting in a low average reflectance of 4.2% – without an additional antireflective coating. A simple kinetic Monte-Carlo model shows that nano-dendritic structures can be formed due to low etching rate of side walls and evolve into tapered structures over a longer run time. Refractive index profiles built from our simulated patterns and surface morphology of the samples yield calculated reflectance curves that correlate well with experimental results.
The effect of herd mentality on dairy heifers conditioned to traffic through audio cues
Authors: Russell W. T. , Kerrisk K. L. , Whitty M. A.
Published: May 2017

The objective for the present trial was to understand whether dairy heifers could be trained to respond to an audio cue paired with a feed reward. The use of acoustic conditioning to induce cattle movement has not previously been tested with animal-mounted devices to call cattle both individually and as a group. Five heifers underwent testing for 6 days as part of an 18-day field trial (12 days of conditioning). The 6-day testing and data-collection period involved the heifers being called via a smartphone device mounted on the cheek strap of a halter. Heifers were called either as individuals or as a group. When the audio cue was sent, heifers were expected to traffic from a group-holding area to a feeding area (~80-m distance) to receive an allocation of a grain-based concentrate. Heifers were significantly (P = 0.001) more likely to approach the feeding area when called as a group (91% response rate) than when they were called as individuals (67% response rate). When heifers did respond to being called, their time to traffic to the feed area was quicker (P < 0.001) when they were called as a group (77.9 ± 55.4 s) than when they were called as individuals (139.3 ± 89.2 s). The present trial has shown that animals can be trained to respond to an audio cue paired to a feed reward, highlighting the potential for acoustic conditioning to improve voluntary cow movement with an animal-mounted device. It also highlights the limitations of cattle responding to being called individually compared with being called as a group.
A comparison of the effects of post-mortem aging on breast meat from Cobb 500 and Hubbard ISA broilers
Authors: Mello J. L. M. , Souza R. A. , Paschoalin G. C. , Ferrari F. B. , Machado B. M. , Giampietro-Ganeco A. , Souza P. A. , Borba H.
Published: May 2017

We compared the physical and chemical characteristics of the pectoralis major muscle from Cobb 500 and Hubbard ISA broilers and evaluated the effect of aging process for up to 7 days on meat quality. We used breast samples from male Cobb 500 (42 days of age; n = 60) and Hubbard ISA (85 days of age; n = 60) broilers. Twenty samples of each genotype were analysed 4 h post-slaughter (Control group). Another 20 samples of each genotype were aged in an incubator (2 ± 0.5°C) for 3 and for 7 days. Breast fillets were 23% heavier in the Cobb 500 group (306 g vs 248 g; P = 0.0009). Before aging, meat from Hubbard ISA broilers had higher (P < 0.001) water-holding capacity, which promotes the production of less exudate and possibly reduces nutritional losses during storage, which may be beneficial to the poultry industry. Despite being initially less tender, breast meat from Hubbard ISA broilers showed, during the aging process, a reduction (P < 0.05) of shear force (48.46–15.04 N), total collagen amount (6.0–4.8 g/kg) and myofibrillar fragmentation index (150.17–97.42) and had the same (P = 0.134) fat concentration (0.87 g/100 g) as that of breast meat from Cobb 500 broilers (0.93 g/100 g, respectively). Breast meat from Hubbard ISA broilers had a higher (P < 0.001) polyunsaturated fatty acid concentration, especially docosahexaenoic acid, which is beneficial to human health. Aging breast fillets for 3 days at 2°C is sufficient to tenderise the meat without reducing its juiciness, which suggests that the aging process can add value to free-range meat.
Performance of Arabidopsis thaliana under different light qualities: comparison of light-emitting diodes to fluorescent lamp
Authors: Köhl Karin , Tohge Takayuki , Schöttler Mark Aurel
Published: May 2017

For precise phenotyping, Arabidopsis thaliana (L.) Heynh. is grown under controlled conditions with fluorescent lamps as the predominant light source. Replacement by systems based on light emitting diodes (LED) could improve energy efficiency and stability of light quality and intensity. To determine whether this affects the reproducibility of results obtained under fluorescent lamps, four Arabidopsis accessions and a phytochrome mutant were grown and phenotyped under two different LED types or under fluorescent lamps. All genotypes had significantly higher rosette weight and seed mass and developed faster under LED light than under fluorescent lamps. However, differences between genotypes were reproducible independent of the light source. Chlorophyll content, photosynthetic complex accumulation and light response curves of chlorophyll fluorescence parameters were indistinguishable under LED and fluorescent light. Principal component analysis of leaf metabolite concentrations revealed that the effect of a change from fluorescent light to LED light was small compared with the diurnal effect, which explains 74% of the variance and the age effect during vegetative growth (12%). Altogether, the replacement of fluorescent lamps by LED allowed Arabidopsis cultivation and reproduction of results obtained under fluorescent light.
Dutch learner English in close-up
Authors: van Vuuren Sanne , Laskin Lyuben
Published: May 2017

This study presents a longitudinal Bayesian analysis of pre-subject adverbial (PSA) use in a 571,174-word corpus of Dutch learner English. Overall, learners use more circumstance and linking adverbials, but fewer stance adverbials than both novice and expert native writers. Learners also use more ‘local anchors’, i.e. adverbials that serve a cohesive purpose by linking back to an antecedent in the directly preceding discourse. Interestingly, untimed essays are more native-like than timed essays in their use of each of the adverbial types considered. Although learners generally develop in the direction of native writing, the use of linking adverbials in learners’ literature essays develops in the opposite direction. L1 transfer may account for more frequent use of some categories of adverbials, particularly local anchors, but the widening gap between learners and native speakers (NSs) in the use of linking adverbials suggests that the potential role of textbook and curriculum design warrants further research.
Strategy training and mind-mapping facilitates children’s hypertext comprehension
Authors: Fesel Sabine S. , Segers Eliane , de Leeuw Linda , Verhoeven Ludo
Published: May 2017

Children in primary school read hypertext for comprehension. However, children typically are taught reading strategies for linear
text, while these strategies are not automatically transferrable one-to-one to hypertext. In the present study, a training group
of 55 sixth-graders were taught four hypertext reading strategies (planning, monitoring, evaluation and elaboration) via mind
mapping and the usage of a prompting paper-card. A control group of 29 children received no strategy training. We examined to what
extent strategy training influenced children’s strategy use and learning outcomes: (1) number of pages read and reading time per
text, (2) literal / inferential reading comprehension scores and (3) knowledge representations (relatedness judgment task and mind
maps). At posttest, the training group showed higher scores on a self-reported strategy usage questionnaire, and higher
comprehension scores as compared to the control group. Hypertext strategy training in combination with mind-mapping supports
children’s hypertext comprehension.
SHOTGUN: converting words into triplets
Authors: Beeksma Merijn , Neijt Anneke , Zuidema Johan
Published: May 2017

Software systems convert between graphemes and phonemes using lexicon-based, rule-based or data-driven techniques. SHOTGUN combines these techniques in a hybrid system which converts between graphemes and phonemes bi-directionally, adds linguistic and educational information about the relationships between graphemes and phonemes and provides estimates about the likelihood that the generated output is correct. We describe the components from which SHOTGUN is built and determine its accuracy by running tests on two data sources, the BasisSpellingBank and CELEX, comparing the results to Nunn’s (1998) rule-based conversion system. SHOTGUN converts phonemes to graphemes and vice versa with precision of 81% and 86% when tested on the BasisSpellingBank, and 80% and 81% when tested on CELEX. SHOTGUN proves to be a powerful new conversion tool.
Punctuation and syntactic structure inobwohlandweilclauses in nonstandard written German
Authors: Schäfer Roland , Sayatz Ulrike
Published: May 2017

In this paper, we analyze written sentences containing the German particlesobwohl(“although”) andweil(“because”). In standard written German, these particles embed clauses in verb-last constituent order, which is characteristic of subordinated clauses. In spoken and – as we show – nonstandard written German, they embed clauses in verb-second constituent order, which is characteristic of independent sentences. Our usage-based approach to the syntax – graphemics interface includes a large-scale corpus analysis of the patterns of punctuation in the nonstandard variants that provides clues to the syntactic structure and degree of sentential independence of the nonstandard variants. Our corpus study confirms and refines hypotheses from existing theoretical approaches by clearly showing that writers markobwohlclauses with verb-second order systematically as independent sentences, whereasweilclauses with verb-second order are much less strongly marked as independent. This work suggests that similar corpus studies could provide deeper insight into the interplay between syntax and graphemics.
The syllabary used by the Kickapoo in Mexico
Authors: Unseth Peter
Published: May 2017

Kickapoo who moved from the USA into northern Mexico since 1839 have written in a syllabary they identified as created by Sequoyah for the Cherokee. Possible scenarios for how the Kickapoo may have learned the Cherokee syllabary are examined. However, some authors have reported that the Kickapoo in Mexico used the less famous Great Lakes Algonquian Syllabary (GLAS), not the Cherokee syllabary. A new line of evidence is presented concerning the label that the Kickapoo use to name the syllabary, evidence that proves the syllabary they have used is the GLAS, not Sequoyah’s. Building on this evidence, new insights about the unexpected shape of some of the GLAS symbols are presented, along with clues about the creator(s) of the GLAS.
Nesprin 1α2 is essential for mouse postnatal viability and nuclear positioning in skeletal muscle
Authors: Stroud Matthew J. , Feng Wei , Zhang Jianlin , Veevers Jennifer , Fang Xi , Gerace Larry , Chen Ju
Published: May 2017

The position of the nucleus in a cell is controlled by interactions between the linker of nucleoskeleton and cytoskeleton (LINC) complex and the cytoskeleton. Defects in nuclear positioning and abnormal aggregation of nuclei occur in many muscle diseases and correlate with muscle dysfunction. Nesprin 1, which includes multiple isoforms, is an integral component of the LINC complex, critical for nuclear positioning and anchorage in skeletal muscle, and is thought to provide an essential link between nuclei and actin. However, previous studies have yet to identify which isoform is responsible. To elucidate this, we generated a series of nesprin 1 mutant mice. We showed that the actin-binding domains of nesprin 1 were dispensable, whereas nesprin 1α2, which lacks actin-binding domains, was crucial for postnatal viability, nuclear positioning, and skeletal muscle function. Furthermore, we revealed that kinesin 1 was displaced in fibers of nesprin 1α2–knockout mice, suggesting that this interaction may play an important role in positioning of myonuclei and functional skeletal muscle.
GLANET: genomic loci annotation and enrichment tool
Authors: Otlu Burçak , Firtina Can , Keleş Sündüz , Tastan Oznur
Published: May 2017

Motivation

Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations.

Results

We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately. GLANET annotates and performs enrichment analysis on these loci with a rich library. We introduce and perform novel data-driven computational experiments for assessing the power and Type-I error of its enrichment procedure which show that GLANET has attained high statistical power and well-controlled Type-I error rate. As a key feature, users can easily extend its library with new gene sets and genomic intervals. Other key features include assessment of impact of single nucleotide variants (SNPs) on TF binding sites and regulation based pathway enrichment analysis.

Availability and implementation

GLANET can be run using its GUI or on command line. GLANET’s source code is available at https://github.com/burcakotlu/GLANET. Tutorials are provided at https://glanet.readthedocs.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
Flexbar 3.0 – SIMD and multicore parallelization
Authors: Roehr Johannes T , Dieterich Christoph , Reinert Knut
Published: May 2017

Motivation

High-throughput sequencing machines can process many samples in a single run. For Illumina systems, sequencing reads are barcoded with an additional DNA tag that is contained in the respective sequencing adapters. The recognition of barcode and adapter sequences is hence commonly needed for the analysis of next-generation sequencing data. Flexbar performs demultiplexing based on barcodes and adapter trimming for such data. The massive amounts of data generated on modern sequencing machines demand that this preprocessing is done as efficiently as possible.

Results

We present Flexbar 3.0, the successor of the popular program Flexbar. It employs now twofold parallelism: multi-threading and additionally SIMD vectorization. Both types of parallelism are used to speed-up the computation of pair-wise sequence alignments, which are used for the detection of barcodes and adapters. Furthermore, new features were included to cover a wide range of applications. We evaluated the performance of Flexbar based on a simulated sequencing dataset. Our program outcompetes other tools in terms of speed and is among the best tools in the presented quality benchmark.

Availability and implementation

https://github.com/seqan/flexbar
Integrity of immunoglobulin variable regions is supported by GANP during AID-induced somatic hypermutation in germinal center B cells
Authors: Eid Mohammed Mansour Abbas , Shimoda Mayuko , Singh Shailendra Kumar , Almofty Sarah Ameen , Pham Phuong , Goodman Myron F. , Maeda Kazuhiko , Sakaguchi Nobuo
Published: May 2017

Immunoglobulin affinity maturation depends on somatic hypermutation (SHM) in immunoglobulin variable (IgV) regions initiated by activation-induced cytidine deaminase (AID). AID induces transition mutations by C→U deamination on both strands, causing C:G→T:A. Error-prone repairs of U by base excision and mismatch repairs (MMRs) create transversion mutations at C/G and mutations at A/T sites. In Neuberger’s model, it remained to be clarified how transition/transversion repair is regulated. We investigate the role of AID-interacting GANP (germinal center-associated nuclear protein) in the IgV SHM profile. GANP enhances transition mutation of the non-transcribed strand G and reduces mutation at A, restricted to GYW of the AID hotspot motif. It reduces DNA polymerase η hotspot mutations associated with MMRs followed by uracil-DNA glycosylase. Mutation comparison between IgV complementary and framework regions (FWRs) by Bayesian statistical estimation demonstrates that GANP supports the preservation of IgV FWR genomic sequences. GANP works to maintain antibody structure by reducing drastic changes in the IgV FWR in affinity maturation.
Quantifying tidal stream disruption in a simulated Milky Way
Authors: Sandford Emily , Küpper Andreas H. W. , Johnston Kathryn V. , Diemand Jürg
Published: May 2017

Simulations of tidal streams show that close encounters with dark matter subhaloes induce density gaps and distortions in on-sky path along the streams. Accordingly, observing disrupted streams in the Galactic halo would substantiate the hypothesis that dark matter substructure exists there, while in contrast, observing collimated streams with smoothly varying density profiles would place strong upper limits on the number density and mass spectrum of subhaloes. Here, we examine several measures of stellar stream ‘disruption' and their power to distinguish between halo potentials with and without substructure and with different global shapes. We create and evolve a population of 1280 streams on a range of orbits in the Via Lactea II simulation of a Milky Way-like halo, replete with a full mass range of Λcold dark matter subhaloes, and compare it to two control stream populations evolved in smooth spherical and smooth triaxial potentials, respectively. We find that the number of gaps observed in a stellar stream is a poor indicator of the halo potential, but that (i) the thinness of the stream on-sky, (ii) the symmetry of the leading and trailing tails and (iii) the deviation of the tails from a low-order polynomial path on-sky (‘path regularity') distinguish between the three potentials more effectively. We furthermore find that globular cluster streams on low-eccentricity orbits far from the galactic centre (apocentric radius ∼30–80 kpc) are most powerful in distinguishing between the three potentials. If they exist, such streams will shortly be discoverable and mapped in high dimensions with near-future photometric and spectroscopic surveys.
CO excitation in the Seyfert galaxy NGC 7130
Authors: Pozzi F. , Vallini L. , Vignali C. , Talia M. , Gruppioni C. , Mingozzi M. , Massardi M. , Andreani P.
Published: May 2017

We present a coherent multiband modelling of the carbon monoxide (CO) spectral energy distribution of the local Seyfert galaxy NGC 7130 to assess the impact of the active galactic nucleus (AGN) activity on the molecular gas. We take advantage of all the available data from X-ray to the submillimetre, including ALMA data. The high-resolution (∼0.2 arcsec) ALMA CO(6–5) data constrain the spatial extension of the CO emission down to an ∼70 pc scale. From the analysis of the archival Chandra and NuSTAR data, we infer the presence of a buried, Compton-thick AGN of moderate luminosity, L2–10 keV  ∼ 1.6 × 1043 erg s−1. We explore photodissociation and X-ray-dominated-region (PDR and XDR) models to reproduce the CO emission. We find that PDRs can reproduce the CO lines up to J ∼ 6; however, the higher rotational ladder requires the presence of a separate source of excitation. We consider X-ray heating by the AGNs as a source of excitation, and find that it can reproduce the observed CO spectral energy distribution. By adopting a composite PDR+XDR model, we derive molecular cloud properties. Our study clearly indicates the capabilities offered by the current generation of instruments to shed light on the properties of nearby galaxies by adopting state-of-the-art physical modelling.
Intracranial Infectious and Inflammatory Diseases Presenting as Neurosurgical Pathologies
Authors: Rapalino Otto , Mullins Mark E.
Published: May 2017

There are many infectious and inflammatory processes affecting the central nervous system that can simulate other neurosurgical pathologies (e.g. tumor) and may precipitate a brain biopsy for definitive diagnosis if not suspected a priori. The challenge for the healthcare team is to recognize imaging features that support a nonsurgical pathology to avoid unnecessary interventions. This review aims to give a general overview of some common inflammatory and infectious entities that affect the central nervous system, with illustrative examples and highlighting important pearls and pitfalls.
Genomic relatedness of Staphylococcus pettenkoferi isolates of different origins
Authors: Månsson Emeli , Hellmark Bengt , Stegger Marc , Skytt Andersen Paal , Sundqvist Martin , Söderquist Bo
Published: May 2017

Purpose. The aim of the study was to characterize clinical and environmental Staphylococcus pettenkoferi isolates with regard to genomic diversity and antibiotic susceptibility pattern. Repetitive-sequence-based PCR and core genome phylogenetic analysis of whole-genome sequencing (WGS) data verified the presence of distinct clades comprising closely related S. pettenkoferi isolates from different geographical locations and origins.

Methodology. Phylogenetic relationships between 25 S
. pettenkoferi isolates collected from blood cultures and intra-operative air sampling were determined by repetitive-sequence-based PCR typing and analysis of ~157 000 SNPs identified in the core genome after WGS. Antibiotic susceptibility testing and tests for biofilm production (microtitre plate assay) were performed.

Results. Repetitive-sequence-based PCR as well as WGS data demonstrated the close relatedness of clinically significant blood culture isolates to probable contaminants, as well as to environmental isolates. Antibiotic-susceptibility testing demonstrated a low level of antimicrobial resistance. The mecA gene was present in two cefoxitin-resistant isolates. No isolates were found to produce biofilm.

Conclusion. Close genomic relatedness of S. pettenkoferi isolates from different geographical locations and origins were found within clades, but with substantial genomic difference between the two major clades. The ecological niche of S. pettenkoferi remains unconfirmed, but the presence of S. pettenkoferi in the air of the operating field favours the suggestion of a role in skin flora. Identification of S. pettenkoferi in clinical samples should, in a majority of cases, most likely be regarded as a probable contamination, and its role as a possible pathogen in immunocompromised hosts remains to be clarified.
Microbe Profile: Akkermansia muciniphila: a conserved intestinal symbiont that acts as the gatekeeper of our mucosa
Authors: de Vos Willem M
Published: May 2017

Akkermansia muciniphila is an abundant inhabitant of the intestinal tract of humans and many other animals. It is the sole intestinal representative of the verrucomicrobia in human stools and depleted in adults suffering from obesity, diabetes and several other diseases. A. muciniphila degrades intestinal mucin into mainly propionic and acetic acid, and lives in symbiosis with its host, marked by signalling to immune and metabolic pathways, priming trophic chains and likely providing competitive exclusion at the host–microbe interface. Since its recent discovery, A. muciniphila has increasingly been studied and recognized as a true intestinal symbiont promoting beneficial interactions in the intestinal tract.
Mark Hepworth: in memoriam
Authors: Jackson Thomas , Willett Peter
Published: May 2017

Purpose

The purpose of this paper is to honour the contributions of Mark Hepworth to library and information science (LIS).

Design/methodology/approach

The personal views of the two authors, both of whom knew Hepworth for many years.

Findings

The significance of Hepworth’s research in LIS, in particular to studies of information behaviour and information literacy.

Originality/value

Demonstrates the community’s appreciation of Hepworth’s contributions to the discipline.