bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating free vs bound oxygen on ignition of nano-aluminum based energetics leads to a critical reaction rate criterion
Authors: Zhou Wenbo , DeLisio Jeffery B. , Wang Xizheng , Egan Garth C. , Zachariah Michael R.
Published: September 2015

This study investigates the ignition of nano-aluminum (n-Al) and n-Al based energetic materials (nanothermites) at varying O2 pressures (1–18 atm), aiming to differentiate the effects of free and bound oxygen on ignition and to assess if it is possible to identify a critical reaction condition for ignition independent of oxygen source. Ignition experiments were conducted by rapidly heating the samples on a fine Pt wire at a heating rate of ∼105 °C s−1 to determine the ignition time and temperature. The ignition temperature of n-Al was found to reduce as the O2 pressure increased, whereas the ignition temperatures of nanothermites (n-Al/Fe2O3, n-Al/Bi2O3, n-Al/K2SO4, and n-Al/K2S2O8) had different sensitivities to O2 pressure depending on the formulations. A phenomenological kinetic/transport model was evaluated to correlate the concentrations of oxygen both in condensed and gaseous phases, with the initiation rate of Al-O at ignition temperature. We found that a constant critical reaction rate (5 × 10−2 mol m−2 s−1) for ignition exists which is independent to ignition temperature, heating rate, and free vs bound oxygen. Since for both the thermite and the free O2 reaction the critical reaction rate for ignition is the same, the various ignition temperatures are simply reflecting the conditions when the critical reaction rate for thermal runaway is achieved.
Dynamics of an oscillating turbulent jet in a confined cavity
Authors: Righolt B. W. , Kenjereš S. , Kalter R. , Tummers M. J. , Kleijn C. R.
Published: September 2015

We demonstrate how the self-sustained oscillation of a confined jet in a thin cavity can be quantitatively described by a zero-dimensional model of the delay differential equation type with two a priori predicted model constants. This model describes the three phases in self-sustained oscillations: (i) pressure driven growth of the oscillation, (ii) amplitude limitation by geometry, and (iii) delayed destruction of the recirculation zone. The two parameters of the model are the growth rate of the jet angle by a pressure imbalance and the delay time for the destruction of this pressure imbalance. We present closed relations for both model constants as a function of the jet Reynolds number Re, the inlet velocity vin, the cavity width W, and the cavity width over inlet diameter W/d and we demonstrate that these model constants do not depend on other geometric ratios. The model and the obtained model constants have been successfully validated against three dimensional large eddy simulations, and planar particle image velocimetry measurements, for 1600 < Re ≤ 7100 and 20 ≤ W/d < 50. The presented model inherently contains the transition to a non-oscillating mode for decreasing Reynolds numbers or increasing W/d-ratios and allows for the quantitative prediction of the corresponding critical Reynolds number and critical W/d.
Numerical study of oblique detonation wave initiation in a stoichiometric hydrogen-air mixture
Authors: Wang Tao , Zhang Yining , Teng Honghui , Jiang Zonglin , Ng Hoi Dick
Published: September 2015

Two-dimensional, oblique detonations induced by a wedge are simulated using the reactive Euler equations with a detailed chemical reaction model. The focus of this study is on the oblique shock-to-detonation transition in a stoichiometric hydrogen-air mixture. A combustible, gas mixture at low pressure and high temperature, corresponding to the realistic, inflow conditions applied in oblique detonation wave engines, is presented in this study. At practical flight conditions, the present numerical results illustrate that oblique detonation initiation is achieved through a smooth transition from a curved shock, which differs from the abrupt transition depicted in the previous studies. The formation mechanism of this smooth transition is discussed and a quantitative analysis is carried out by defining a characteristic length for the initiation process. The dependence of the initiation length on different parameters including the wedge angle, flight Mach number, and inflow Mach number is discussed. Despite the hypothetical nature of the simulation configuration, the present numerical study uses parameters we deem relevant to practical conditions and provides important observations for which future investigations can benefit from in reaching toward a rigorous theory of the formation and self-sustenance of oblique detonation waves.
Interplay between the local information based behavioral responses and the epidemic spreading in complex networks
Authors: Liu Can , Xie Jia-Rong , Chen Han-Shuang , Zhang Hai-Feng , Tang Ming
Published: September 2015

The spreading of an infectious disease can trigger human behavior responses to the disease, which in turn plays a crucial role on the spreading of epidemic. In this study, to illustrate the impacts of the human behavioral responses, a new class of individuals, SF, is introduced to the classical susceptible-infected-recovered model. In the model, SF state represents that susceptible individuals who take self-initiate protective measures to lower the probability of being infected, and a susceptible individual may go to SF state with a response rate when contacting an infectious neighbor. Via the percolation method, the theoretical formulas for the epidemic threshold as well as the prevalence of epidemic are derived. Our finding indicates that, with the increasing of the response rate, the epidemic threshold is enhanced and the prevalence of epidemic is reduced. The analytical results are also verified by the numerical simulations. In addition, we demonstrate that, because the mean field method neglects the dynamic correlations, a wrong result based on the mean field method is obtained—the epidemic threshold is not related to the response rate, i.e., the additional SF state has no impact on the epidemic threshold.
Magnetic anisotropy induced by crystal distortion in Ge1−xMnxTe/PbTe//KCl (001) ferromagnetic semiconductor layers
Authors: Knoff W. , Łusakowski A. , Domagała J. Z. , Minikayev R. , Taliashvili B. , Łusakowska E. , Pieniążek A. , Szczerbakow A. , Story T.
Published: September 2015

Ferromagnetic resonance (FMR) study of magnetic anisotropy is presented for thin layers of IV-VI diluted magnetic semiconductor Ge1−xMnxTe with x = 0.14 grown by molecular beam epitaxy on KCl (001) substrate with a thin PbTe buffer. Analysis of the angular dependence of the FMR resonant field reveals that an easy magnetization axis is located near to the normal to the layer plane and is controlled by two crystal distortions present in these rhombohedral Ge1−xMnxTe layers: the ferroelectric distortion with the relative shift of cation and anion sub-lattices along the [111] crystal direction and the biaxial in-plane, compressive strain due to thermal mismatch.
Laser irradiance scaling in polar direct drive implosions on the National Ignition Facility
Authors: Murphy T. J. , Krasheninnikova N. S. , Kyrala G. A. , Bradley P. A. , Baumgaertel J. A. , Cobble J. A. , Hakel P. , Hsu S. C. , Kline J. L. , Montgomery D. S. , Obrey K. A. D. , Shah R. C. , Tregillis I. L. , Schmitt M. J. , Kanzleiter R. J. , Batha S. H. , Wallace R. J. , Bhandarkar S. D. , Fitzsimmons P. , Hoppe M. L. , Nikroo A. , Hohenberger M. , McKenty P. W. , Rinderknecht H. G. , Rosenberg M. J. , Petrasso R. D.
Published: September 2015

Polar-direct-drive experiments conducted at the National Ignition Facility [E. I. Moses, Fusion Sci. Technol. 54, 361 (2008)] performed at laser irradiance between 1 and 2×1015 W/cm2 exhibit increased hard x-ray emission, decreased neutron yield, and reduced areal density as the irradiance is increased. Experimental x-ray images at the higher irradiances show x-ray emission at the equator, as well as degraded symmetry, that is not predicted in hydrodynamic simulations using flux-limited energy transport, but that appear when non-local electron transport together with a model to account for cross beam energy transfer (CBET) is utilized. The reduction in laser power for equatorial beams required in the simulations to reproduce the effects of CBET on the observed symmetry also reproduces the yield degradation consistent with experimental data.
Low temperature rate coefficients of the H + CH+ → C+ + H2 reaction: New potential energy surface and time-independent quantum scattering
Authors: Werfelli Ghofran , Halvick Philippe , Honvault Pascal , Kerkeni Boutheïna , Stoecklin Thierry
Published: September 2015

The observed abundances of the methylidyne cation, CH+, in diffuse molecular clouds can be two orders of magnitude higher than the prediction of the standard gas-phase models which, in turn, predict rather well the abundances of neutral CH. It is therefore necessary to investigate all the possible formation and destruction processes of CH+ in the interstellar medium with the most abundant species H, H2, and e−. In this work, we address the destruction process of CH+ by hydrogen abstraction. We report a new calculation of the low temperature rate coefficients for the abstraction reaction, using accurate time-independent quantum scattering and a new high-level ab initio global potential energy surface including a realistic model of the long-range interaction between the reactants H and CH+. The calculated thermal rate coefficient is in good agreement with the experimental data in the range 50 K–800 K. However, at lower temperatures, the experimental rate coefficient takes exceedingly small values which are not reproduced by the calculated rate coefficient. Instead, the latter rate coefficient is close to the one given by the Langevin capture model, as expected for a reaction involving an ion and a neutral species. Several recent theoretical works have reported a seemingly good agreement with the experiment below 50 K, but an analysis of these works show that they are based on potential energy surfaces with incorrect long-range behavior. The experimental results were explained by a loss of reactivity of the lowest rotational states of the reactant; however, the quantum scattering calculations show the opposite, namely, a reactivity enhancement with rotational excitation.
Analysis of organic vapors with laser induced breakdown spectroscopy
Authors: Nozari Hadi , Rezaei Fatemeh , Tavassoli Seyed Hassan
Published: September 2015

In this paper, laser induced breakdown spectroscopy (LIBS) is utilized in the study of acetone, ethanol, methanol, cyclohexane, and nonane vapors. Carbon, hydrogen, oxygen, and nitrogen atomic emission spectra have been recorded following laser-induced breakdown of the organic vapors that are mixed with air inside a quartz chamber at atmospheric pressure. The plasma is generated with focused, Q-switched Nd:YAG radiation at the wavelength of 1064 nm. The effects of ignition and vapor pressure are discussed in view of the appearance of the emission spectra. The recorded spectra are proportional to the vapor pressure in air. The hydrogen and oxygen contributions diminish gradually with consecutive laser-plasma events without gas flow. The results show that LIBS can be used to characterize organic vapor.
Communication: Hole localization in Al-doped quartz SiO2 within ab initio hybrid-functional DFT
Authors: Gerosa Matteo , Di Valentin Cristiana , Bottani Carlo Enrico , Onida Giovanni , Pacchioni Gianfranco
Published: September 2015

We investigate the long-standing problem of hole localization at the Al impurity in quartz SiO2, using a relatively recent DFT hybrid-functional method in which the exchange fraction is obtained ab initio, based on an analogy with the static many-body COHSEX approximation to the electron self-energy. As the amount of the admixed exact exchange in hybrid functionals has been shown to be determinant for properly capturing the hole localization, this problem constitutes a prototypical benchmark for the accuracy of the method, allowing one to assess to what extent self-interaction effects are avoided. We obtain good results in terms of description of the charge localization and structural distortion around the Al center, improving with respect to the more popular B3LYP hybrid-functional approach. We also discuss the accuracy of computed hyperfine parameters, by comparison with previous calculations based on other self-interaction-free methods, as well as experimental values. We discuss and rationalize the limitations of our approach in computing defect-related excitation energies in low-dielectric-constant insulators.
Experimental and numerical study on hydrodynamic performance of a wave energy converter using wave-induced motion of floating body
Authors: Peng Wei , Lee Kwang-Ho , Mizutani Norimi , Huang Xiaoyun
Published: September 2015

This paper presents results from experimental and numerical investigations on the wave potential extraction of an energy conversion device subjected to regular waves in intermediate water depth. The device is based on a pontoon-type floating breakwater with asymmetric mooring plates. The numerical model is built based on the Navier-Stokes solver coupled with immersed boundary method, volume of fluid method and the mechanics model of energy device. The data obtained in the laboratory investigation suggest that reactive control methods must be employed to optimize the load of the power take off system and maintain the wave energy converter near resonance, which plays an important role in capturing higher wave power. The energy conversion efficiency can reach 14% during experimental runs with only one dynamo installed. Furthermore, by comparing with the experimental results, the applicability of the developed numerical model is demonstrated in predicting the interactions between water waves and the wave power device. With the help of snapshots of water particle velocity field and the wave pressure field from numerical calculation, the flow pattern and external forces from the fluid field can also be estimated. Finally, the effects of mooring angle and the length of floating body on the performance of the energy device are highlighted.
Study of confined coherent acoustic phonon modes in a free-standing cubic GaN membrane by femtosecond spectroscopy
Authors: He Chuan , Grossmann Martin , Brick Delia , Schubert Martin , Novikov Sergei V. , Foxon C. Thomas , Gusev Vitalyi , Kent Anthony J. , Dekorsy Thomas
Published: September 2015

Confined longitudinal coherent acoustic phonon modes are excited and detected in a sub-μm-thick free-standing cubic GaN membrane by femtosecond pump-probe spectroscopy. After fs laser excitation, Brillouin oscillation and thickness oscillation with frequencies up to 100 GHz are observed and studied in the time domain. We found an initial expansion of the membrane upon optical excitation at 400 nm. Our experimental results confirmed earlier existing theoretical predictions and experimental observations that the hydrostatic deformation potential of cubic GaN is positive.
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
Authors: Abdollahipour Babak , Abouie Jahanfar , Ebrahimi Navid
Published: September 2015

We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields.
Role of Helium Droplets in Mass Spectra of Diatomics: Suppression of Dissociative Reactions
Authors: Ellis Andrew M. , Yang Sheng-fu
Published: September 2015

It is generally accepted that electron impact of doped helium nanodroplets initially produces a positively charged helium atom, which then ionizes the dopant if the two come into contact. In effect the He+ can initiate ion-molecule reactions. However, the effect of the surrounding helium on ion-molecule reactions remains ambiguous. To explore this, electron-induced chemistry has been investigated for the diatomic molecules O2, CO and N2. The helium is found to significantly suppress dissociative ion product channels.
Interaction between Potassium Phosphate Buffer Solution and Modeling Cell Membrane Investigated by Sum Frequency Generation Vibrational Spectroscopy
Authors: Yang Weilai , Tian Kangzhen , Ye Shuji
Published: September 2015

Potassium phosphate buffer solution has been widely used in the biological experiments, which represents an important process of the interaction between ions and biomolecules, yet the influences of potassium phosphate on biomolecules such as the cell membrane are still poorly understood at the molecular level. In this work, we have applied sum frequency generation vibrational spectroscopy and carried out a detailed study on the interaction between potassium phosphate buffer solution (PBS) and negative 1,2-dimyristoyl-d54-sn-glycero-3-[phospho-rac-(1-glycerol)] (d54-DMPG) lipid bilayer in real time. The PBS-induced dynamic change in the molecular structure of d54-DMPG lipid bilayer was monitored using the spectral features of CD2, CD3, lipid head phosphate, and carbonyl groups for the first time. It is found that K+ can bind to the cell membrane and cause the signal change of CD2, CD3, lipid head phosphate, and carbonyl groups quickly. Potassium PBS interacts with lipid bilayers most likely by formation of toroidal pores inside the bilayer matrix. This result can provide a molecular basis for the interpretation of the effect of PBS on the ion-assisted transport of protein across the membrane.
Photoelectron Imaging Spectroscopy of ZrO− Diatomic Anion
Authors: Liu Qing-yu , Hu Lian-rui , Chen Hui , He Sheng-gui
Published: September 2015

The diatomic ZrO− anion has been prepared by laser ablation and studied by photoelectron imaging spectroscopy combined with quantum chemistry calculations. The observed photoelectron spectra can be well assigned on the basis of reported optical spectroscopy and high-level ab initio calculations. The ground state of ZrO− is a 2Δ state with spin-orbit splitting of 578±12 cm−1. The electron affinity of ZrO is 1.249±0.005 eV. For the first time, the c3∑− state of ZrO has been experimentally observed at 13316±24 cm−1 with respect to the X1∑+ ground state. A comparison between ZrO and the isoelectronic molecule NbN has been made.
SP3-Hybridization Feature of Ag4 Superatom in Superatomic Molecules
Authors: Yan Li-juan , Cheng Long-jiu , Yang Jin-long
Published: September 2015

Analogous to atoms, superatoms can be used as building blocks to compose molecules and materials. To demonstrate this idea, the possibility of using tetrahedral Ag4 cluster to form a series of superatomic molecules Ag4X4 (X=H, Li, Na, K, Cu, Ag, Au and F, Cl, Br) is discussed. Based on the super valence bond model, a tetrahedral Ag4 cluster can be viewed as a 4-electron superatom, which can mimic a sp3 hybridization C atom. By comparison of the representative superatomic molecules Ag4X4 (X=Au, Cl) with the corresponding simple molecules CX4 (X=H, Cl), the similarities in terms of chemical bonding patterns and molecular orbitals (MOs) are conspicuous. Energy calculations predict that the Ag4 superatom can bind with all the involved ligands. Furthermore, the stabilities of superatomic molecules are enhanced by the large gaps of the highest occupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO gaps) and high aromaticity. Our studies may find applications in assembling materials with superatoms.
Linear and Nonlinear Spectra in Photosynthetic Light Harvesting Complexes: Benchmark Tests of Modified Redfield Method
Authors: Jing Yuan-yuan , Song Kai , Bai Shu-ming , Shi Qiang
Published: September 2015

We employ the numerically exact hierarchical equations of motion (HEOM) method to perform benchmark tests for the popular modified Redfield method in calculating linear and nonlinear spectroscopic signals of molecular aggregates in photosynthetic light harvesting complexes. It is currently well known that the perturbative and Markovian approximations involved in the modified Redfield equation may give inappropriate description of the excitation energy transfer processes in the intermediate coupling regime. An interesting topic is thus to test the validity of the modified Redfield method in calculating various types of spectroscopic signals. By using model dimers with different sets of parameters and a model of the Fenna-Matthews-Olson complex, we calculate and compare the absorption, emission, and 2D spectra using the modified Redfield and HEOM methods. It is found that results from the modified Redfield method agree well with the HEOM ones in a wide range of parameter regimes. The comparison also helps to understand the quantum beating signals in the 2D spectra of the photosynthetic light harvesting complexes.
Construction of the Apparatus for Two Dimensional Electronic Spectroscopy and Characterization of the Instrument
Authors: Yue Shuai , Wang Zhuan , He Xiao-chuan , Zhu Gang-bei , Weng Yu-xiang
Published: September 2015

This work describes the construction of a phase-stable two dimensional electronic spectrometer operating in a photon echo mode with optical heterodyne detection, where the diffractive optics were used to realize the passive phase stabilization. In addition, a high speed and sensitive EMCCD was configured for shot-to-shot measurement which effectively improved signal-to-noise ratio. Consequently, the phase stability between a pulse pair split by the diffractive optics was determined in terms of standard deviation to be λ/200 during an observation period of 30 min, while the phase stability of the photon echo signal measured with IR140 is λ/90 in 19 min. In addition, a method of phase-shift in the pump pulse is also presented, which can effectively remove the interference from scattering light in collection of pump-probe transient absorption spectrum. The phase-shift method can improve the accuracy of phase adjustment in 2D electronic spectrum of scattering samples.
State to State Photodissociation Dynamics of Vibrationally Excited D2O in B Band
Authors: Han Shan-yu , Zhou Lin-sen , Xie Dai-qian
Published: September 2015

The state-to-state photodissociassion dynamics for the B band of D2O have been explored from quantum dynamical calculations including the electronic ̃X and ̃B states. The calculations were carried out using a Chebyshev real wave packet method. The calculated absorption spectra, product state distributions, and branching ratios from different initial vibrational states show different dynamic features, due to the different shapes of the vibrational wavefunctions. The initial bending mode (0,1,0) generates two lobes with a shallow minimum on the absorption spectrum and a slight inverted vibrational population of OD(̃X) product at high total energies. The rotational state distributions of OD(̃X, v=0) product are highly inverted and depend weakly on the initial state and total energy. On the other hand, the ro-vibrational distributions of OD(̃A) product strongly oscillate with the total energy, which are dominated by the long-living resonances and depend sensitively on the potential surfaces. The antisymmetric stretching mode (0,0,1) has large OD(̃A)/OD(̃X) branching ratios at high total energies, which indicates that the B band dissociation proceeds mainly via the adiabatic pathway in some cases.
Direct Observation of Ethanol Photocatalysis on Rutile TiO2(110) Surface
Authors: Wei Dong , Jin Xian-chi , Dai Dong-xu , Ma Zhi-bo , Yang Xue-ming
Published: September 2015

Photocatalytic dissociation of ethanol molecules on the rutile TiO2(110) surface after UV irradiation has been investigated by scanning tunneling microscope at 80 K. Most of the ethanol molecules adsorb molecularly at Ti sites, similar to the case of methanol. After UV irradiation, two different protrusions of products were observed, one of them has been identified by the technique of tip manipulation, which was likely composed of an acetaldehyde in the middle and two bridge-bonded hydroxyls on both neighbored oxygen sites. Multi-time irradiation experiments have also been performed to further understand the relationship between the two protrusions and the process of ethanol photocatalytic dissociation. These results provide detailed insights into the photocatalysis of ethanol on rutile TiO2(110), which would help us to understand how phtotocatalytic reactions of ethnaol proceed at the fundamental level.
Habitat associations of a rare South Australian sea star (Parvulastra parvivipara) and a co-occurring chiton (Ischnochiton variegatus): implications for conservation
Authors: Liversage Kiran
Published: September 2015

The sea star Parvulastra parvivipara is a small-range endemic known from only seven granitic headlands in South Australia. Evidence from previous studies suggests that its unstable boulder habitat will experience increased disturbance as sea levels rise. This study investigated distributional and ontogenetic patterns of P. parvivipara across different-sized boulders that vary in physical stability and susceptibility to disturbance. To develop a better understanding of community dynamics in P. parvivipara habitat, patterns were also assessed for a chiton with which the sea star commonly co-occurs (Ischnochiton variegatus), and assemblages of encrusting species were also measured, as these can vary amongst boulder sizes and influence mobile animals. Large boulders had many tubeworms, contributing to a significant boulder-size effect on encrusting species assemblage structure. P. parvivipara was most abundant on the smallest boulders; there was no evidence that abundances were influenced by encrusters. I. variegatus abundances were unaffected by boulder size, but a positive correlation between lengths of individuals and encruster cover occurred on the smallest boulders. Overall, physical habitat features, not encrusting biota, likely caused an association of P. parvivipara with small boulders, while I. variegatus displayed apparent ontogenetic use of encruster-related habitat features. As P. parvivipara uses mostly small boulders that are particularly susceptible to disturbances that are increasing with rising sea levels, future ecological restoration efforts to protect this rare species may be required. Such efforts can be properly informed about necessary habitat requirements from these results.
Demeanor indexicals, interpretive discourses and the “Kong Girl” stereotype
Authors: Chen Katherine H.Y , Kang M. Agnes
Published: September 2015

Focusing on a Hong Kong online discussion involving ‘Jenny’, who was later described as the ‘Kong Girl’ prototype, we demonstrate a method to study gender stereotype as both semiotically and discursively constructed. We trace the perceivable signs in online posts as demeanor indexicals (Goffman 1956, Agha 2007), and discuss how forum participants collectively develop Jenny’s public persona as a woman who is materialistic and has an entitlement attitude, qualities that later become emblematic of the Kong Girl stereotype. Our analysis proposes a framework for how interpretive discourses mediate between the situated social media context and gender ideologies, and contributes to an understanding of the role of demeanor indexicals in the construction of a stereotype that is not associated with a linguistic register. We provide insights into local gender dynamics and illustrate how a private dispute becomes entangled in a public consensus building process that is necessarily selective, emergent, and positioned.
Combating privilege, regulating language
Authors: VanderStouwe Chris
Published: September 2015

Despite recent claims that (public) gay spaces as we know them no longer need to exist (Aguirre-Livingston 2011), many queer
scholars have shown that this is not historically the case (e.g. Manalansan 2003). In order to examine the issue of language and
sexuality in public spaces, this paper uses ethnographic data collected among members of a university queer group in southern
California to demonstrate role and regulation of ‘inclusive language’ — language that seeks to remain gender-neutral and
non-exclusionary for personal identity labels — in the attempts to create what are known as safe spaces, both private and public.
While a need for such spaces comes from a reaction to social privilege and normative expectations commonly found in public spaces,
in many respects, the material reality of safe spaces would not be possible without regulating language used in this setting.
ICT: isotope correction toolbox
Authors: Jungreuthmayer Christian , Neubauer Stefan , Mairinger Teresa , Zanghellini Jürgen , Hann Stephan
Published: September 2015

Summary: Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences—in particular for complex isotopic systems—is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms.

Availability and implementation: Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/

Contact: {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at}

Supplementary information:  Supplementary data are available at Bioinformatics online.
NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles
Authors: Leggett Richard M. , Heavens Darren , Caccamo Mario , Clark Matthew D. , Davey Robert P.
Published: September 2015

Motivation: The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to provide comprehensive alignment-based quality control and error profile analysis—something that is extremely important given the speed with which the platform is evolving.

Results: NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF report including error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it is easily extensible to include others.

Availability and implementation: NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https://github.com/TGAC/NanoOK. A VirtualBox VM containing all dependencies and the DH10B read set used in this article is available from http://opendata.tgac.ac.uk/nanook/. A Docker image is also available from Docker Hub—see program documentation https://documentation.tgac.ac.uk/display/NANOOK.

Contact:  richard.leggett@tgac.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Expression of Malic Enzymes in Sebaceous Lesions
Authors: Su Ting-Fu , Gao Hong-Wei
Published: September 2015

Malic enzymes (MEs) are involved in fatty acid biosynthesis and lipid accumulation, and their expression in sebocytes and sebaceous lesions has not been investigated. The aims of this study were to examine ME1 and ME2 expression in normal skin and sebaceous lesions. A total of 68 cases including 5 specimens of normal skin, 12 facial lesions showing sebaceous hyperplasia, 18 sebaceous adenomas, 10 sebaceomas, 13 steatocystomas, and 10 sebaceous carcinomas were examined for the expression of ME1 and ME2. All benign and malignant sebaceous lesions showed ME1+(vesicular) in clear cells and ME2+(granular) in nonclear cells, respectively. ME1−/ME2+ phenotype is seen in basal sebocytes, basal keratinocytes, sweat glands, and outer root sheath cells and hence not specific. This study demonstrates that ME1+(vesicular)/ME2+(granular) expression phenotype may have a potential to be a valuable marker for sebaceous differentiation. It is necessary to perform large-scale studies including skin tumors with a clear cell morphology that may mimic sebaceous differentiation.
When dogs look back: inhibition of independent problem-solving behaviour in domestic dogs (
Canis lupus familiaris
) compared with wolves (
Canis lupus
)
Authors: Udell Monique A. R.
Published: September 2015

Domestic dogs have been recognized for their social sensitivity and aptitude in human-guided tasks. For example, prior studies have demonstrated that dogs look to humans when confronted with an unsolvable task; an action often interpreted as soliciting necessary help. Conversely, wolves persist on such tasks. While dogs' ‘looking back’ behaviour has been used as an example of socio-cognitive advancement, an alternative explanation is that pet dogs show less persistence on independent tasks more generally. In this study, pet dogs, shelter dogs and wolves were given up to three opportunities to open a solvable puzzle box: when subjects were with a neutral human caretaker, alone and when encouraged by the human. Wolves were more persistent and more successful on this task than dogs, with 80% average success rate for wolves versus a 5% average success rate for dogs in both the human-in and alone conditions. Dogs showed increased contact with the puzzle box during the encouragement condition, but only a moderate increase in problem-solving success. Social sensitivity appears to play an important role in pet and shelter dogs' willingness to engage in problem-solving behaviour, which could suggest generalized dependence on, or deference to, human action.
Proper symmetric and asymmetric endoplasmic reticulum partitioning requires astral microtubules
Authors: Smyth Jeremy T. , Schoborg Todd A. , Bergman Zane J. , Riggs Blake , Rusan Nasser M.
Published: September 2015

Mechanisms that regulate partitioning of the endoplasmic reticulum (ER) during cell division are largely unknown. Previous studies have mostly addressed ER partitioning in cultured cells, which may not recapitulate physiological processes that are critical in developing, intact tissues. We have addressed this by analysing ER partitioning in asymmetrically dividing stem cells, in which precise segregation of cellular components is essential for proper development and tissue architecture. We show that inDrosophilaneural stem cells, called neuroblasts, the ER asymmetrically partitioned to centrosomes early in mitosis. This correlated closely with the asymmetric nucleation of astral microtubules (MTs) by centrosomes, suggesting that astral MT association may be required for ER partitioning by centrosomes. Consistent with this, the ER also associated with astral MTs in meioticDrosophilaspermatocytes and during syncytial embryonic divisions. Disruption of centrosomes in each of these cell types led to improper ER partitioning, demonstrating the critical role for centrosomes and associated astral MTs in this process. Importantly, we show that the ER also associated with astral MTs in cultured human cells, suggesting that this centrosome/astral MT-based partitioning mechanism is conserved across animal species.
Exploring the evolution of a trade-off between vigilance and foraging in group-living organisms
Authors: Olson Randal S. , Haley Patrick B. , Dyer Fred C. , Adami Christoph
Published: September 2015

Even though grouping behaviour has been actively studied for over a century, the relative importance of the numerous proposed fitness benefits of grouping remain unclear. We use a digital model of evolving prey under simulated predation to directly explore the evolution of gregarious foraging behaviour according to one such benefit, the ‘many eyes’ hypothesis. According to this hypothesis, collective vigilance allows prey in large groups to detect predators more efficiently by making alarm signals or behavioural cues to each other, thereby allowing individuals within the group to spend more time foraging. Here, we find that collective vigilance is sufficient to select for gregarious foraging behaviour as long there is not a direct cost for grouping (e.g. competition for limited food resources), even when controlling for confounding factors such as the dilution effect. Furthermore, we explore the role of the genetic relatedness and reproductive strategy of the prey and find that highly related groups of prey with a semelparous reproductive strategy are the most likely to evolve gregarious foraging behaviour mediated by the benefit of vigilance. These findings, combined with earlier studies with evolving digital organisms, further sharpen our understanding of the factors favouring grouping behaviour.
Why pair? Evidence of aggregative mating in a socially monogamous marine fish (Siganus doliatus, Siganidae)
Authors: Fox Rebecca J. , Bellwood David R. , Jennions Michael D.
Published: September 2015

Many species live in stable pairs, usually to breed and raise offspring together, but this cannot be assumed. Establishing whether pairing is based on mating, or an alternative cooperative advantage, can be difficult, especially where species show no obvious sexual dimorphism and where the act of reproduction itself is difficult to observe. In the tropical marine fishes known as rabbitfish (Siganidae), half of extant species live in socially monogamous, territorial pairs. It has been assumed that partnerships are for mating, but the reproductive mode of pairing rabbitfish is currently unconfirmed. Using passive acoustic telemetry to track movements of fishes belonging to one such species (Siganus doliatus), we provide the first evidence that paired adult fish undertake highly synchronized migrations with multiple conspecifics on a monthly cycle. All tagged individuals migrated along the same route in three consecutive months and were absent from home territories for 2–3 days just after the new moon. The timing and directionality of migrations suggest thatS. doliatusmay form spawning aggregations, offering the potential for exposure to multiple reproductive partners. The finding raises fundamental questions about the basis of pairing, mate choice and partnership longevity in this family.
Quantifying uncertainty in the phylogenetics of Australian numeral systems
Authors: Zhou Kevin , Bowern Claire
Published: September 2015

Researchers have long been interested in the evolution of culture and the ways in which change in cultural systems can be reconstructed and tracked. Within the realm of language, these questions are increasingly investigated with Bayesian phylogenetic methods. However, such work in cultural phylogenetics could be improved by more explicit quantification of reconstruction and transition probabilities. We apply such methods to numerals in the languages of Australia. As a large phylogeny with almost universal ‘low-limit' systems, Australian languages are ideal for investigating numeral change over time. We reconstruct the most likely extent of the system at the root and use that information to explore the ways numerals evolve. We show that these systems do not increment serially, but most commonly vary their upper limits between 3 and 5. While there is evidence for rapid system elaboration beyond the lower limits, languages lose numerals as well as gain them. We investigate the ways larger numerals build on smaller bases, and show that there is a general tendency to both gain and replace 4 by combining 2 + 2 (rather than inventing a new unanalysable word ‘four'). We develop a series of methods for quantifying and visualizing the results.
In a warmer Arctic, mosquitoes avoid increased mortality from predators by growing faster
Authors: Culler Lauren E. , Ayres Matthew P. , Virginia Ross A.
Published: September 2015

Climate change is altering environmental temperature, a factor that influences ectothermic organisms by controlling rates of physiological processes. Demographic effects of warming, however, are determined by the expression of these physiological effects through predator–prey and other species interactions. Using field observations and controlled experiments, we measured how increasing temperatures in the Arctic affected development rates and mortality rates (from predation) of immature Arctic mosquitoes in western Greenland. We then developed and parametrized a demographic model to evaluate how temperature affects survival of mosquitoes from the immature to the adult stage. Our studies showed that warming increased development rate of immature mosquitoes (Q10= 2.8) but also increased daily mortality from increased predation rates by a dytiscid beetle (Q10= 1.2–1.5). Despite increased daily mortality, the model indicated that faster development and fewer days exposed to predators resulted in an increased probability of mosquito survival to the adult stage. Warming also advanced mosquito phenology, bringing mosquitoes into phenological synchrony with caribou. Increases in biting pests will have negative consequences for caribou and their role as a subsistence resource for local communities. Generalizable frameworks that account for multiple effects of temperature are needed to understand how climate change impacts coupled human–natural systems.
Genetic perturbation of key central metabolic genes extends lifespan in
Drosophila
and affects response to dietary restriction
Authors: Talbert Matthew E. , Barnett Brittany , Hoff Robert , Amella Maria , Kuczynski Kate , Lavington Erik , Koury Spencer , Brud Evgeny , Eanes Walter F.
Published: September 2015

There is a connection between nutrient inputs, energy-sensing pathways, lifespan variation and aging. Despite the role of metabolic enzymes in energy homeostasis and their metabolites as nutrient signals, little is known about how their gene expression impacts lifespan. In this report, we use P-element mutagenesis in
Drosophila
to study the effect on lifespan of reductions in expression of seven central metabolic enzymes, and contrast the effects on normal diet and dietary restriction. The major observation is that for five of seven genes, the reduction of gene expression extends lifespan on one or both diets. Two genes are involved in redox balance, and we observe that lower activity genotypes significantly extend lifespan. The hexokinases also show extension of lifespan with reduced gene activity. Since both affect the ATP/ADP ratio, this connects with the role of AMP-activated protein kinase as an energy sensor in regulating lifespan and mediating caloric restriction. These genes possess significant expression variation in natural populations, and our experimental genotypes span this level of natural activity variation. Our studies link the readout of energy state with the perturbation of the genes of central metabolism and demonstrate their effect on lifespan.
Adaptation to different host plant ages facilitates insect divergence without a host shift
Authors: Zhang Bin , Segraves Kari A. , Xue Huai-Jun , Nie Rui-E , Li Wen-Zhu , Yang Xing-Ke
Published: September 2015

Host shifts and subsequent adaption to novel host plants are important drivers of speciation among phytophagous insects. However, there is considerably less evidence for host plant-mediated speciation in the absence of a host shift. Here, we investigated divergence of two sympatric sister elm leaf beetles,
Pyrrhalta maculicollis
and
P. aenescens
, which feed on different age classes of the elm
Ulmus pumila
L. (seedling versus adult trees)
.
Using a field survey coupled with preference and performance trials, we show that these beetle species are highly divergent in both feeding and oviposition preference and specialize on either seedling or adult stages of their host plant. An experiment using artificial leaf discs painted with leaf surface wax extracts showed that host plant chemistry is a critical element that shapes preference. Specialization appears to be driven by adaptive divergence as there was also evidence of divergent selection; beetles had significantly higher survival and fecundity when reared on their natal host plant age class. Together, the results identify the first probable example of divergence induced by host plant age, thus extending how phytophagous insects might diversify in the absence of host shifts.
Saturating effects of species diversity on life-history evolution in bacteria
Authors: Fiegna Francesca , Scheuerl Thomas , Moreno-Letelier Alejandra , Bell Thomas , Barraclough Timothy G.
Published: September 2015

Species interactions can play a major role in shaping evolution in new environments. In theory, species interactions can either stimulate evolution by promoting coevolution or inhibit evolution by constraining ecological opportunity. The relative strength of these effects should vary as species richness increases, and yet there has been little evidence for evolution of component species in communities. We evolved bacterial microcosms containing between 1 and 12 species in three different environments. Growth rates and yields of isolates that evolved in communities were lower than those that evolved in monocultures, consistent with recent theory that competition constrains species to specialize on narrower sets of resources. This effect saturated or reversed at higher levels of richness, consistent with theory that directional effects of species interactions should weaken in more diverse communities. Species varied considerably, however, in their responses to both environment and richness levels. Mechanistic models and experiments are now needed to understand and predict joint evolutionary dynamics of species in diverse communities.