bluuebunny/crossref_metadata_2025 huggingface dataset:
Radar coincidence imaging by exploiting the continuity of extended target
Authors: Zhou Xiaoli , Wang Hongqiang , Cheng Yongqiang , Qin Yuliang
Published: May 2016

Radar coincidence imaging (RCI) is a recently developed concept of radar imaging, which introduces the optical coincidence imaging to traditional microwave imaging. Conventional RCI methods ignore the structure information of complex extended target, which limits its applications in high resolution imaging, thus an adaptive clustered sparse Bayesian learning algorithm is proposed in this study. To exploit the continuity of extended target, a hierarchical correlated Gaussian prior model is introduced to take into account both the sparse prior and the cluster prior, and then the algorithm alternates between steps of target reconstruction and parameter optimisation under the variational Bayesian expectation–maximisation framework. Therefore, the reconstruction of each coefficient involves its immediate neighbours, and the parameter indicating the pattern relevance among neighbouring scatterers is updated adaptively during the iterations. Experimental results demonstrate that the proposed algorithm could realise high resolution imaging effectively for extended target.
Orthogonal frequency division multiplexing linear frequency modulation signal design with optimised pulse compression property of spatial synthesised signals
Authors: Li Hui , Zhao Yongbo , Cheng Zengfei , Feng Da‐Zheng
Published: May 2016

Orthogonal frequency division multiplexing (OFDM) linear frequency modulation (LFM) waveform is widely studied due to its application potentials in multiple‐input–multiple‐output (MIMO) radar, but its effective design is still a challenge. Considering the critical role, the pulse compression property of spatial synthesised signals plays in MIMO radar, a detailed analysis is made using OFDM LFM signals, resulting in the radical reasons for the high grating sidelobes. Then, a joint optimisation method for OFDM LFM signal design based on genetic algorithm and sequential quadratic programming is proposed to degrade the sidelobe level dramatically. Furthermore, to nullify the grating sidelobes thoroughly, a modification is performed through optimising the relaxed frequency steps of the OFDM LFM waveform, which involves a balance between sidelobe property and orthogonality. Numerical results validate the theoretic analysis and show the superior performance of the designed OFDM LFM waveforms in pulse compression properties of spatial synthesised signals.
Effects of thickness on switching current for (Pb0.97La0.02)(Zr0.95Ti0.05)O3 antiferroelectric films under thermo‐electric coupled field
Authors: An Kun , Wang Erwei , He Jian , Chou Xiujian , Xue Chenyang , Zhang Wendong
Published: May 2016

Homogeneous and compact antiferroelectric (AFE) (Pb, La)(Zr, Ti)O3 thick films in large area with different thicknesses were successfully fabricated by the sol–gel processing on Pt(111)/Ti/SiO2/Si(100) substrates. The characteristics of switching current of samples with different thicknesses under thermo‐electric coupled field were investigated in detail. The experimental result shows that the peak of switching current density increased with the increase of temperature in three samples. Moreover, it is found that the thickness of the films has a big effect on the current density. Therefore, the peak of switching current density increased with increasing in the thickness at the same temperatures. The maximum switching current density of film with the thickness of 2254 nm is 4.35 × 10−5A/cm2. These results are quite important and necessary for design and preparation of the AFE materials applied on high sensitivity and intelligent micro‐sensors and micro‐actuators.
A cylindrically symmetric “micro-Mott” electron polarimeter
Authors: Clayburn N. B. , Brunkow E. , Burtwistle S. J. , Rutherford G. H. , Gay T. J.
Published: May 2016

A small, novel, cylindrically symmetric Mott electron polarimeter is described. The effective Sherman function, Seff, or analyzing power, for 20 kV Au target bias with a 1.3 keV energy loss window is 0.16 ± 0.01, where uncertainty in the measurement is due primarily to uncertainty in the incident electron polarization. For an energy loss window of 0.5 keV, Seff reaches its maximum value of 0.24 ± 0.02. The device’s maximum efficiency, I/Io, defined as the detected count rate divided by the incident particle rate, is 3.7 ± 0.2 × 10−4 at 20 keV. The figure-of-merit of the device, η, is defined as Seff2IIo and equals 9.0 ± 1.6 × 10−6. Potential sources of false asymmetries due to detector electronic asymmetry and beam misalignment have been investigated. The new polarimeter’s performance is compared to published results for similar compact retarding-field Mott polarimeters, and it is concluded that this device has a relatively large Seff and low efficiency. SIMION® electron trajectory simulations and Sherman function calculations are presented to explain the differences in performance between this device and previous designs. This design has an Seff that is insensitive to spatial beam fluctuations and, for an energy loss window >0.5 keV, negligible background due to spurious ion and X-ray production at the target.
Growth of sinuous waves on thin liquid sheets: Comparison of predictions with experiments
Authors: Majumdar Nayanika , Tirumkudulu Mahesh S.
Published: May 2016

A recent theory [M. S. Tirumkudulu and M. Paramati, “Stability of a moving radial liquid sheet: Time dependent equations,” Phys. Fluids 25(10), 102–107 (2013)] has shown that a radially expanding liquid sheet is unstable to sinuous wave disturbances due to the thinning of the liquid sheet while ignoring the presence of a surrounding gas phase. In this work, we compare the predictions of the aforementioned theory with the measurements of Crapper et al. [“Large amplitude Kelvin-Helmholtz waves on thin liquid sheets,” Proc. R. Soc. London, Ser. A 342(1629), 209–224 (1975)] who measured the amplitude and spatial growth rates of sinuous waves induced in radially expanding liquid sheets produced by fan spray nozzles. The predicted growth rates are remarkably close to the measurements over a range of forcing frequencies and amplitudes even though the experiments were performed in the presence of a surrounding gas phase. This is in contrast to large discrepancies observed by Crapper et al. when the same measurements were compared with the predictions of a spatial stability analysis for a moving liquid sheet that accounts for the inertia of the surrounding gas phase but ignores the thickness variation of the sheet.
Wetting states of superhydrophobic surfaces made of polygonal pores or posts
Authors: Hemeda A. A. , Amrei M. M. , Vahedi Tafreshi H.
Published: May 2016

In this work, a mathematical framework is developed to describe some of the important intermediate wetting states of a superhydrophobic surface between the two extreme states of Cassie and Wenzel. The superhydrophobic surfaces considered here are comprised of sharp-edged polygonal pores or posts. Two different critical pressures are defined in this work, and used to distinguish pinned, partially pinned, and de-pinned air–water interfaces from one another. This information, in particular, is used to develop predictive expressions for the critical pressure and wetted area of the surfaces. Good agreement is observed between the predictions of our expressions and those obtained from numerical calculations or experiment. The work presented here compares the pressure-dependent performances of the superhydrophobic surfaces having different pore or post designs with one another.
A simple counter-flow cooling system for a supersonic free-jet beam source assembly
Authors: Barr M. , Fahy A. , Martens J. , Dastoor P. C.
Published: May 2016

A simple design for an inexpensive, cooled, free-jet beam source is described. The source assembly features an integrated cooling system as supplied by a counter-flow of chilled nitrogen, and is composed primarily of off-the-shelf tube fittings. The design facilitates rapid implementation and eases subsequent alignment with respect to any downstream beamline aperture. The source assembly outlined cools the full length of the stagnation volume, offering temperature control down to 100 K and long-term temperature stability better than ±1 K.
Approximate method for stochastic chemical kinetics with two-time scales by chemical Langevin equations
Authors: Wu Fuke , Tian Tianhai , Rawlings James B. , Yin George
Published: May 2016

The frequently used reduction technique is based on the chemical master equation for stochastic chemical kinetics with two-time scales, which yields the modified stochastic simulation algorithm (SSA). For the chemical reaction processes involving a large number of molecular species and reactions, the collection of slow reactions may still include a large number of molecular species and reactions. Consequently, the SSA is still computationally expensive. Because the chemical Langevin equations (CLEs) can effectively work for a large number of molecular species and reactions, this paper develops a reduction method based on the CLE by the stochastic averaging principle developed in the work of Khasminskii and Yin [SIAM J. Appl. Math. 56, 1766–1793 (1996); ibid. 56, 1794–1819 (1996)] to average out the fast-reacting variables. This reduction method leads to a limit averaging system, which is an approximation of the slow reactions. Because in the stochastic chemical kinetics, the CLE is seen as the approximation of the SSA, the limit averaging system can be treated as the approximation of the slow reactions. As an application, we examine the reduction of computation complexity for the gene regulatory networks with two-time scales driven by intrinsic noise. For linear and nonlinear protein production functions, the simulations show that the sample average (expectation) of the limit averaging system is close to that of the slow-reaction process based on the SSA. It demonstrates that the limit averaging system is an efficient approximation of the slow-reaction process in the sense of the weak convergence.
New insight into the microstructure and doping of unintentionally n-type microcrystalline silicon carbide
Authors: Pomaska Manuel , Köhler Florian , Zastrow Uwe , Mock Jan , Pennartz Frank , Muthmann Stefan , Astakhov Oleksandr , Carius Reinhard , Finger Friedhelm , Ding Kaining
Published: May 2016

Microcrystalline silicon carbide (μc-SiC:H) deposited by hot wire chemical vapor deposition (HWCVD) and plasma-enhanced chemical vapor deposition (PECVD) provide advantageous opto-electronic properties, making it attractive as a window layer material in silicon thin-film and silicon heterojunction solar cells. However, it is still not clear which electrical transport mechanisms yield dark conductivities up to 10−3 S/cm without the active use of any doping gas and how the transport mechanisms are related to the morphology of μc-SiC:H. To investigate these open questions systematically, we investigated HWCVD and PECVD grown layers that provide a very extensive range of dark conductivity values from 10−12 S/cm to 10−3 S/cm. We found out by secondary ion mass spectrometry measurements that no direct correlation exists between oxygen or nitrogen concentrations and high dark conductivity σd, high charge carrier density n, and low activation energy Ea. Higher σd seems to rise from lower hydrogen concentrations or/and larger coherent domain sizes LSiC. On the one hand, the decrease of σd with increasing hydrogen concentration might be due to the inactivation of donors by hydrogen passivation that gives rise to decreased n. On the other hand, qualitatively consistent with the Seto model, the lower σd and lower n might be caused by smaller LSiC, since the fraction of depleted grain boundaries with higher Ea increases accordingly.
A mechanistic interpretation of the resonant wave-particle interaction
Authors: Chim Chi Yung , O'Neil Thomas M.
Published: May 2016

This paper provides a simple mechanistic interpretation of the resonant wave-particle interaction of Landau. For the simple case of a Langmuir wave in a Vlasov plasma, the non-resonant electrons satisfy an oscillator equation that is driven resonantly by the bare electric field from the resonant electrons, and in the case of wave damping, this complex driver field is of a phase to reduce the oscillation amplitude. The wave-particle resonant interaction also occurs in waves governed by 2D E × B drift dynamics, such as a diocotron wave. In this case, the bare electric field from the resonant electrons causes E × B drift motion back in the core plasma, reducing the amplitude of the wave.
Gyrokinetic particle simulation of fast-electron driven beta-induced Aflvén eigenmode
Authors: Cheng Junyi , Zhang Wenlu , Lin Zhihong , Holod Ihor , Li Ding , Chen Yang , Cao Jintao
Published: May 2016

The fast-electron driven beta-induced Alfvén eigenmode (e-BAE) in toroidal plasmas is investigated for the first time using global gyrokinetic particle simulations, where the fast electron is described by the drift kinetic equation. The simulation shows that the e-BAE propagates in the fast electron diamagnetic direction and its polarization is close to an ideal MHD mode. The phase space structure shows that only the fast electron processional resonance is responsible for the e-BAE excitations while fast-ion driven BAE can be excited through all the channels, including transit, bounce, and processional resonance.
Flow-induced polymer translocation through a nanopore from a confining nanotube
Authors: Ding Mingming , Chen Qiaoyue , Duan Xiaozheng , Shi Tongfei
Published: May 2016

We study the flow-induced polymer translocation through a nanopore from a confining nanotube, using a hybrid simulation method that couples point particles into a fluctuating lattice-Boltzmann fluid. Our simulation illustrates that the critical velocity flux of the polymer linearly decreases with the decrease in the size of the confining nanotube, which corresponds well with our theoretical analysis based on the blob model of the polymer translocation. Moreover, by decreasing the size of the confining nanotube, we find a significantly favorable capture of the polymer near its ends, as well as a longer translocation time. Our results provide the computational and theoretical support for the development of nanotechnologies based on the ultrafiltration and the single-molecule sequencing.
X-ray photoelectron spectroscopy analysis of boron defects in silicon crystal: A first-principles study
Authors: Yamauchi Jun , Yoshimoto Yoshihide , Suwa Yuji
Published: May 2016

We carried out a comprehensive study on the B 1s core-level X-ray photoelectron spectroscopy (XPS) binding energies and formation energies for boron defects in crystalline silicon by first-principles calculation with careful evaluation of the local potential boundary condition for the model system using the supercell corresponding to 1000 Si atoms. It is reconfirmed that the cubo-octahedral B12 cluster in silicon crystal is unstable and exists at the saddle point decaying to the icosahedral and S4 B12 clusters. The electrically active clusters without any postannealing of ion-implanted Si are identified as icosahedral B12 clusters. The experimentally proposed threefold coordinated B is also identified as a ⟨001⟩B-Si defect. For an as-doped sample prepared by plasma doping, the calculated XPS spectra for complexes consisting of vacancies and substitutional B atoms are consistent with the experimental spectra. It is proposed that, assuming that the XPS peak at 187.1 eV is due to substitutional B (Bs), the experimental XPS peaks at 187.9 and 186.7 eV correspond to interstitial B at the H-site and ⟨001⟩B-Si defects, respectively. In the annealed samples, the complex of Bs and interstitial Si near the T-site is proposed as a candidate for the experimental XPS peak at 188.3 eV.
Incorporation of dopant impurities into a silicon oxynitride matrix containing silicon nanocrystals
Authors: Ehrhardt Fabien , Ulhaq-Bouillet Corinne , Muller Dominique , Slaoui Abdelilah , Ferblantier Gérald
Published: May 2016

Dopant impurities, such as gallium (Ga), indium (In), and phosphorus (P), were incorporated into silicon-rich silicon oxynitride (SRSON) thin films by the ion implantation technique. To form silicon nanoparticles, the implanted layers were thermally annealed at temperatures up to 1100 °C for 60 min. This thermal treatment generates a phase separation of the silicon nanoparticles from the SRSON matrix in the presence of the dopant atoms. We report on the position of the dopant species within the host matrix and relative to the silicon nanoparticles, as well as on the effect of the dopants on the crystalline structure and the size of the Si nanoparticles. The energy-filtered transmission electron microscopy technique is thoroughly used to identify the chemical species. The distribution of the dopant elements within the SRSON compound is determined using Rutherford backscattering spectroscopy. Energy dispersive X-ray mapping coupled with spectral imaging of silicon plasmons was performed to spatially localize at the nanoscale the dopant impurities and the silicon nanoparticles in the SRSON films. Three different behaviors were observed according to the implanted dopant type (Ga, In, or P). The In-doped SRSON layers clearly showed separated nanoparticles based on indium, InOx, or silicon. In contrast, in the P-doped SRSON layers, Si and P are completely miscible. A high concentration of P atoms was found within the Si nanoparticles. Lastly, in Ga-doped SRSON the Ga atoms formed large nanoparticles close to the SRSON surface, while the Si nanoparticles were localized in the bulk of the SRSON layer. In this work, we shed light on the mechanisms responsible for these three different behaviors.
Negative differential thermal conductance and thermal rectification effects across a graphene-based superconducting junction
Authors: Zhou Xingfei , Zhang Zhi
Published: May 2016

We study the heat transport in a graphene-based normal-superconducting junction by solving the Bogoliubov-de Gennes (BdG) equation. There are two effects, the competitive and cooperative effects, which come from the interaction between the temperature-dependent energy-gap function in the superconducting region and the occupation difference of quasiparticles. It is found that the competitive effect can not only bring the negative differential thermal conductance effect but also the thermal rectification effect. By contrast, the cooperative effect just causes the thermal rectification effect. Furthermore, the thermal rectification ratio and the magnitude of heat current should be seen as two inseparable signs for characterizing the thermal rectification effect. These discoveries can add more application for the graphene-based superconducting junction, such as heat diode and heat transistor, at cryogenic temperatures.
Communication: Adiabatic and non-adiabatic electron-nuclear motion: Quantum and classical dynamics
Authors: Albert Julian , Kaiser Dustin , Engel Volker
Published: May 2016

Using a model for coupled electronic-nuclear motion we investigate the range from negligible to strong non-adiabatic coupling. In the adiabatic case, the quantum dynamics proceeds in a single electronic state, whereas for strong coupling a complete transition between two adiabatic electronic states takes place. It is shown that in all coupling regimes the short-time wave-packet dynamics can be described using ensembles of classical trajectories in the phase space spanned by electronic and nuclear degrees of freedom. We thus provide an example which documents that the quantum concept of non-adiabatic transitions is not necessarily needed if electronic and nuclear motion is treated on the same footing.
A multimode terahertz-Orotron with the special Smith–Purcell radiation
Authors: Liu Weihao , Lu Yalin , Wang Lin , Jia Qika
Published: May 2016

We proposed and investigated a terahertz Orotron, which is based on the recently revealed special Smith–Purcell radiation. It overcomes the main obstacles of the traditional Orotron in the terahertz region—unreachable high starting-current-density and low radiation power. With the experimentally available electron beam and facilities, its average output power can reach hundreds of milliwatts and even several watts in terahertz region, which is many orders of magnitude higher than that of the traditional Orotron. Additionally, it can be controlled to operate in ether the first or the second order mode, and the radiation frequency can extend from 0.1 THz to 1 THz. These remarkable advantages make it a promising terahertz source for practical applications.
Effect of the ratio of maize cob and husk to napier Pakchong 1 silage on nutritive value and in vitro gas production of rumen fluid of Thai native cattle
Authors: Yammuen-art S. , Somrak P. , Phatsara C.
Published: May 2016

The present study evaluated the chemical composition and in vitro ruminal digestibility of napier Pakchong 1 silage combined with maize cob and husk in different ratios. The napier Pakchong 1 grass was harvested at 45 days of maturity. The napier Pakchong 1 grass was ensiled with maize cob and husk at ratios of 1:5, 1:10 and 1:15. Three rumen fistulated Thai native cattle (White Lamphun cattle) with an average weight of 154 ± 4.7 kg were used to determine ruminal digestibility by in vitro gas-production technique. Gas production was recorded after incubating for 2, 4, 8, 12, 24, 48, 72 and 96 h. The microbial biomass yield was determined after incubating for 24 h. DM, NDF and ADF of maize cob and husk mixed with napier Pakchong 1 silage declined by increasing the proportion of napier Pakchong 1 grass, while gas production after 4–10 h of incubating maize cob and husk mixed with napier Pakchong 1 grass increased by increasing the proportion of napier Pakchong 1 grass. The metabolisable energy, organic matter digestibility and microbial biomass yield did not differ among the different ratios. The results of the study suggested a recommended ratio of maize cob and husk to napier Pakchong 1 grass of 1:10. The ensiling fermentation increased the proportion of protein in the roughage, which lead to increased in vitro gas production of roughage.
Canola integration into semi-arid wheat cropping systems of the inland Pacific Northwestern USA
Authors: Pan W. L. , Young F. L. , Maaz T. M. , Huggins D. R.
Published: May 2016

The inland Pacific Northwestern USA (iPNW) wheat-producing region has a diversity of environments and soils, yet it lacks crop diversity and is one of the few semi-arid wheat-growing regions without significant integration of oilseeds. Four major agroecological zones, primarily characterised by water availability, feature distinctly different fallowed and annually cropped systems, each presenting different challenges and opportunities to integrate winter and spring canola. Although major interests in regional energy crops and rotational diversification spurred feasibility research on iPNW canola food, feed and fuel production in the 1970s, commercial canola adaptation has lagged behind other semi-arid wheat regions for various socioeconomic, ecophysiological and agronomic reasons. New federal crop insurance policies will reduce economic risks in new crop adaptation, and oilseed processing facilities are creating new local markets. Although canola management largely relies on wheat farm equipment, agronomic approaches require strategic adjustments to account for physiological differences between canola and cereals including seed size, seedling morphology and responses to temperature extremes. Climate change predictions for the region threaten to exacerbate current hot and dry summers and research aims to develop and adapt flexible winter and spring canola-based systems to regional water and temperature stressors in each zone. Adaptation will require novel planting, fertilisation and weed control strategies to successfully establish improved winter canola cultivars in hot dry summers that survive cold winters, and spring canola cultivars direct-seeded in cool wet springs. The adaptation of winter and spring canola will somewhat mirror the rotational placement of winter and spring cereals within each zone. Economic analysis of oilseed break crop benefits such as weed and disease control will help to demonstrate the medium-term economic benefits of crop diversification to support the growth of a regional canola industry in the iPNW.
Nitrogen responses of canola in low to medium rainfall environments of Western Australia
Authors: Seymour Mark , Sprigg Sally , French Bob , Bucat Jackie , Malik Raj , Harries Martin
Published: May 2016

Canola (Brassica napus L.) is widely grown throughout all rainfall zones in south-western Australia. Yields are low by world standards, and variable in low-rainfall (<350 mm annual rainfall) and medium-rainfall (350–450 mm) zones, so that minimising production costs is a major consideration for growers in these areas. One of the major input costs is nitrogen (N) fertiliser. Fifteen N rate × application time × canola plant-type experiments were conducted in the low- and medium-rainfall zones between 2012 and 2014. In most experiments, five rates of N were tested, of ranges 0–75, 0–100, or 0–150 kg N/ha. Nitrogen was applied at four different times (seeding, or 4, 8 or 12 weeks after sowing) or split between these timings. Each experiment compared triazine-tolerant (TT), open-pollinated (OP) canola with Roundup Ready (RR) hybrid canola, and one experiment included TT hybrid and RR OP canola types. On average, RR hybrid produced 250 kg/ha, or 23% more seed and 2.2% more oil than TT OP canola, and the average gross margin of RR hybrid was AU$65/ha more than TT OP. However, seed yield and gross margin differences between RR hybrid and TT OP canola were reduced when seed yields were <1400 kg/ha.
Canola growth (dry matter) and seed yield responded positively to N fertiliser in most experiments, with 90% of maximum seed yield achieved at an average of 46 kg N/ha (s.e. 6). However, 90% of maximum gross margin was achieved at a lower average N rate of 17 kg N/ha, due primarily to the relatively small yield increase compared with the reduction in concentration of oil in the seed with N applied. Because canola growers of south-western Australia are now paid an uncapped premium for canola grain with oil concentration >42%, decreases in oil percentage have a significant financial effect, and recommended rates of N should be lower than those calculated to optimise seed yield. In 80% of cases, the first 10 kg N/ha applied provided a return on investment in N >$1.50 for every $1 invested. The next 20 kg N/ha applied provided a return on investment of $1.25 for every $1 invested 80% of the time, and further increases would most likely break even. The timing of N application had a minor effect on yield, oil and financial returns, but delaying N application would allow farmers to reduce risk under poor conditions by reducing or eliminating further inputs. Overall, our work demonstrates that a conservative approach to N supply mindful of the combined impacts of N on yield and oil is necessary in south-western Australia and that split and delayed applications are a viable risk-management strategy.
Canola yield improvement on the Canadian Prairies from 2000 to 2013
Authors: Morrison M. J. , Harker K. N. , Blackshaw R. E. , Holzapfel C. J. , O'Donovan J. T.
Published: May 2016

During the period from 2000 to 2013, average canola yields from Canadian farms increased from 1330 to 2025 kg ha–1, or 54 kg ha–1 year–1. The objective of this review was to propose likely reasons behind this increase by examining genotypic, environmental and agronomic factors. During this period, hybrid canola cultivars with herbicide tolerance (HY-HT) expanded from 80% to >95% of the area sown to canola. Genetic gain from switching from open-pollinated cultivars to HY-HT cultivars was estimated to account for 32 kg ha–1 year–1. When some key environmental factors were examined, there were no significant linear changes in growing season temperature, although the linear increase in April and May precipitation was significant and likely responsible for an increase of 12 kg ha–1 year–1. When coupled with the yield increase from changes in atmospheric CO2 (3 kg ha–1 year–1), the environment was estimated to account for ~15 kg ha–1 year–1. Ignoring all main-factor interactions, changes due to management accounted for the remainder, or 7 kg ha–1 year–1. The expanded use of HY-HT varieties has resulted in better weed control, and an increase in the use of minimum tillage, leading to greater water-use efficiency and higher yield. It is likely that many of the effects of changes in management were hidden in the interaction with genotype and environment main effects. It is difficult to estimate these interactions without designing experiments to do so. The design and implementation of experiments to understand the interaction among main factors should be a priority. Future yield targets of 25 Mt canola by 2025 will require an increase in yield per ha beyond the current rate, or an increase in the land seeded to canola, or a combination of the two factors. Continued progress with canola yield depends on active plant-breeding programs, agronomic research using new varieties, favourable environmental conditions, and high world commodity prices.
Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic
TP53
mutations in noncancerous tissues
Authors: Krimmel Jeffrey D. , Schmitt Michael W. , Harrell Maria I. , Agnew Kathy J. , Kennedy Scott R. , Emond Mary J. , Loeb Lawrence A. , Swisher Elizabeth M. , Risques Rosa Ana
Published: May 2016

Significance

The detection of rare tumor-specific somatic mutations in “liquid biopsies” is limited by the high error rate of DNA sequencing technologies. By sequencing peritoneal fluid from women with high-grade serous ovarian cancer, we demonstrate that duplex sequencing, currently the most accurate sequencing technology, is able to detect one cancer cell among tens of thousands of normal cells. This unprecedented sensitivity also revealed a striking prevalence of extremely low frequency
TP53
mutations in normal tissue. Women with and without cancer harbored
TP53
mutations of pathogenic consequences, both in peritoneal fluid and peripheral blood. These mutations likely represent a premalignant mutational background that accumulates in cancer and aging.
Nagorny Karabakh conflict: Prospects for conflict transformation
Authors: Ayunts Artak , Zolyan Mikayel , Zakaryan Tigran
Published: May 2016

The article explores the current stalemate in the Nagorny Karabakh conflict, and perspectives for conflict transformation. As the conflict has remained dormant for more than 20 years, the political systems of the countries engaged in the conflict have adjusted to the conflict situation. The conflict is often used by the political elites in order to legitimize their power, consolidate support, marginalize opponents, and neutralize democratizing pressures. Since the status quo serves the interests of the authorities, the ruling regimes do not have strong incentives to seek conflict resolution. In these conditions, conflict transformation approaches are considered a necessary means to deal with the conflict. Given that political elites have little incentive to implement such transformation, civil society actors come increasingly to the fore. Only through multitrack initiatives supported by civil society actors, we argue, can conflict transformation practices advance and subsequently bring peace to the region.
Association of Liver Hemangiosarcoma and Secondary Iron Overload in B6C3F1 Mice—The National Toxicology Program Experience
Authors: Nyska Abraham , Haseman Joseph K. , Kohen Roni , Maronpot Robert R.
Published: May 2016

The literature evidencing the role of iron in promoting a range of neoplasms in humans and animals prompted us to search for a possible association between chemically induced hemosiderosis and hemangiosarcomas in the liver of mice in selected studies conducted by the National Toxicology Program (NTP). Its historical control database was examined for studies in which treatment-related liver hemangiosarcoma was noted; 130 consecutive NTP studies in B6C3F1 mice from Technical Report (TR)-340 to TR-493 were evaluated. Three compounds (2-butoxyethanol, p-nitroaniline, and para-chloroaniline) were associated with a relatively high incidence of Kupffer cell pigmentation consisting of hemosiderin in both sexes; only the male mice developed a relatively low incidence of treatment-related hemangiosarcoma. With a fourth compound (o-nitroanisole), a relatively low incidence (16/50, high-dose males) of chemical-related hemosiderosis was noted, with no associated increase of hemangiosarcoma. Two chemicals (pentachlorophenol and tetrafluoroethylene) increased the incidence of liver hemangiosarcoma in male and female mice, with no increase in Kupffer cell pigmentation. The overall association between liver hemangiosarcoma and Kupffer cell pigmentation was highly significant (p < 0.001). The cause for hemosiderosis in all cases was the erythrocytic hemolytic effect of the compounds. The reason for the sex-increased susceptibility for development of hemangiosarcoma is unknown but may be due to a hormone-related, reduced antioxidative defensive capacity through modulation of the activities of antioxidative enzymes.
On a conjecture of Kimoto and Wakayama
Authors: Long Ling , Osburn Robert , Swisher Holly
Published: May 2016

We prove a conjecture due to Kimoto and Wakayama from 2006 concerning Apéry-like numbers associated to a special value of a spectral zeta function. Our proof uses hypergeometric series and

p
p

-adic analysis.
DOGMA: domain-based transcriptome and proteome quality assessment
Authors: Dohmen Elias , Kremer Lukas P.M. , Bornberg-Bauer Erich , Kemena Carsten
Published: May 2016

Motivation: Genome studies have become cheaper and easier than ever before, due to the decreased costs of high-throughput sequencing and the free availability of analysis software. However, the quality of genome or transcriptome assemblies can vary a lot. Therefore, quality assessment of assemblies and annotations are crucial aspects of genome analysis pipelines.

Results: We developed DOGMA, a program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides information about domain content for further analysis. DOGMA provides a very fast way to do quality assessment within seconds.

Availability and Implementation: DOGMA is implemented in Python and published under GNU GPL v.3 license. The source code is available on https://ebbgit.uni-muenster.de/domainWorld/DOGMA/ .

Contacts:  e.dohmen@wwu.de or c.kemena@wwu.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades
Authors: Wren Jonathan D.
Published: May 2016

Motivation : To analyze the relative proportion of bioinformatics papers and their non-bioinformatics counterparts in the top 20 most cited papers annually for the past two decades.

Results : When defining bioinformatics papers as encompassing both those that provide software for data analysis or methods underlying data analysis software, we find that over the past two decades, more than a third (34%) of the most cited papers in science were bioinformatics papers, which is approximately a 31-fold enrichment relative to the total number of bioinformatics papers published. More than half of the most cited papers during this span were bioinformatics papers. Yet, the average 5-year JIF of top 20 bioinformatics papers was 7.7, whereas the average JIF for top 20 non-bioinformatics papers was 25.8, significantly higher ( P  < 4.5 × 10 −29 ). The 20-year trend in the average JIF between the two groups suggests the gap does not appear to be significantly narrowing. For a sampling of the journals producing top papers, bioinformatics journals tended to have higher Gini coefficients, suggesting that development of novel bioinformatics resources may be somewhat ‘hit or miss’. That is, relative to other fields, bioinformatics produces some programs that are extremely widely adopted and cited, yet there are fewer of intermediate success.

Contact : jdwren@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
RCP: a novel probe design bias correction method for Illumina Methylation BeadChip
Authors: Niu Liang , Xu Zongli , Taylor Jack A.
Published: May 2016

Motivation: The Illumina HumanMethylation450 BeadChip has been extensively utilized in epigenome-wide association studies. This array and its successor, the MethylationEPIC array, use two types of probes—Infinium I (type I) and Infinium II (type II)—in order to increase genome coverage but differences in probe chemistries result in different type I and II distributions of methylation values. Ignoring the difference in distributions between the two probe types may bias downstream analysis.

Results: Here, we developed a novel method, called Regression on Correlated Probes (RCP), which uses the existing correlation between pairs of nearby type I and II probes to adjust the beta values of all type II probes. We evaluate the effect of this adjustment on reducing probe design type bias, reducing technical variation in duplicate samples, improving accuracy of measurements against known standards, and retention of biological signal. We find that RCP is statistically significantly better than unadjusted data or adjustment with alternative methods including SWAN and BMIQ.

Availability: We incorporated the method into the R package ENmix , which is freely available from the Bioconductor website ( https://www.bioconductor.org/packages/release/bioc/html/ENmix.html ).

Contact:  niulg@ucmail.uc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Metallo-β-Lactamase (MBL)-Producing Enterobacteriaceae in United States Children
Authors: Logan Latania K. , Bonomo Robert A.
Published: May 2016

Metallo-β-lactamases (MBLs) are emerging as the most notable resistance determinants in Enterobacteriaceae. In many cases, the genes encoding MBLs are part of complex, mobile genetic elements that carry other resistance determinants. In the United States, there are increasing reports of MBL-producing Enterobacteriaceae, with New Delhi MBLs (NDMs) accounting for the majority of transmissible MBL infections. Many infections caused by NDM-producing bacteria are associated with international travel and medical tourism. However, little recognition of the introduction of MBL-producing Enterobacteriaceae into the pediatric community has followed. Reports suggest that this occurred as early as 2002. Here, we reflect on the unwelcome emergence of MBL-producing Enterobacteriaceae in US children and the available clinical and molecular data associated with spread. Since 2002, there have been disturbing reports that include the most readily transmissible MBLs, blaIMP, blaVIM, and blaNDM types. In the majority of children with available data, a history of foreign travel is absent.
Genetic evidence for natural selection in humans in the contemporary United States
Authors: Beauchamp Jonathan
Published: May 2016

Recent findings from molecular genetics now make it possible to test directly for natural selection by analyzing whether genetic variants associated with various phenotypes have been under selection. I leverage these findings to construct polygenic scores that use individuals’ genotypes to predict their body mass index, educational attainment (EA), glucose concentration, height, schizophrenia, total cholesterol, and (in females) age at menarche. I then examine associations between these scores and fitness to test whether natural selection has been occurring. My study sample includes individuals of European ancestry born between 1931 and 1953 in the Health and Retirement Study, a representative study of the US population. My results imply that natural selection has been slowly favoring lower EA in both females and males, and are suggestive that natural selection may have favored a higher age at menarche in females. For EA, my estimates imply a rate of selection of about -1.5 months of education per generation (which pales in comparison with the increases in EA observed in contemporary times). Though they cannot be projected over more than one generation, my results provide additional evidence that humans are still evolving—albeit slowly, especially when compared to the rapid secular changes that have occurred over the past few generations due to cultural and environmental factors.
Lysis, Lysogeny, and Virus-Microbe Ratios
Authors: Weitz Joshua S. , Beckett Stephen J. , Brum Jennifer R. , Cael B. B. , Dushoff Jonathan
Published: May 2016

We show that neither the Piggyback-the-Winner model nor coral reef virome data presented in Knowles et al. [1] support a mechanistic link between increases in lysogeny, suppression of lysis, and the decline of the virus-to-microbial cell ratio (VMR) at high microbial cell densities across environmental and human-associated systems.
Estimating effective population size from temporal allele frequency changes in experimental evolution
Authors: Jónás Ágnes , Taus Thomas , Kosiol Carolin , Schlötterer Christian , Futschik Andreas
Published: May 2016

The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-termNe. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related toNe. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-Seq). Pool-Seq is cost-effective and outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling increasing the estimated allele frequency variance. We propose a new estimator ofNe, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurateNeestimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wideNeestimates, we extend our method using a recursive partitioning approach to estimateNelocally along the chromosome. Since type I error is accounted for, our method permits the identification of genomic regions that differ significantly inNe. We present an application to Pool-Seq data from experimental evolution withDrosophila, and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R-package athttps://github.com/ThomasTaus/Nest.
Two tautomeric forms of 2-amino-5,6-dimethylpyrimidin-4-one
Authors: Hall Victoria M. , Bertke Jeffery A. , Swift Jennifer A.
Published: May 2016

Derivatives of 4-hydroxypyrimidine are an important class of biomolecules. These compounds can undergo keto–enol tautomerization in solution, though a search of the Cambridge Structural Database shows a strong bias toward the 3H-keto tautomer in the solid state. Recrystallization of 2-amino-5,6-dimethyl-4-hydroxypyrimidine, C6H9N3O, from aqueous solution yielded triclinic crystals of the 1H-keto tautomer, denoted form (I). Though not apparent in the X-ray data, the IR spectrum suggests that small amounts of the 4-hydroxy tautomer are also present in the crystal. Monoclinic crystals of form (II), comprised of a 1:1 ratio of both the 1H-keto and the 3H-keto tautomers, were obtained from aqueous solutions containing uric acid. Forms (I) and (II) exhibit one-dimensional and three-dimensional hydrogen-bonding motifs, respectively.
Crystal structure of phenyl 2,4,5-trichlorobenzenesulfonate
Authors: Riley Sean , Staples Richard J. , Biros Shannon M. , Ngassa Felix N.
Published: May 2016

The title compound, C12H7Cl3O3S, was synthesizedviaa nucleophilic substitution reaction between phenol and 2,4,5-trichlorobenzenesulfonyl chloride. The two aryl rings are orientedgaucheto one another around the sulfonate S—O bond, with a C—S—O—C torsion angle of −70.68 (16)°, and the two rings are inclined to one another by 72.40 (7)°. In the crystal, molecules are linkedviavarious C—Cl...π interactions, forming ribbons propagating along [100]. Neighboring ribbons are linked by a weak C—Cl...π interaction, forming layers parallel to (010).
(E)-2-Phenyl-N-(thiophen-2-ylmethylidene)imidazo[1,2-a]pyridin-3-amine
Authors: Elaatiaoui Abdelmalik , Elkalai Fouad , Benchat Noureddine , Saadi Mohamed , El Ammari Lahcen
Published: May 2016

The asymmetric unit of the title compound, C18H13N3S, is build up from two independent molecules slightly inclined to each other. In each molecule, the imidazo[1,2-a]pyridine ring system is almost planar, with the largest deviation from the mean plane being 0.022 (1) Å in the first molecule and 0.018 (1) Å in the second molecule. The fused-ring system belonging to the first molecule makes dihedral angles of 24.06 (7) and 40.52 (8)° with the thiophenyl and phenyl rings, respectively. The corresponding values observed in the second molecule are nearly the same, namely 25.20 (7) and 38.99 (7)°, respectively. The dihedral angle between the thiophenyl and phenyl rings is 63.47 (9)° in the first molecule and 47.49 (9)° in the second. The cohesion of the crystal structure is ensured by two C—H...N hydrogen bonds between molecules and by three C—H...π interactions, forming a three-dimensional network.
(E)-4-Hydroxy-6-methyl-3-[1-(2-phenylhydrazinylidene)ethyl]-2H-pyran-2-one
Authors: Rahmouni Samra , Djedouani Amel , Touzani Rachid , Fleutot Solenne , Bendaas Abderrahmen
Published: May 2016

The title compound, C14H14N2O3, crystallized with three crystallographically independent molecules (A,BandC) in the asymmetric unit. The three molecules each have anEconformation about the C=N bond but differ in the orientation of the phenyl and pyran rings. The dihedral angles between the phenyl and pyran ring planes are 14.30 (1), 28.38 (1) and 25.58 (1)° in moleculesA,BandC, respectively. There is an intramolecular O—H...N hydrogen bond in each molecule with anS(6) ring motif. In the crystal, molecules are linked by N—H...O and C—H...O hydrogen bonds, forming layers parallel to (001), enclosingR22(8) andR33(21) ring motifs. The layers are linkedviaC—H...π interactions, forming bilayers, which are joined by a further C—H...π interaction, forming a three-dimensional structure.
Public Information Precision and Coordination Failure: An Experiment
Authors: BANERJEE SANJAY , MAIER MICHAEL
Published: May 2016

More precise public disclosure reduces uncertainty about economic fundamentals, but it can increase uncertainty about other agents' actions, leading to coordination failure. We conducted a laboratory experiment to study the effects of public information precision and strategic complementarity on coordination failure. Information precision is operationalized in terms of “granularity” (level of detail). We found that (1) granular public disclosure, which is disaggregated and precise, increases the likelihood of coordination failure and decreases coordination efficiency when public information is pessimistic about future economic prospects; (2) the deleterious effect of granular disclosure is stronger when strategic complementarity is high; and (3) higher levels of strategic complementarity decrease coordination efficiency. Overall, the observed likelihood of coordination failure is higher and coordination efficiency is lower than predicted by theory. Our findings have implications for the Federal Reserve's decision to publicly disclose detailed stress test results for distressed banks, and the debate on whether the Public Company Accounting Oversight Board should publicly release reports on firm‐specific quality‐control deficiencies of audit firms.