bluuebunny/crossref_metadata_2025 huggingface dataset:
Atypical temperature-dependence of symmetry transformation observed in a uranyl phosphonate
Authors: Zheng Tao , Gao Yang , Gui Daxiang , Chen Lanhua , Sheng Daopeng , Diwu Juan , Chai Zhifang , Albrecht-Schmitt Thomas E. , Wang Shuao
Published: May 2016

The first example of phase transformation from a centrosymmetric space group at LT to a chiral space group at HT is reported, which was clearly resolved in a single-crystal-to-single-crystal manner in a 3D uranyl(vi) phosphonate compound.
Tuning the reactivity of Sp1 zinc fingers with platinum complexes
Authors: Du Zhifeng , de Paiva Raphael E. F. , Qu Yun , Farrell Nicholas
Published: May 2016

The microenvironment around a zinc finger coordination unit affects the reactivity of apparently similar ZFs with Lewis acid platinum electrophiles. The unique dicysteine-bridged dinuclear platinum unit is the product of the reaction of [PtCl2(en)] and the F3 of the transcription factor Sp1.
Single-ion magnet behaviour in mononuclear and two-dimensional dicyanamide-containing cobalt(ii) complexes
Authors: Świtlicka-Olszewska Anna , Palion-Gazda Joanna , Klemens Tomasz , Machura Barbara , Vallejo Julia , Cano Joan , Lloret Francesc , Julve Miguel
Published: May 2016

The magneto-structural features of one mononuclear and two layered Co(ii) complexes being new examples of Single-Ion Magnets (SIMs) are reported.
Orthophosphate-P in the nutrient impacted River Taw and its catchment (SW England) between 1990 and 2013
Authors: Tappin Alan D. , Comber Sean , Worsfold Paul J.
Published: May 2016

Excess dissolved phosphorus (as orthophosphate-P) contributes to reduced river water quality within Europe and elsewhere.
A direct and vicinal functionalization of the 1-methyl-2-quinolone framework: 4-alkoxylation and 3-chlorination
Authors: Hao Feiyue , Asahara Haruyasu , Nishiwaki Nagatoshi
Published: May 2016

Bis(functionalization), 4-alkoxylation and 3-chlorination, of the 1-methyl-2-quinolone framework was achieved by a sequential treatment of 3-nitrated 2-quinolones with sodium alkoxide and NCS.
Highly enantioselective synthesis of dihydrocoumarin-fused dihydropyrans via the phosphine-catalyzed [4 + 2] annulation of allenones with 3-aroylcoumarins
Authors: Han Xiaoyu , Ni Huanzhen , Chan Wai-Lun , Gai Xikun , Wang Yongjiang , Lu Yixin
Published: May 2016

Phosphine-catalyzed [4 + 2] annulation between 3-aroylcoumarins and allenones has been developed.
Ribosome-inactivating proteins (RIPs) and their important health promoting property
Authors: Wang Shuzhen , Li Zhiliang , Li Shiming , Di Rong , Ho Chi-Tang , Yang Guliang
Published: May 2016

Ribosome-inactivating proteins (RIPs), widely present in plants, certain fungi and bacteria, can inhibit protein synthesis by removing one or more specific adenine residues from the large subunit of ribosomal RNAs (rRNAs).
Assessment of gas production from natural gas hydrate using depressurization, thermal stimulation and combined methods
Authors: Song Yongchen , Zhang Lunxiang , Lv Qin , Yang Mingjun , Ling Zheng , Zhao Jiafei
Published: May 2016

The largest sources of hydrocarbons worldwide are distributed in the permafrost and submarine in the form of methane hydrates, but exploitation of these hydrocarbons is still years away from industrial production; thus, further research is needed.
Facile one pot synthesis of mesoporous organic–inorganic hybrid aluminosilicate spheres with ultra-high aluminium contents and their enhanced adsorption behavior for methylene blue
Authors: Zeng Shangjing , Wang Runwei , Zhang Zongtao , Qiu Shilun
Published: May 2016

An facile approach to synthesize mesoporous organo-aluminosilicate spheres with high aluminium content has been developed under static conditions.
Improved H2 uptake capacity of transition metal doped benzene by boron substitution
Authors: Deshmukh Amol , Konda Ravinder , Kalamse Vijayanand , Chaudhari Ajay
Published: May 2016

The effect of boron substitution on hydrogen storage capacity of transition metal (TM) doped benzene is studied using density functional theory and the second order Møller–Plesset method with aug-cc-pVDZ basis set.
Covalent immobilization of KR-12 peptide onto a titanium surface for decreasing infection and promoting osteogenic differentiation
Authors: Nie Bin'en , Ao Haiyong , Chen Chi , Xie Kai , Zhou Jianliang , Long Teng , Tang Tingting , Yue Bing
Published: May 2016

Covalent immobilization of KR-12 peptide onto titanium surface for anti-bacteria and promoting osteogenic differentiation.
A facile approach for the fabrication of nano-attapulgite/poly(vinyl pyrrolidone)/biopolymers core–sheath ultrafine fibrous mats for drug controlled release
Authors: Zhu Tonghe , Yu Kui , Bhutto M. Aqeel , Wang Juan , Shen Wei , Song Wei , Zhou Xiangxiang , EI-Hamshary Hany , Al-Deyab Salem S. , Mo Xiumei
Published: May 2016

Herein, we report a facile method for the fabrication of flurbiprofen axetil (FA)-loaded core–sheath composite ultrafine fibers for drug sustained release.
In situ growth of biocidal AgCl crystals in the top layer of asymmetric polytriazole membranes
Authors: Villalobos Luis Francisco , Chisca Stefan , Cheng Hong , Hong Pei-Ying , Nunes Suzana , Peinemann Klaus-Viktor
Published: May 2016

Scalable fabrication strategies to concentrate biocidal materials in only the surface of membranes are highly desirable.
Kinetic analysis of Fe3+reduction coupled with nitrate removal by Klebsiella sp. FC61 under different conditions
Authors: Su Jun feng , Cheng Ce , Ma Fang , Huang Ting lin , Lu Jin suo , Shao Si cheng
Published: May 2016

Klebsiellasp. FC61, a newly found iron-reducing bacterium, has the ability of simultaneously reducing Fe3+and nitrate under different pH and temperature conditions.
Linear polarisation property and fusion method for target recognition in passive millimetre‐wave polarimetric imaging
Authors: Cheng Yayun , Hu Fei , Gui Liangqi , Su Jinlong , Qi Bo , Liu Siyuan , Huang Manman
Published: May 2016

The millimetre‐wave (mmW) linear polarisation property of a typical stereoscopic object is investigated theoretically. The mmW brightness temperatures (BTs) of the target at different linear polarisations are simulated using ray tracing. Based on the distribution characteristics of linear polarisation images, a linear polarisation fusion (LPF) method is presented to improve the BT contrast between the target area and the background area. The simulation results indicate that the LPF method is capable for achieving good image quality to improve the ability of recognising the target.
Constant time‐delay control technique for switching dc–dc converters
Authors: Wang Jinping , Hou Liangkui , Bao Bo‐Cheng , He Yigang
Published: May 2016

A novel constant time‐delay control technique for switching dc–dc converters is presented. The controller with simple implementation only consists of a comparator and a delay module. Compared output voltage with a reference voltage and then delayed for a preset time interval, a control pulse for driving main power switch is finally generated. Taking constant time‐delay controlled buck converter as an example, theoretical analyses and PSIM circuit simulations are performed, which indicates that the proposed control technique has the advantages including well regulation, fast transient response and robust stability.
Graph‐based approach to scene text localisation and tracking in videos
Authors: Kim Y.G. , Koo H.I.
Published: May 2016

A text localisation and tracking method is presented that finds text‐regions in videos and assigns unique IDs to their trajectories. For the goal, a graph‐based framework that can work with existing text detection methods is developed. To be precise, graphs are built where vertices are image‐level text detection results and edges represent the correspondence scores of the vertices. From these graphs, text‐region trajectories by using the graph‐cut algorithm are extracted. This approach allows considering false positives and misses, as well as their patch‐based tracking results at the same time, and text trajectories are reliably extracted. Finally, the results are refined by interpolating misses and filtering out false positives. The proposed method is submitted to the International Conference on Document Analysis and Recognition 2015 robust reading competition (video text localisation) and the method showed the best performance in terms of CLEAR MOT metrics and was ranked third place according to VACE metrics among the seven participating methods.
2.5 mW 2.73 GHz non‐overlapping multi‐phase clock generator with duty‐cycle correction in 0.13 µm CMOS
Authors: Yu Xiao‐Peng , Fang Yun , Shi Zheng
Published: May 2016

A high‐speed low power multi‐phase clock generator with a simple duty‐cycle correction circuit is presented. By adding tail transistors driven by the out‐phase signal as a discharge path to correct the phase overlapping in the conventional design, 25% duty cycle multi‐phase clocks are obtained with <1° phase error. Thanks to this simple topology, the proposed work is featured with fast‐speed, low power with a small silicon area. Fabricated in a 0.13 µm RF CMOS process, the proposed clock generator has a measured operating frequency up to 2.73 GHz with a maximum power consumption of 2.5 mW from a 1.2 V supply.
Optimisation of subcarrier intensity modulation binary phase‐shift keying free space optical link with avalanche photodiode receiver influenced by gamma–gamma atmospheric turbulence and pointing errors
Authors: Petkovic Milica I. , Milic Dejan N. , Djordjevic Goran T.
Published: May 2016

This study presents the average bit error rate (BER) performance analysis of free space optical (FSO) systems employing subcarrier intensity modulation with binary phase‐shift keying and avalanche photodiode (APD) receiver. Intensity fluctuations of received optical signal are assumed to originate from both the gamma–gamma atmospheric turbulence and pointing errors. Besides theoretical derivation of the average BER expression, numerical integration is performed assuming specified relative calculation errors. Numerical results are presented and validated by Monte Carlo simulations. Furthermore, closed‐form expressions are derived for thermal noise and shot noise limited conditions, which represent special cases of the system under investigation. On the basis of the presented results, effects of the FSO link and receiver parameters on BER performance are investigated and discussed. It is shown that optimal values of laser beam waist and average APD gain exist for minimising the average BER. The optimal values of laser beam waist depend strongly on the normalised jitter standard deviation, while the optimal values of APD gain are mostly dependent on receiver noise temperature, bit rate and atmospheric conditions.
Detection of current transformer saturation based on variational mode decomposition analysis
Authors: Abdoos Ali Akbar
Published: May 2016

Sometimes, current transformers (CTs) are saturated in power systems due to increase of flux passing through the CT core. The distorted CT secondary current can lead to maloperation of protective relays. In this study, a new algorithm is proposed for detection of saturation interval by analysing secondary current signal using variational mode decomposition (VMD). The VMD can decompose signals into different modes which are concentrated around centre frequencies. The start and end points of saturation regions are estimated by using decomposed modes signals. Comprehensive simulations are implemented in PSCAD/EMTDC environment while the main parameters which have direct effect on saturation levels are considered in simulation studies. The performance of the proposed method is evaluated in different conditions: light, moderate, severe and AC CT saturation conditions. The promising obtained results of real data test show that the proposed method can detect the CT saturation time intervals with high accuracy in practical applications.
Numerical approach to estimate the maximum power point of a photovoltaic array
Authors: Sahu Himanshu Sekhar , Nayak Sisir Kumar
Published: May 2016

This study presents a novel approach to estimate the maximum power point (MPP) of a photovoltaic (PV) array on an hourly basis using meteorological data. The estimation of MPP of a PV array based on its characteristic equation is done by using Levenberg–Marquardt (LM) method. The monthly averaged daily and hourly global solar irradiation during sunshine hours of Guwahati city is estimated by taking relative humidity and ambient temperature data using empirical relations. The actual and estimated maximum powers of a PV array of monthly averaged daily and hourly basis is calculated using MATLAB. It is demonstrated that each of the estimated maximum power of a PV array on an hourly basis is nearly equal to each of the actual maximum power. The MPP of a PV module estimated by the LM method is validated with the actual and experimental results. A comparative study of MPP of a PV module estimated from the proposed method with perturb‐and‐observe based on proportional–integral, genetic algorithm and Gauss–Seidel is performed. The performance of the proposed algorithm for estimation of MPP of a PV array ensures the accuracy and faster convergence.
Synchrophasor measurement‐based correlation approach for dominant mode identification in bulk power systems
Authors: Jiang Tao , Bai Linquan , Li Fangxing , Jia Hongjie , Hu Qinran , Jin Xiaolong
Published: May 2016

This study proposes a novel synchrophasor measurement‐based correlation approach to identify the dominant oscillation modes in bulk power systems. In the proposed approach, the reference channel (RC) of cross‐correlation (CC) is optimally selected based on residue analysis. With the selected RC, the CC of field‐measurement data is formed to extract the free‐decay system responses. Then, eigensystem realisation algorithm (ERA) is applied to the extracted responses to estimate the system state‐space model. A practical model order selection strategy for ERA is proposed to determine the system model order. Further, cross‐coherence spectrum is employed to distinguish the dominant modes from the eigenvalues of the estimated state‐space model. The proposed method can achieve accurate and robust solutions in the presence of different levels of errors and noises in measurement data. The effectiveness of the proposed method has been verified in a 16‐generator, 68‐bus test system as well as the China Southern Power Grid system.
Study of the operation characteristics of a point absorbing direct driven permanent magnet linear generator deployed in the Baltic Sea
Authors: Lejerskog Erik , Strömstedt Erland , Savin Andrej , Boström Cecilia , Leijon Mats
Published: May 2016

To experimentally study how a wave energy converter (WEC) behaves when parameters such as weighton the translator and buoy volume are changing is of significant importance whentrying to optimise the WEC system. This study presents results from a WECdeployed at the Baltic Sea near the island of Åland. Compared with earlierexperiments, the weight on the translator has been significantly increased tosuit the buoy volume. Experimental results show that the power output betweenthe upward and the downward motions are comparable up to the maximum speed forthe downward motion of the translator. To study the speed of the translator indownward direction a model has been derived. The model has also been used tostudy the impact of having a changing active area. Moreover, finite element (FE) simulations done on the generator have been compared withexperimental data and show a good agreement, but at high speeds of thetranslator the FE simulations start to deviate from theexperiments.
Cylindrical coordinate rocket trajectory profiles and line‐of‐sight projective coordinates for tracking ballistic missiles from satellite infrared sensor line‐of‐sight observations
Authors: Danchick Roy
Published: May 2016

In this paper the authors apply the concept of cylindrical coordinate trajectory profiles to the accurate and efficient estimation of the launch parameter state of an intercontinental ballistic missiles from line‐of sight observations that are assembled by a pair of geo‐stationary satellite infrared sensors. To estimate the four‐parameter launch state (geodetic latitude, longitude, direction, time) they introduce the notion of a two‐coordinate projective coordinate representation of line‐of‐sight from observing sensor to observed target instead of the usual two angular coordinates such as local azimuth and elevation. They also introduce the notion of optimally combining launch parameter states, each state estimated from the observations of one of the pair. Finally, they investigate the performance of a nine‐component inertial state (position vector, velocity vector, mass, mass rate, drag coefficient) extended Kalman filter that is primed by the optimal state estimate. The extended Kalman filter processes interleaved line‐of‐sight projective coordinate observations. A numerical experiment is presented with the simulated fly‐out of a notional three stage North Korean intercontinental Ballistic Missile as observed by a dual viewing pair of geo‐stationary satellite infrared sensors separated by approximately 90 degrees in longitude.
Interactive clutter measurement density estimator for multitarget data association
Authors: Kim Woo Chan , Song Taek Lyul
Published: May 2016

Clutter measurement density (CMD) is an environmental parameter required for target tracking algorithms, but it is a priori unknown and as such needs to be estimated for tracking accuracy. The authors propose an interactive CMD estimator which is based on a Gaussian mixture probability hypothesis density filter. The proposed algorithm estimates the intensity of the clutter generators which generate the clutter measurements in the surveillance space. Since the estimated intensity is evaluated from the set of the components that consists the kinematic information for the clutter generators, the proposed algorithm can be applied to the dynamic cluttered environments. Furthermore, the proposed algorithm utilises the clutter measurement probabilities calculated from the target tracker to eliminate the target originated measurements for CMD estimation. An improved multitarget tracking performance of the proposed algorithm is verified by a Monte Carlo simulation study.
Differences between Manufacturers of Computed Tomography–Based Computer-Assisted Surgery Systems Do Exist
Authors: Nooh Anas , Lubov Joushua , Aoude Ahmed , Aldebeyan Sultan , Jarzem Peter , Ouellet Jean , Weber Michael H.
Published: May 2016

Study Design

Literature review.

Objective

Several studies have shown that the accuracy of pedicle screw placement significantly improves with use of computed tomography (CT)-based navigation systems. Yet, there has been no systematic review directly comparing accuracy of pedicle screw placement between different CT-based navigation systems. The objective of this study is to review the results presented in the literature and compare CT-based navigation systems relative only to screw placement accuracy.

Methods

Data sources included CENTRAL, Medline, PubMed, and Embase databases. Studies included were randomized clinical trials, case series, and case–control trials reporting the accuracy of pedicle screws placement using CT-based navigation. Two independent reviewers extracted the data from the selected studies that met our inclusion criteria. Publications were grouped based on the CT-based navigation system used for pedicle screw placement.

Results

Of the 997 articles we screened, only 26 met all of our inclusion criteria and were included in the final analysis, which showed a significant statistical difference ( p < 0.0001, 95% confidence interval 0.92 to 1.23) in accuracy of pedicle screw placement between three different CT-based navigation systems. The mean (weighted) accuracy of pedicle screws placement based on the CT-based navigation system was found to be 97.20 ± 2.1% in StealthStation (Medtronic, United States) and 96.1 ± 3.9% in VectorVision (BrainLab, Germany).

Conclusion

This review summarizes results presented in the literature and compares screw placement accuracy using different CT-based navigation systems. Although certain factors such as the extent of the procedure and the experience and skills of the surgeon were not accounted for, the differences in accuracy demonstrated should be considered by spine surgeons and should be validated for effects on patients’ outcome.
Dysphagia Rates after Anterior Cervical Diskectomy and Fusion: A Systematic Review and Meta-Analysis
Authors: Shriver Michael F. , Lewis Daniel J. , Kshettry Varun R. , Rosenbaum Benjamin P. , Benzel Edward C. , Mroz Thomas E.
Published: May 2016

Study Design

 Systematic review and meta-analysis.

Objective

Anterior cervical diskectomy and fusion (ACDF) is an effective surgical option for patients with cervical radiculopathy, myelopathy, or deformity. Although ACDF is generally safe, dysphagia is a common complication. Despite its high incidence, prolonged postoperative dysphagia is poorly understood; its etiology remains relatively unknown, and its risk factors are widely debated.

Methods

We searched MEDLINE, Scopus, Web of Science, and Embase for studies reporting complications for cervical diskectomy with plating. We recorded dysphagia events from all included studies and calculated effect summary values, 95% confidence intervals (CIs), Q values, and I2 values.

Results

Of the 7,780 retrieved articles, 14 met inclusion criteria. The overall dysphagia rate was 8.5% (95% CI 5.7 to 11.3%). The rate of moderate or severe dysphagia was 4.4% (0.4 to 8.4%). Follow-up times of <12, 12 to 24, and >24 months reported rates of 19.9% (6.0 to 33.7%), 7.0% (5.2 to 8.7%), and 7.6% (1.4 to 13.8%), respectively. Studies utilizing the Bazaz Dysphagia Score resulted in an increase in dysphagia diagnosis relative to studies with no outlined criteria (19.8%, 5.9 to 33.7% and 6.9%, 3.7 to 10.0%, respectively), indicating that the criteria used for dysphagia identification are critical. There was no difference in dysphagia rate with the use of autograft versus allograft.

Conclusions

This review represents a comprehensive estimation of the actual incidence of dysphagia across a heterogeneous group of surgeons, patients, and criteria. The classification scheme for dysphagia varied significantly within the literature. To ensure its diagnosis and identification, we recommend the use of a standardized, well-outlined method for dysphagia diagnosis.
Reference Correlation of the Viscosity of ortho-Xylene from 273 to 673 K and up to 110 MPa
Authors: Cao F. L. , Meng X. Y. , Wu J. T. , Vesovic V.
Published: May 2016

A new correlation for the viscosity of ortho-xylene (o-xylene) is presented. The correlation is based upon a body of experimental data that has been critically assessed for internal consistency and for agreement with theory. It is applicable in the temperature range from 273 to 673 K at pressures up to 110 MPa. The overall uncertainty of the proposed correlation, estimated as the combined expanded uncertainty with a coverage factor of 2, varies from 1% for the viscosity at atmospheric pressure to 5% for the highest temperatures and pressures of interest. Tables of the viscosity generated by the relevant equations, at selected temperatures and pressures and along the saturation line, are provided.
Detecting leaks in gas-filled pressure vessels using acoustic resonances
Authors: Gillis K. A. , Moldover M. R. , Mehl J. B.
Published: May 2016

We demonstrate that a leak from a large, unthermostatted pressure vessel into ambient air can be detected an order of magnitude more effectively by measuring the time dependence of the ratio p/f2 than by measuring the ratio p/T. Here f is the resonance frequency of an acoustic mode of the gas inside the pressure vessel, p is the pressure of the gas, and T is the kelvin temperature measured at one point in the gas. In general, the resonance frequencies are determined by a mode-dependent, weighted average of the square of the speed-of-sound throughout the volume of the gas. However, the weighting usually has a weak dependence on likely temperature gradients in the gas inside a large pressure vessel. Using the ratio p/f2, we measured a gas leak (dM/dt)/M ≈ − 1.3 × 10−5 h−1 = − 0.11 yr−1 from a 300-liter pressure vessel filled with argon at 450 kPa that was exposed to sunshine-driven temperature and pressure fluctuations as large as (dT/dt)/T ≈ (dp/dt)/p ≈ 5 × 10−2 h−1 using a 24-hour data record. This leak could not be detected in a 72-hour record of p/T. (Here M is the mass of the gas in the vessel and t is the time.)
Fast time-resolved electrostatic force microscopy: Achieving sub-cycle time resolution
Authors: Karatay Durmus U. , Harrison Jeffrey S. , Glaz Micah S. , Giridharagopal Rajiv , Ginger David S.
Published: May 2016

The ability to measure microsecond- and nanosecond-scale local dynamics below the diffraction limit with widely available atomic force microscopy hardware would enable new scientific studies in fields ranging from biology to semiconductor physics. However, commercially available scanning-probe instruments typically offer the ability to measure dynamics only on time scales of milliseconds to seconds. Here, we describe in detail the implementation of fast time-resolved electrostatic force microscopy using an oscillating cantilever as a means to measure fast local dynamics following a perturbation to a sample. We show how the phase of the oscillating cantilever relative to the perturbation event is critical to achieving reliable sub-cycle time resolution. We explore how noise affects the achievable time resolution and present empirical guidelines for reducing noise and optimizing experimental parameters. Specifically, we show that reducing the noise on the cantilever by using photothermal excitation instead of piezoacoustic excitation further improves time resolution. We demonstrate the discrimination of signal rise times with time constants as fast as 10 ns, and simultaneous data acquisition and analysis for dramatically improved image acquisition times.
Instability analysis of pointing accuracy and power imbalance of spherical hohlraum
Authors: Duan Hao , Wu Changshu , Pei Wenbing , Zou Shiyang
Published: May 2016

An analytic model to describe the statistic behavior of flux asymmetry on the capsule shell under the influence of random fluctuation of laser spots' position and laser energy is developed. Based on our previous work [Duan et al., Phys. Plasmas 22, 092704 (2015)] and a diagram technique, the expectation, variance, and probability density function of flux asymmetry raised by laser pointing accuracy and laser power imbalance of 4, 6, and 8 laser entrance holes (LEHs) spherical hohlraums are shown. For spherical hohlraums with different numbers of LEHs, it is found that the random part of flux asymmetry is proportional to the ratio between laser energy and square root of total spots' number ELaser/Nt, and angle-of-incidence θ0, which indicates that a choice of small θ0 and a great number of Nt can reduce the random flux asymmetry. In order to achieve a cumulative probability in which each l-order flux asymmetry can meet corresponding requirements [Gu et al., Phys. Plasmas 21, 012704 (2014)] beyond 90% in the condition of a 1000 μm capsule and 4000 μm hohlraum, the power imbalance, i.e., the ratio between standard derivation and expectation of laser spots power ΔF/Fspot for 4, 6, and 8 LEHs spherical hohlraums must not exceed 8.1%, 9.1%, and 8.5%, corresponding pointing accuracy rHΔθ must not exceed 79 μm, 102 μm, and 96 μm along the êθ direction, and rH sin 2θ0Δϕ must not exceed 77 μm, 99 μm, and 94 μm along the êϕ direction, respectively.
Exploring biological effects of MoS2 nanosheets on native structures of α-helical peptides
Authors: Gu Zonglin , Li Weifeng , Hong Linbi , Zhou Ruhong
Published: May 2016

Recent reports of mono- and few-layer molybdenum disulfide (MoS2), a representative transition metal dichacogenide (TMD), as antibacterial and anticancer agents have shed light on their potential in biomedical applications. To better facilitate these promising applications, one needs to understand the biological effects of these TMDs as well, such as their potential adverse effects on protein structure and function. Here, we sought to understand the interaction of MoS2 nanosheets with peptides using molecular dynamics simulations and a simple model polyalanine with various lengths (PAn, n = 10, 20, 30, and 40; mainly α − helices). Our results demonstrated that MoS2 monolayer has an exceptional capability to bind all peptides in a fast and strong manner. The strong attraction from the MoS2 nanosheet is more than enough to compensate the energy needed to unfold the peptide, regardless of the length, which induces drastic disruptions to the intra-peptide hydrogen bonds and subsequent secondary structures of α − helices. This universal phenomenon may point to the potential nanotoxicity of MoS2 when used in biological systems. Moreover, these results aligned well with previous findings on the potential cytotoxicity of TMD nanomaterials.
Smart darting diffusion Monte Carlo: Applications to lithium ion-Stockmayer clusters
Authors: Christensen H. M. , Jake L. C. , Curotto E.
Published: May 2016

In a recent investigation [K. Roberts et al., J. Chem. Phys. 136, 074104 (2012)], we have shown that, for a sufficiently complex potential, the Diffusion Monte Carlo (DMC) random walk can become quasiergodic, and we have introduced smart darting-like moves to improve the sampling. In this article, we systematically characterize the bias that smart darting moves introduce in the estimate of the ground state energy of a bosonic system. We then test a simple approach to eliminate completely such bias from the results. The approach is applied for the determination of the ground state of lithium ion-n–dipoles clusters in the n = 8–20 range. For these, the smart darting diffusion Monte Carlo simulations find the same ground state energy and mixed-distribution as the traditional approach for n < 14. In larger systems we find that while the ground state energies agree quantitatively with or without smart darting moves, the mixed-distributions can be significantly different. Some evidence is offered to conclude that introducing smart darting-like moves in traditional DMC simulations may produce a more reliable ground state mixed-distribution.
Numerical study of the structural and vibrational properties of amorphous Ta2O5 and TiO2-doped Ta2O5
Authors: Damart T. , Coillet E. , Tanguy A. , Rodney D.
Published: May 2016

Using classical molecular dynamics simulations, we synthesized amorphous Ta2O5 and amorphous TiO2-doped Ta2O5. We show that Ta2O5 is composed primarily of six-folded Ta atoms forming octahedra that are either organized in chain-like structures or share edges or faces. When Ta2O5 is doped with TiO2, Ti atoms form equally five- and six-folded polyhedra that perturb but do not break the network structure of the glass. Performing a vibrational eigenmode analysis and projecting the eigenmodes on the rocking, stretching, and bending motions of the Ta-2O and Ta-3O bonds, we provide an atomic-scale analysis that substantiates the interpretations of Raman spectra of amorphous Ta2O5. This eigenmode analysis also reveals the key role played by Ti atoms in the 5 to 12 THz range.
Zinc requirement for two phytoplankton strains of the Tasman Sea
Authors: Sinoir Marie , Bowie Andrew R. , Mongin Mathieu , Butler Edward C. V. , Hassler Christel S.
Published: May 2016

Zinc has been proposed as a limiting, or co-limiting, micronutrient for phytoplankton. In the Tasman Sea, extremely low zinc concentrations have been reported, raising the possibility there of limitation of phytoplankton growth by zinc. The pennate diatom Nitzschia closterium (CS-1) and the coccolithophorid Emiliania huxleyi (CS-812) were cultured in two low zinc concentrations (Zn2+ = 1.5 pmolL–1 and Zn2+ = 1.5 nmolL–1) mimicking conditions found in coastal and pelagic Tasman Sea. To monitor phytoplankton health and productivity, the maximum quantum yield (Fv/Fm), growth rate and cell size were analysed. These parameters showed that both strains were able to adapt and still grow. Short-term uptake experiments revealed an effect on Zn biological transport, with consequences for its bioavailability. When grown at low Zn2+ concentrations, E. huxleyi showed an induction of a two-transporter system, highly dependent on photosynthetic energy for Zn uptake. N. closterium was able to survive without inducing a higher-affinity Zn transporter. Its Zn uptake was also highly dependent on cellular energy and the ability to potentially access labile complexed forms of Zn. This strategy, thus, represented an advantage over E. huxleyi. Results are discussed in the context of the conditions found in the Tasman Sea.
Outreach youth health service in school setting: a retrospective case study
Authors: Stanzel Karin A.
Published: May 2016

This case study documents the journey of an outreach youth clinic from its inception to its current practice. It reviews the barriers and enablers to attending the outreach youth clinic as well as determining the health concerns that have prompted young people to access the service. A case study method was applied to review agency evaluation reports and open-ended feedback surveys completed by service users. An ongoing reflective health practitioner’s journal was also kept by the clinicians. The results identify sexual and reproductive health, and mental health, as the main concerns for which young people seek help. Additionally, confidentiality and privacy issues are of concern, while parental and caregiver’s understanding acts as an enabler for young people to obtain better health. Multi-agency collaboration is highlighted while the significance of a robust connection between the collaborating services and leadership from the school is also recognised. The outreach youth clinic is providing a youth-specific service that has had good utilisation. However, a solid collaboration with the school and the community health sector is crucial if a service such as this is to be maintained and sustained.
Effects of culling on vigilance behaviour and endogenous stress response of female fallow deer
Authors: Pecorella I. , Ferretti F. , Sforzi A. , Macchi E.
Published: May 2016

Context
Human activities can induce behavioural and stress responses in wild animals. Information is scarce on the effects of culling on anti-predator behaviour and endogenous stress response of wild ungulates.

Aims
In a Mediterranean area, we evaluated the effects of culling on vigilance, foraging and endogenous stress response of female fallow deer (Dama dama).

Methods
Effects of culling were evaluated through behavioural observations and hormone analyses of faecal samples.

Key results
In an area where culling occurred (C), individuals showed significantly greater vigilance rates and foraged closer to wood than in an area with no culling (NC). In C, 24 h after culling, faecal cortisol concentrations were greater than those recorded in NC, but they decreased significantly to values comparable to (48 h post-shot) and lower than (72 h post-shot) those observed in NC.

Conclusions
Most likely, culling determined behavioural responses in female fallow deer, but did not trigger long-term physiological effects.

Implications
Increased anti-predator behaviour may complicate the implementation of long-term culling programs.
Relativistic BEC-BCS Crossover in a magnetized Nambu-Jona-Lasinio Model
Authors: Duarte Dyana C. , Farias R.L.S. , Manso Patricía H.A. , Ramos Rudnei O.
Published: May 2016

The BEC-BCS crossover in the NJL model is studied in the presence of an external magnetic field. Particular attention is given to two different regularization schemes used in the literature and we show how they compare to each other. The comparison is made for the case of a cold and magnetized two color NJL model. We also make a brief discussion about the Nc
= 3 case without magnetic fields, as an extension of this work in the future.
Spectral identification of topological domains
Authors: Chen Jie , Hero Alfred O. , Rajapakse Indika
Published: May 2016

Motivation: Topological domains have been proposed as the backbone of interphase chromosome structure. They are regions of high local contact frequency separated by sharp boundaries. Genes within a domain often have correlated transcription. In this paper, we present a computational efficient spectral algorithm to identify topological domains from chromosome conformation data (Hi-C data). We consider the genome as a weighted graph with vertices defined by loci on a chromosome and the edge weights given by interaction frequency between two loci. Laplacian-based graph segmentation is then applied iteratively to obtain the domains at the given compactness level. Comparison with algorithms in the literature shows the advantage of the proposed strategy.

Results: An efficient algorithm is presented to identify topological domains from the Hi-C matrix.

Availability and Implementation: The Matlab source code and illustrative examples are available at http://bionetworks.ccmb.med.umich.edu/

Contact: indikar@med.umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm
Authors: Luo Huimin , Wang Jianxin , Li Min , Luo Junwei , Peng Xiaoqing , Wu Fang-Xiang , Pan Yi
Published: May 2016

Motivation: Drug repositioning, which aims to identify new indications for existing drugs, offers a promising alternative to reduce the total time and cost of traditional drug development. Many computational strategies for drug repositioning have been proposed, which are based on similarities among drugs and diseases. Current studies typically use either only drug-related properties (e.g. chemical structures) or only disease-related properties (e.g. phenotypes) to calculate drug or disease similarity, respectively, while not taking into account the influence of known drug–disease association information on the similarity measures.

Results: In this article, based on the assumption that similar drugs are normally associated with similar diseases and vice versa, we propose a novel computational method named MBiRW, which utilizes some comprehensive similarity measures and Bi-Random walk (BiRW) algorithm to identify potential novel indications for a given drug. By integrating drug or disease features information with known drug–disease associations, the comprehensive similarity measures are firstly developed to calculate similarity for drugs and diseases. Then drug similarity network and disease similarity network are constructed, and they are incorporated into a heterogeneous network with known drug–disease interactions. Based on the drug–disease heterogeneous network, BiRW algorithm is adopted to predict novel potential drug–disease associations. Computational experiment results from various datasets demonstrate that the proposed approach has reliable prediction performance and outperforms several recent computational drug repositioning approaches. Moreover, case studies of five selected drugs further confirm the superior performance of our method to discover potential indications for drugs practically.

Availability and Implementation:  http://github.com//bioinfomaticsCSU/MBiRW .

Contact:  jxwang@mail.csu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
MEANS: python package for Moment Expansion Approximation, iNference and Simulation
Authors: Fan Sisi , Geissmann Quentin , Lakatos Eszter , Lukauskas Saulius , Ale Angelique , Babtie Ann C. , Kirk Paul D. W. , Stumpf Michael P. H.
Published: May 2016

Motivation: Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system’s moments and apply a closure ansatz to obtain a closed set of differential equations; that can become the basis for the deterministic analysis of the moments of the outputs of stochastic systems.

Results: We present a free, user-friendly tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment. Our package enables the analysis of complex stochastic systems without any constraints on the number of species and moments studied and the type of rate laws in the system. In addition to the approximation method our package provides numerous tools to help non-expert users in stochastic analysis.

Availability and implementation:  https://github.com/theosysbio/means

Contacts:  m.stumpf@imperial.ac.uk or e.lakatos13@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ensemble squid habitat model using three-dimensional ocean data
Authors: Alabia Irene D. , Saitoh Sei-Ichi , Igarashi Hiromichi , Ishikawa Yoichi , Usui Norihisa , Kamachi Masafumi , Awaji Toshiyuki , Seito Masaki
Published: May 2016

Neon flying squid (Ommastrephes bartramii) is a large pelagic squid internationally harvested in the North Pacific. Here, we examined its potential habitat in the central North Pacific using an ensemble modelling approach. Initially, ten statistical models were constructed by combining the squid fishing points, selected vertical layers of the sea temperature and salinity, sea surface height (SSH), and SSH gradient from the multi-variate ocean variational estimation system for the western North Pacific from June to July 1999–2011. The variable selection analyses have captured the importance of vertical temperature and salinity layers at the upper 300 and 440 m, respectively, coinciding with the reported vertical ranges of diel migration for the squid's primary prey species in the North Pacific. The evaluation of the habitat predictions using the independent sets of the presence data from 2012 to 2014 showed significant variability in the predictive accuracy, which is likely reflective of the interannual differences in environmental conditions across the validation periods. Our findings from ensemble habitat model approach using three-dimensional oceanographic data were able to characterize the near- and subsurface habitats of the neon flying squid. Moreover, our results underpinned the possible link between interannual environmental variability and spatio-temporal patterns of potential squid habitats. As such, these further suggest that an ensemble model approach could present a promising tool for operational fishery application and squid resource management.
Meta-analysis reveals pathway signature of Septic Shock
Authors: Mukhopadhyay Samanwoy , Pandey Abhaydeep , Thatoi Pravat K , Das Bidyut K , Ravindran Balachandran , Bhattacharjee Samsiddhi , Mohapatra Saroj K
Published: May 2016

Septic shock is a major medical problem with high morbidity and mortality and incompletely understood biology. Availability of genome-wide expression data from different studies on septic shock empowers the quest for hitherto unidentified pathways by integration and meta-analysis of multiple data sets. Electronic search was performed on medical literature and gene expression databases. Selection of studies was based on the organism (human subjects), tissue of origin (circulating leukocytes) and the platform technology (gene expression microarray). Gene-level meta-analysis was conducted on the six selected studies to identify the genes consistently differentially expressed in septic shock. These genes were then subjected to pathway analysis. The identified up-regulated pathwayhsa04380 (Osteoclast Differentiation) was validated in an independent cohort of patients. A simplified model was generated showing the major gene-modules dysregulated in SS.
Membrane state diagrams make electrophysiological models simple
Authors: Law Robert , Jones Stephanie R.
Published: May 2016

Ion channels are ubiquitous in living systems. Through interactions with membrane potential, ion channels both control metabolic events and mediate cell communication. Consequentially, membrane bioelectricity bears on fields ranging from cancer etiology to computational neuro-science. Conductance models have proven successful in quantitatively capturing these dynamics but are often considered difficult, with interpretation relegated to specialists. To facilitate research in membrane dynamics, especially in fields where roles for ion channels are just beginning to be quantified, we must make these models easy to understand.

Here, we show that the membrane differential equation central to conductance models can be understood using simple circular geometry. The membrane state diagrams we construct are compact, faithful representations of conductance model state, designed to look like circular “cells” with currents flowing in and out. Every feature of a membrane state diagram corresponds to a physiological variable, so that insight taken from a diagram can be translated back to the underlying model. The construction is elementary: we convert conductances to angles subtended on the circle and potentials to radii; currents are then areas of the enclosed annular sectors.

Our method clarifies a powerful but prohibitive modeling approach and has the potential for widespread use in both electrophysiological research and pedagogy. We illustrate how membrane state diagrams can augment traditional methods in the stability analysis of voltage equilibria and in depicting the Hodgkin-Huxley action potential, and we use the diagrams to infer the possibility of nontrivial fixed-voltage channel population dynamics by visual inspection rather than linear algebra.
Allowance for uncollectible accounts as a tool for earnings management
Authors: Lee Hyun-Ah , Choi Won-Wook
Published: May 2016

Purpose

This study aims to verify the circumstances under which managing the allowance for uncollectible accounts is used as a tool of earnings management.

Design/methodology/approach

The authors investigate whether bad debt expense, which is an income statement counterpart of allowance for uncollectible accounts, is adjusted downward when pre-managed earnings is slightly above zero earnings, prior year’s earnings or analysts’ forecasts.

Findings

The findings of this study show that firms manage bad debt expense downward to avoid losses, sustain the prior year’s earnings and meet or beat analysts’ forecasts. The authors also find that the understatement of bad debt expense to meet earnings benchmarks is pronounced for firms with high tax costs.

Social implications

Standard setters and auditors can gain a better understanding in detail of the practices and methods of managing earnings via the allowance for uncollectible accounts.

Originality/value

This study is the first to examine earnings management via the allowance for uncollectible accounts in non-financial Korean firms. In addition, the findings provide the evidence that firms prefer to use the allowance for uncollectible accounts as a strategic tool to meet benchmarks, especially when their tax costs are high.