bluuebunny/crossref_metadata_2025 huggingface dataset:
Fast identification of partial discharge sources using blind source separation and kurtosis
Authors: Au M. , Agba B.L. , Gagnon F.
Published: November 2015

A technique for the fast identification of partial discharge (PD) sources is proposed for the detection of mechanical failure or damage to insulation materials by using wireless remote control and monitoring systems in substations. An estimation of the number of PD sources can help to evaluate the insulation performance and lifetime of power equipment. Multiple PD sources can be generated during the operating voltage where their electromagnetic radiations are highly impulsive, non‐Gaussian noise and the resulting probability distribution function is heavy‐tailed. Multiple PD sources can be estimated by their electromagnetic radiations via blind source separation (BSS) and measuring the excess kurtosis using low‐cost wireless intelligent electronic devices. The efficiency and performance of the proposed method is demonstrated by simulating PD sources based on the spatial Poisson point process where the number of sources is a random variable not known by the receiver. Assuming non‐white and decorrelated or non‐Gaussian and independent sources, results show that the number of significant PD sources can be estimated with low error rate. Underdetermined problems in BSS can affect performances.
Calibrating sample and hold stages with pruned Volterra kernels
Authors: Centurelli F. , Monsurrò P. , Rosato F. , Ruscio D. , Trifiletti A.
Published: November 2015

Switched capacitor sample and hold (SHA) stages in deep submicron technologies can achieve hundreds of mega samples per second of sampling frequency, but are affected by several nonlinear effects which reduce their signal‐to‐noise‐and‐distortion ratio (SNDR): CMOS switch non‐idealities, amplifier nonlinearity, and incomplete settling. It is possible to model and correct distortions using Volterra kernels, which can be rather resource‐consuming as the number of parameters to estimate rapid increases with the order and length of the kernels. In this reported work, it is shown that a switched capacitor SHA, simulated using the 45 nm process by STMicroelectronics, can be calibrated to achieve a 10–24 dB improvement in SNDR. Computational costs are kept low using a different lag value for each kernel, and iteratively pruning the elements of the Volterra kernels which affect linearity the least. A technique for estimation and out‐of‐sample validation is presented and robustness checks are performed. A performance gain of 8.5 dB can be achieved with as few as 17 correction parameters, while 21 coefficients are enough to gain 12.2 dB, and 36 to gain 18.4 dB.
Design of dual‐bandpass filters using stepped‐impedance circular ring resonator
Authors: Wang Wensong , Cao Qunsheng , Yang Chenchen , Wang Yi , Chen Yinchao
Published: November 2015

A stepped‐impedance circular ring resonator (SICRR) with two pairs of stubs is proposed for the design of a dual‐bandpass filter. This quad‐mode resonator is applied to produce two passbands. It is found that the centre frequencies and bandwidths of the two passbands can be tuned by varying the lengths of the stubs. Simulation results show that the defined impedance ratio K and the electrical length ratio α of between the SICRR segments can affect the frequency separation between the two passbands. A prototype filter centred at 3.4 and 5.56 GHz is designed and fabricated. Good agreement between the simulated and measured results was achieved for the SICRR filter.
Joint optimal power allocation and relay location for decode‐and‐forward multi‐hop relaying over log‐normal channel
Authors: Kundu Chinmoy , Bose Ranjan
Published: November 2015

A joint optimisation of power allocation (PA) and relay location is proposed for decode‐and‐forward relaying over multi‐hop, independent, log‐normal fading channels. Optimisation is carried out at high signal‐to‐noise ratio (SNR) and low SNR scenarios to minimise the outage probability with a constraint on total transmit power and end‐to‐end relaying distance. End‐to‐end average bit error rate is also minimised assuming the same constraints. Optimisation is carried out to find optimal PA (OPA) for a given relay location, optimal relay location (ORL) for a given PA and joint OPA and relay location. All the optimisation problems reformulated from the original problems are shown to be convex except relay location optimisation minimising outage probability at low SNR scenario. It is then solved using properties of concave minimisation. Optimal allocation factors do not depend on the instantaneous channel state information. It also does not depend on total available power in the system except allocation factors evaluated by optimising outage at high SNR. It is observed that OPA allocates more power to weaker links and ORL allocates less distance to weaker links. It is also observed that performance improvement increases with increase in link unbalance and distance‐based allocation is most effective.
Improved droop control method with precise current sharing and voltage regulation
Authors: Chiang Hsuang‐Chang , Jen Kuo‐Kuang , You Gwo‐Huei
Published: November 2015

The droop control method is one of the simplest methods for load sharing control of multiple converters. Although the current sharing precision can be adjusted to be well through the droop parameter, the voltage regulation precision is hard to be maintained well due to the voltage droop. In addition, the stability and dynamic response is usually degraded since the small‐signal model of multiple converter system is usually changed significantly. To cope with these two limitations, this study presents an improved droop control method with automatic master to correct the voltage regulation. A robust control scheme is also provided to maintain a good stability and dynamic response as the design of the normal condition. The proposed method is confirmed with some simulation and experimental results.
Impact of high penetration of variable renewable generation on frequency dynamics in the continental Europe interconnected system
Authors: Wang Ye , Silva Vera , Lopez‐Botet‐Zulueta Miguel
Published: November 2015

This study addresses the development and operation of the European continental electricity system with a high penetration of wind and photovoltaic (PV) generation. The main focus of the work is the assessment of the impact of inertia reduction, due to wind and PV power electronics interface, on frequency stability indicators, as the rate of change of frequency and the frequency nadir following a large generation loss. The analysis is based on dynamic frequency stability studies, performed for every hour of the year and over a large number of weather scenarios. The outputs of these simulations are used to perform statistical analysis of these indicators and to estimate the critical instantaneous penetration rate of wind and PV, which the European continental synchronous area can accommodate from a system dynamics point of view. The results show that a single critical instantaneous penetration rate cannot be defined, since the frequency dynamic behaviour depends on parameters that change from one period to the following. Instead, this critical penetration rate should be calculated for every dispatch period. This study also highlights the growing importance of load self‐regulating effect's contribution to frequency stability in the future system.
Operational assessment and adaptive selection of micro‐Doppler features
Authors: Gürbüz Sevgi Zübeyde , Erol Barış , Çağlıyan Bahri , Tekeli Bürkan
Published: November 2015

A key challenge for radar surveillance systems is the discrimination of ground‐based targets, especially humans from animals, as well as different types of human activities. For this purpose, target micro‐Doppler signatures have been shown to yield high automatic target classification rates; however, performance is typically only given for near‐optimal operating conditions using a fixed set of features. Over the past few decades dozens of micro‐Doppler features have been proposed, when in fact utilisation of all possible features does not guarantee the maximum classification performance and the selection of an optimal subset of features is scenario dependent. In this work, a comprehensive survey of micro‐Doppler features and their dependence upon system parameters and operational conditions – such as transmit frequency, range and Doppler resolution, antenna–target geometry, signal‐to‐noise ratio, and dwell time – is given. Algorithms for optimising classification performance for a reduced number of features are presented. Performance gains achievable using adaptive feature selection are assessed for a case study of interest.
Ternary static random access memory using quantum dot gate field‐effect transistor
Authors: Karmakar Supriya , Jain Faquir C.
Published: November 2015

Quantum dot gate field‐effect transistor (QDGFET) generates three states in their transfer characteristics. A successful model can explain the generation of third state in the transfer characteristics of the QDGFET. The innovative circuit design using QDGFET can be used to design different ternary logic. This Letter discusses the design of ternary logic static random access memory using QDGFET.
Low‐temperature selective catalytic reduction of NO over carbon nanotubes supported MnO2 fabricated by co‐precipitation method
Authors: Lu Xiulian , Zheng Yuying , Zhang Yanbing , Qiu Hongfeng , Zou Haiqiang
Published: November 2015

A series of MnO2/carbon nanotubes (CNTs) catalysts were prepared to use for the selective catalytic reduction (SCR) of NO with NH3 via liquid‐phase redox method at ambient temperature. The resulting samples possessed an amorphous MnO2 and, a higher SCR activity than that obtained by wet impregnation technique.
Nonlinear circuit analysis technique for microelectromechanical systems with a time‐variant capacitor and an AC power source
Authors: Li Chong , Dean Robert Neal , Flowers George T.
Published: November 2015

Microelectromechanical systems (MEMS) utilise time‐variant capacitors as transducers in many applications. However, this kind of component can introduce harmonics and disturbances into the circuit with an AC power source, which is difficult to evaluate through closed‐form solutions. This Letter proposes an iterative solution to analyse the dynamics of MEMS devices which contain a time‐variant capacitor and an AC source. First, the expressions of the time‐variant capacitor, AC source and their derivatives with respect to time are determined. Then, an initial solution that is sufficiently close to the actual solution is determined using linear circuit analysis. On the basis of the previous steps and the principles of the iterative method, an approximated solution combining the initial solution and its iteratively‐derived higher‐order terms is reached. Adding additional higher‐order terms can improve the accuracy of the solution. A case study considering a MEMS device which has an AC power source and sinusoidal motion was performed using MATLAB Simulink. The simulation study further demonstrated that: (i) this iterative solution can effectively analyse the dynamics of MEMS devices with a time‐variant capacitor and an AC power source; and (ii) computing additional higher‐order terms derived from the initial solution can further improve the solution's accuracy.
A parallel algorithm for implicit depletant simulations
Authors: Glaser Jens , Karas Andrew S. , Glotzer Sharon C.
Published: November 2015

We present an algorithm to simulate the many-body depletion interaction between anisotropic colloids in an implicit way, integrating out the degrees of freedom of the depletants, which we treat as an ideal gas. Because the depletant particles are statistically independent and the depletion interaction is short-ranged, depletants are randomly inserted in parallel into the excluded volume surrounding a single translated and/or rotated colloid. A configurational bias scheme is used to enhance the acceptance rate. The method is validated and benchmarked both on multi-core processors and graphics processing units for the case of hard spheres, hemispheres, and discoids. With depletants, we report novel cluster phases in which hemispheres first assemble into spheres, which then form ordered hcp/fcc lattices. The method is significantly faster than any method without cluster moves and that tracks depletants explicitly, for systems of colloid packing fraction ϕc < 0.50, and additionally enables simulation of the fluid-solid transition.
A test on reactive force fields for the study of silica dimerization reactions
Authors: Moqadam Mahmoud , Riccardi Enrico , Trinh Thuat T. , Åstrand Per-Olof , van Erp Titus S.
Published: November 2015

We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization. The initial configurations for the force field optimization are usually the minimum energy structures of the ab initio database. Hence, the ab initio method dictates which structures are being examined and force field parameters are being adjusted in order to minimize the differences with the ab initio data. As a result, this approach will not exclude the possibility that the force field predicts stable geometries or low transition states which are realistically very high in energy and, therefore, never considered by the ab initio method. Our analysis reveals the existence of such unphysical geometries even at unreactive conditions where the distance between the reactants is large. To test the effect of these discrepancies, we launched molecular dynamics simulations using DFT and ReaxFF and observed spurious reactions for both ReaxFF force fields. Our results suggest that the standard procedures for parameter fitting need to be improved by a mutual comparative method.
The entropic forces and dynamic integrity of single file water in hydrophobic nanotube confinements
Authors: Sahu Pooja , Ali Sk. M.
Published: November 2015

Water in nanotube exhibits remarkably different properties from the bulk phase, which can be exploited in various nanoconfinement based technologies. The properties of water within nanotube can be further tuned by varying the nanotube electrostatics and functionalization of nanotube ends. Here, therefore, we investigate the effect of quantum partial charges and carbon nanotube (CNT) termination in terms of associated entropic forces. An attempt has been made to correlate the entropic forces with various dynamical and structural properties. The simulated structural features are consistent with general theoretical aspects, in which the interfacial water molecules at H terminated CNT are found to be distributed in a different way as compared to other CNTs. The rotational entropy components for different cases of CNTs are well corroborated by the decay time of hydrogen bond (HB) correlation functions. A part of this event has been explained in terms of orientation of water molecules in the chain, i.e., the change in direction of dipole moment of water molecules in the chain and it has been revealed that the HBs of CNT confined water molecules show long preserving correlation if their rotations inside CNT are restricted. Furthermore, the translational entropy components are rationally integrated with the differing degree of translational constraints, added by the CNTs. To the best of our information, perhaps this is the first study where the thermodynamic effects introduced by H-termination and induced dipole of CNT have been investigated. Additionally, we present a bridge relation between “translational diffusivity and configurational entropy” for water transport from bulk phase to inside CNTs.
Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom
Authors: Bross David H. , Parmar Payal , Peterson Kirk A.
Published: November 2015

The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set limit using new all-electron correlation consistent basis sets. The latter was carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons has been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. The final ionization potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV) and thus more reliable than the current experimental values of IP3 through IP6.
Geodesic mode instability driven by electron and ion fluxes in tokamaks
Authors: Elfimov A. G. , Camilo de Souza F. , Galvão R. M. O.
Published: November 2015

The effect of the parallel electron current and plasma flux on Geodesic Acoustic Modes (GAM) in a tokamak is analyzed by kinetic theory taking into the account the ion Landau damping and diamagnetic drifts. It is shown that the electron current and plasma flow, modeled by shifted Maxwell distributions of electrons and ions, may overcome the ion Landau damping generating the GAM instability when the parallel electron current velocity is larger than the effective parallel GAM phase velocity of sidebands, Rqω. The instability is driven by the electron current and the parallel ion flux cross term. Possible applications to tokamak experiments are discussed. The existence of the geodesic ion sound mode due to plasma flow is shown.
Torsional wave propagation in a circular plate of piezoelectric radial phononic crystals
Authors: Shu Haisheng , Zhao Lei , Shi Xiaona , Liu Wei , Shi Dongyan , Kong Fankai
Published: November 2015

Piezoelectric rings are periodically introduced and inserted in a base plate along the radial direction, forming a one-dimensional circular plate of piezoelectric radial phononic crystals (CPPRPC). The transfer matrix of the torsional wave between adjacent units is derived in cylindrical coordinates. Then, by introducing Lyapunov exponents, the phenomenon of the torsional wave band gap is analyzed with consideration of outer control. Furthermore, the effects of some factors, namely, radial span ratio, inner radius of the plate, open-circuit, and short-circuit statuses of the piezoelectric ceramics, on the torsional wave band gap are also discussed in detail. The results show that the distinct band gaps are obtained for torsional waves propagating in CPPRPC. Together with the outer control gain, structural and piezoelectric parameters have significant effects on the band gaps. In particular, middle-low frequency band gaps can be effectively obtained by rationally varying the outer active control gain.
Influence of phase transition on shock-induced spallation in nanocrystalline iron
Authors: Gunkelmann Nina , Bringa Eduardo M. , Urbassek Herbert M.
Published: November 2015

Intense shock waves may lead to spallation of the sample. Recent experiments show differences of shock spallation in iron depending on whether the samples underwent the pressure-induced bcc-hcp phase transformation or not. In this study, we perform molecular dynamics simulations of shock-induced spallation in polycrystalline iron. Our results show that the phase transformation decreases the probability of multiple spallation and crack formation. In agreement with experiments, the phase transformation changes the surface morphology showing smoother spallation surfaces.
Direct observation of strain in InAs quantum dots and cap layer during molecular beam epitaxial growth using in situ X-ray diffraction
Authors: Shimomura Kenichi , Suzuki Hidetoshi , Sasaki Takuo , Takahasi Masamitu , Ohshita Yoshio , Kamiya Itaru
Published: November 2015

Direct measurements on the growth of InAs quantum dots (QDs) and various cap layers during molecular beam epitaxy are performed by in situ X-ray diffraction (XRD). The evolution of strain induced both in the QDs and cap layers during capping is discussed based on the XRD intensity transients obtained at various lattice constants. Transients with different features are observed from those obtained during InGaAs and GaAs capping. The difference observed is attributed to In-Ga intermixing between the QDs and the cap layer under limited supply of In. Photoluminescence (PL) wavelength can be tuned by controlling the intermixing, which affects both the strain induced in the QDs and the barrier heights. The PL wavelength also varies with the cap layer thickness. A large redshift occurs by reducing the cap thickness. The in situ XRD observation reveals that this is a result of reduced strain. We demonstrate how such information about strain can be applied for designing and preparing novel device structures.
Note: Thermally stable thin-film filters for high-power extreme-ultraviolet applications
Authors: Tarrio C. , Berg R. F. , Lucatorto T. B. , Lairson B. , Lopez H. , Ayers T.
Published: November 2015

We investigated several types of thin-film filters for high intensity work in the extreme-ultraviolet (EUV) spectral range. In our application, with a peak EUV intensity of 2.7 W cm−2, Ni-mesh-backed Zr filters have a typical lifetime of 20 h, at which point they suffer from pinholes and a 50% loss of transmission. Initial trials with Si filters on Ni meshes resulted in rupture of the filters in less than an hour. A simple thermal calculation showed that the temperature rise in those filters to be about 634 K. A similar calculation indicated that using a finer mesh with thicker wires and made of Cu reduces the temperature increase to about 60 K. We have exposed a Si filter backed by such a mesh for more than 60 h with little loss of transmission and no leaks.
A reliable, compact, and repetitive-rate high power microwave generation system
Authors: Li Wei , Li Zhi-qiang , Sun Xiao-liang , Zhang Jun
Published: November 2015

A compact high power microwave (HPM) generation system is described in this paper. The main parts of the HPM system are a Marx generator with a pulse forming line and a magnetron with diffraction output. The total weight and length of the system are 250 kg and 120 cm, respectively. The output microwave power of the HPM system at 550 kV of applied voltage and 0.33 T of magnetic field reaches 1 GW at 2.32 GHz of central frequency with 38 ns of pulse duration, 23% of power conversion efficiency, and Gaussian radiation pattern. In the bursts operation, both time and amplitude jitters are less than 4 ns and lower than 1.5 dB, respectively.
Communication: Slow supramolecular mode in amine and thiol derivatives of 2-ethyl-1-hexanol revealed by combined dielectric and shear-mechanical studies
Authors: Adrjanowicz K. , Jakobsen B. , Hecksher T. , Kaminski K. , Dulski M. , Paluch M. , Niss K.
Published: November 2015

In this paper, we present results of dielectric and shear-mechanical studies for amine (2-ethyl-1-hexylamine) and thiol (2-ethyl-1-hexanethiol) derivatives of the monohydroxy alcohol, 2-ethyl-1-hexanol. The amine and thiol can form hydrogen bonds weaker in strength than those of the alcohol. The combination of dielectric and shear-mechanical data enables us to reveal the presence of a relaxation mode slower than the α-relaxation. This mode is analogous to the Debye mode seen in monohydroxy alcohols and demonstrates that supramolecular structures are present for systems with lower hydrogen bonding strength. We report some key features accompanying the decrease in the strength of the hydrogen bonding interactions on the relaxation dynamics close to the glass-transition. This includes changes (i) in the amplitude of the Debye and α-relaxations and (ii) the separation between primary and secondary modes.
Collisional excitation of NH(X3Σ−) by Ne: Potential energy surface, scattering calculations, and comparison with experiments
Authors: Bouhafs Nezha , Lique François
Published: November 2015

We present a new three-dimensional potential energy surface (PES) for the NH(X3Σ−)–Ne van der Waals system, which explicitly takes into account the NH vibrational motion. Ab initio calculations of the NH–Ne PES were carried out using the open-shell single- and double-excitation coupled cluster approach with non-iterative perturbational treatment of triple excitations [RCCSD(T)]. The augmented correlation-consistent quadruple zeta (aug-cc-pVQZ) basis set was employed. Mid-bond functions were also included in order to improve the accuracy in the van der Waals well. Using this new PES, we have studied the collisional excitation of NH(X3Σ−) by Ne. Close-coupling calculations of the collisional excitation cross sections of the fine-structure levels of NH by Ne are performed for energies up to 3000 cm−1, which yield, after thermal average, rate coefficients up to 350 K. The propensity rules between fine-structure levels are reported, and it is found that F-conserving cross sections are larger than F-changing cross sections even if the propensity rules are not as strong as for the NH–He system. The calculated rate coefficients are compared with available experimental measurements at room temperature and a fairly good agreement is found between experimental and theoretical data, confirming the good quality of the scattering calculations and also the accuracy of the potential energy surface used in this work.
Patterning of high mobility electron gases at complex oxide interfaces
Authors: Trier F. , Prawiroatmodjo G. E. D. K. , von Soosten M. , Christensen D. V. , Jespersen T. S. , Chen Y. Z. , Pryds N.
Published: November 2015

Oxide interfaces provide an opportunity for electronics. However, patterning of electron gases at complex oxide interfaces is challenging. In particular, patterning of complex oxides while preserving a high electron mobility remains underexplored and inhibits the study of quantum mechanical effects where extended electron mean free paths are paramount. This letter presents an effective patterning strategy of both the amorphous-LaAlO3/SrTiO3 (a-LAO/STO) and modulation-doped amorphous-LaAlO3/La7/8Sr1/8MnO3/SrTiO3 (a-LAO/LSM/STO) oxide interfaces. Our patterning is based on selective wet etching of amorphous-LSM (a-LSM) thin films, which acts as a hard mask during subsequent depositions. Strikingly, the patterned modulation-doped interface shows electron mobilities up to ∼8 700 cm2/V s at 2 K, which is among the highest reported values for patterned conducting complex oxide interfaces that usually are ∼1 000 cm2/V s at 2 K.
Root-to-shoot signalling: integration of diverse molecules, pathways and functions
Authors: Shabala Sergey , White Rosemary G. , Djordjevic Michael A. , Ruan Yong-Ling , Mathesius Ulrike
Published: November 2015

Plant adaptive potential is critically dependent upon efficient communication and co-ordination of resource allocation and signalling between above- and below-ground plant parts. Plant roots act as gatekeepers that sense and encode information about soil physical, chemical and biological factors, converting them into a sophisticated network of signals propagated both within the root itself, and also between the root and shoot, to optimise plant performance for a specific set of conditions. In return, plant roots receive and decode reciprocal information coming from the shoot. The communication modes are highly diverse and include a broad range of physical (electric and hydraulic signals, propagating Ca2+ and ROS waves), chemical (assimilates, hormones, peptides and nutrients), and molecular (proteins and RNA) signals. Further, different signalling systems operate at very different timescales. It remains unclear whether some of these signalling systems operate in a priming mode(s), whereas others deliver more specific information about the nature of the signal, or whether they carry the same ‘weight’. This review summarises the current knowledge of the above signalling mechanisms, and reveals their hierarchy, and highlights the importance of integration of these signalling components, to enable optimal plant functioning in a dynamic environment.
Generalised dihedral subalgebras from the Monster
Authors: Rehren Felix
Published: November 2015

The conjugacy classes of the Monster which occur in the McKay observation correspond to the isomorphism types of certain

2
2

-generated subalgebras of the Griess algebra. Sakuma, Ivanov and others showed that these subalgebras match the classification of vertex algebras generated by two Ising conformal vectors, or of Majorana algebras generated by two axes. In both cases, the eigenvalues

α
,
β

\alpha ,\beta

parametrising the theory are fixed to

1
4

\frac {1}{4}

,

1
32

\frac {1}{32}

. We generalise these parameters and the algebras which depend on them, in particular finding the largest possible (nonassociative) axial algebras which satisfy the same key features, by working extensively with the underlying rings. The resulting algebras admit an associating symmetric bilinear form and satisfy the same

6
6

-transposition property as the Monster;

1
4

\frac {1}{4}

,

1
32

\frac {1}{32}

turns out to be distinguished.
The Effectiveness of Psychoeducational Intervention on Managing Symptom Clusters in Patients With Cancer
Authors: Xiao Wenli , Chow Ka Ming , So Winnie K. W. , Leung Doris Y. P. , Chan Carmen W. H.
Published: November 2015

Background:

Managing symptom clusters instead of single symptoms could be more beneficial in cancer care. Psychoeducational intervention (PEI) has been highlighted as a promising symptom intervention, but the effect of PEI in the management of cancer symptom clusters remains unknown.

Objective:

The aim of this study was to evaluate the effectiveness of PEI on managing symptom clusters in patients with cancer.

Methods:

Six databases were searched, together with hand searching, to identify eligible randomized controlled trials from the year 2001 to July 2014. Data selection, quality appraisal of studies, and data extraction were conducted independently by 2 reviewers. Data were synthesized by use of a systematic narrative approach, and meta-analysis was conducted when this was possible.

Results:

Four eligible studies involving 343 cancer patients were included in the review. The methodological quality of the studies was generally fair. Symptom clusters seemed to improve with the provision of PEI. Meta-analysis shows significant improvement in functional performance.

Conclusions:

The evidence that PEI could alleviate cancer symptom clusters is encouraging but inconclusive in this review. Future well-designed investigations testing some commonly used PEI such as progressive muscle relaxation and patient education on various types of cancer symptom clusters are warranted.

Implications for Practice:

This review suggests a promising role of PEI in managing cancer symptom clusters. Healthcare providers should increase their awareness of managing symptom clusters using PEI to yield more effective and efficient cancer care.
Validation of Illumina’s Isaac variant calling workflow
Authors: Mainzer Liudmila S. , Chapman Brad A. , Hofmann Oliver , Rendon Gloria , Stephens Zachary D. , Jongeneel C. Victor
Published: November 2015

As the pace of implementing personalized medicine concepts increases, high-throughput variant calling on hundreds of individual genomes per day is a reality that will likely be faced by sequencing facilities across the country in the near future. While the scientific best practices for human variant calling workflows have been well defined, they also pose serious computational challenges at this high scale. Therefore, efforts in both academia and the private sector have focused on developing alternative workflows that may substantially reduce the computational cost per individual genome. Isaac is an “ultra-fast” variant calling workflow, designed by Illumina, Inc, and is claimed to be six times faster than BWA-GATK, with comparable sensitivity and specificity. This report is an independent review of Isaac, mainly focused on the accuracy of variant calls. We note that Isaac is indeed quite fast, and provide some benchmarks on a few hardware architectures. The overall conclusion from our analysis is that the Isaac workflow has undergone substantial improvement from version 01.14.11.27 to Isaac_2.0. The call accuracy is especially high on NA12878, however exomes tend to have a high fraction of false positive calls. We did not manage to reproduce the 99% sensitivity and specificity reported in the Illumina whitepaper, however that might be improved with further tweaking of the options. This report includes the information about some of the command-line parameters and documentation.
Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome
Authors: Zhang Bin , Wolynes Peter G.
Published: November 2015

We derive an unbiased information theoretic energy landscape for chromosomes at metaphase using a maximum entropy approach that accurately reproduces the details of the experimentally measured pair-wise contact probabilities between genomic loci. Dynamical simulations using this landscape lead to cylindrical, helically twisted structures reflecting liquid crystalline order. These structures are similar to those arising from a generic ideal homogenized chromosome energy landscape. The helical twist can be either right or left handed so chiral symmetry is broken spontaneously. The ideal chromosome landscape when augmented by interactions like those leading to topologically associating domain (TAD) formation in the interphase chromosome reproduces these behaviors. The phase diagram of this landscape shows the helical fiber order and the cylindrical shape persist at temperatures above the onset of chiral symmetry breaking which is limited by the TAD interaction strength.
Modeling Small Non-canonical RNA Motifs with the Rosetta FARFAR Server
Authors: Yesselman Joseph D. , Das Rhiju
Published: November 2015

Non-canonical RNA motifs help define the vast complexity of RNA structure and function, and in many cases, these loops and junctions are on the order of only 10 nucleotides in size. Unfortunately, despite their small size, there is no reliable method to determine the ensemble of lowest energy structures of junctions and loops at atomic accuracy. This chapter outlines straightforward protocols using a webserver for Rosetta Fragment Assembly of RNA with Full Atom Refinement (FARFAR) (http://rosie.rosettacommons.org/rna_denovo/submit) to model the 3D structure of small non-canonical RNA motifs for use in visualizing motifs and for further refinement or filtering with experimental data such as NMR chemical shifts.
Micro-Pharmacodynamics: BridgingIn VitroandIn VivoExperimental Scales in Testing Drug Efficacy and Resistance
Authors: Rejniak Katarzyna A.
Published: November 2015

Systemic chemotherapy is one of the main anticancer treatments used for most kinds of clinically diagnosed tumors. However, the efficacy of these drugs can be hampered by the physical attributes of the tumor tissue that can impede the transport of therapeutic agents to tumor cells in sufficient quantities. As a result, drugs that work wellin vitrooften fail at clinical trials when confronted with the complexities of interstitial transport within the tumor microenvironment. ThemicroPDmodel that we developed is used to investigate the penetration of drug molecules through the tumor tissue and influenced by the physical and metabolic properties of tumor microenvironment, and how it affects drug efficacy and the emergence of drug resistance.
Progressive lengthening of 3′ untranslated regions of mRNAs by alternative cleavage and polyadenylation in cellular senescence of mouse embryonic fibroblasts
Authors: Han Miao , Lv Guoliang , Nie Hongbo , Shen Ting , Niu Yichi , Li Xueping , Chen Meng , Zheng Xia , Li Wei , Ding Chen , Wei Gang , Gu Jun , Tian Xiao-Li , Zheng Yufang , Liu Xinhua , Hu Jinfeng , Tao Wei , Ni Ting
Published: November 2015

Background

Cellular senescence has historically been viewed as an irreversible cell cycle arrest that acts to prevent cancer. Recent discoveries demonstrated that cellular senescence also played a vital role in normal embryonic development, tissue renewal and senescence-related diseases. Alternative cleavage and polyadenylation (APA) is an important layer of post-transcriptional regulation, which has been found playing an essential role in development, activation of immune cells and cancer progression. However, the role of APA in the process of cellular senescence remains unclear.

Materials and Methods

We applied high-throughput paired-end polyadenylation sequencing (PA-seq) and strand-specific RNA-seq sequencing technologies, combined systematic bioinformatics analyses and experimental validation to investigate APA regulation in different passages of mouse embryonic fibroblasts (MEFs) and in aortic vascular smooth muscle cells of rats (VSMCs) with different ages.

Results

Based on PA-seq, we found that genes in senescent cells tended to use distal pA sites and an independent bioinformatics analysis for RNA-seq drew the same conclusion. In consistent with these global results, both the number of genes significantly preferred to use distal pAs in senescent MEFs and VSMCs were significantly higher than genes tended to use proximal pAs. Interestingly, the expression levels of genes preferred to use distal pAs in senescent MFEs and VSMCs tended to decrease, while genes with single pAs did not show such trend. More importantly, genes preferred to use distal pAs in senescent MFEs and VSMCs were both enriched in common senescence-related pathways, including ubiqutin mediated proteolysis, regulation of actin cytoskeleton, cell cycle and wnt signaling pathway. By cis-elements analyses, we found that the longer 3′ UTRs of the genes tended to use distal pAs progressively can introduce more conserved binding sites of senescence-related miRNAs and RBPs. Furthermore, 375 genes with progressive 3′ UTR lengthening during MEF senescence tended to use more strong and conserved polyadenylation signal (PAS) around distal pA sites and this was accompanied the observation that expression level of core factors involved in cleavage and polyadenylation complex was decreased.

Conclusions

Our finding that genes preferred distal pAs in senescent mouse and rat cells provide new insights for aging cells’ posttranscriptional gene regulation in the view of alternative polyadenylation given senescence response was thought to be a tumor suppression mechanism and more genes tended to use proximal pAs in cancer cells. In short, APA was a hidden layer of post-transcriptional gene expression regulation involved in cellular senescence.
Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs
Authors: Chen Jenny , Shishkin Alexander A. , Zhu Xiaopeng , Kadri Sabah , Maza Itay , Hanna Jacob H. , Regev Aviv , Garber Manuel
Published: November 2015

BACKGROUND

Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across multitudes of species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: 1) identifying truly noncoding genes fromde novoreconstructed transcriptomes, and 2) prioritizing hundreds of resulting putative lncRNAs from each sample for downstream experimental interrogation.

RESULTS

We presentslnckv, a computational lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-Sequencing data and further prioritizes lncRNAs by characterizing selective constraint as a proxy for function. Our filtering pipeline is comparable to manual curation efforts and more sensitive than previously published approaches. Further, we develop, for the first time, a sensitive alignment pipeline for aligning lncRNA loci and propose new evolutionary metrics relevant for both sequence and transcript evolution. Our analysis reveals that selection acts in several distinct patterns, and uncovers two notable classes of lncRNAs: one showing strong purifying selection at RNA sequence and another where constraint is restricted to the regulation but not the sequence of the transcript.

CONCLUSION

Our novel comparative methods for lncRNAs reveals 233 constrained lncRNAs out of tens of thousands of currently annotated transcripts, which we believe should be prioritized for further interrogation. To aid in their analysis we provide theslncky Evolution Browseras a resource for experimentalists.
A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer
Authors: Mucaki Eliseos J. , Caminsky Natasha G. , Perri Ami M. , Lu Ruipeng , Laederach Alain , Halvorsen Matthew , Knoll Joan HM. , Rogan Peter K.
Published: November 2015

Background

Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significantly increases the number of VUS detected. While prior studies have emphasized protein coding variants, non-coding sequence variants have also been proven to significantly contribute to high penetrance disorders, such as hereditary breast and ovarian cancer (HBOC). We present a strategy for analyzing different functional classes of non-coding variants based on information theory (IT).

Methods

We captured and enriched for coding and non-coding variants in genes known to harbor mutations that increase HBOC risk. Custom oligonucleotide baits spanning the complete coding, non-coding, and intergenic regions 10 kb up- and downstream ofATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2,andTP53were synthesized for solution hybridization enrichment. Unique and divergent repetitive sequences were sequenced in 102 high-risk patients without identified mutations inBRCA1/2.Aside from protein coding changes, IT-based sequence analysis was used to identify and prioritize pathogenic non-coding variants that occurred within sequence elements predicted to be recognized by proteins or protein complexes involved in mRNA splicing, transcription, and untranslated region (UTR) binding and structure. This approach was supplemented byin silicoand laboratory analysis of UTR structure.

Results

15,311 unique variants were identified, of which 245 occurred in coding regions. With the unified IT-framework, 132 variants were identified and 87 functionally significant VUS were further prioritized. We also identified 4 stop-gain variants and 3 reading-frame altering exonic insertions/deletions (indels).

Conclusions

We have presented a strategy for complete gene sequence analysis followed by a unified framework for interpreting non-coding variants that may affect gene expression. This approach distills large numbers of variants detected by NGS to a limited set of variants prioritized as potential deleterious changes.
Does country-level governance enhance ethical behaviour of firms? An African perspective
Authors: Agyemang Otuo Serebour , Fantini Giulia , Frimpong Joyce
Published: November 2015

Purpose

– The purpose of this paper is to examine the relationship between country-level governance and ethical behaviour of firms in African countries in the period 2009-2012.

Design/methodology/approach

– It uses a broad set of country-level governance ratings by the World Bank and data on ethical behaviour of firms by the World Economic Forum’s report on Global Competitiveness. Full data of a total of 39 African economies out of the 54 (including two disputed) economies over the sample period were obtained for this analysis.

Findings

– The authors find a statistically significant and positive relationship between country-level rule of law, regulatory quality, control of corruption and democracy, and firm ethical behaviour of firms in African economies. This implies that improvement in country-level rule of law, regulatory quality, control of corruption and democracy tends to be associated with sound ethical behaviour of firms in African economies. However, the authors did not find any statistically significant relationship between country-level accountability, political stability, outsider model of governance and ethical behaviour of firms.

Practical implications

– As a continent that is yet to fully discover its potential, the practice of good governance is particularly germane, as this may not only help ensure sound ethical standards of corporations, but may also aid the continent to attract foreign investors, which will beneficially impact economic growth and development of African economies. In this respect, efforts by governments across the continent to ensuring good governance are laudable. One possible way is to ensure an effective and transparent enforcement of laws to stimulate compliance in a specifically clear-cut manner by crafting costs for non-compliance (for instance, legal costs, investigation cost, imprisonment, dent to image and fines).

Originality/value

– This paper reinforces the belief that the existence of country-level good governance could provide and enhance cohesive and internally consistent ethical standards of companies.
Non-parametric decomposition and the choice of reference group
Authors: Anspal Sten
Published: November 2015

Purpose

– The Ñopo (2008) method of non-parametric decomposition, a matching-based alternative to Oaxaca (1973) and Blinder’s (1973) method of wage gap decomposition, is subject to the so-called “index number problem” common to the Oaxaca-Blinder and many related methods: its results are sensitive to the (arbitrary) choice of either male or female sex as the reference category in decomposition. The purpose of this paper is to address this issue by proposing an extension to the method that is invariant to the choice of reference category.

Design/methodology/approach

– The Ñopo method is modified such that the wage structure of the average worker instead of either male or female worker’s is used as the reference, enabling one to distinguish the “male advantage” and “female advantage” portions of the gender wage gap. As an illustration, a decomposition of the gender wage gap is performed with the modified method, using data from 15 OECD countries.

Findings

– The empirical results using the Ñopo decomposition indicate substantial differences in estimates of the unexplained gap depending on which sex is used as the reference category. Moreover, this disparity varies significantly with the choice of covariates used in the decomposition. This confirms there is significant cross-country variation in the asymmetry between male advantage and female disadvantage and that a decomposition method making this explicit would be relevant in real world settings.

Originality/value

– The extension of the Ñopo method proposed in this paper offers a way of decomposing the wage gaps in a way that is not sensitive to the choice of the reference category.