bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative study of electron motion and stability for different focusing regimes in a free-electron laser with three-dimensional helical wiggler
Authors: Xu Jing-Yue , Wang S.-J. , Xu Y.-G. , Ji Y.-P. , Liu X.-X. , Zhang Shi-Chang
Published: July 2015

Since the electromagnetic energy gained by the laser wave in a free-electron laser (FEL) is transferred from the kinetic energy loss of a relativistic electron beam, the stability of electron motion is one of the key factors that affect FEL performance. In this paper the stability of electron motion is compared for different focusing regimes. It is demonstrated that the natural focusing regime of a three-dimensional wiggler is easily broken by the self-field of the electron beam. The magnetic focusing regime of an axial guide magnetic field is based on the superposition of a strong Larmor rotation on the transverse quiver motion of the electrons, while the electric focusing regime of an ion-channel guiding field generates an electric force to counteract the divergent effect of the beam self-field. In comparison with the magnetic focusing regime of an external magnetic system, the electric focusing regime of an ion-channel guiding field may yield smaller instantaneous Larmor radius and slighter Larmor-centre deviation from the axis and provide better motion stability.
Low-power radio-frequency excitation as a plasma source in a Penning–Malmberg trap: a systematic study
Authors: Maero G. , Chen S. , Pozzoli R. , Romé M.
Published: July 2015

A novel method was experimentally demonstrated to produce a low-density electron plasma in a Penning–Malmberg trap, exploiting the static electric and magnetic confinement fields together with a periodic excitation with amplitudes as low as 0.5–5 V and frequencies in the MHz range. This unusual technique proved to be applicable as a replacement for conventional electron sources in Penning devices and presents interesting aspects both in terms of basic science and technological applications. Nevertheless, the experimental observations demonstrate the high sensitivity of plasma features of interest (charge, mean density and density distribution) to the experimental conditions, namely trap configuration and excitation parameters, and as a consequence clear trends have not been identified so far. We present an experimental campaign of measurements where several parameters were systematically changed leading to a better assessment of the plasma production mechanism and to the identification of common trends.
Radially anisotropic systems with forces: equilibrium states
Authors: Di Cintio Pierfrancesco , Ciotti L. , Nipoti C.
Published: July 2015

We continue the study of collisionless systems governed by additive$r^{-{\it\alpha}}$interparticle forces by focusing on the influence of the force exponent${\it\alpha}$on radial orbital anisotropy. In this preparatory work, we construct the radially anisotropic Osipkov–Merritt phase-space distribution functions for self-consistent spherical Hernquist models with$r^{-{\it\alpha}}$forces and$1\leqslant {\it\alpha}<3$. The resulting systems are isotropic at the centre and increasingly dominated by radial orbits at radii larger than the anisotropy radius$r_{a}$. For radially anisotropic models we determine the minimum value of the anisotropy radius$r_{ac}$as a function of${\it\alpha}$for phase-space consistency (such that the phase-space distribution function is nowhere negative for$r_{a}\geqslant r_{ac}$). We find that$r_{ac}$decreases for decreasing${\it\alpha}$, and that the amount of kinetic energy that can be stored in the radial direction relative to that stored in the tangential directions for marginally consistent models increases for decreasing${\it\alpha}$. In particular, we find that isotropic systems are consistent in the explored range of${\it\alpha}$. By means of direct$N$-body simulations, we finally verify that the isotropic systems are also stable.
Lagrangian coherent structures and plasma transport processes
Authors: Falessi M. V. , Pegoraro F. , Schep T. J.
Published: July 2015

A dynamical system framework is used to describe transport processes in plasmas embedded in a magnetic field. For periodic systems with one degree of freedom, the Poincaré map provides a splitting of the phase space into regions where particles have different kinds of motion: periodic, quasi-periodic or chaotic. The boundaries of these regions are transport barriers, i.e. a trajectory cannot cross such boundaries throughout the evolution of the system. Lagrangian coherent structures generalize this method to systems with the most general time dependence, splitting the phase space into regions with different qualitative behaviours. This leads to the definition of finite-time transport barriers, i.e. trajectories cannot cross the barrier for a finite amount of time. This methodology can be used to identify fast recirculating regions in the dynamical system and to characterize the transport between them.
Solitary waves in asymmetric electron–positron–ion plasmas
Authors: Lu Ding , Li Zi-Liang , Xie Bai-Song
Published: July 2015

By solving the coupled equations of the electromagnetic field and electrostatic potential, we investigate solitary waves in an asymmetric electron–positron plasma and/or electron–positron–ion plasmas with delicate features. It is found that the solutions of the coupled equations can capture multipeak structures of solitary waves in the case of cold plasma, which are left out by using the long-wavelength approximation. By considering the effect of ion motion with respect to non-relativistic and ultra-relativistic temperature plasmas, we find that the ions’ mobility can lead to larger-amplitude solitary waves; especially, this becomes more obvious for a high-temperature plasma. The effects of asymmetric temperature between electrons and positrons and the ion fraction on the solitary waves are also studied and presented. It is shown that the amplitudes of solitary waves decrease with positron temperature in asymmetric temperature electron–positron plasmas and decrease also with ion concentration.
Electron inertia effect on incompressible plasma flow in a planar channel
Authors: Gavrikov M. B. , Taiurskii A. A.
Published: July 2015

In this paper, we consider a one-fluid model of electromagnetic hydrodynamics (EMHD) of quasi-neutral plasma, with ion and electron inertia fully taken into account. The EMHD and the MHD models are compared with regard to solving the classical problem of steady flow of incompressible plasma in a planar channel. In the MHD theory, the solution is given by the Hartmann flow, whereas in the EMHD model, the diagram of the longitudinal velocity is shown to be significantly different from the Hartmann profile: in particular, near-wall flows and a counterflow appear, while the flow velocity may significantly deviate from the direction of the antigradient pressure causing plasma to flow (the so-called hydrodynamic ‘Hall effect’). This study shows that the EMHD and the MHD planar channel theories are practically the same for liquid metal plasma and are very different for gas plasma.
Nonlinear dust acoustic travelling waves in dusty plasmas due to dust charge fluctuations
Authors: Saha Asit , Chatterjee Prasanta , Pal Nikhil
Published: July 2015

Dust acoustic solitary waves, blow-up solitary waves and periodic waves have been investigated in unmagnetized dusty plasmas with Maxwell-distributed electrons and ions, considering dust charge fluctuations using the bifurcation theory of planar dynamical systems. The basic equations are transformed to an ordinary differential equation involving the electrostatic potential. Applying the bifurcation theory of planar dynamical systems, we have established the existence of solitary, blow-up solitary and periodic waves. Four exact solutions of the solitary, blow-up solitary and periodic waves are derived depending on the physical parameters. Regarding the solitary, blow-up solitary and periodic waves, we have presented the combined effects of the density ratio of electrons and ions (${\it\alpha}$), the temperature ratio of electrons and ions $({\it\beta})$ and the speed of the travelling wave ($v$) on the characteristics of dust acoustic solitary, blow-up solitary and periodic waves.
Guiding-centre transformation of the radiation–reaction force in a non-uniform magnetic field
Authors: Hirvijoki E. , Decker J. , Brizard A. J. , Embréus O.
Published: July 2015

In this paper, we present the guiding-centre transformation of the radiation–reaction force of a classical point charge travelling in a non-uniform magnetic field. The transformation is valid as long as the gyroradius of the charged particles is much smaller than the magnetic field non-uniformity length scale, so that the guiding-centre Lie-transform method is applicable. Elimination of the gyromotion time scale from the radiation–reaction force is obtained with the Poisson-bracket formalism originally introduced by Brizard (Phys. Plasmas, vol. 11, 2004, 4429–4438), where it was used to eliminate the fast gyromotion from the Fokker–Planck collision operator. The formalism presented here is applicable to the motion of charged particles in planetary magnetic fields as well as in magnetic confinement fusion plasmas, where the corresponding so-called synchrotron radiation can be detected. Applications of the guiding-centre radiation–reaction force include tracing of charged particle orbits in complex magnetic fields as well as the kinetic description of plasma when the loss of energy and momentum due to radiation plays an important role, e.g. for runaway-electron dynamics in tokamaks.
Nonlinear dynamics of ion acoustic waves in quantum pair-ion plasmas
Authors: Sahu Biswajit , Pal Barnali , Poria Swarup , Roychoudhury Rajkumar
Published: July 2015

The nonlinear properties of the ion acoustic waves (IAWs) in a three-component quantum plasma comprising electrons, and positive and negative ions are investigated analytically and numerically by employing the quantum hydrodynamic (QHD) model. The Sagdeev pseudopotential technique is applied to obtain the small-amplitude soliton solution. The effects of the quantum parameter$H$, positive to negative ion density ratio${\it\beta}$and Mach number on the nonlinear structures are investigated. It is found that these factors can significantly modify the properties of the IAWs. The existence of quasi-periodic and chaotic oscillations in the system is established. Switching from quasi-periodic to chaotic is possible with the variation of Mach number or quantum parameter$H$.
Ion-acoustic shocks with reflected ions: modelling and particle-in-cell simulations
Authors: Liseykina T. V. , Dudnikova G. I. , Vshivkov V. A. , Malkov M. A.
Published: July 2015

Non-relativistic collisionless shock waves are widespread in space and astrophysical plasmas and are known as efficient particle accelerators. However, our understanding of collisionless shocks, including their structure and the mechanisms whereby they accelerate particles, remains incomplete. We present here the results of numerical modelling of an ion-acoustic collisionless shock based on the one-dimensional kinetic approximation for both electrons and ions with a real mass ratio. Special emphasis is paid to the shock-reflected ions as the main driver of shock dissipation. The reflection efficiency, the velocity distribution of reflected particles and the shock electrostatic structure are studied in terms of the shock parameters. Applications to particle acceleration in geophysical and astrophysical shocks are discussed.
Magnetorotational instability in cool cores of galaxy clusters
Authors: Nipoti Carlo , Posti L. , Ettori S. , Bianconi M.
Published: July 2015

Clusters of galaxies are embedded in halos of optically thin, gravitationally stratified, weakly magnetized plasma at the system’s virial temperature. Owing to radiative cooling and anisotropic heat conduction, such intracluster medium (ICM) is subject to local instabilities, which are combinations of the thermal, magnetothermal and heat-flux-driven buoyancy instabilities. If the ICM rotates significantly, its stability properties are substantially modified and, in particular, also the magnetorotational instability (MRI) can play an important role. We study simple models of rotating cool-core clusters and we demonstrate that the MRI can be the dominant instability over significant portions of the clusters, with possible implications for the dynamics and evolution of the cool cores. Our results give further motivation for measuring the rotation of the ICM with future X-ray missions such as ASTRO-H and ATHENA.
Nucleation and growth of nanoparticles in a plasma by laser ablation in liquid
Authors: Taccogna Francesco
Published: July 2015

Modelling the nucleation and growth of nanoparticles in liquid-phase laser ablation is very important to optimize and control the size and the structure of nanoparticles. However, the detailed formation process of nanoparticles after laser ablation is still unclear. In the present study we investigated for the first time the kinetic growth of nanoparticles synthesized by laser ablation in water, emphasizing the leading role of the plasma medium and in particular the electrostatic agglomeration due to the charging of the nanoparticle in the plasma plume. The importance of the confining role of the liquid medium on the plasma plume is revealed, showing how an isothermal expansion is able to produce smaller nanoparticles compared to an adiabatic cooling.
Generation of zonal flow and magnetic field in the ionospheric E-layer
Authors: Kahlon L. Z. , Kaladze T. D.
Published: July 2015

We review the generation of zonal flow and magnetic field by coupled electromagnetic ultra-low-frequency waves in the Earth’s ionospheric E-layer. It is shown that, under typical ionospheric E-layer conditions, different planetary low-frequency waves can couple with each other. Propagation of coupled internal-gravity–Alfvén, coupled Rossby–Khantadze and coupled Rossby–Alfvén–Khantadze waves is revealed and studied. A set of appropriate equations describing the nonlinear interaction of such waves with sheared zonal flow is derived. The conclusion on the instability of short-wavelength turbulence of such coupled waves with respect to the excitation of low-frequency and large-scale perturbation of the sheared zonal flow and sheared magnetic field is deduced. The nonlinear mechanism of the instability is based on the parametric triple interaction of finite-amplitude coupled waves leading to the inverse energy cascade towards longer wavelength. The possibility of generation of an intense mean magnetic field is shown. Obtained growth rates are discussed for each case of the considered coupled waves.
Measurement of the angle, temperature and flux of fast electrons emitted from intense laser–solid interactions
Authors: Rusby D. R. , Wilson L. A. , Gray R. J. , Dance R. J. , Butler N. M. H. , MacLellan D. A. , Scott G. G. , Bagnoud V. , Zielbauer B. , McKenna P. , Neely D.
Published: July 2015

High-intensity laser–solid interactions generate relativistic electrons, as well as high-energy (multi-MeV) ions and x-rays. The directionality, spectra and total number of electrons that escape a target-foil is dependent on the absorption, transport and rear-side sheath conditions. Measuring the electrons escaping the target will aid in improving our understanding of these absorption processes and the rear-surface sheath fields that retard the escaping electrons and accelerate ions via the target normal sheath acceleration (TNSA) mechanism. A comprehensive Geant4 study was performed to help analyse measurements made with a wrap-around diagnostic that surrounds the target and uses differential filtering with a FUJI-film image plate detector. The contribution of secondary sources such as x-rays and protons to the measured signal have been taken into account to aid in the retrieval of the electron signal. Angular and spectral data from a high-intensity laser–solid interaction are presented and accompanied by simulations. The total number of emitted electrons has been measured as $2.6\times 10^{13}$ with an estimated total energy of $12\pm 1~\text{J}$ from a $100~{\rm\mu}\text{m}$ Cu target with 140 J of incident laser energy during a $4\times 10^{20}~\text{W}~\text{cm}^{-2}$ interaction.
Roberts on Depletion: How Much Better Can We Do for Future People?
Authors: GREENE MARK E.
Published: July 2015

Suppose that Depletion will reduce the well-being of future people. Many of us would like to say that Depletion is wrong because of the harm to future people. However, it can easily be made to seem that Depletion is actually harmless – this is the non-identity problem. I discuss a particularly ingenious attempt by Melinda Roberts to attribute a harm to Depletion. I will argue that the magnitude of Roberts's harm is off target by many orders of magnitude: it is just too tiny to explain the intuitive wrong of Depletion.
New AIE-active dinuclear Ir(iii) complexes with reversible piezochromic phosphorescence behaviour
Authors: Li Guangfu , Ren Xinyao , Shan Guogang , Che Weilong , Zhu Dongxia , Yan Likai , Su Zhongmin , Bryce Martin R.
Published: July 2015

Two new AIE-active cationic dinuclear Ir(iii) complexes exhibit highly reversible piezochromic phosphorescence behaviour enabling the construction of a re-writable phosphorescence data recording device.
Phosphonate monoesters on a thiacalix[4]arene framework as potential inhibitors of protein tyrosine phosphatase 1B
Authors: Trush Viacheslav V. , Kharchenko Sergiy G. , Tanchuk Vsevolod Yu. , Kalchenko Vitaly I. , Vovk Andriy I.
Published: July 2015

Monoester derivatives of thiacalix[4]arene tetrakis(methylphosphonic) acid were found to be capable of inhibiting protein tyrosine phosphatase 1B. In addition, these compounds can strongly bind to human serum albumin.
Chlorine/UV induced photochemical degradation of total ammonia nitrogen (TAN) and process optimization
Authors: Zhang Xinran , Li Weiguang , Ren Pengfei , Wang Xiaoju
Published: July 2015

Three independent factors have significant interaction effects on TAN photodecomposition.
Furthering the chemosensing of silver nanoclusters for ion detection
Authors: Ding Weihua , Huang Saipeng , Guan Lingmei , Liu Xianhu , Luo Zhixun
Published: July 2015

An eco-friendly silver nanocluster chemosensor for Mn2+and I−ion detection, differentiation and bioimaging was synthesized. The chemosensing mechanisms were elucidated by microscopic characterization and spectral analyses.
Entanglement and Energy for Vibrationally Localized States in Molecule CS2
Authors: Yang Zi-xin , Shen Xing , Hou Xi-wen
Published: July 2015

The dynamics of quantum entanglement described by the von Neumann entropy is studied for the localized states of Fermi-resonance coupling vibrations in molecule CS2, where the interacting energy between the stretching and the bending modes is considered to establish a connection between entanglement and energy. It is shown that entanglement reveals dominant anti-correlation with the interacting energy for the stretch-localized state, while that exhibits dominantly positive correlation for the bend-localized state. The entanglement and the energy for the dislocalized states are discussed as well. Those are useful for molecular quantum computing and quantum information in high dimensional states.
Senior staff perspectives of a quality indicator program in public sector residential aged care services: a qualitative cross-sectional study in Victoria, Australia
Authors: Chadwick Liam M. , MacPhail Aleece , Ibrahim Joseph E. , McAuliffe Linda , Koch Susan , Wells Yvonne
Published: July 2015

Objective
The aims of the present study were to describe the views of senior clinical and executive staff employed in public sector residential aged care services (RACS) about the benefits and limitations of using quality indicators (QIs) for improving care, and to identify any barriers or enablers to implementing the QI program.

Methods
A cross-sectional qualitative study using semistructured interviews and direct observation of key informants involved in the QI program was performed across 20 public sector RACS in Victoria, Australia. Participants included senior clinical, executive and front-line staff at the RACS. The main outcome measures were perceived benefits and the enablers or barriers to the implementation of a QI program.

Results
Most senior clinical and executive staff respondents reported substantive benefits to using the QIs and the QI program. A limited number of staff believed that the QI program failed to improve the quality of care and that the resource requirements outweighed the benefits of the program, resulting in disaffected staff.

Conclusions
The QIs and QI program acted as a foundation for improving standards of care when used at the front line or point of care. Senior executive engagement in the QI program was vital to successful implementation.

What is known about this topic?
QIs measure the structures, processes or outcomes of care and identify issues that need further investigation or improvement. QIs are increasingly being adopted throughout the world. In Australia, the public sector RACS QIs project was implemented in 2006. It is yet to be formally evaluated.

What does this paper add?
Perceived benefits and limitations of the QI program were identified, together with barriers to successful implementation of the program and recommendations for future improvements. QI data were reported to improve quality culture and assist with identifying clinical areas for improvement. However, the QI program was associated with significantly increased workload and some stakeholders questioned its usefulness. The QI program studied could be improved through better access to education and training for those responsible for data collection and results dissemination to appropriate training and resources; and revision of the QI definitions and reporting methods.

What are the implications for clinicians?
QI data are useful for identifying opportunities for quality improvement. Despite data limitations, public sector RACS can use data for internal benchmarking, staff education and targeting of quality improvement interventions. At the policy level, revising the QI definitions and simplifying data collection and reporting would improve and strengthen the program. At the clinician and executive level, there is also a strong preference for QI data that allow comparison and benchmarking between facilities.
Application and implications of Mental Health Act 2007 (NSW) certificate use in acute generalist settings
Authors: Lamont Scott , Brunero Scott , Sharma Swapnil
Published: July 2015

Objective
This retrospective study aimed to explore the appropriate application and implications of Mental Health Act 2007 (NSW) (MHA) certificate use in a metropolitan generalist hospital in New South Wales.

Methods
A de-identified MHA certificate review was undertaken within acute generalist medical and surgical specialties between June 2012 and May 2013. To assess differences, data were separated into two categories according to whether certificates were completed by psychiatry trainees or generalist medical officers. Analysis of indications for detention was also undertaken and qualitatively matched against legislative criteria.

Results
A total of 43 MHA certificates were included in the review, which highlighted missing elements in most certificates. Differences were found when professional consensus by the researchers was used to match documentation to legislative criteria. The researchers disagreed with nine of the 16 indications (mental illness/mental disorder) by the generalist medical officers and only one indication by a psychiatry trainee. Six of the certificates appeared to be related to lack of capacity and need for treatment of medical conditions, thus more related to Guardianship Act 1987 (NSW) applications.

Conclusion
This study highlights inconsistencies in legislative knowledge and requirements between professional groups. Education and training opportunities have been identified to ensure greater consistency in application of the MHA, preservation of patient rights and avoidance of stigma. MHA use in this setting should be exercised with caution and by appropriately trained individuals.

What is known about the topic?
The MHA and its state and territory counterparts provide for the treatment, care and support of people who have a mental illness and the protection of a person’s rights therein. Despite not being intended for application in generalist facilities, mental health legislation is widely used in generalist facilities and certificates are completed by generalist health professionals with limited training in this area of practice.

What does this paper add?
This study adds to the limited body of knowledge in relation to MHA detention in acute generalist facilities. Disparate preparation of medical officers in the use of this legislation has been identified, which has potential wider implications for patients beyond immediate care.

What are the implications for practitioners?
Inadequate attention to correct completion of MHA certificates and associated documentation could potentially invalidate detention, leaving healthcare professionals and institutions open to litigious claims that restrictive or coercive practices subsequent to the certificate’s completion were technically unlawful. Further, detention under the MHA, albeit temporarily, has potential human rights issues attached and wrongful detention could lead to longstanding issues relating to stigma.
Acute rehospitalisation during the first 3 months of in-patient rehabilitation for traumatic brain injury
Authors: Andraweera Nalinda , Seemann Richard
Published: July 2015

Objective Unplanned re-admission to acute care hospitals during in-patient rehabilitation causes disruption to the rehabilitation program and increases the cost of health care. The aims of the present study were to identify the frequency, reasons and duration of disruption to rehabilitation because of acute re-admissions during the first 3 months of in-patient rehabilitation for traumatic brain injury (TBI) and to investigate the correlation between the duration of acute rehospitalisation and the discharge functional independence measure (FIM) score. Methods A retrospective study was conducted on patients admitted for in-patient rehabilitation following TBI to a rehabilitation hospital in Auckland, New Zealand, between January 2009 and August 2013. Data on duration and reasons for acute rehospitalisation, as well as admission and discharge FIM scores, were obtained from electronic patient records. Pearson correlation was used to evaluate the relationship between the duration of acute rehospitalisation and the discharge FIM score. Results Of the 628 patients admitted for brain injury rehabilitation, 71 (11.3%) required acute rehospitalisation within the first 3 months. The main reasons for acute rehospitalisation were preventable medical causes (43.8%), including urinary tract infections, respiratory tract infections and coronary artery disease. Of the acute re-admissions, 76.6% were within the first month of admission to the rehabilitation centre and 46.6% needed in-patient treatment in the acute care hospital for >5 days. There was a moderately strong negative correlation between the duration of stay in the acute care hospital and the discharge FIM score (r = – 0.412; P = 0.0005). Conclusion A significant number of patients admitted for in-patient rehabilitation following TBI require acute rehospitalisation due to preventable medical causes. Because the duration of acute rehospitalisation has a negative impact on rehabilitation functional gain, preventive measures and surveillance need to be further investigated and optimised. What is known about the topic? The incidence of acute rehospitalisation of patients in the community following brain injury rehabilitation is 20%–25%, with approximately half the re-admissions being for elective reasons, including orthopaedic and reconstructive surgery. What does this paper add? Unplanned acute rehospitalisation during first 3 months of in-patient rehabilitation following TBI is due to preventable causes and results in lower FIM scores on discharge. What are the implications for practitioners? An uninterrupted rehabilitation programme is vital for achieving functional outcomes.
DFT and SERS Study of Adsorption of 1,4-Dimethoxy-2-nitro-3-methylanthracene-9,10-dione onto Silver Nanoparticles
Authors: Geetha K. , Rekha T. N. , Umadevi M. , Rajkumar Beulah J.M. , Sathe G.V. , Vanelle P. , Terme T. , Khoumeri O.
Published: July 2015

Surface-enhanced Raman scattering (or spectroscopy), commonly known as SERS, has been employed to investigate the adsorption mechanism and orientation of 1,4-dimethoxy-2-nitro-3-methylanthracene-9,10-dione (DMNMAD) molecule onto silver. Silver nanoparticles (Ag NPs) were synthesized based on a solution combustion method using citric acid as a fuel. Scanning electron microscopy and transition electron microscopy studies confirm the crystalline nature and morphology of the synthesized silver nanoparticles. Theoretical normal Raman spectra (nRs) and SERS spectra of the DMNMAD molecule, simulated based on DFT/B3PW91 level of theory were validated experimentally. Experimental and theoretical vibrational modes correlate well, confirming the reliable assignments of the vibrational bands. Enhancement of C=O stretching and C–H in-plane vibrational modes in the SERS spectrum indicates the ‘stand-on’ orientation of the molecule on the silver nanoparticles after adsorption. The frontier molecular orbitals confirm the charge transfers between the molecule and silver nanoparticles following the process of adsorption. As anthraquinone derivatives have been recently used as potent anti-tumour drugs, the adsorption studies reported in the current investigation can pave way to the potential application of DMNMAD in drug delivery.
Effects of grazing by large herbivores on plant diversity and productivity of semi-arid alpine steppe on the Qinghai-Tibetan Plateau
Authors: Ganjurjav Hasbagan , Duan Min-jie , Wan Yun-fan , Zhang Wei-na , Gao Qing-zhu , Li Yue , Jiangcun Wang-zha , Danjiu Luo-bu , Guo Hong-bao
Published: July 2015

Grazing by large herbivores may have a strong impact on plant diversity and productivity, but the effects are expected to vary with grazing pressure. The changes in productivity and species diversity of Stipa purpurea-dominated semi-arid alpine steppe grassland were measured under four different stocking rates of Tibetan sheep [no grazing, light (2.4 sheep units ha–1), moderate (3.6 sheep units ha–1), and heavy (6.0 sheep units ha–1) grazing] in a 5-year (2006–2010) grazing experiment on the Qinghai-Tibetan Plateau, China. Herbage mass and aboveground net primary productivity of alpine steppe declined significantly with increasing stocking rate (P < 0.05). Over the 5 years of the experiment, the proportion of forbs and sedges increased significantly under light and moderate grazing; the proportion of grasses decreased significantly, whereas the proportion of S. purpurea did not change compared with the no grazing treatment. Species diversity was highest under moderate grazing and was significantly higher than the no grazing treatment in 2 years (2008 and 2010). Moderate grazing enhanced the species diversity of the plant community due to an increase in the proportion of forbs. There were significant positive linear correlations between herbage mass and species diversity under no and light grazing. Species diversity was not related to productivity under moderate and heavy grazing. In conclusion, grazing by sheep reduced plant productivity; plant diversity increased under low and moderate grazing, and was as a result of changes in the composition of the plant community of a semi-arid alpine steppe.
Condom-associated erection problems: behavioural responses and attributions in young, heterosexual men
Authors: Hill Brandon J. , Sanders Stephanie A. , Crosby Richard A. , Ingelhart Kara N. , Janssen Erick
Published: July 2015

Background
Previous studies have associated men who experience condom-associated erection problems (CAEP) with incomplete condom use and/or foregoing using condoms altogether. However, how men respond to CAEP and what they attribute CAEP to, remains unclear. Understanding young men’s CAEP responses and attributions could help improve sexually transmissible infections (STI)/HIV prevention programs and interventions. Methods: Behavioural responses to, and attributions for, CAEP during application (CAEP-Application) and/or during penile-vaginal intercourse (CAEP-PVI) were reported using an online questionnaire by 295 young, heterosexual men (aged 18–24 years) who were recruited via social media websites and university Listservs across major cities in the Midwestern USA. Results: Behavioural responses to CAEP-Application included receiving oral or manual stimulation, stimulating a partner, self-stimulation, foregoing condom use and applying the condom after starting intercourse. Attributions for CAEP-Application included: distraction, fit and feel problems, application taking too long and having consumed too much alcohol. Behavioural responses to CAEP-PVI included increasing the intensity of intercourse, removing the condom to receive oral or manual stimulation and removing condom and continuing intercourse. Attributions for CAEP-PVI included: lack of sensation, taking too long to orgasm, not being ‘turned on’ enough, fit and feel problems and partner-related factors. Conclusions: Men who report CAEP respond with both STI/HIV risk-reducing and potentially risk-increasing behaviours (e.g. forgoing condom use). Men attribute their experiences to a wide range of individual- and partner-level factors. Addressing men’s CAEP behavioural responses and attributions may increase the efficacious value of condom programs and STI/HIV prevention interventions – particularly among men who experience CAEP.
Conformational kinetics reveals affinities of protein conformational states
Authors: Daniels Kyle G. , Suo Yang , Oas Terrence G.
Published: July 2015

Significance

Despite 50 years of studies of coupled binding and conformational change reactions in proteins and nucleic acids, there has been no detailed analysis of the affinities of the multiple conformational states involved. The relationship between these affinities and the dynamics of conformational change has also been largely overlooked. We perform rigorous kinetic analysis of protein conformational change coupled to binding to concomitantly determine binding affinities of individual conformational states and rate constants for conformational changes. The results point to an inextricable link between affinities of the individual states and the change in conformational dynamics upon binding. The difference in affinities of conformational states is critical for driving conformational change and has implications in molecular recognition, allostery, and drug development.
SomaticSignatures: inferring mutational signatures from single-nucleotide variants
Authors: Gehring Julian S. , Fischer Bernd , Lawrence Michael , Huber Wolfgang
Published: July 2015

Summary: Mutational signatures are patterns in the occurrence of somatic single-nucleotide variants that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable and easy-to-use tools that identify such signatures in cancer sequencing data. It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing methods for pattern decomposition, supports extension through user-defined approaches and integrates with existing Bioconductor workflows.

Availability and implementation: The R package SomaticSignatures is available as part of the Bioconductor project. Its documentation provides additional details on the methods and demonstrates applications to biological datasets.

Contact:  julian.gehring@embl.de, whuber@embl.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
C-It-Loci: a knowledge database for tissue-enriched loci
Authors: Weirick Tyler , John David , Dimmeler Stefanie , Uchida Shizuka
Published: July 2015

Motivation: Increasing evidences suggest that most of the genome is transcribed into RNAs, but many of them are not translated into proteins. All those RNAs that do not become proteins are called ‘non-coding RNAs (ncRNAs)’, which outnumbers protein-coding genes. Interestingly, these ncRNAs are shown to be more tissue specifically expressed than protein-coding genes. Given that tissue-specific expressions of transcripts suggest their importance in the expressed tissue, researchers are conducting biological experiments to elucidate the function of such ncRNAs. Owing greatly to the advancement of next-generation techniques, especially RNA-seq, the amount of high-throughput data are increasing rapidly. However, due to the complexity of the data as well as its high volume, it is not easy to re-analyze such data to extract tissue-specific expressions of ncRNAs from published datasets.

Results: Here, we introduce a new knowledge database called ‘C-It-Loci’, which allows a user to screen for tissue-specific transcripts across three organisms: human, mouse and zebrafish. C-It-Loci is intuitive and easy to use to identify not only protein-coding genes but also ncRNAs from various tissues. C-It-Loci defines homology through sequence and positional conservation to allow for the extraction of species-conserved loci. C-It-Loci can be used as a starting point for further biological experiments.

Availability and implementation: C-It-Loci is freely available online without registration at http://c-it-loci.uni-frankfurt.de.

Contact:  uchida@med.uni-frankfurt.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Application of learning to rank to protein remote homology detection
Authors: Liu Bin , Chen Junjie , Wang Xiaolong
Published: July 2015

Motivation: Protein remote homology detection is one of the fundamental problems in computational biology, aiming to find protein sequences in a database of known structures that are evolutionarily related to a given query protein. Some computational methods treat this problem as a ranking problem and achieve the state-of-the-art performance, such as PSI-BLAST, HHblits and ProtEmbed. This raises the possibility to combine these methods to improve the predictive performance. In this regard, we are to propose a new computational method called ProtDec-LTR for protein remote homology detection, which is able to combine various ranking methods in a supervised manner via using the Learning to Rank (LTR) algorithm derived from natural language processing.

Results: Experimental results on a widely used benchmark dataset showed that ProtDec-LTR can achieve an ROC1 score of 0.8442 and an ROC50 score of 0.9023 outperforming all the individual predictors and some state-of-the-art methods. These results indicate that it is correct to treat protein remote homology detection as a ranking problem, and predictive performance improvement can be achieved by combining different ranking approaches in a supervised manner via using LTR.

Availability and implementation: For users’ convenience, the software tools of three basic ranking predictors and Learning to Rank algorithm were provided at http://bioinformatics.hitsz.edu.cn/ProtDec-LTR/home/

Contact:  bliu@insun.hit.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Qualitative network models in support of ecosystem approaches to bivalve aquaculture
Authors: Reum Jonathan C. P. , McDonald P. Sean , Ferriss Bridget E. , Farrell Dara M. , Harvey Chris J. , Levin Phillip S.
Published: July 2015

Predicting the effects of aquaculture development for coastal ecosystems remains challenging, particularly for data-limited systems, and tools that account for complex ecological interactions are needed to support ecosystem approaches to aquaculture. Here, we used qualitative network models (QNMs) to examine the potential community effects of increasing bivalve aquaculture in South Puget Sound, a large estuarine system in Washington, United States. QNMs are formalized conceptual models that require only a qualitative understanding of how variables composing a system interact (that is, the sign of interactions: +, –, and 0) and are therefore well-suited to data-limited systems. Specifically, we examined community-wide responses to scenarios in which bivalve cultivation effort increased for three different bivalve species (Manila clam Venerupis philippinarum, Pacific oyster Crassostrea gigas, and geoduck Panopea generosa). Further, we evaluated community-wide responses to the removal of benthic bivalve predators, a future increase in nutrient loadings, and combinations of these scenarios acting simultaneously. The scenarios enabled identification of potential trade-offs between increased aquaculture and shifts in the abundance of community members and assessment of the possible effects of different management actions. We also analysed the QNM to identify key interactions that influence the sign outcome of community responses to press perturbations, highlighting potential points for management intervention and linkages deserving of more focused quantitative study. QNMs are mathematically robust and highly flexible, but remain underutilized. We suggest that they may serve as valuable tools for supporting ecosystem approaches to aquaculture.
A critique of the balanced harvesting approach to fishing
Authors: Froese Rainer , Walters Carl , Pauly Daniel , Winker Henning , Weyl Olaf L. F. , Demirel Nazli , Tsikliras Athanassios C. , Holt Sidney J.
Published: July 2015

The approach to fisheries termed “balanced harvesting” (BH) calls for fishing across the widest possible range of species, stocks, and sizes in an ecosystem, in proportion to their natural productivity, so that the relative size and species composition is maintained. Such fishing is proposed to result in higher catches with less negative impact on exploited populations and ecosystems. This study examines the models and the empirical evidence put forward in support of BH. It finds that the models used unrealistic settings with regard to life history (peak of cohort biomass at small sizes), response to fishing (strong compensation of fishing mortality by reduced natural mortality), and economics (uniform high cost of fishing and same ex-vessel price for all species and sizes), and that empirical evidence of BH is scarce and questionable. It concludes that evolutionary theory, population dynamics theory, ecosystem models with realistic assumptions and settings, and widespread empirical evidence do not support the BH proposal. Rather, this body of evidence suggests that BH will not help but will hinder the policy changes needed for the rebuilding of ecosystems, healthy fish populations, and sustainable fisheries.
Sessions 8–10
Authors: Ladouceur Robert , Lachance Stella
Published: July 2015

Chapter 7 discusses sessions eight to ten of the treatment program. These sessions explore erroneous cognitions that lead to gambling, the development of skills to challenging and casting doubt on these thoughts, and empowering the client to make decisions about their own gambling behaviours.
Psychiatric Comorbidity Is Associated Prospectively with Diminished Opioid Analgesia and Increased Opioid Misuse in Patients with Chronic Low Back Pain
Authors: Wasan Ajay D. , Michna Edward , Edwards Robert R. , Katz Jeffrey N. , Nedeljkovic Srdjan S. , Dolman Andrew J. , Janfaza David , Isaac Zach , Jamison Robert N.
Published: July 2015

AbstractAbstract

In 81 patients with chronic low back pain prospectively studied for 6½ months with placebo followed by opioids, those with high negative affect were prescribed larger average daily doses of opioids, had less improvement in pain, and had a greater rate of opioid misuse than those with low negative affect. These prospective data support previous cross-sectional data to suggest that negative affect presents an important risk factor in inadequate analgesia from opioids and opioid misuse.

Background:

Opioids are frequently prescribed for chronic low back pain (CLBP), but there are little prospective data on which patient subgroups may benefit. Psychiatric comorbidity, such as high levels of depression and anxiety symptoms (termed comorbid negative affect [NA]), is a common presentation and may predict diminished opioid analgesia and/or increased opioid misuse.

Methods:

The authors conducted a 6½-month prospective cohort study of oral opioid therapy, with an active drug/placebo run-in period, in 81 CLBP patients with low, moderate, and high levels of NA. Treatment included an opioid titration phase with a prescribing physician blinded to NA group assignment and a 4-month continuation phase, during which subjects recorded daily pain levels using an electronic diary. The primary outcome was the percent improvement in average daily pain, summarized weekly.

Results:

There was an overall 25% dropout rate. Despite the high NA group being prescribed a higher average daily dose of morphine equivalents, linear mixed model analysis revealed that the 24 study completers in each of the high NA and low NA groups had an average 21 versus 39% improvement in pain, respectively (P < 0.01). The high NA group also had a significantly greater rate of opioid misuse (39 vs. 8%, P < 0.05) and significantly more and intense opioid side effects (P < 0.01).

Conclusions:

These results indicate that the benefit and risk considerations in CLBP patients with high NA versus low NA are distinctly different. Thus, NA is an important phenotypic variable to characterize at baseline, before deciding whether to prescribe opioids for CLBP.
An Anatomic Study of the Greater Trochanter Starting Point for Intramedullary Nailing in the Skeletally Immature
Authors: Park Paul J. , Weinberg Douglas S. , Petro Kathleen F. , Liu Raymond W.
Published: July 2015

Background:

Trochanteric entry femoral nails have been increasing in popularity in the pediatric population for stabilization in fractures and osteotomies. The proper position for entry point in the coronal plane has been well studied; however, the sagittal plane in the pediatric population has not yet been well characterized.

Methods:

Eighty-eight cadaveric femora aged 8 to 20 years were studied in an apparent neck-shaft angle (ANSA) position, with distal condyles flat on the surface, and a true neck-shaft angle (TNSA) position, with internal rotation to neutralize femoral anteversion. Anterior and lateral offset were measured on lateral and anteroposterior photographs, respectively, as the perpendicular distance from the greater trochanter apex to the center of the intramedullary canal. The effect of rotational position (ANSA vs. TNSA) of the proximal femur was compared using the intraclass correlation coefficient for anterior and lateral offset. Correlations between age, demographics, anteversion, and greater trochanter morphology with anterior and lateral offset were evaluated with multiple regression analysis.

Results:

The mean age was 15.8±3.8 years. The mean anterior displacement of the trochanteric apex was 4.8±3.0 and 4.6±3.2 mm in the ANSA and TNSA positions, respectively. The mean lateral displacement was 10.6±4.2 and 9.7±4.0 mm in the ANSA and TNSA positions, respectively. The intraclass coefficient for anterior offset in the ANSA versus TNSA position was 0.704 and 0.900 for lateral offset. Change was minimal for anterior offset in the ANSA and TNSA positions versus age (standardized beta values 0.240, 0.241, respectively). There was a significant correlation with increasing lateral offset in the ANSA and TNSA positions with increasing age (standardized beta values 0.500, 0.385 respectively).

Conclusions:

In the pediatric population, the tip of the greater trochanter is consistently anterior by approximately 5 mm. The mean lateral displacement was approximately 10 mm and increased with increasing age.

Clinical Relevance:

Nail entry at the pediatric greater trochanter apex would likely result in anterior placement. We recommend inserting the guidewire 5 mm posterior to the apex of the trochanter and confirming coronal and sagittal position with fluoroscopy.