bluuebunny/crossref_metadata_2025 huggingface dataset:
Calculations for the practical applications of quadratic helicity in MHD
Authors: Akhmet'ev Petr M. , Candelaresi Simon , Smirnov Alexandr Yu
Published: October 2017

For the quadratic helicity χ(2), we present a generalization of the Arnol'd inequality which relates the magnetic energy to the quadratic helicity, which poses a lower bound. We then introduce the quadratic helicity density using the classical magnetic helicity density and its derivatives along magnetic field lines. For practical purposes, we also compute the flow of the quadratic helicity and show that for an α2-dynamo setting, it coincides with the flow of the square of the classical helicity. We then show how the quadratic helicity can be extended to obtain an invariant even under compressible deformations. Finally, we conclude with the numerical computation of χ(2) which show cases the practical usage of this higher order topological invariant.
Pinhole induced efficiency variation in perovskite solar cells
Authors: Agarwal Sumanshu , Nair Pradeep R.
Published: October 2017

Process induced efficiency variation is a major concern for all thin film solar cells, including the emerging perovskite based solar cells. In this article, we address the effect of pinholes or process induced surface coverage aspects on the efficiency of such solar cells through detailed numerical simulations. Interestingly, we find that the pinhole size distribution affects the short circuit current and open circuit voltage in contrasting manners. Specifically, while the JSC is heavily dependent on the pinhole size distribution, surprisingly, the VOC seems to be only nominally affected by it. Further, our simulations also indicate that, with appropriate interface engineering, it is indeed possible to design a nanostructured device with efficiencies comparable to those of ideal planar structures. Additionally, we propose a simple technique based on terminal I–V characteristics to estimate the surface coverage in perovskite solar cells.
Determination of plasma displacement based on eddy current diagnostics for the Keda Torus eXperiment
Authors: Tu Cui , Li Hong , Liu Adi , Li Zichao , Zhang Yuan , You Wei , Tan Mingsheng , Luo Bing , Adil Yolbarsop , Hu Jintong , Wu Yanqi , Yan Wentan , Xie Jinlin , Lan Tao , Mao Wenzhe , Ding Weixing , Xiao Chijin , Zhuang Ge , Liu Wandong
Published: October 2017

The measurement of plasma displacement is one of the most basic diagnostic tools in the study of plasma equilibrium and control in a toroidal magnetic confinement configuration. During pulse discharge, the eddy current induced in the vacuum vessel and shell will produce an additional magnetic field at the plasma boundary, which will have a significant impact on the measurement of plasma displacement using magnetic probes. In the newly built Keda Torus eXperiment (KTX) reversed field pinch device, the eddy current in the composite shell can be obtained at a high spatial resolution. This device offers a new way to determine the plasma displacement for KTX through the multipole moment expansion of the eddy current, which can be obtained by unique probe arrays installed on the inner and outer surfaces of the composite shell. In an ideal conductor shell approximation, the method of multipole moment expansion of the poloidal eddy current for measuring the plasma displacement in toroidal coordinates, is more accurate than the previous method based on symmetrical magnetic probes, which yielded results in cylindrical coordinates. Through an analytical analysis of many current filaments and numerical simulations of the current distribution in toroidal coordinates, the scaling relation between the first moment of the eddy current and the center of gravity of the plasma current is obtained. In addition, the origin of the multipole moment expansion of the eddy current in KTX is retrieved simultaneously. Preliminary data on the plasma displacement have been collected using these two methods during short pulse discharges in the KTX device, and the results of the two methods are in reasonable agreement.
Experimental study on self-pulsing in flow-induced atmospheric pressure plasma jet
Authors: Cui Ruilin , He Feng , Miao Jinsong , Ouyang Jiting
Published: October 2017

In this paper, we present an experimental study on the self-pulsing phenomenon in a flow-induced atmospheric pressure plasma jet (APPJ) in a hollow electrode configuration driven by dc voltage supply. The current-voltage curve, the typical waveforms of current and voltage of self-pulsing, the time-resolved images, and the repetition frequency were measured under different experimental conditions. The results show that the APPJ of a hollow electrode can sustain in a stable, repeatable self-pulsing regime. The waveform of the pulsed current is very stable with nearly constant rising time and decay time at different discharge averaged currents. Although the pulsing frequency increases linearly with the averaged current and the gas flow rate, it decreases with the electrode gap. An equivalent electric circuit consisting of a capacitor and two resistors was used to model the self-pulsing discharge plasma. The simulation results and the time-resolved images recorded using an ICCD camera show that the pulsed process of the hollow electrode APPJ contains the evolutions of gas breakdown, discharge development, and decay of a glow plasma. A weak discharge is maintained during the time interval between two pulses, indicating that the self-pulsing in this APPJ is a mode transition between glow and weak discharge.
Intermittent ion leakage from a Penning trap during potential barrier closure
Authors: Himura H. , Kawai S. , Akaike K. , Okada S. , Aoki J. , Masamune S.
Published: October 2017

Intermittent leakages of trapped ions from a Penning trap are clearly explained. Two mechanisms are revealed by considering both experimental and numerical results. The initial leakage is due to ions energized by the potential barrier that is just closing to form a positive potential well. The following leakage is induced by an axial average oscillation of the bulk of the trapped ions. Some individual bounce ions are pushed out of the potential barriers owing to the space potential of the bulk.
Damping of vibrational excitations in glasses at terahertz frequency: The case of 3-methylpentane
Authors: Baldi Giacomo , Benassi Paola , Fontana Aldo , Giugni Andrea , Monaco Giulio , Nardone Michele , Rossi Flavio
Published: October 2017

We report a compared analysis of inelastic X ray scattering (IXS) and of low frequency Raman data of glassy 3-methylpentane. The IXS spectra have been analysed allowing for the existence of two distinct excitations at each scattering wavevector obtaining a consistent interpretation of the spectra. In particular, this procedure allows us to interpret the linewidth of the modes in terms of a simple model which relates them to the width of the first sharp diffraction peak in the static structure factor. In this model, the width of the modes arises from the blurring of the dispersion curves which increases approaching the boundary of the first pseudo-Brillouin zone. The position of the boson peak contribution to the density of vibrational states derived from the Raman scattering measurements is in agreement with the interpretation of the two excitations in terms of a longitudinal mode and a transverse mode, the latter being a result of the mixed character of the transverse modes away from the center of the pseudo-Brillouin zone.
Annealing-induced interfacial atomic intermixing in InAs/GaSb type II superlattices
Authors: Li Xiaochao , Zhang Yong , Jiang Dongwei , Guo Fengyun , Zhao Liancheng
Published: October 2017

We have investigated the effect of post-growth rapid thermal annealing (RTA) on the interface structure and atomic intermixing of InAs/GaSb type II superlattices (T2SLs). It is found that the mechanism of interfacial atomic interdiffusion of the anion (In/Ga) and the cation (As/Sb) is different. The activation energies of 0.62 eV and 0.27 eV are calculated to describe the In/Ga and As/Sb interdiffusion. In T2SLs, RTA will promote As/Sb intermixing across the interfaces between 450 and 480 °C, while In/Ga intermixing will be activated at 500 °C annealing. This demonstrates that the appropriate In/Ga intermixing is important to control the deterioration of the interfacial quality and the formation of dislocations, which is very crucial for the device performance.
Configuration path integral Monte Carlo approach to the static density response of the warm dense electron gas
Authors: Groth Simon , Dornheim Tobias , Bonitz Michael
Published: October 2017

Precise knowledge of the static density response function (SDRF) of the uniform electron gas serves as key input for numerous applications, most importantly for density functional theory beyond generalized gradient approximations. Here we extend the configuration path integral Monte Carlo (CPIMC) formalism that was previously applied to the spatially uniform electron gas to the case of an inhomogeneous electron gas by adding a spatially periodic external potential. This procedure has recently been successfully used in permutation blocking path integral Monte Carlo simulations (PB-PIMC) of the warm dense electron gas [T. Dornheim et al., Phys. Rev. E 96, 023203 (2017)], but this method is restricted to low and moderate densities. Implementing this procedure into CPIMC allows us to obtain highly accurate finite temperature results for the SDRF of the electron gas at high to moderate densities closing the gap left open by the PB-PIMC data. In this paper, we demonstrate how the CPIMC formalism can be efficiently extended to the spatially inhomogeneous electron gas and present the first data points. Finally, we discuss finite size errors involved in the quantum Monte Carlo results for the SDRF in detail and present a solution how to remove them that is based on a generalization of ground state techniques.
Evaluation of covalency of ions in lead-free perovskite-type dielectric oxides
Authors: Takesue Naohisa , Ishibashi Kazuya , Asakura Kazuki
Published: October 2017

Electronic states of ions in lead-free perovskite-type dielectric oxides have been investigated with a first-principle cluster calculation. For this calculation a double-perovskite cluster model based upon the simple cubic ABO3 was used; A and B are both the cations, and O is the oxygen anion. Systematic variations of ionic species for A and B, and lengths of the model cube edge were given to the model. Results of charge transfers of the ions show that their magnitudes depend on the edge length; the lager length leads to the higher transfer magnitude. This tendency implies spatial tolerance of the ions to the clusters, and are expected to correlate with electric polarizability and dipole reversibility of this kind of oxides. The density of states and the overlap population indicate that the higher cation valence causes the higher covalency of the anions. Considering all results together provides us an idea to obtain lead-free high-performance ferroelectrics, as high as the lead-based solid solutions.
Effect of the orientation of the harbor seal vibrissa based biomimetic cylinder on hydrodynamic forces and vortex induced frequency
Authors: Kim HyoJu , Yoon Hyun Sik
Published: October 2017

The present study considered the geometric disturbance inspired by a harbor seal vibrissa of which undulated surface structures (HSV) are known as a detecting device to capture the water movement induced by prey fish. As an original research can extend to the flow control based on the biomimetic, this study aims at finding the effect of the angle of attack (AOA) on flow characteristics around the harbor seal vibrissa shaped cylinder, to cover the change of flow direction during the harbor seal’s movements and surrounding conditions. Therefore, we considered a wide range of AOA varying from 0 to 90 degree. We carried out large eddy simulation (LES) to investigate the flow around inclined vibrissa shaped cylinder for the Reynolds number (Re) of 500. The elliptic cylinder is considered for the purpose of the comparison. The difference of force coefficients between the HSV and the elliptic cylinder can be classified into three regimes of one large variation region, two invariant regimes according to AOA. In contrast to the elliptic cylinder showing the monotonically decrease of the vortex shedding frequency in AOA, the HSV reveals the increasing and then decreasing behavior of the vortex shedding frequency along the AOA. The same decreasing profile of the vortex shedding frequency means that the HSV lost the unique function on the vortex shedding frequency. The shear layers for the HSV is much longer than that of shear layers for the elliptic cylinder at low angles of the attack. With increasing AOA, the difference of the vortical structures in the wake between the HSV and the elliptic cylinder becomes minor. Thus, it can be concluded that as AOA increases, the bluff body flow overcomes the flow induced by the HSV shape, resulting in the appearance of almost the same flow with the elliptic cylinder.
Structurally embedded reflectors and mirrors for elastic wave focusing and energy harvesting
Authors: Tol S. , Degertekin F. L. , Erturk A.
Published: October 2017

The harvesting of elastic waves propagating in structures can be enhanced dramatically via spatial focusing using mirror and lens concepts. Recent efforts on the mirror design have employed cylindrical stubs that form elliptical and parabolic geometries to focus structure-borne waves originating from a point source and incident plane waves, respectively. In those first-generation heuristic efforts, bulky cylindrical attachments served as effective reflectors while drastically altering thin host structures. Enabling structurally embedded mirror (SEM) configurations that avoid substantial modification of the host system requires a thorough understanding of the elastic mirror dynamics. This work presents a detailed investigation of SEM design, analysis, and experimental validation for enhanced elastic wave energy harvesting, among other applications that can benefit from spatially focused wave intensity. The SEM concept proposed in this effort uses metallic spheres (e.g., tungsten, lead, and steel) inserted into blind holes in a flat aluminum plate domain. The results show that, while SEM performance improves with property mismatch between the inclusion and the host materials, transmission resonances of the inclusions are detrimental to reflection performance and have to be avoided. A relationship between elastic mirror geometry and wavelength is unveiled to minimize the energy concentration in the side lobes around the intended focus, enabling small-sized and simple harvester design. These basic concepts and principles, demonstrated through finite-element simulations, are validated experimentally over a range of frequencies. Dramatic enhancement of the harvested power (by an order of magnitude) is also demonstrated using an elliptical SEM made from spherical tungsten inclusions in an aluminum plate. The case of a perforated mirror is also addressed briefly.
Preface: Special Topic: From Quantum Mechanics to Force Fields
Authors: Piquemal Jean-Philip , Jordan Kenneth D.
Published: October 2017

This Special Topic issue entitled “From Quantum Mechanics to Force Fields” is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.
Elastic electron scattering from nitrobenzene
Authors: Maioli Leticia S. , Bettega Márcio H. F.
Published: October 2017

We present integral, momentum transfer, and differential cross sections for an elastic scattering of electrons by nitrobenzene. Our calculations employed the Schwinger multichannel method with pseudopotentials and were performed in the static-exchange and static-exchange plus polarization approximations. The cross sections were computed for impact energies up to 10 eV. We observed four resonances in the static-exchange calculations, and three when polarization effects were included. This result indicates that the low-lying resonance in the B1 symmetry of C2v group, observed in the static-exchange calculation, became a bound state when polarization was taken into account. Our calculations including polarization effects assigned the low-lying resonance located at 0.92 eV to the A2 symmetry and the other two resonances, located at 2.07 eV and 6 eV, to the B1 symmetry. These results compare well with the attachment energies obtained through electron transmission spectroscopy data and with dissociative electron attachment results for the NO2− sub-product, suggesting for the latter that the π* resonances mediate the dissociation process.
Performance, hepatic function and efficiency of nutrient utilisation of grazing dairy cows supplemented with alkaline-treated Jatropha curcas L. meal
Authors: Souza Jocely G. , Olini Lucas M. G. , Araujo Claudio V. , Mendonça Simone , Zervoudakis Joanis T. , Cabral Luciano S. , Ogunade Ibukun M. , Oliveira André S.
Published: October 2017

Jatropha meal is an emergent source of protein for ruminant feed, but the presence mainly of phorbol esters limits its use. We hypothesised that alkaline treatment of Jatropha curcas L. meal will reduce phorbol esters and allow its use as a concentrate supplement for dairy cows. We evaluated the effects of four levels of Jatropha meal treated with 70 g of sodium hydroxide/kg [JMT; 0.145 mg phorbol ester g/kg dry matter (DM)] in a concentrate supplement (0, 100, 200 and 300 g/kg DM; 4 kg cow/day as fed) on performance and efficiency of nutrient utilisation in grazing dairy cows. The alkaline treatment reduced the phorbol esters content of the toxic Jatropha meal by 67.7%. The JMT level linearly reduced the supplement intake (P < 0.01), but it did not affect pasture intake (P = 0.73) or blood hepatic transaminase (P > 0.10). As a result, the JMT level linearly reduced apparent total-tract nutrient digestibility (P ≤ 0.05), ruminal microbial protein synthesis (P = 0.05) and milk yield (P < 0.01). However, it did not affect milk composition (P > 0.05) and nitrogen balance (P = 0.29). Alkaline treatment substantially reduces the phorbol ester in Jatropha meal by 67.7%, but its inclusion in supplements reduces diet digestibility and performance of dairy cows.
Influence of climatic factors on variation in the Normalised Difference Vegetation Index in Mongolian Plateau grasslands
Authors: Cao Xu-Juan , Gao Qing-Zhu , Hasbagan Ganjurjav , Liang Yan , Li Wen-Han , Hu Guo-Zheng
Published: October 2017

Climate change will affect how the Normalised Difference Vegetation Index (NDVI), which is correlated with climate factors, varies in space and over time. The Mongolian Plateau is an arid and semi-arid area, 64% covered by grassland, which is extremely sensitive to climate change. Its climate has shown a warming and drying trend at both annual and seasonal scales. We analysed NDVI and climate variation characteristics and the relationships between them for Mongolian Plateau grasslands from 1981 to 2013. The results showed spatial and temporal differences in the variation of NDVI. Precipitation showed the strongest correlation with NDVI (43% of plateau area correlated with total annual precipitation and 44% with total precipitation in the growing season, from May to September), followed by potential evapotranspiration (27% annual, and 30% growing season), temperature (7% annual, 16% growing season) and cloud cover (10% annual, 12% growing season). These findings confirm that moisture is the most important limiting factor for grassland vegetation growth on the Mongolian Plateau. Changes in land use help to explain variations in NDVI in 40% of the plateau, where no correlation with climate factors was found. Our results indicate that vegetation primary productivity will decrease if warming and drying trends continue but decreases will be less substantial if further warming, predicted as highly likely, is not accompanied by further drying, for which predictions are less certain. Continuing spatial and temporal variability can be expected, including as a result of land use changes.
Biological conservation law as an emerging functionality in dynamical neuronal networks
Authors: Podobnik Boris , Jusup Marko , Tiganj Zoran , Wang Wen-Xu , Buldú Javier M. , Stanley H. Eugene
Published: October 2017

Significance

Living complex systems create functionalities by pairing up complementary processes, one to build and another to correct and clean the space for more building. When these processes are embedded into mutually exclusive phases, establishing a balance between them requires a phase flipping mechanism. For a simple neuronal network composed of neurons and synapses, we demonstrate that flipping between excited and resting phases gives rise to a statistical conservation law of synaptic strength. Furthermore, this law is selected by evolution regardless of the network’s initial state, thus reconciling biology with the physical concept of self-organized criticality.
Efficient synthesis of phycocyanobilin in mammalian cells for optogenetic control of cell signaling
Authors: Uda Youichi , Goto Yuhei , Oda Shigekazu , Kohchi Takayuki , Matsuda Michiyuki , Aoki Kazuhiro
Published: October 2017

Significance

Optical control of cell signaling has attracted much attention in recent years. Most optogenetic systems exploit blue light, as do fluorescent indicators such as FRET-based biosensors. Phytochrome B (PhyB)–phytochrome-interacting factor (PIF) is a red/far-red light-switchable heterodimerization system. However, PhyB requires phytochromobilin or phycocyanobilin (PCB) as a chromophore, which must be externally added to mammalian cells. To overcome this difficulty, we developed a system for an efficient synthesis of PCB in mammalian cells. Eventually, we found that PCB was synthesized by introducing all
PcyA
,
HO1
,
Fd
, and
Fnr
genes. The knockout or knockdown of biliverdin reductase A further enhanced PCB synthesis. This genetically encoded PCB synthesis system allowed us to manipulate cell signaling by red/far-red light without exogenous PCB addition.
Species richness accelerates marine ecosystem restoration in the Coral Triangle
Authors: Williams Susan L. , Ambo-Rappe Rohani , Sur Christine , Abbott Jessica M. , Limbong Steven R.
Published: October 2017

Significance

The exceptional diversity of species in the coral reefs, seagrass meadows, and mangrove forests of the Coral Triangle and the many ecological functions and benefits to humans they provide have made them a high priority for conservation and fisheries management. Nevertheless, their degradation continues and calls for effective restoration. In an experimental restoration, we demonstrated that planting mixtures of diverse seagrass species improves their overall survival and growth and thus the trajectory toward successful restoration. Incorporating species diversity into restoration heralds a shift in practice from establishing a single founder species, and recognizes the widely documented positive effects that biodiversity has on ecosystem function and services. Biodiversity is often a restoration goal, but it also promises a means to improve success.
Effects of various strengthening methods on the properties of Cu–Ti–B alloys
Authors: Jiang Yihui , Li Dan , Zhang Xinnan , Zou Juntao , Xiao Peng , Liang Shuhua
Published: October 2017

A copper alloy of Cu–1.9 wt-%Ti–0.7 wt-%B was fabricated by vacuum induction melting and casting followed by cold working and annealing. Four strengthening methods has been involved during the preparation of the alloy, and the combined action of these methods results in the alloy with the tensile strength of 530 ± 24 MPa and the electrical conductivity (EC) of 48.0 ± 2.1% International Annealed Copper Standard. The specific contribution (or deterioration) of different strengthening methods to hardness and EC was quantitatively evaluated. With regard to combined properties of Cu–Ti–B alloys, age hardening and forming TiB2 particles are two effective methods to improve hardness and to maintain EC at a relatively high level simultaneously, but solid solution strengthening and work hardening are two inferior strengthening methods.
Satellite and Airborne Remote Sensing Applications for Freshwater Fisheries
Authors: Dauwalter Daniel C. , Fesenmyer Kurt A. , Bjork Robin , Leasure Douglas R. , Wenger Seth J.
Published: October 2017

Remote sensing has been pivotal to our understanding of freshwater fisheries, and we review this rapidly changing field with a focus on satellite and airborne applications. Historical applications emphasized spatial variation in the environment (e.g., watershed land use and in situ primary productivity), but improved access to imagery archives facilitates better change detection over time. New sensor platforms and technology now yield imagery with higher spatial, temporal, and spectral resolutions than ever before, which has accelerated development of remote sensing products that more accurately characterize aquatic environments. Free access to imagery archives, cloud computing, and availability of derived products linked to national hydrography databases are all removing historical barriers to its use by fisheries professionals. These advances in remote sensing have allowed new questions to be answered at finer spatial resolutions across broader landscapes and longer time frames, providing a new big-picture perspective to freshwater fisheries conservation and management.
Molecular mechanisms of developmentally programmed crinophagy in Drosophila
Authors: Csizmadia Tamás , Lőrincz Péter , Hegedűs Krisztina , Széplaki Szilvia , Lőw Péter , Juhász Gábor
Published: October 2017

At the onset of metamorphosis, Drosophila salivary gland cells undergo a burst of glue granule secretion to attach the forming pupa to a solid surface. Here, we show that excess granules evading exocytosis are degraded via direct fusion with lysosomes, a secretory granule-specific autophagic process known as crinophagy. We find that the tethering complex HOPS (homotypic fusion and protein sorting); the small GTPases Rab2, Rab7, and its effector, PLEKHM1; and a SNAP receptor complex consisting of Syntaxin 13, Snap29, and Vamp7 are all required for the fusion of secretory granules with lysosomes. Proper glue degradation within lysosomes also requires the Uvrag-containing Vps34 lipid kinase complex and the v-ATPase proton pump, whereas Atg genes involved in macroautophagy are dispensable for crinophagy. Our work establishes the molecular mechanism of developmentally programmed crinophagy in Drosophila and paves the way for analyzing this process in metazoans.
Membrane curvature directs the localization of Cdc42p to novel foci required for cell–cell fusion
Authors: Smith Jean A. , Hall Allison E. , Rose Mark D.
Published: October 2017

Cell fusion is ubiquitous in eukaryotic fertilization and development. The highly conserved Rho–GTPase Cdc42p promotes yeast fusion through interaction with Fus2p, a pheromone-induced amphiphysin-like protein. We show that in prezygotes, Cdc42p forms a novel Fus2p-dependent focus at the center of the zone of cell fusion (ZCF) and remains associated with remnant cell walls after initial fusion. At the ZCF and during fusion, Cdc42p and Fus2p colocalized. In contrast, in shmoos, both proteins were near the cortex but spatially separate. Cdc42p focus formation depends on ZCF membrane curvature: mutant analysis showed that Cdc42p localization is negatively affected by shmoo-like positive ZCF curvature, consistent with the flattening of the ZCF during fusion. BAR-domain proteins such as the fusion proteins Fus2p and Rvs161p are known to recognize membrane curvature. We find that mutations that disrupt binding of the Fus2p/Rvs161p heterodimer to membranes affect Cdc42p ZCF localization. We propose that Fus2p localizes Cdc42p to the flat ZCF to promote cell wall degradation.
Unsupervised multiple kernel learning for heterogeneous data integration
Authors: Mariette Jérôme , Villa-Vialaneix Nathalie
Published: October 2017

Motivation

Recent high-throughput sequencing advances have expanded the breadth of available omics datasets and the integrated analysis of multiple datasets obtained on the same samples has allowed to gain important insights in a wide range of applications. However, the integration of various sources of information remains a challenge for systems biology since produced datasets are often of heterogeneous types, with the need of developing generic methods to take their different specificities into account.

Results

We propose a multiple kernel framework that allows to integrate multiple datasets of various types into a single exploratory analysis. Several solutions are provided to learn either a consensus meta-kernel or a meta-kernel that preserves the original topology of the datasets. We applied our framework to analyse two public multi-omics datasets. First, the multiple metagenomic datasets, collected during the TARA Oceans expedition, was explored to demonstrate that our method is able to retrieve previous findings in a single kernel PCA as well as to provide a new image of the sample structures when a larger number of datasets are included in the analysis. To perform this analysis, a generic procedure is also proposed to improve the interpretability of the kernel PCA in regards with the original data. Second, the multi-omics breast cancer datasets, provided by The Cancer Genome Atlas, is analysed using a kernel Self-Organizing Maps with both single and multi-omics strategies. The comparison of these two approaches demonstrates the benefit of our integration method to improve the representation of the studied biological system.

Availability and implementation

Proposed methods are available in the R package mixKernel, released on CRAN. It is fully compatible with the mixOmics package and a tutorial describing the approach can be found on mixOmics web site http://mixomics.org/mixkernel/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Generalized anxiety disorder
Authors: Wells Adrian , Butler Gillian
Published: October 2017

Chapter 7 discusses generalized anxiety disorder (GAD), and argues for an improved conceptual understanding of GAD, based on experimental and clinical observations. It first outlines the nature of the problem, and the development of existing psychological treatments, before focusing on experimental and theoretical work on generalized anxiety and worry. A cognitive model of GAD is discussed, along with its treatment implications, and the concepts used in constructing models of vulnerability to stress in general, and of GAD in particular, are discussed in relation to models of cognition in disorders such as obsessive-compulsive disorder (OCD) and schizophrenia.
Chronic fatigue
Authors: Sharpe Michael
Published: October 2017

Chapter 16 explores chronic fatigue. It outlines the nature of chronic fatigue (fatigue as a symptom, fatigue as an illness, and chronic fatigue syndrome (CFS)), the aetiology of CFS, treatments for chronic fatigue (physical therapies and psychotherapies), a cognitive behavioural approach to CFS, and future directions for research.
Regulation-Dysregulation Theory and Condition Triggering
Authors: McGuire Michael , Troisi Alfonso
Published: October 2017

This chapter discusses regulation-dysregulation theory (RDT) and condition triggering. It outlines how specific types of social interactions influence CNS physiology, infrastructural functionality, cognition, and behavior; how the behavior of others in seemingly normal social environments trigger the onset of conditions in individuals who are either condition-predisposed or condition-vulnerable; and how the behavior of others in extremely adverse environments explains the onset of conditions in individuals who are neither predisposed nor vulnerable to conditions
Schizophrenia
Authors: McGuire Michael , Troisi Alfonso
Published: October 2017

This chapter has introduces a number of evolutionary views of schizophrenia, and illustrates how evolutionary concepts can alter how existing research data are interpreted and provides new insights into the possible causes and functions of disorders.
Dysthymic Disorder: A Study of Infrastructural Suboptimality
Authors: McGuire Michael , Troisi Alfonso
Published: October 2017

Chapter 14 outlines a study of dysthymic disorder (DD) from the evolutionary context, including the study design and procedure (structured interviews, psychological, psychophysiological, and neuropsychological tests), ethological studies, symptom change, and a causal analysis of DD.
Getting Things Done On Time
Authors: Ferrari Joseph R.
Published: October 2017

This chapter explores procrastination. It outlines a brief history of the procrastination concept, reviews the prevalence of two major categories of procrastination, followed by a discussion of the reasons why people procrastinate. Lastly, it describes what people can do about overcoming procrastination.
Coping with the Inevitability of Death
Authors: Strachan Eric , Pyszczynski Tom , Greenberg Jeff , Solomon Sheldon
Published: October 2017

This chapter explores methods of coping with the inevitability of death. It discusses Terror Management Theory, the mortality salience hypothesis and anxiety buffer hypothesis, proximal and distal defenses. The chapter also outlines the mismanagement of terror, which can manifest as anxiety disorders, neuroticism, and excessive fear.
Comparing Favorably
Authors: Wills Thomas Ashby , Sandy James M.
Published: October 2017

This chapter considers how people may use social comparison to cope with psychological distress arising from sources such as negative life events, failure experiences, and threats to self-esteem. It includes the theory of social comparison, the theory of downward comparison, and the mechanisms of downward comparison (selection of target, constructed comparisons, derogation of an outgroup, counterfactual thinking), as well as current issues in social comparison research.
A Look at the Coping Strategies and Styles of Asian Americans
Authors: Chang Edward C.
Published: October 2017

This chapter explores cultural differences in coping, and focuses on the coping strategies and styles of Asian Americans by applying various models of coping (including Lazarus and Folkman’s stress and coping model, Epstein’s constructive thinking model, and D’Zurilla’s rational coping model)
Finding My Mind
Authors: White Ruth C.
Published: October 2017

Chapter 2 explores the confusion, denial, and terror accompanying the realization that the contributor’s life’s predominant style—brilliance, lightning-quick turnaround of ideas and projects—signals, at a deeper level, a history of not just ADHD and depression but also manic-depressive illness (bipolar disorder).
Weeping Mother
Authors: Agee Jarralynne
Published: October 2017

Chapter 9 explores the depression of the contributor’s mother, the poverty in which the family found itself for many years, and the impact of these early experiences on the contributor’s life and career.
Performing Human
Authors: Lucas Janet
Published: October 2017

Chapter 13 explores the dilemmas experienced by victims of severe abuse in “closed” family systems, and provides a portrayal of the kinds of violence and neglect the contributor experienced during childhood.
Session 1: Welcome!
Authors: Wells Karen C. , Lochman John E. , Lenhart Lisa A.
Published: October 2017

Chapter 1 presents an introduction to the Coping Power Program for parents. It outlines the Coping Power Program itself, the corresponding child group, group rules, and introduces the topic of how to provide academic support in the home for the child.
Session 7: Giving Your Child Good Instructions
Authors: Wells Karen C. , Lochman John E. , Lenhart Lisa A.
Published: October 2017

Chapter 7 focuses on giving the child good instructions. It again applies the ABC model (using instructions as an antecedent to behavior), and discusses the differences between instructions that do and don’t work.
Session 16: The End of the Coping Power Program
Authors: Wells Karen C. , Lochman John E. , Lenhart Lisa A.
Published: October 2017

Chapter 16 discusses the end of the Coping Power Program. It explores planning for the long term, and resources that are available after the conclusion of the program, and reviews the topics that have been covered throughout the program.
Data Collection
Authors: Piechowski Lisa Drago
Published: October 2017

This chapter focuses on data collection as part of the evaluation of disability, with emphasis on the specific methodology for obtaining data from various sources such as written records and documents, self-report data from the claimant, psychological testing and neuropsychological testing, and information from collaterals such as interviews and treatment providers including psychiatrists, psychologists, and psychotherapists. It also describes instruments commonly used in assessing psychopathology and cognitive functioning during disability evaluation. Finally, it considers formal assessment of the claimant's response style as an integral part of the independent medical examination.
Finding the Right Board Certification for You
Authors: Boll Thomas J.
Published: October 2017

Chapter 5 explores a number of questions in order to determine which ABPP board certification is appropriate for an individual. Questions include, “Am I qualified to be board certified?” “Does it make sense or do I want to be board certified?” “How many board certifications should I consider?” and “Which certification is rightfor me or which one should I do first?”
Giving Back to the ABPP
Authors: Nelson W. Michael , Hart Kathleen J.
Published: October 2017

This chapter outlines what a newly-certified psychologistcan do following their ABPP examination. It includes the standards for displaying ABPP credentials, and information on acting as a role model or mentor, and involvement in specialty boards or academies.
Undergraduate Education in Psychology
Authors: Dunn Dana S. , Beins Bernard C. , McCarthy Maureen A. , Hill G. William
Published: October 2017

This chapter presents an introductory overview to the title. It discusses the structure and content of each section within the title, along with the importance of continuity within psychology education, and the presentation throughout of psychology as a science.
Addressing the Multiple Demands of Teaching Introductory Psychology
Authors: Stoloff Michael L.
Published: October 2017

This chapter identifies the special demands of teaching introductory psychology and presents suggestions for orchestrating successful learning, such as course organization, learning objectives, motivation, class size, and dealing with academic dishonesty.
Engaging Students in Psychology
Authors: Gurung Regan A. R. , Wilson-Doenges Georjeanna
Published: October 2017

This chapter presents an effective strategy to engage first-year students at the level of the class and the university. The strategy is designed to energize students with a passion for learning and to better connect them to the university, and engage students with the curriculum.
Displacing Wikipedia
Authors: Harris Charles M. , Cameron S. Lynn
Published: October 2017

This chapter discusses information literacy for first-year students, including the use of Wikipedia as a source of information, definitions of information literacy, case examples of information literacy curricula, and methods of assessing information literacy.
The Capstone Research Course
Authors: Messer Wayne S. , Porter David B.
Published: October 2017

This chapter discusses capstone research courses, and offers an account of experiences to benefit those who may find themselves in the position of developing and teaching such a course, including learning goals, the benefits of undergraduate research experiences, and common challenges.
Capping the Undergraduate Experience
Authors: Grayson Joann H.
Published: October 2017

This chapter discusses fieldwork as an undergraduate capstone option, including why fieldwork should be offered, how a capstone field placement can be planned, negotiation with agencies for placements, student selection, expectations for student success, stages of fieldwork, and the importance of teaching best practices to students.
The Caregiver’s Own Role Transition
Authors: Miller Mark D.
Published: October 2017

Chapter 10 explores the role transition of the caregiver in interpersonal psychotherapy (IPT). This includes outlines of transitions to caregivers for adult child caregivers, spouse caregivers, siblings, and friends, which are illustrated using case vignettes.
Reaching Steady State and Long-Term Planning
Authors: Miller Mark D.
Published: October 2017

Chapter 12 discusses steady states maintenance and long-term planning in interpersonal therapy for cognitive impairment (IPT-ci). It discusses planning for future contingencies, last wills and testaments, and advanced directives.
What Would She Think?
Authors: Shapiro Dan
Published: October 2017

This case discusses ethical standards bearing on maintaining confidentiality, disclosures (of confidential information), and the maintenance, dissemination, and disposal of confidential records of professional and scientific work, especially following the death of a client. The chapter presents a discussion of the key ethical issues, a summary of the primary ethical conundrums prevalent in the work setting, and a final reflection in retrospect regarding how the ethical quandary was handled.
Now You See It, Now You Don’t
Authors: Gonsiorek John C.
Published: October 2017

This case describes the ethical issues in a situation in forensic psychological practice where the client rescinds access to releases of information. The chapter presents a discussion of the key ethical issues, a summary of the primary ethical conundrums prevalent in the work setting, and a final reflection in retrospect regarding how the ethical quandary was handled.
Second Chances
Authors: Farley Lisa M.
Published: October 2017

This case involves beneficence and nonmaleficence, and respect for people's rights and dignity in the context of pediatric organ transplantation. The chapter presents a discussion of the key ethical issues, a summary of the primary ethical conundrums prevalent in the work setting, and a final reflection in retrospect regarding how the ethical quandary was handled.
Establishing Rapport With an “Enemy Combatant”
Authors: Kennedy Carrie H.
Published: October 2017

This case discusses the issues of mixed agency in military psychology, confidentiality, and cultural competency. The chapter presents a discussion of the key ethical issues, a summary of the primary ethical conundrums prevalent in the work setting, and a final reflection in retrospect regarding how the ethical quandary was handled.
A Disaster in a Suit and Tie
Authors: Morgan III Charles A.
Published: October 2017

This case discusses the issues that can occur when organizational policies undermine a therapist's ethical obligations to their client. The chapter presents a discussion of the key ethical issues, a summary of the primary ethical conundrums prevalent in the work setting, and a final reflection in retrospect regarding how the ethical quandary was handled.
Doing Good Versus Avoiding Harm
Authors: Green Alan G.
Published: October 2017

This case explores the issues involved in avoiding harm/nonmaleficence, and minimising danger to the client in the context of reporting a case to Child Protection Services. The chapter presents a discussion of the key ethical issues, a summary of the primary ethical conundrums prevalent in the work setting, and a final reflection in retrospect regarding how the ethical quandary was handled.
Knocked Off Kilter
Authors: Thomas Janet T.
Published: October 2017

This case describes supervision of a colleague following complaints from clients of sexual boundary violations. The chapter presents a discussion of the key ethical issues, a summary of the primary ethical conundrums prevalent in the work setting, and a final reflection in retrospect regarding how the ethical quandary was handled.
Implementation of Evidence-Based Psychological Treatments in the Veterans Health Administration
Authors: Ruzek Josef I. , Karlin Bradley E. , Zeiss Antonette
Published: October 2017

Chapter 5 describes the innovative approaches taken to facilitate implementation and maintenance of best practices for anxiety, depression, and severe mental illness in the Veterans Health Administration, the largest integrated health care system in the United States.
Integrating the neurobiological and neuropsychological dimensions of autism
Authors: Robbins T. W.
Published: October 2017

This chapter discusses the integration of the neurobiological and neuropsychological dimensions of autism. It includes a survey of the major neural theories of autism (medial temporal lobe hypothesis, the cerebellar hypothesis, the frontostriatal hypothesis, and evidence from neuroimaging and neuropsychology), and a summary of research suggestions (neuroimaging in a cognitive context, functional connectivity from neuroimaging, and cluster analysis of autistic symptoms).
Semi-structured interviewing
Authors: Fylan Fiona
Published: October 2017

This chapter presents a guide to conducting effective semi-structured interviews. It discusses the nature of semi-structured interviews and why they should be used, as well as preparation, the logistics of conducting the interview, and reflexivity.
Experimental methods in clinical and health research
Authors: Field Andy P. , Davey Graham C. L.
Published: October 2017

This chapter looks at experimental methods and why they are important in clinical research. It begins by looking at how experiments allow causal inferences and concludes by looking at how such causal inferences are essential in clinical psychology to unearth the mechanisms that drive abnormal behaviour.
General and generalised linear models
Authors: Miles Jeremy
Published: October 2017

This chapter discusses general and generalised linear models (GLM and GLZ respectively). It outlines GLMs (mean, properties of GLMs and the mean), samples and populations, comparison of two groups of data, multiple regression and the GLM, analysis of variance (ANOVA) and the GLM, GLM in SPSS, and the GLZ).
Survival analysis
Authors: Watson Peter
Published: October 2017

This chapter explores survival analysis. It includes data censoring, functions of duration time (the survival function, and hazard function), Cox’s proportional hazards model, log-linearity, time varying predictors, and odds ratios.
Memory
Authors: Harvey Allison G. , Watkins Edward , Mansell Warren , Shafran Roz
Published: October 2017

Chapter 3 explores memory. It outlines the nature of memory (implicit and explicit, perceptually-driven and conceptually-driven tasks, working memory, verbally accessible and situationally accessible memories), stimuli and selective memory, and the influence on memory of anxiety disorders, somatoform disorders, eating disorders, mood disorders, and substance-related disorders. Overgeneral memory, avoidant encoding and retrieval, recurrent memories are also discussed, as well as clinical implications.
Reasoning
Authors: Harvey Allison G. , Watkins Edward , Mansell Warren , Shafran Roz
Published: October 2017

Chapter 4 discusses reasoning. This includes the interpretation of ambiguous stimuli, self-report paradigms, cognitive-experimental paradigms, attributions, expectancies and heuristics, covariation and illusory correlation, and the evidence for the presence of these reasoning processes across psychological disorders (anxiety disorders, somatoform disorders, eating disorders, mood disorders, psychotic disorders, and substance-related disorders).