bluuebunny/crossref_metadata_2025 huggingface dataset:
Linear and nonlinear dielectric theory for a slab: The connections between the phenomenological coefficients and the susceptibilities
Authors: Fulton Robert L.
Published: August 2016

The response of dielectric media to electromagnetic fields can be described by using either the response to a Maxwell field E or to an externally produced field E. The former response is measured by phenomenological (dielectric) coefficients and the latter by susceptibilities. With the purpose of clarifying some recent proposals, the connections between the linear (two-point) and first non-vanishing nonlinear (four-point) dielectric coefficients and the susceptibilities for media confined to a slab are examined using a general procedure developed sometime ago. Unlike the relations found for correlations between a local polarization density and the integrated polarization densities (total polarizations), the point-point connections give rise to non-vanishing cross correlations between polarization densities which are parallel and perpendicular to the slab surfaces. The cross correlations in the two-point connections vanish when one polarization density is integrated to form the correlations between a local polarization density and the total polarization thereby losing angular information. The integrated parallel and perpendicular correlations remain different. When the four-point connections are similarly integrated most, but not all, cross correlations vanish. The angular correlations induced by the slab surfaces render the use of point-point correlations that are valid for isotropic media invalid for use in the integrated slab densities. In addition, the nonlinear fluctuations in the perpendicular components are drastically reduced relative to those in the parallel components or in isotropic media.
Network inoculation: Heteroclinics and phase transitions in an epidemic model
Authors: Yang Hui , Rogers Tim , Gross Thilo
Published: August 2016

In epidemiological modelling, dynamics on networks, and, in particular, adaptive and heterogeneous networks have recently received much interest. Here, we present a detailed analysis of a previously proposed model that combines heterogeneity in the individuals with adaptive rewiring of the network structure in response to a disease. We show that in this model, qualitative changes in the dynamics occur in two phase transitions. In a macroscopic description, one of these corresponds to a local bifurcation, whereas the other one corresponds to a non-local heteroclinic bifurcation. This model thus provides a rare example of a system where a phase transition is caused by a non-local bifurcation, while both micro- and macro-level dynamics are accessible to mathematical analysis. The bifurcation points mark the onset of a behaviour that we call network inoculation. In the respective parameter region, exposure of the system to a pathogen will lead to an outbreak that collapses but leaves the network in a configuration where the disease cannot reinvade, despite every agent returning to the susceptible class. We argue that this behaviour and the associated phase transitions can be expected to occur in a wide class of models of sufficient complexity.
Global existence and explosion of the stochastic viscoelastic wave equation driven by multiplicative noises
Authors: Liang Fei , Chen Yucong , Li Junbing
Published: August 2016

In this paper, we discuss an initial boundary value problem of stochastic viscoelastic wave equation driven by multiplicative noise involving the nonlinear damping term utq−2ut and a source term of the type up−2u. We first establish the local existence and uniqueness of solution by the iterative technique truncation function method. Moreover, we also show that the solution is global for q ≥ p. Lastly, by modifying the energy functional, we give sufficient conditions such that the local solution of the stochastic equations will blow up with positive probability or explode in energy sense for p > q.
Measurement of diagnostic neutral beam parameters on J-TEXT
Authors: Wang J. R. , Cheng Z. F. , Li Z. , Li Y. , Luo J. , Zhang X. L. , Zhuang G.
Published: August 2016

A Doppler frequency shift spectrum (DFSS) system composed of two spectrometers has been developed for the joint Texas experimental tokamak to measure diagnostic neutral beam parameters including the beam energy fractions, intensity distributions, and divergences. The beam energy fractions are derived from measurements of H-alpha (Hα) emission using collisional excitation cross sections. The beam intensity distributions are obtained using an 11-channel measurement with a reconstruction technique. The beam divergences are obtained from spectrum broadening and geometric calculations. The results of preliminary investigations indicate that the DFSS system works well and can be used to obtain all of these parameters simultaneously. According to the preliminary experiment, the one-third energy fraction has the largest proportion (about 45%) of the beam energy and the full energy fraction is about 10%. The beam diameter is about 8.1 cm at a distance of 2.04 m from the accelerator. The beam divergence angle is about 3.3°. The current beam parameters are insufficient for charge-exchange measurements.
Dark current investigation in thin P-i-N InGaAs photodiodes for nano-resonators
Authors: Verdun Michaël , Beaudoin Grégoire , Portier Benjamin , Bardou Nathalie , Dupuis Christophe , Sagnes Isabelle , Haïdar Riad , Pardo Fabrice , Pelouard Jean-Luc
Published: August 2016

We investigated the dark current components of thin planar InGaAs photodiodes grown by metalorganic vapor-phase epitaxy for optical nano-resonators. Owing to their high electric field enhancement, nano-resonators make it possible to substantially reduce the thickness of the active region to about 100 nm all the while maintaining high quantum efficiency. In the present study, to cover a broad spectral band, we combined several resonance peaks induced by guided-mode resonances in a given spectral range. This type of geometry allowed us to introduce InAlAs at the edge of a thin InGaAs active region in order to drastically reduce both the diffusion current and the generation/recombination current. We found that, in such devices, tunneling dark current components increase as the thickness of the active layer is reduced and dominate the reverse dark current. By optimizing the epitaxial stack, while keeping its total thickness constant (the optical properties of the nano-resonator remained unchanged), we showed that we are already able to achieve a specific detectivity of up to 1×1013 cmHz W−1 for λ=1.55 μm.
Fully kinetic model of breakdown during sheath expansion after interruption of vacuum arcs
Authors: Wang Zhenxing , Wang Haoran , Zhou Zhipeng , Tian Yunbo , Geng Yingsan , Wang Jianhua , Liu Zhiyuan
Published: August 2016

Research on sheath expansion is critical to the understanding of the dielectric recovery process in a vacuum interrupter after interruption of vacuum arcs. In this paper, we investigated how residual plasma affects breakdown in the sheath expansion period after the current zero. To simulate sheath expansion and breakdown, we developed a fully kinetic particle-in-cell Monte Carlo collision model with one spatial dimension and three velocity dimensions. The model accounted for various collisions, including ionization, excitation, elastic collisions, charge exchange, and momentum exchange, and we added an external circuit to the model to make the calculations self-consistent. The existence of metal vapor slowed the sheath expansion in the gap and caused high electric field formation in front of the cathode surface. The initial residual plasma, which was at sufficiently low density, seemed to have a limited impact on breakdown, and the metal vapor dominated the breakdown in this case. Additionally, the breakdown probability was sensitive to the initial plasma density if the value exceeded a specific threshold, and plasma at sufficiently high density could mean that breakdown would occur more easily. We found that if the simulation does not take the residual plasma into account, it could overestimate the critical value of the metal vapor density, which is always used to describe the boundary of breakdown after interruption of vacuum arcs. We discussed the breakdown mechanism in sheath expansion, and the breakdown is determined by a combination of metal vapor, residual plasma, and the electric field in front of the cathode surface.
GaN Schottky diodes with single-crystal aluminum barriers grown by plasma-assisted molecular beam epitaxy
Authors: Tseng H. Y. , Yang W. C. , Lee P. Y. , Lin C. W. , Cheng Kai-Yuan , Hsieh K. C. , Cheng K. Y. , Hsu C.-H.
Published: August 2016

GaN-based Schottky barrier diodes (SBDs) with single-crystal Al barriers grown by plasma-assisted molecular beam epitaxy are fabricated. Examined using in-situ reflection high-energy electron diffractions, ex-situ high-resolution x-ray diffractions, and high-resolution transmission electron microscopy, it is determined that epitaxial Al grows with its [111] axis coincident with the [0001] axis of the GaN substrate without rotation. In fabricated SBDs, a 0.2 V barrier height enhancement and 2 orders of magnitude reduction in leakage current are observed in single crystal Al/GaN SBDs compared to conventional thermal deposited Al/GaN SBDs. The strain induced piezoelectric field is determined to be the major source of the observed device performance enhancements.
The characteristics of MBE-grown InxAl1−xN/GaN surface states
Authors: Jiao Wenyuan , Kong Wei , Li Jincheng , Collar Kristen , Kim Tong-Ho , Losurdo Maria , Brown April S.
Published: August 2016

The density and energy distribution of InxAl1−xN/GaN surface donor states are studied for InxAl1−xN structures with varying indium compositions. The results support a surface states model with a constant energy distribution of 2.17–2.63 eV below the conduction band minimum and a concentration of 4.64–8.27 × 1013 cm−2 eV−1. It is shown that the properties of the surface states are affected by the surface indium composition xs, as opposed to the bulk composition, xb (InxAl1−xN). Higher surface indium composition xs increases the density of surface states and narrows their energy distribution.
Nanoparticle-density-dependent field emission of surface-decorated SiC nanowires
Authors: Dong Qizheng , Chen Shanliang , Chen Qiang , Gao Fengmei , Wang Lin , Xie Zhipeng , Yang Weiyou
Published: August 2016

Increasing the electron emission site density of nanostructured emitters with limited field screening effects is one of the key issues for improving the field emission (FE) properties. In this work, we reported the Au-nanoparticles-density-dependent field emission behaviors of surface-decorated SiC nanowires. The Au nanoparticles (AuNPs) decorated around the surface of the SiC nanowires were achieved via an ion sputtering technique, by which the densities of the isolated AuNPs could be adjusted by controlling the fixed sputtering times. The measured FE characteristics demonstrated that the turn-on fields of the SiC nanowires were tuned to be of 2.06, 1.14, and 3.35 V/μm with the increase of the decorated AuNPs densities, suggesting that a suitable decorated AuNPs density could render the SiC nanowires with totally excellent FE performances by increasing the emission sites and limiting the field screening effects.
Research Update: Enhanced energy storage density and energy efficiency of epitaxial Pb0.9La0.1(Zr0.52Ti0.48)O3 relaxor-ferroelectric thin-films deposited on silicon by pulsed laser deposition
Authors: Nguyen Minh D. , Houwman Evert P. , Dekkers Matthijn , Nguyen Chi T. Q. , Vu Hung N. , Rijnders Guus
Published: August 2016

Pb0.9La0.1(Zr0.52Ti0.48)O3 (PLZT) relaxor-ferroelectric thin films were grown on SrRuO3/SrTiO3/Si substrates by pulsed laser deposition. A large recoverable storage density (Ureco) of 13.7 J/cm3 together with a high energy efficiency (η) of 88.2% under an applied electric field of 1000 kV/cm and at 1 kHz frequency was obtained in 300-nm-thick epitaxial PLZT thin films. These high values are due to the slim and asymmetric hysteresis loop when compared to the values in the reference undoped epitaxial lead zirconate titanate Pb(Zr0.52Ti0.48)O3 ferroelectric thin films (Ureco = 9.2 J/cm3 and η = 56.4%) which have a high remanent polarization and a small shift in the hysteresis loop, under the same electric field.
Growth of InN hexagonal microdisks
Authors: Yang Chen-Chi , Lo Ikai , Hu Chia-Hsuan , Huang Hui-Chun , Chou Mitch M. C.
Published: August 2016

InN hexagonal thin wurtzite disks were grown on γ-LiAlO2 by plasma-assisted molecular-beam epitaxy at low temperature (470oC). The (0001¯) InN thin disk was established with the capture of N atoms by the β¯-dangling bonds of most-outside In atoms, and then the lateral over-growth of the In atoms were caught by the β¯-dangling bonds of the N atoms. From the analyses of high-resolution transmission electron microscopy, the lateral over-grown width was extended to three unit cells at [11¯00]InN direction for a unit step-layer, resulting in an oblique surface with 73o off c-axis.
Avoiding polar catastrophe in the growth of polarly orientated nickel perovskite thin films by reactive oxide molecular beam epitaxy
Authors: Yang H. F. , Liu Z. T. , Fan C. C. , Yao Q. , Xiang P. , Zhang K. L. , Li M. Y. , Liu J. S. , Shen D. W.
Published: August 2016

By means of the state-of-the-art reactive oxide molecular beam epitaxy, we synthesized (001)- and (111)-orientated polar LaNiO3 thin films. In order to avoid the interfacial reconstructions induced by polar catastrophe, screening metallic Nb-doped SrTiO3 and iso-polarity LaAlO3 substrates were chosen to achieve high-quality (001)-orientated films in a layer-by-layer growth mode. For largely polar (111)-orientated films, we showed that iso-polarity LaAlO3 (111) substrate was more suitable than Nb-doped SrTiO3. In situ reflection high-energy electron diffraction, ex situ high-resolution X-ray diffraction, and atomic force microscopy were used to characterize these films. Our results show that special attentions need to be paid to grow high-quality oxide films with polar orientations, which can prompt the explorations of all-oxide electronics and artificial interfacial engineering to pursue intriguing emergent physics like proposed interfacial superconductivity and topological phases in LaNiO3 based superlattices.
Bidirectional threshold switching characteristics in Ag/ZrO2/Pt electrochemical metallization cells
Authors: Du Gang , Wang Chao , Li Hongxia , Mao Qinan , Ji Zhenguo
Published: August 2016

A bidirectional threshold switching (TS) characteristic was demonstrated in Ag/ZrO2/Pt electrochemical metallization cells by using the electrochemical active Ag electrode and appropriate programming operation strategies The volatile TS was stable and reproducible and the rectify ratio could be tuned to ∼107 by engineering the compliance current. We infer that the volatile behavior is essentially due to the moisture absorption in the electron beam evaporated films, which remarkably improved the anodic oxidation as well as the migration of Ag+ ions. The resultant electromotive force would act as a driving force for the metal filaments dissolution, leading to the spontaneous volatile characteristics. Moreover, conductance quantization behaviors were also achieved owing to formation and annihilation of atomic scale metal filaments in the film matrix. Our results illustrate that the Ag/ZrO2/Pt device with superior TS performances is a promising candidate for selector applications in passive crossbar arrays.
Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state
Authors: Vlasic Thomas M. , Servio Phillip , Rey Alejandro D.
Published: August 2016

This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.
Martensitic transformation of pure iron at a grain boundary: Atomistic evidence for a two-step Kurdjumov-Sachs–Pitsch pathway
Authors: Meiser Jerome , Urbassek Herbert M.
Published: August 2016

Using classical molecular dynamics simulations and the Meyer-Entel interaction potential, we study the martensitic transformation pathway in a pure iron bi-crystal containing a symmetric tilt grain boundary. Upon cooling the system from the austenitic phase, the transformation starts with the nucleation of the martensitic phase near the grain boundary in a plate-like arrangement. The Kurdjumov-Sachs orientation relations are fulfilled at the plates. During further cooling, the plates expand and merge. In contrast to the orientation relation in the plate structure, the complete transformation proceeds via the Pitsch pathway.
Feeding management, production and performance of 13 pasture-based dairy farms in a Mediterranean environment
Authors: McDonnell R. P. , Staines M. vH. , Edmunds B. E. , Morris R.
Published: August 2016

Physical performance data from 13 dairy farms in Western Australia, six feeding all concentrate in the milking parlour and seven feeding a portion of concentrate in a partial mixed ration (PMR) with forage, were collected between March 2012 and June 2013. Each farm was visited 13 times at intervals of 4–6 weeks, and feed intake and milk production was recorded on each visit. Four farms had access to fresh pasture all year round via irrigation. Milk yield (MY) and composition data was calculated daily from milk processor records. Pasture dry matter intake (DMI) was estimated based on metabolisable energy supply and requirements according to published feeding standards. All milk and feed-related measures were significantly affected by visit date (P < 0.01). Mean annual concentrate intake and MY was 2082 ± 344 kg/cow and 7679 ± 684 kg/cow, respectively. Daily concentrate DMI was greatest in May 2012 (8.9 ± 2.2 kg/cow), near the end of the non-grazing season, and lowest in August 2012 (5.1 ± 1.5 kg/cow). On an average annual basis, PMR farms provided 22 ± 15% of total concentrate fed as part of a PMR, and 28 ± 11% of total concentrates and by-products fed as part of a PMR. Daily grazed pasture DMI was highest on all farms in September 2012 (12.9 ± 2.4 kg/cow), and averaged 6.6 kg/cow on the four irrigated farms between January and May. Daily yield of energy-corrected milk was highest in September 2012 (26.9 kg/cow) and lowest in January 2013 (21.9 kg/cow). Milk fat content was highest in summer and lowest in winter; the reverse was true of milk protein. Feed conversion efficiency was significantly affected by visit date, but mean feed conversion efficiency was the same (1.37) for in-parlour and PMR farms. Overall there was some evidence that PMR feeding systems on Western Australian dairy farms are not optimised to their full potential, but a high degree of variability in performance between all farms was also apparent.
Direct observation of aqueous secondary organic aerosol from biomass-burning emissions
Authors: Gilardoni Stefania , Massoli Paola , Paglione Marco , Giulianelli Lara , Carbone Claudio , Rinaldi Matteo , Decesari Stefano , Sandrini Silvia , Costabile Francesca , Gobbi Gian Paolo , Pietrogrande Maria Chiara , Visentin Marco , Scotto Fabiana , Fuzzi Sandro , Facchini Maria Cristina
Published: August 2016

Significance

Organic aerosol (OA) is a dominant component of atmospheric aerosol worldwide, and it is recognized as a key factor affecting air quality and possibly climate. Observations indicate that more than one-half of the global OA is of secondary origin. Traditional models typically underpredict secondary organic aerosol (SOA) mass, suggesting that a complete knowledge of SOA formation mechanisms is lacking. We show that aqueous-phase processing of biomass-burning emissions contributes to SOA formation. Such aqueous SOA absorbs UV and visible light more efficiently that other OA components. Aqueous chemistry processing of biomass-burning emissions should be taken into account in air quality and climate models for a correct description of the global OA budget and its climate-relevant optical properties.
Sandwich-structured polymer nanocomposites with high energy density and great charge–discharge efficiency at elevated temperatures
Authors: Li Qi , Liu Feihua , Yang Tiannan , Gadinski Matthew R. , Zhang Guangzu , Chen Long-Qing , Wang Qing
Published: August 2016

Significance

Polymers are the materials of choice for high-energy capacitive storage devices due to their inherent advantages such as being lightweight, their ease of processing, and their high dielectric strength. Yet, their performance deteriorates significantly with increasing operating temperature, which falls short of emerging energy applications under harsh conditions. Here we demonstrate the sandwich-structured polymer nanocomposites with greatly improved energy densities, high power densities, and remarkable charge–discharge efficiencies that far exceed those of the existing polymer-based dielectrics at 150 °C, a temperature oriented toward electric vehicle applications. The development of polymer-based dielectric materials capable of high-temperature operation represents a key element in meeting the technological challenges and fulfilling the requirements of advanced electronics and electrical power systems.
Power in everyday life
Authors: Smith Pamela K. , Hofmann Wilhelm
Published: August 2016

Significance

Although power is a fundamental part of human relations, little is known about power in daily life. We studied the everyday experience of power by surveying individuals multiple times over 3 d regarding their subjective feelings of power and positional power. Power dynamics were a common, though not constant, experience. Rather than power being concentrated among a few individuals, almost half of participants reported sometimes holding high-power positions. People’s feelings of power did not always map onto the positions they held. Most variability in power was related to people’s changing situations rather than their stable traits. Low power negatively affected mood and cognition. Contrary to negative stereotypes of powerholders, higher power was associated with greater feelings of responsibility.
Using the shortwave infrared to image middle ear pathologies
Authors: Carr Jessica A. , Valdez Tulio A. , Bruns Oliver T. , Bawendi Moungi G.
Published: August 2016

Significance

Imaging with shortwave infrared (SWIR) light has great potential for visualizing biological structures previously undetectable with visible light. To demonstrate the clinical potential of SWIR imaging, we developed a medical otoscope sensitive to SWIR light. We show that the unique transmission of SWIR light through tissue improves resolution of anatomical structures lying behind thin tissue membranes like the ear drum. We therefore significantly improve imaging of underlying middle ear anatomy. SWIR imaging also allows identification of disease characterized by fluid accumulation, as in the diagnosis of otitis media. With successful diagnosis of otitis media estimated at 51% for US pediatricians, objectifying this diagnosis could curb the antibiotic resistance associated with an estimated 2 million overdiagnoses each year.
Disulfide cross-linking influences symbiotic activities of nodule peptide NCR247
Authors: Shabab Mohammed , Arnold Markus F. F. , Penterman Jon , Wommack Andrew J. , Bocker Hartmut T. , Price Paul A. , Griffitts Joel S. , Nolan Elizabeth M. , Walker Graham C.
Published: August 2016

Significance

Terminal differentiation of endocytosed rhizobia into nitrogen-fixing bacteroids inside of legume root nodules is orchestrated by a large family of host-encoded cysteine-rich signaling peptides. These peptides have diverse effects on bacteria, but their molecular mechanisms of action are still unknown. The presence of highly conserved cysteine motifs in this peptide family results in an additional layer of complexity because each individual peptide can potentially form several disulfide–cross-linked regioisomers under oxidative conditions. By demonstrating several distinct patterns of relative activities between the three disulfide–cross-linked regioisomers of NCR247, its reduced form, and a variant lacking cysteines, our work suggests that disulfide cross-linking can augment the rich complexity ofRhizobium-legume chemical communication required for symbiosis.
Embryogenesis and Early Growth of Pure Strains and Hybrids of Sharptooth Catfish Clarias gariepinus and Sampa Heterobranchus longifilis
Authors: Olufeagba S O , Okomoda V T , Shuibu G
Published: August 2016

The embryonic development, early growth and survival of pure and reciprocal hybrid crosses of Sharptooth Catfish Clarias gariepinus and Sampa Heterobranchus longifilis were studied. The morula and blastula stages occurred 5 and 10 min earlier, respectively, in pure crosses (at 4 h, 10 min and 5 h after fertilization, respectively) than in hybrids. Timing of gastrulation in pure strain H. longifilis and the ♀ H. longifilis × ♂ C. gariepinus cross was earlier (9 h) than in pure strain C. gariepinus and ♀C. gariepinus × ♂ H. longifilis (9 h, 25 min), but similar timings were recorded during the somite stages (18 h). Hatching started at 23 h in H. longifilis, at 23 h, 10 min in C. gariepinus, and at 23 h, 15 min in the hybrids. Yolk absorption was complete in 4 d, but exogenous feeding began on the third day (72 h) when larvae weighed 0.7± 0.01 mg (mean ± SE). After 4 weeks of feeding ad libitum with shell-free Artemia, pure crosses of both species grew better than the hybrids, and C. gariepinus recorded the highest weight (83.33 mg). The hybrids, however, showed significantly higher survival than did the pure strains.
Increased Discriminability of Authenticity from Multimodal Laughter is Driven by Auditory Information
Authors: Lavan Nadine , McGettigan Carolyn
Published: August 2016

We present an investigation of the perception of authenticity in audiovisual laughter, in which we contrast spontaneous and volitional samples and examine the contributions of unimodal affective information to multimodal percepts. In a pilot study, we demonstrate that listeners perceive spontaneous laughs as more authentic than volitional ones, both in unimodal (audio-only, visual-only) and multimodal contexts (audiovisual). In the main experiment, we show that the discriminability of volitional and spontaneous laughter is enhanced for multimodal laughter. Analyses of relationships between affective ratings and the perception of authenticity show that, while both unimodal percepts significantly predict evaluations of audiovisual laughter, it is auditory affective cues that have the greater influence on multimodal percepts. We discuss differences and potential mismatches in emotion signalling through voices and faces, in the context of spontaneous and volitional behaviour, and highlight issues that should be addressed in future studies of dynamic multimodal emotion processing.
Transcription Factors, Transcriptional Coregulators, and Epigenetic Modulation in the Control of Pulmonary Vascular Cell Phenotype: Therapeutic Implications for Pulmonary Hypertension (2015 Grover Conference Series)
Authors: Pullamsetti Soni S. , Perros Frédéric , Chelladurai Prakash , Yuan Jason , Stenmark Kurt
Published: August 2016

Pulmonary hypertension (PH) is a complex and multifactorial disease involving genetic, epigenetic, and environmental factors. Numerous stimuli and pathological conditions facilitate severe vascular remodeling in PH by activation of a complex cascade of signaling pathways involving vascular cell proliferation, differentiation, and inflammation. Multiple signaling cascades modulate the activity of certain sequence‐specific DNA‐binding transcription factors (TFs) and coregulators that are critical for the transcriptional regulation of gene expression that facilitates PH‐associated vascular cell phenotypes, as demonstrated by several studies summarized in this review. Past studies have largely focused on the role of the genetic component in the development of PH, while the presence of epigenetic alterations such as microRNAs, DNA methylation, histone levels, and histone deacetylases in PH is now also receiving increasing attention. Epigenetic regulation of chromatin structure is also recognized to influence gene expression in development or disease states. Therefore, a complete understanding of the mechanisms involved in altered gene expression in diseased cells is vital for the design of novel therapeutic strategies. Recent technological advances in DNA sequencing will provide a comprehensive improvement in our understanding of mechanisms involved in the development of PH. This review summarizes current concepts in TF and epigenetic control of cell phenotype in pulmonary vascular disease and discusses the current issues and possibilities in employing potential epigenetic or TF‐based therapies for achieving complete reversal of PH.
PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets
Authors: Yu Jinchao , Guerois Raphaël
Published: August 2016

Motivation: Protein–protein docking methods are of great importance for understanding interactomes at the structural level. It has become increasingly appealing to use not only experimental structures but also homology models of unbound subunits as input for docking simulations. So far we are missing a large scale assessment of the success of rigid-body free docking methods on homology models.

Results: We explored how we could benefit from comparative modelling of unbound subunits to expand docking benchmark datasets. Starting from a collection of 3157 non-redundant, high X-ray resolution heterodimers, we developed the PPI4DOCK benchmark containing 1417 docking targets based on unbound homology models. Rigid-body docking by Zdock showed that for 1208 cases (85.2%), at least one correct decoy was generated, emphasizing the efficiency of rigid-body docking in generating correct assemblies. Overall, the PPI4DOCK benchmark contains a large set of realistic cases and provides new ground for assessing docking and scoring methodologies.

Availability and Implementation: Benchmark sets can be downloaded from http://biodev.cea.fr/interevol/ppi4dock/

Contact:  guerois@cea.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Overwinter shifts in the feeding ecology of juvenile Chinook salmon
Authors: Hertz Eric , Trudel Marc , Tucker Strahan , Beacham Terry D. , Mazumder Asit
Published: August 2016

Winter is thought to be a critical period for many fish in the ocean, but their ecology during this time tends to be poorly understood. We quantified the feeding ecology of juvenile Chinook salmon (Oncorhynchus tshawytscha) off the west coast of Vancouver Island in British Columbia, Canada, in autumn and winter to determine how seasonality could affect diet. Using stomach contents and stable isotopes, we tested the hypothesis that the winter diet of juvenile Chinook salmon differs from that of the autumn diet. Stomach-content data showed a shift from a primary reliance on amphipods in autumn to euphausiids in winter. This finding was generally corroborated by the stable isotope analysis, although mixing models suggested a greater contribution of fish prey to the diet in both autumn and winter. Understanding the diet of fish during winter may provide useful information for management as a first step in understanding the factors influencing mortality across life stages.
Ecosystem considerations in Alaska: the value of qualitative assessments
Authors: Zador Stephani G. , Holsman Kirstin K. , Aydin Kerim Y. , Gaichas Sarah K.
Published: August 2016

The application of ecosystem considerations, and in particular ecosystem report cards, in federal groundfish fisheries management in Alaska can be described as an ecosystem approach to fisheries management (EAFM). Ecosystem information is provided to managers to establish an ecosystem context within which deliberations of fisheries quota occur. Our goal is to make the case for the need for qualitative ecosystem assessments in EAFM, specifically that qualitative synthesis has advantages worthy to keep a permanent place at the fisheries management table. These advantages include flexibility and speed in responding to and synthesizing new information from a variety of sources. First, we use the development of indicator-based ecosystem report cards as an example of adapting ecosystem information to management needs. Second, we review lessons learned and provide suggestions for best practices for applying EAFM to large and diverse fisheries in multiple marine ecosystems. Adapting ecosystem indicator information to better suit the needs of fisheries managers resulted in succinct report cards that summarize ecosystem trends, complementing more detailed ecosystem information to provide context for EAFM. There were several lessons learned in the process of developing the ecosystem report cards. The selection of indicators for each region was influenced by geography, the extent of scientific knowledge/data, and the particular expertise of the selection teams. Optimizing the opportunity to qualitatively incorporate ecosystem information into management decisions requires a good understanding of the management system in question. We found that frequent dialogue with managers and other stakeholders leads to adaptive products. We believe that there will always be a need for qualitative ecosystem assessment because it allows for rapid incorporation of new ideas and data and unexpected events. As we build modelling and predictive capacity, we will still need qualitative synthesis to capture events outside the bounds of current models and to detect impacts of the unexpected.
Estimating uncertainty of data limited stock assessments
Authors: Kokkalis Alexandros , Eikeset Anne Maria , Thygesen Uffe H. , Steingrund Petur , Andersen Ken H.
Published: August 2016

Many methods exist to assess the fishing status of data-limited stocks; however, little is known about the accuracy or the uncertainty of such assessments. Here we evaluate a new size-based data-limited stock assessment method by applying it to well-assessed, data-rich fish stocks treated as data-limited. Particular emphasis is put on providing uncertainty estimates of the data-limited assessment. We assess four cod stocks in the North-East Atlantic and compare our estimates of stock status (F/Fmsy) with the official assessments. The estimated stock status of all four cod stocks followed the established stock assessments remarkably well and the official assessments fell well within the uncertainty bounds. The estimation of spawning stock biomass followed the same trends as the official assessment, but not the same levels. We conclude that the data-limited assessment method can be used for stock assessment and that the uncertainty estimates are reliable. Further work is needed to quantify the spawning biomass of the stock.
A Tutorial in Consumer Research: Process Theorization in Cultural Consumer Research
Authors: Giesler Markus , Thompson Craig J.
Published: August 2016

How do researchers studying the cultural aspects of consumption theorize change? We propose four analytical workbench modes of process theorization in combination with nine genres of process-oriented consumer research, each presenting a distinctive combination of assumptions about the nature of change in market and consumption systems and consumers’ role in these processes. Through this framework, we provide consumer researchers with a useful interpretive tool kit for deriving a process-oriented theorization from the unwieldy complexity of longitudinal data.
How Multiple Imputation Makes a Difference
Authors: Lall Ranjit
Published: August 2016

Political scientists increasingly recognize that multiple imputation represents a superior strategy for analyzing missing data to the widely used method of listwise deletion. However, there has been little systematic investigation ofhowmultiple imputation affects existing empirical knowledge in the discipline. This article presents the first large-scale examination of the empirical effects of substituting multiple imputation for listwise deletion in political science. The examination focuses on research in the major subfield of comparative and international political economy (CIPE) as an illustrative example. Specifically, I use multiple imputation to reanalyze the results of almost every quantitative CIPE study published during a recent five-year period inInternational OrganizationandWorld Politics, two of the leading subfield journals in CIPE. The outcome is striking: in almost half of the studies, key results “disappear” (by conventional statistical standards) when reanalyzed.
Molecular Size Distribution and Amylase Resistance of Maize Starch Nanoparticles Prepared by Acid Hydrolysis
Authors: Perez Herrera Mariana , Vasanthan Thava , Hoover Ratnajothi , Izydorczyk Marta
Published: August 2016

The molecular size distribution of maize starch nanoparticles (SNP) prepared by acid hydrolysis (3.16M H2SO4) and their amylase‐resistant counterparts, before and after debranching, was investigated. The weight average molecular weight (Mw) and linear chain length distribution were determined by high‐performance size‐exclusion chromatography (HPSEC) and high‐performance anion‐exchange chromatography (HPAEC), respectively. The objective was to understand the role of amylose involvement in the formation of SNP showing different crystalline structures (A‐ and B‐types). The HPSEC profiles of SNP before debranching from waxy, normal, and high‐amylose maize starches showed broad monomodal peaks. Debranched SNP from waxy maize eluted in a single narrow peak, whereas those from nonwaxy starches showed a multimodal distribution. Similar trends were also observed for the chain length distribution patterns, for which the longest detectable chains (degree of polymerization [DP] 31) in waxy maize were significantly lower than those of nonwaxy maize starches (DP 55–59). This indicated the potential amylose involvement in the SNP structure of normal and high‐amylose starches. Further evidence of amylose involvement was ascribed to the resistance of SNP toward amylolysis (Hylon VII > Hylon V > normal > waxy). The amylase‐resistant residues of SNP from high‐amylose maize starches were composed of both low Mw linear and branched chains.
An Emerging Disease Caused by Pseudomonas syringae pv. phaseolicola Threatens Mung Bean Production in China
Authors: Sun Suli , Zhi Ye , Zhu Zhendong , Jin Jing , Duan Canxing , Wu Xiaofei , Xiaoming Wang
Published: August 2016

An emerging bacterial disease with symptoms resembling those of halo blight is threatening mung bean production in China. This study was conducted to investigate the disease’s geographic distribution in China using consecutive multiyear field surveys and to confirm the causative agents’ identity. The surveys were conducted in 15 provinces covering seven geographic regions from 2009 to 2014. The survey results revealed that the emerging mung bean disease has rapidly spread and is prevalent in three of the main Chinese geographic regions, which contain more than 90% of the mung-bean-growing areas in China. To confirm the causal agent, diseased mung bean leaves were collected from the surveyed fields and used to isolate the pathogen. A bacterium was consistently isolated from all of the collected leaves. Based on the phenotypic characteristics, the physiological and biochemical properties, pathogenicity tests, and fatty acid composition, in combination with specific polymerase chain reactions and 16S-23S ribosomal DNA sequence analyses, the bacterium was identified as Pseudomonas syringae pv. phaseolicola. To our knowledge, this is the first report of P. syringae pv. phaseolicola causing halo blight on mung bean in China. The results indicate that P. syringae pv. phaseolicola is likely of epidemiological significance on mung bean in China.
Occurrence, Distribution, and Molecular Characterization of Citrus yellow vein clearing virus in China
Authors: Zhou Y. , Chen H. M. , Cao M. J. , Wang X. F. , Jin X. , Liu K. H. , Zhou C. Y.
Published: August 2016

In 2009, a new citrus viral disease caused by Citrus yellow vein clearing virus (CYVCV) was discovered in China. To more effectively monitor the presence of CYVCV, a survey was conducted in 166 citrus orchards from 11 major citrus-growing provinces in China from May 2014 to April 2016. In all, 458 of a total of 2,350 citrus samples tested positive for CYVCV, demonstrating that the virus is widely distributed in China. In this study, the complete genome sequences of 19 CYVCV isolates from different provinces and hosts were sequenced and characterized. Comparisons of the whole-genome sequences of these 19 CYVCV isolates as well as 4 isolates previously reported from around the world revealed that the sequence identity ranged from 97.1 to 99.8%, indicating that there is a very low level of sequence heterogeneity among CYVCV isolates of different geographic origins and hosts. Phylogenetic analysis of these 23 genomic sequences suggested that all of the isolates from China were clustered into the same clade, clearly apart from the CYVCV isolates from Turkey and Pakistan. To our knowledge, this is the first extensive survey conducted in China for CYVCV incidence.
A Proposal for a Genome Similarity-Based Taxonomy for Plant-Pathogenic Bacteria that Is Sufficiently Precise to Reflect Phylogeny, Host Range, and Outbreak Affiliation Applied to Pseudomonas syringae sensu lato as a Proof of Concept
Authors: Vinatzer Boris A. , Weisberg Alexandra J. , Monteil Caroline L. , Elmarakeby Haitham A. , Sheppard Samuel K. , Heath Lenwood S.
Published: August 2016

Taxonomy of plant pathogenic bacteria is challenging because pathogens of different crops often belong to the same named species but current taxonomy does not provide names for bacteria below the subspecies level. The introduction of the host range-based pathovar system in the 1980s provided a temporary solution to this problem but has many limitations. The affordability of genome sequencing now provides the opportunity for developing a new genome-based taxonomic framework. We already proposed to name individual bacterial isolates based on pairwise genome similarity. Here, we expand on this idea and propose to use genome similarity-based codes, which we now call life identification numbers (LINs), to describe and name bacterial taxa. Using 93 genomes of Pseudomonas syringae sensu lato, LINs were compared with a P. syringae genome tree whereby the assigned LINs were found to be informative of a majority of phylogenetic relationships. LINs also reflected host range and outbreak association for strains of P. syringae pathovar actinidiae, a pathovar for which many genome sequences are available. We conclude that LINs could provide the basis for a new taxonomic framework to address the shortcomings of the current pathovar system and to complement the current taxonomic system of bacteria in general.
Incidence of Pleural Fluid and Its Associated Risk Factors After Posterior Spinal Fusion in Patients With Adolescent Idiopathic Scoliosis
Authors: Hayashi Kazunori , Terai Hidetomi , Toyoda Hiromitsu , Suzuki Akinobu , Hoshino Masatoshi , Tamai Koji , Ohyama Shoichiro , Nakamura Hiroaki
Published: August 2016

Study Design.

Retrospective review of prospectively-collected data.

Objective.

To determine the incidence pleural fluid (PF) and its associated risk factors after posterior corrective spinal fusion (PCSF) in patients with adolescent idiopathic scoliosis (AIS).

Summary of Background Data.

Subclinical PF is often observed after PCSF in AIS patients. However, a few reports have been published regarding the incidence, characteristics, and associated risk factors.

Methods.

A total of 76 AIS patients who underwent PCSF and followed up for a minimum of 1 year were enrolled in this study. The volume of PF in each thorax was detected with thoracolumbar CT images taken preoperatively, at 1 week and 3 months follow up. Patient demographics, comorbidities, operation factors, serum albumin levels, scoliotic parameters, occurrence of malposition of pedicle screw insertion, and complications were collected and analyzed with univariate and multivariate analyses.

Results.

There were 71 female and five male patients (mean age, 16.2 yrs). All cases had a right convex curve in thoracic spine. Other causes of PF were not observed. PF was detected in 54 cases (71%) at 1 week postsurgery. It accumulated bilaterally in 36 cases, only in the right thorax in 13 cases, and only in the left thorax in five cases. There was significant difference between the depth of PF in the right and left sides (P < 0.001). The independent risk factor for PF was increased number of fused levels (OR: 3.88, 95% CI: 1.31–11.47). The mean coronal curve correction rate and other scoliotic factors were not significantly correlated.

Conclusion.

PF was observed in 71% of the patients who underwent PCSF for AIS. The right thorax was more commonly involved than the left. A higher number of fused levels (11 or more) was an independent risk factor of PF.

Level of Evidence: 3