bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic elastic moduli in magnetic gels: Normal modes and linear response
Authors: Pessot Giorgio , Löwen Hartmut , Menzel Andreas M.
Published: September 2016

In the perspective of developing smart hybrid materials with customized features, ferrogels and magnetorheological elastomers allow a synergy of elasticity and magnetism. The interplay between elastic and magnetic properties gives rise to a unique reversible control of the material behavior by applying an external magnetic field. Albeit few works have been performed on the time-dependent properties so far, understanding the dynamic behavior is the key to model many practical situations, e.g., applications as vibration absorbers. Here we present a way to calculate the frequency-dependent elastic moduli based on the decomposition of the linear response to an external stress in normal modes. We use a minimal three-dimensional dipole-spring model to theoretically describe the magnetic and elastic interactions on the mesoscopic level. Specifically, the magnetic particles carry permanent magnetic dipole moments and are spatially arranged in a prescribed way, before they are linked by elastic springs. An external magnetic field aligns the magnetic moments. On the one hand, we study regular lattice-like particle arrangements to compare with previous results in the literature. On the other hand, we calculate the dynamic elastic moduli for irregular, more realistic particle distributions. Our approach measures the tunability of the linear dynamic response as a function of the particle arrangement, the system orientation with respect to the external magnetic field, as well as the magnitude of the magnetic interaction between the particles. The strength of the present approach is that it explicitly connects the relaxational modes of the system with the rheological properties as well as with the internal rearrangement of the particles in the sample, providing new insight into the dynamics of these remarkable materials.
Kinetics of fragmentation and dissociation of two-strand protein filaments: Coarse-grained simulations and experiments
Authors: Zaccone A. , Terentjev I. , Herling T. W. , Knowles T. P. J. , Aleksandrova A. , Terentjev E. M.
Published: September 2016

While a significant body of investigations have been focused on the process of protein self-assembly, much less is understood about the reverse process of a filament breaking due to thermal motion into smaller fragments, or depolymerization of subunits from the filament ends. Indirect evidence for actin and amyloid filament fragmentation has been reported, although the phenomenon has never been directly observed either experimentally or in simulations. Here we report the direct observation of filament depolymerization and breakup in a minimal, calibrated model of coarse-grained molecular simulation. We quantify the orders of magnitude by which the depolymerization rate from the filament ends koff is larger than fragmentation rate k− and establish the law koff/k− = exp[(ε‖ − ε⊥)/kBT] = exp[0.5ε/kBT], which accounts for the topology and energy of bonds holding the filament together. This mechanism and the order-of-magnitude predictions are well supported by direct experimental measurements of depolymerization of insulin amyloid filaments.
Direct laser acceleration in an inhomogeneous cylindrical plasma channel
Authors: Zhang Rong , Cheng Li-Hong , Tang Rong-An , Xue Ju-Kui
Published: September 2016

We discuss the development of the instability for electron acceleration and energy gain of electrons from laser waves in both homogeneous and inhomogeneous non-planar cylindrical plasma channels. We find that the instability (i.e., electron acceleration) in the cylindrical plasma channel can be developed more quickly and strongly than that in the planar two-dimensional plasma channel. Then, enhancement of energy gain and shortening of acceleration length in the cylindrical plasma channel are observed. For the cylindrical plasma channel, the electron in the inhomogeneous plasma channel can gain more energy from the laser and the acceleration length can be shortened by adjusting the width of the laser and the inhomogeneous charge density distributions.
Effects of electric field on structures and dynamics in a two-dimensional dust dipole particle system
Authors: Hou X. N. , Liu Y. H. , Huang F. , Jiang S. Z. , Chen Z. Y. , Zhang R. Y.
Published: September 2016

Effects of radial electric field on the structures and dynamics of dust dipoles are studied by molecular dynamics simulations. The dipoles' configuration and mean distance to the system center are used to illustrate the structures of the whole system. It is shown that the dipole particles can arrange themselves into ring-like structures in the absence of external electric field, which can gradually transform to vortex, and then to radial arrangement with the increase of the strength of electric field. The trajectories, mean square displacement, and the mean speed in radial and tangential directions of dipoles are investigated to depict the effects of the radial electric filed on the collective motion of dust dipolar particles, which are closely associated with the growth of dust particle, especially for the formation of rod-like and some other complex fractal dust particles.
Temperature dependence of viscosity in a two-dimensional dusty plasma without the effects of shear thinning
Authors: Haralson Zach , Goree J.
Published: September 2016

An experiment was designed to measure viscosity and its temperature dependence in a two-dimensional dusty plasma. To avoid shear thinning while maintaining a uniform temperature, the shear flow and heating were provided separately, using different kinds of laser manipulation. The viscosity was found to be significantly higher than that was reported in three previous experiments most similar to ours, probably due to our avoidance of shear thinning. The viscosity increases linearly with the inverse temperature Γ, as predicted by simulations for a liquid-like strongly coupled plasma at low temperatures.
Current convective instability in detached divertor plasma
Authors: Krasheninnikov S. I. , Smolyakov A. I.
Published: September 2016

The asymmetry of inner and outer divertors, which cause the inner divertor to detach first, while the outer one is still attached, results in the large temperature difference between the vicinities of inner and outer targets and the onset of large electric potential drop through detached plasma of the inner divertor. A large potential drop along with the inhomogeneity of the resistivity of detached plasma across the divertor leg drives the current convective instability in the inner divertor and subsequent fluctuations of radiation loss similar to that observed in experiments. The estimates of the frequency of plasma parameter fluctuations due to the current convective instability are in a reasonable agreement with experimental data. Once the outer divertor also detaches, the temperature difference between the vicinities of inner and outer targets disappears, and the driving force for the current convective instability, and resulting oscillations of radiation loss, vanishes. This feature is indeed observed in experiments.
Communication: Uncovering correlated vibrational cooling and electron transfer dynamics with multidimensional spectroscopy
Authors: Guo Zhenkun , Giokas Paul G. , Cheshire Thomas P. , Williams Olivia F. , Dirkes David J. , You Wei , Moran Andrew M.
Published: September 2016

Analogues of 2D photon echo methods in which two population times are sampled have recently been used to expose heterogeneity in chemical kinetics. In this work, the two population times sampled for a transition metal complex are transformed into a 2D rate spectrum using the maximum entropy method. The 2D rate spectrum suggests heterogeneity in the vibrational cooling (VC) rate within the ensemble. In addition, a cross peak associated with VC and back electron transfer (BET) dynamics reveals correlation between the two processes. We hypothesize that an increase in the strength of solute-solvent interactions, which accelerates VC, drives the system toward the activationless regime of BET.
Influence of the Nb growth surface on the allotropic Ti phase transformation in Nb/Ti/Nb nanolaminates
Authors: Wan Li , Yu Xiao-xiang , Thompson Gregory
Published: September 2016

As the thickness of a thin film is decreased, the interfacial structure becomes paramount and crystals can undergo phase transformations. Molecular dynamic simulations have been performed to capture how such transformation could occur under the growth surface of a film. An hcp to bcc transition in Ti for Ti/Nb multilayers was used as the case studies. The simulations had good agreement with experiments. The simulations further predicted a mixed phase state for Ti for particular equal layer thicknesses.
Enhanced axial confinement in a monolithically integrated self-rolled-up SiNx vertical microring photonic coupler
Authors: Yu Xin , Goddard Lynford L. , Li Xiuling , Chen Xiaogang
Published: September 2016

We report an efficient method to introduce enhanced axial confinement in the self-rolled-up SiNx vertical microtube coupler by depositing a thin layer of high refractive index material strip within the coupling section and effectively forming a vertical microring. Three times wider mode spacing is observed in such a vertical microring coupler monolithically integrated with a silicon nitride ridge waveguide as compared to the one without such axial confinement. More importantly, single mode operation within the telecomm C-band and S-band is achieved.
Explaining the distribution, structure and species composition of snow-patch vegetation in Tasmania, Australia
Authors: Parry Jared , Kirkpatrick Jamie B. , Marsden-Smedley Jon
Published: September 2016

The term ‘snow patch’ indicates an area in an alpine zone with distinct vegetation because snow persists there longer than in the surrounding areas. Snow patches are a well known rare and threatened ecosystem on mainland Australia, but little is known of their distribution and vegetation in Tasmania. We describe, and determine the environmental relationships of, snow patches and their vegetation in Tasmania. There are 119 snow patches in Tasmania, covering 86 ha in toto, 43 of which have some fjaeldmark vegetation and the rest of which have a complete vegetation cover. Snow patches are confined to the taller, more continental mountains where they occur on north-east- to east-facing slopes, with the surrounding alpine vegetation usually being free of persistent snow. Their considerable floristic and structural variability relates to substrate and climate. Within Tasmania, several species are largely restricted to snow patches. The high degree of Tasmanian endemism in the snow-patch vegetation makes it distinct from the snow-patch vegetation of mainland Australia. The Tasmanian snow patches are also distinct in their environmental conditions. In Tasmania, snow does not usually persist over the winter outside the 119 snow patches. There are five floristic communities in these patches, all being distinct from those in mainland Australian snow patches. The Tasmanian snow patches merit listing as a threatened ecosystem on the basis of their distinctiveness and restricted extent.
Effect of Alkyl Chain Length of Imidazolium Cation on the Electroreduction of CO2 to CO on Ag Electrode in Acetonitrile
Authors: Wang Qianqian , Chen Chengzhen , Zhong Juhua , Zhang Bo , Cheng Zhenmin
Published: September 2016

The effect of imidazolium-based ionic liquid on the electroreduction of CO2 to CO over a Ag electrode in acetonitrile catholyte was investigated. The voltage–current profiles clearly indicate that the electroreduction of CO2 is sensitive to the alkyl chain length at the N1-position in imidazolium cation (MIM+). Density functional theory computation suggests that the onset potential of CO2 reduction is related to the association degree between MIM+ and CO2•– species. More importantly, preparative scale electrolysis shows that the selectivity and output rate for the target product CO are also significantly affected by MIM+. With the elongation of the alkyl group in MIM+ from ethyl to octyl, the Faradaic efficiency for CO remarkably increases from 87 ± 4 % to 97 ± 2 % and then remains almost unchanged. However, the curve of the current density with respect to the chain length of alkyl group shows a convex style. These results indicate the dependence of CO2 reduction efficiency on the MIM+ adsorbed on the Ag electrode surface.
The effect of soil moisture extremes on the pathways and forms of phosphorus lost in runoff from two contrasting soil types
Authors: Simmonds B. , McDowell R. W. , Condron L. M.
Published: September 2016

Soil moisture and Olsen P concentrations play an important role in phosphorus (P) losses in runoff. Under moisture-rich anaerobic conditions, the reduction of Fe-oxides dissolves P from the soil into solution that may be available for loss by transport processes. Under very dry conditions, soil hydrophobicity induced by soil organic C can exacerbate infiltration-excess surface flow and soil erosion. Our hypotheses were as follows: (1) rainfall applied to a dry soil would cause greater particulate P losses in surface runoff due to hydrophobicity; (2) P losses from a wet soil would be dominated by drainage and filtered P; and (3) both runoff processes would result in environmentally unacceptable P losses at agronomically productive Olsen P concentrations depending on the sorption capacity (anion storage capacity; ASC) of the soil. Superphosphate was added to a Brown and Organic soil (Olsen P initially 7 and 13mgL–1 respectively) to create a range of Olsen P concentrations. Soils were placed in boxes, soil moisture adjusted (<10% or 90% available water holding capacity) and artificial rainfall applied at a rate equivalent to a storm event (5-year return interval; 30–35mmh–1) and surface runoff and drainage collected. Surface runoff was measured as infiltration-excess surface flow from dry Organic soil (water drop penetration time >3600s), and as saturation-excess surface flow from the wet Brown soil (water drop penetration time <5s). Total P (TP) concentrations in surface flow from both soils increased linearly with Olsen P concentration. Compared with dry Organic soil, the wet Brown soil lost a greater proportion of TP as particulate via surface runoff. However, due to the high hydraulic conductivity and low ASC, the most important pathway for the Organic soil, wet or dry, was filtered P loss in drainage. These data can be used to more effectively target strategies to mitigate P losses.
Visual assessments of fuel loads are poorly related to destructively sampled fuel loads in eucalypt forests
Authors: Volkova Liubov , Sullivan Andrew L. , Roxburgh Stephen H. , Weston Christopher J.
Published: September 2016

Fire managers around the world commonly use visual assessment of forest fuels to aid prediction of fire behaviour and plan for hazard reduction burning. In Australia, fuel hazard assessment guides also allow conversion of visual assessments to indicative fuel loads, which is essential for some rate of spread models and calculation of fireline intensity or emissions. The strength of correlation between fuel hazard and destructively sampled (directly measured) fuel load was tested using a comprehensive dataset of >500 points from across a range of eucalypt forests in Australia. Overall, there was poor correlation between the assigned fuel hazard rating and measured biomass for surface, near-surface and elevated fuel components, with a clear tendency for these systems to under-predict fuel load at low hazard ratings, and over-predict it at high hazard ratings. Visual assessment of surface fuels was not statistically different from a random allocation of hazard level. The considerable overlap in fuel load between hazard ratings at higher ranges suggests the need to reduce the number of hazard classes to provide clearer differentiation of fuel hazard. To accurately assess forest fuel condition, improvements in fuel hazard descriptions and calibration of visual assessment with destructively measured fuels is essential.
Soil heating during the complete combustion of mega-logs and broadcast burning in central Oregon USA pumice soils
Authors: Smith Jane E. , Cowan Ariel D. , Fitzgerald Stephen A.
Published: September 2016

The environmental effect of extreme soil heating, such as occurs with the complete combustion of large downed wood during wildfires, is a post-fire management concern to forest managers. To address this knowledge gap, we stacked logs to create ‘mega-log’ burning conditions and compared the temperature, duration and penetration of the soil heat pulse in nine high intensity burned (HB) plots paired with adjacent masticated and broadcast burned low intensity burned (LB) plots at different soil depths (0, 5, 10 and 30 cm) in a Pinus ponderosa stand with volcanic pumice soils. Maximum soil surface temperatures ranges were 424–1168°C with a mean and standard error of 759 ± 9°C in the HB treatment and 42–360°C (107 ± 43°C) in the LB treatment. In the HB treatment, temperatures causing fine root and soil organism mortality (>60°C) penetrated the soil to at least 10 cm, but were not recorded at 30 cm. In the HB treatment, mean duration above 60°C at 0–10 cm persisted for 4–13 h (7.61 ± 1.02 h). Soils in the LB treatment experienced lethal temperatures at the surface for about an hour (1.19 ± 0.70 h) and at 5 cm were mostly well below lethal temperatures with the exception of one at 57°C and another at 100°C that remained above 60°C for 1.4 h. Large areas of high burn severity may affect long-term forest productivity. Our quantification of soil heating establishes conditions for ongoing studies investigating the effects of soil burn severity on tree seedling growth, soil fungi and nutrients.
Anthropogenic influence on wildfire activity in Alberta, Canada
Authors: Robinne François-Nicolas , Parisien Marc-André , Flannigan Mike
Published: September 2016

The boreal forest of Alberta, Canada, is under pressure from a rapid expansion of the wildland–human interface driven by natural resources exploitation. The specific impact of these changes on area burned remains poorly understood. We addressed this issue by modelling area burned for the 1980–2010 period using variables accounting for various anthropogenic effects. We hypothesise that an ecological frontier exists in the areas of intermediate to low human influence in northern Alberta, which implies a new influx of human-caused ignitions coinciding with continuous flammable vegetation, hence promoting area burned. Using a statistical control approach, we assessed the importance of each anthropogenic variable by adding them to a biophysical regression model. Our results show that there is a diversity of responses of area burned to the different anthropogenic factors considered. Distance to the transportation network, human footprint and density of the energy network significantly improved the model predictions. The area burned in the ecological frontier showed clusters of higher predictions by anthropogenic models, which supports our hypothesis of an ecological frontier and suggests that human and natural ignitions have an additive, albeit temporary, effect on landscape fire susceptibility.
Role of dystroglycan in limiting contraction-induced injury to the sarcomeric cytoskeleton of mature skeletal muscle
Authors: Rader Erik P. , Turk Rolf , Willer Tobias , Beltrán Daniel , Inamori Kei-ichiro , Peterson Taylor A. , Engle Jeffrey , Prouty Sally , Matsumura Kiichiro , Saito Fumiaki , Anderson Mary E. , Campbell Kevin P.
Published: September 2016

Significance

Dystroglycan (DG) is an extracellular matrix receptor that is linked to the cytoskeleton and critical for the development of skeletal muscle. DG deficiency throughout development is associated with multiple pathological features and muscular dystrophy. However, the direct consequence of DG disruption in mature muscle is not known. Here, we investigate muscles of transgenic mice after genetic knockdown of DG at maturity. The results demonstrate early susceptibility to contraction-induced injury accompanied by reduced passive tension and decreased titin immunostaining, rather than increased necrosis, excitation–contraction uncoupling, or sarcolemmal fragility. These results suggest a need for critical rethinking of both current theories regarding contraction-induced injury in muscular dystrophy and therapeutic strategies.
High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization
Authors: Moffitt Jeffrey R. , Hao Junjie , Wang Guiping , Chen Kok Hao , Babcock Hazen P. , Zhuang Xiaowei
Published: September 2016

Significance

Image-based approaches to single-cell transcriptomics offer the ability to quantify not only the copy number of RNAs within cells but also the intracellular RNA location and the spatial organization of cells within cultures or tissues. Here we report advances in multiplexed error-robust fluorescence in situ hybridization (MERFISH) that increase the measurement throughput by two orders of magnitude and allow gene expression profiling of ∼40,000 human cells in a single 18-h measurement. This drastic increase in throughput should facilitate the identification and study of rare populations of cells as well as the characterization of transcriptionally distinct cell types within large tissue regions.
Generalizations of Fourier analysis, and how to apply them
Authors: Gowers W.
Published: September 2016

This is a survey of the use of Fourier analysis in additive combinatorics, with a particular focus on situations where it cannot be straightforwardly applied but needs to be generalized first. Sometimes very satisfactory generalizations exist, while sometimes we have to make do with theories that have some of the desirable properties of Fourier analysis but not all of them. In the latter case, there are intriguing hints that there may be more satisfactory theories yet to be discovered. This article grew out of the Colloquium Lectures at the Joint Meeting of the AMS and the MAA, given in Seattle in January 2016.
Assessment of cancer and virus antigens for cross-reactivity in human tissues
Authors: Jaravine Victor , Raffegerst Silke , Schendel Dolores J , Frishman Dmitrij
Published: September 2016

Motivation

Cross-reactivity (CR) or invocation of autoimmune side effects in various tissues has important safety implications in adoptive immunotherapy directed against selected antigens. The ability to predict CR (on-target and off-target toxicities) may help in the early selection of safer therapeutically relevant target antigens.

Results

We developed a methodology for the calculation of quantitative CR for any defined peptide epitope. Using this approach, we performed assessment of 4 groups of 283 currently known human MHC-class-I epitopes including differentiation antigens, overexpressed proteins, cancer-testis antigens and mutations displayed by tumor cells. In addition, 89 epitopes originating from viral sources were investigated. The natural occurrence of these epitopes in human tissues was assessed based on proteomics abundance data, while the probability of their presentation by MHC-class-I molecules was modelled by the method of Keşmir et al. which combines proteasomal cleavage, TAP affinity and MHC-binding predictions. The results of these analyses for many previously defined peptides are presented as CR indices and tissue profiles. The methodology thus allows for quantitative comparisons of epitopes and is suggested to be suited for the assessment of epitopes of candidate antigens in an early stage of development of adoptive immunotherapy.

Availability and Implementation

Our method is implemented as a Java program, with curated datasets stored in a MySQL database. It predicts all naturally possible self-antigens for a given sequence of a therapeutic antigen (or epitope) and after filtering for predicted immunogenicity outputs results as an index and profile of CR to the self-antigens in 22 human tissues. The program is implemented as part of the iCrossR webserver, which is publicly available at http://webclu.bio.wzw.tum.de/icrossr/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Nanocall: an open source basecaller for Oxford Nanopore sequencing data
Authors: David Matei , Dursi L J , Yao Delia , Boutros Paul C , Simpson Jared T
Published: September 2016

Motivation

The highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls.

Results

To allow offline and private analysis of MinION data, we created Nanocall. Nanocall is the first freely available, open-source basecaller for Oxford Nanopore sequencing data and does not require an internet connection. Using R7.3 chemistry, on two E.coli and two human samples, with natural as well as PCR-amplified DNA, Nanocall reads have ∼68% identity, directly comparable to Metrichor ‘1D’ data. Further, Nanocall is efficient, processing ∼2500 Kbp of sequence per core hour using the fastest settings, and fully parallelized. Using a 4 core desktop computer, Nanocall could basecall a MinION sequencing run in real time. Metrichor provides the ability to integrate the ‘1D’ sequencing of template and complement strands of a single DNA molecule, and create a ‘2D’ read. Nanocall does not currently integrate this technology, and addition of this capability will be an important future development. In summary, Nanocall is the first open-source, freely available, off-line basecaller for Oxford Nanopore sequencing data.

Availability and Implementation

Nanocall is available at github.com/mateidavid/nanocall, released under the MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.
The OGCleaner: filtering false-positive homology clusters
Authors: Fujimoto M Stanley , Suvorov Anton , Jensen Nicholas O , Clement Mark J , Snell Quinn , Bybee Seth M
Published: September 2016

Detecting homologous sequences in organisms is an essential step in protein structure and function prediction, gene annotation and phylogenetic tree construction. Heuristic methods are often employed for quality control of putative homology clusters. These heuristics, however, usually only apply to pairwise sequence comparison and do not examine clusters as a whole. We present the Orthology Group Cleaner (the OGCleaner), a tool designed for filtering putative orthology groups as homology or non-homology clusters by considering all sequences in a cluster. The OGCleaner relies on high-quality orthologous groups identified in OrthoDB to train machine learning algorithms that are able to distinguish between true-positive and false-positive homology groups. This package aims to improve the quality of phylogenetic tree construction especially in instances of lower-quality transcriptome assemblies.

Availability and Implementation

https://github.com/byucsl/ogcleaner

Supplementary information

Supplementary data are available at Bioinformatics online.
Patterns of larval-stage connectivity of Atlantic cod (Gadus morhua) within the Gulf of Maine in relation to current structure and a proposed fisheries closure
Authors: Churchill J. H. , Kritzer J. P. , Dean M. J. , Grabowski J. H. , Sherwood G. D.
Published: September 2016

The decline of the Atlantic cod, Gadus morhua, stock in the Gulf of Maine to a historically low biomass has been coupled with a severe contraction in spatial range. The stock is now largely concentrated in the western Gulf of Maine. This erosion of spatial stock structure may be a factor-inhibiting recovery of Gulf of Maine cod. However, recent efforts to rebuild anadromous forage fish in the coastal Maine region coupled with the proposed creation of a new Eastern Maine Closed Area (EMCA), sited where localized depletion of the cod stock has been especially severe, might enable reestablishment of lost spatial structure of Gulf of Maine cod. We carried out larval transport modeling to examine the potential benefit of recovered cod spawning in the EMCA through supplying larvae to suitable juvenile settlement areas in the Gulf of Maine coastal zone and in the Cashes Ledge Closed Area (CLCA) in the central Gulf of Maine. The results indicate that an appreciable fraction of the larvae spawned in the EMCA are retained, to an age of settlement capability, in the coastal Maine region. Spawning in the EMCA may thus be a contributor of juveniles to a local, eastern Gulf of Maine, cod sub-stock. The results further indicate that spawning in the EMCA may supply a substantial subsidy of larvae to suitable juvenile habitat in the western Gulf of Maine and the CLCA. Protection of spawning stock in the EMCA may thus provide demographic benefits for the wider Gulf of Maine cod stock. Patterns of larval-stage connectivity between various potential spawning regions (including the EMCA) and areas of suitable juvenile habitat exhibit considerable interannual variability, which is predominantly linked to variability in the large-scale Gulf of Maine circulation. This result underscores the value of spatially explicit management as a means of fostering the recovery of the Gulf of Maine cod stock.
Analysis of liver damage from radon, X-ray, or alcohol treatments in mice using a self-organizing map
Authors: Kanzaki Norie , Kataoka Takahiro , Etani Reo , Sasaoka Kaori , Kanagawa Akihiro , Yamaoka Kiyonori
Published: September 2016

In our previous studies, we found that low-dose radiation inhibits oxidative stress–induced diseases due to increased antioxidants. Although these effects of low-dose radiation were demonstrated, further research was needed to clarify the effects. However, the analysis of oxidative stress is challenging, especially that of low levels of oxidative stress, because antioxidative substances are intricately involved. Thus, we proposed an approach for analysing oxidative liver damage via use of a self-organizing map (SOM)—a novel and comprehensive technique for evaluating hepatic and antioxidative function. Mice were treated with radon inhalation, irradiated with X-rays, or subjected to intraperitoneal injection of alcohol. We evaluated the oxidative damage levels in the liver from the SOM results for hepatic function and antioxidative substances. The results showed that the effects of low-dose irradiation (radon inhalation at a concentration of up to 2000 Bq/m3, or X-irradiation at a dose of up to 2.0 Gy) were comparable with the effect of alcohol administration at 0.5 g/kg bodyweight. Analysis using the SOM to discriminate small changes was made possible by its ability to ‘learn’ to adapt to unexpected changes. Moreover, when using a spherical SOM, the method comprehensively examined liver damage by radon, X-ray, and alcohol. We found that the types of liver damage caused by radon, X-rays, and alcohol have different characteristics. Therefore, our approaches would be useful as a method for evaluating oxidative liver damage caused by radon, X-rays and alcohol.
R2P in Theory and Practice
Authors: Bellamy Alex J. , Dunne Tim
Published: September 2016

This introductory chapter charts the evolution of R2P as a response to repeated failure of international society to respond to genocide and mass atrocities in the 1990s. It shows that the principle emerged from attempts to protect civilians from attack whilst protecting principles of order in international society. In doing so, it suggests that over time debates about R2P have shifted away from concerns about the principle’s normative value and meaning towards questions about its implementation in the most difficult of cases. The chapter attempts to introduce the whole book by surveying the principal normative, political, and operational challenges that confront R2P today.
UN General Assembly
Authors: Schmidt Megan
Published: September 2016

With the unanimous endorsement of the responsibility to protect (R2P) heads of state and government recognized that sovereignty entails responsibilities of the state to its people as relates to the protection from genocide, war crimes, crimes against humanity, and ethnic cleansing. Since the endorsement of R2P at the United Nations, progress has occurred at an unprecedented speed at the normative and operational levels with the past ten years also serving to identify challenges for the prevention of and response to atrocities. The United Nations General Assembly (UNGA) has been the central forum for R2P’s normative development, and a growing actor within the UN system for its implementation. This chapter assesses the UNGA’s interaction with R2P, reflecting on how this body has contributed to the conceptual advancement and operationalization of the principle as well as discussing the challenges that have arisen within this forum.
Getting There, Being There
Authors: Luck Edward C.
Published: September 2016

This chapter examines the implementation of R2P within the UN system, focusing especially on the evolving role of the Special Adviser to the UN Secretary-General. It sketches the institutional and political context that shaped the decision to appoint a UN Special Adviser, reflects on how the mandates and practices associated with this position have developed over the years, and assesses how the normative, operational, and institutional challenges ahead are shaping up for the implementation of R2P within the UN. The chapter argues that the position of Special Adviser is still evolving and far from firmly entrenched in the UN bureaucracy. Since its future prospects, and those of the related post of Special Adviser on the Prevention of Genocide, remain to be determined, the chapter addresses the mandates for both positions in some detail and puts forward some suggestions for how they could be further developed in the future.
Responding to Forced Displacement as a Mass Atrocity Crime
Authors: Orchard Phil
Published: September 2016

The protection of forced migrants and the R2P doctrine are inexorably linked. Refugee and internally displaced person forced movements can be triggered directly through mass atrocity crimes, indirectly as people flee mass atrocities, and even by the international use of force triggered by R2P responses. A range of causes of displacement are international crimes and fall within the R2P. However, the international response to internal displacement situations, in particular, tends to highlight legal and humanitarian based forms of protection and assistance, necessarily limited by the issue of sovereignty and state consent. These provide little direct protection in mass atrocity situations. R2P offers a path around the issue of sovereignty not only through the use of force but also by redefining how humanitarian assistance is provided, as demonstrated by Syria.
The Politics of Global Humanitarianism
Authors: Doyle Michael W.
Published: September 2016

The responsibility to protect (R2P) is both a license for and a leash against forcible intervention. It succeeded in widening the scope of legitimate armed intervention by licensing some (protective) interventions but only because it was seen as a leash against other (exploitative) interventions. This chapter traces the origins of the R2P doctrine in the Kosovo and ICISS reports, highlights the special features of the 2005 Outcome Document, notes how the doctrine was strengthened in practice by careful attention to non-coercive measures in Myanmar, Kenya, and Guinea, and then examines the landmark case of its use to sanction and then intervene against Gadhafi’s regime in Libya in 2011. The chapter concludes by drawing lessons for the revision and revival of this important contribution to human security.
Kenya
Authors: Sharma Serena
Published: September 2016

On 28 February 2008, Mwai Kibaki and Raila Odinga signed the Kenyan National Dialogue and Reconciliation Act and the Principles of Partnership establishing a coalition government. These agreements marked the end of one of the darkest moments in Kenyan history: eight weeks of bloodshed following the contested presidential elections of 27 December 2007. This case has generated a significant degree of interest, particularly from the perspective of R2P. The overwhelmingly positive appraisal of this case has, however, generated a number of common misconceptions surrounding the post-election crisis in Kenya. These relate to nearly all aspects of the crisis: from the question of what facilitated the response and how the mediation unfolded to the degree it can be deemed a success story. Consequently, some of the key lessons from this case—which may be relevant for halting atrocities in other contexts—have gone largely unnoticed.
The Genesis of R2P
Authors: Cater Charles , Malone David M.
Published: September 2016

This chapter addresses the evolution of the responsibility to protect concept from September 1999 to its adoption in the World Summit Outcome Document of September 2005. It covers Kofi Annan’s ‘dilemma of intervention’, some early human security initiatives by Canada including the International Commission on Intervention and State Sovereignty (ICISS) and its report The Responsibility to Protect which first articulated the moniker as well as the concept, the High-Level Panel on Threats, Challenges and Change and the Secretary-General’s report In Larger Freedom, the negotiations and Outcome Document of the World Summit, and the early incorporation of protection of civilians within Security Council resolutions. Throughout this narrative, the importance of sustained advocacy by key individuals—including Kofi Annan, Lloyd Axworthy, and Gareth Evans among others—is presented as vital to the evolution (in theory and in practice) of the responsibility to protect.
Nīlakaṇṭha Caturdhara’s Advaita Vedānta
Authors: Minkowski Christopher
Published: September 2016

The Sanskrit author, Nīlakaṇṭha Caturdhara, was active in the seventeenth century. His idiosyncratic works are representative of the lively intellectual scene in Benares in India’s early modern moment, the later era of the Great Mughals. In his writings, Nīlakaṇṭha sought to define an intellectually defensible boundary for the Vedic nondualist philosophy of Advaita Vedānta. His philosophical works are notable for their focus on other nondualist thinkers of the recent past, particularly the south Indian polymath, Appayya Dīkṣita. Nīlakaṇṭha’s philosophical efforts reveal the contentious theological and social context, in which philosophical and exetical arguments about the soul’s relationship to God and its final destiny were central.
Philosophy as a Distinct Cultural Practice
Authors: Smith Justin E. H.
Published: September 2016

This chapter analyzes the cultural features in the ancient world that led to the emergence of philosophy as a distinct cultural activity and examines the way in which Indian philosophy, in contrast to the cases of Greece and China, may be understood in relation to these cultural features. It examines the influence of the technology of writing, as well as of natural-scientific inquiry, especially in the domain of health and medicine, and the transregional importance of literacy and science for the project of philosophy, while also showing that Indian philosophy functions throughout the classical and into the modern period as a relatively discrete intellectual activity. Finally it shows, by comparing the French materialist philosopher Pierre Gassendi with Indian philosophers in the mid-1660s, how differences in the two philosophical traditions’ relationships to literacy and science continued to play a role in the perception of a philosophical divide between these two traditions.
Revisiting a Signaling Game of Legislative–Judiciary Interaction
Authors: Park Hong Min
Published: September 2016

By adding an informational component to the judicial review, Rogers (2001) argued that an independent court can be created and maintained by a legislature. This influential article, however, has one important mistake in its game-theoretical model that changes the equilibrium results and ultimately undermines the theoretical contribution to the discipline. The legislature no longer enjoys informational benefits by having an independent court.
The nature of the X-ray pulsar in M 31: An intermediate-mass X-ray binary?
Authors: Karino Shigeyuki
Published: September 2016

The first finding of the spin period of an accreting neutron star in M 31 was recently reported. The observed spin period is 1.2 s, and it shows 1.27 d modulations due to orbital motion. From the orbital information, the mass donor could not be a giant massive star. On the other hand, its observed properties are very odd as those of typical low-mass X-ray binaries. In this study, we compare the observed binary parameters with theoretical models given by a stellar evolution track, and give a restriction on the possible mass range of the donor. According to the standard stellar evolution model, the donor star should be larger than 1.5 M⊙, which suggests that this system is a new member of a rare category, an intermediate-mass X-ray binary. The magnetic field strength of the neutron star suggested by the spin-up/down tendency in this system supports the possibility of an intermediate-mass donor.
The Residency Application Process: Pursuing Improved Outcomes Through Better Understanding of the Issues
Authors: Katsufrakis Peter J. , Uhler Tara A. , Jones Lee D.
Published: September 2016

The residency application process requires that applicants, their schools, and residency programs exchange and evaluate information to accomplish successful matching of applicants to postgraduate training positions. The different motivations of these stakeholders influence both the types of information provided by medical schools and the perceived value and completeness of information received by residency programs. National standards have arisen to shape the type and format of information reported by medical schools about their students, though criticisms about the candor and completeness of the information remain. Growth in the number of applicants without proportional expansion of training positions and continued increases in the number of applications submitted by each applicant contribute to increases in the absolute number of applications each year, as well as the difficulty of evaluating applicants. Few standardized measures exist to facilitate comparison of applicants, and the heterogeneous nature of provided information limits its utility. Residency programs have been accused of excluding qualified applicants through use of numerical screening methods, such as United States Medical Licensing Examination (USMLE) Step 1 scores. Applicant evaluation includes review of standardized measurements such as USMLE Step 1 scores and other surrogate markers of future success. Proposed potential improvements to the residency application process include limiting applications; increasing the amount and/or types of information provided by applicants and by residency programs; shifting to holistic review, with standardization of metrics for important attributes; and fundamental reanalysis of the residency application process. A solution remains elusive, but these approaches may merit further consideration.
Incidence of Antipsychotic-Associated Side Effects
Authors: Takeuchi Hiroyoshi , Fervaha Gagan , Remington Gary
Published: September 2016

Objective

This study aimed to compare (1) the detection rates of antipsychotic-associated side effects between clinician and patient ratings and (2) differences as a function of change and absolute score definitions.

Methods

Data from phase 1 of the Clinical Antipsychotic Trials of Intervention Effectiveness (N = 1460) were analyzed. In this trial, 18 adverse events were systematically and concurrently assessed by clinicians and patients using a 4-point severity scale ranging from 0 (absent) to 3 (severe). The incidence of antipsychotic-associated side effects was calculated according to 2 definitions: change score (ie, higher score on the scale versus baseline) and absolute score (a score of 2 or 3 on the scale). In addition, patient and clinician concurrent detection rates were examined.

Results

The differences in incidence of antipsychotic-associated side effects between clinician and patient ratings were as small as 5.7% across the 2 definitions. The incidence of all side effects across clinician and patient ratings was approximately 2 times higher when using the change versus absolute score definition. Among the side effects detected by patients, 11 side effects were identified more frequently by clinicians, with 14.3% to 30.2% differences when using the change versus absolute score definition. Conversely, there was no difference of 10% or greater in patient or clinician concurrent detection rate on any item when using the absolute versus change score definition.

Conclusions

Our findings suggest that patient ratings are in line with clinician ratings and that the change score definition may be superior for the assessment of antipsychotic-associated side effects in clinical studies.
Disease transmission promotes evolution of host spatial patterns
Authors: Irvine Michael A. , Bull James C. , Keeling Matthew J.
Published: September 2016

Ecological dynamics can produce a variety of striking patterns. On ecological time scales, pattern formation has been hypothesized to be due to the interaction between a species and its local environment. On longer time scales, evolutionary factors must be taken into account. To examine the evolutionary robustness of spatial pattern formation, we construct a spatially explicit model of vegetation in the presence of a pathogen. Initially, we compare the dynamics for vegetation parameters that lead to competition induced spatial patterns and those that do not. Over ecological time scales, banded spatial patterns dramatically reduced the ability of the pathogen to spread, lowered its endemic density and hence increased the persistence of the vegetation. To gain an evolutionary understanding, each plant was given a heritable trait defining its resilience to competition; greater competition leads to lower vegetation density but stronger spatial patterns. When a disease is introduced, the selective pressure on the plant's resilience to the competition parameter is determined by the transmission of the disease. For high transmission, vegetation that has low resilience to competition and hence strong spatial patterning is an evolutionarily stable strategy. This demonstrates a novel mechanism by which striking spatial patterns can be maintained by disease-driven selection.
Reduced Notch signalling leads to postnatal skeletal muscle hypertrophy in Pofut1cax/caxmice
Authors: Al Jaam Bilal , Heu Katy , Pennarubia Florian , Segelle Alexandre , Magnol Laetitia , Germot Agnès , Legardinier Sébastien , Blanquet Véronique , Maftah Abderrahman
Published: September 2016

Postnatal skeletal muscle growth results from the activation of satellite cells and/or an increase in protein synthesis. The Notch signalling pathway maintains satellite cells in a quiescent state, and once activated, sustains their proliferation and commitment towards differentiation. In mammals, POFUT1-mediatedO-fucosylation regulates the interactions between NOTCH receptors and ligands of the DELTA/JAGGED family, thus initiating the activation of canonical Notch signalling. Here, we analysed the consequences of downregulated expression of thePofut1gene on postnatal muscle growth in mutant Pofut1cax/cax(cax, compact axial skeleton) mice and differentiation of their satellite cell-derived myoblasts (SCDMs). Pofut1cax/caxmice exhibited muscle hypertrophy, no hyperplasia and a decrease in satellite cell numbers compared with wild-type C3H mice. In agreement with these observations, Pofut1cax/caxSCDMs differentiated earlier concomitant with reducedPax7expression and decrease in PAX7+/MYOD−progenitor cells.In vitrobinding assays showed a reduced interaction of DELTA-LIKE 1 ligand (DLL1) with NOTCH receptors expressed at the cell surface of SCDMs, leading to a decreased Notch signalling as seen by the quantification of cleaved NICD and Notch target genes. These results demonstrated that POFUT1-mediatedO-fucosylation of NOTCH receptors regulates myogenic cell differentiation and affects postnatal muscle growth in mice.