bluuebunny/crossref_metadata_2025 huggingface dataset:
Regular aerobic exercise protects against impaired fasting plasma glucose-associated vascular endothelial dysfunction with aging
Authors: DeVan Allison E. , Eskurza Iratxe , Pierce Gary L. , Walker Ashley E. , Jablonski Kristen L. , Kaplon Rachelle E. , Seals Douglas R.
Published: October 2012

In the present study, we tested the hypothesis that age-associated vascular endothelial dysfunction is exacerbated by IFG (impaired fasting plasma glucose) and that regular aerobic exercise prevents this effect. Data were analysed from a cohort of 131 non-smoking men and women without overt clinical disease. Compared with young adult controls (age=24±1 years, n=29; values are means±S.E.M.), brachial artery FMD (flow-mediated dilation), a measure of conduit artery EDD (endothelium-dependent dilation), was 33% lower [7.93±0.33 against 5.27±0.37%Δ (% change), P<0.05] in MA/O (middle-aged/older) adults with NFG (normal fasting plasma glucose) (≤99 mg/dl, 62±1 years, n=35). In MA/O adults with IFG (100–125 mg/dl, 64±1 years, n=28), FMD was 30% lower (3.37±0.35%Δ) than in their peers with NFG and 58% lower than young controls (P<0.05). Brachial artery FMD was greater (6.38±0.35%Δ) in MA/O adults with NFG who regularly performed aerobic exercise (>45 min/day for ≥5 days/week, 62±1 years, n=23) compared with their non-exercising peers and only slightly less than young controls (P<0.05). Most importantly, FMD was completely preserved in MA/O adults with IFG who regularly performed aerobic exercise (6.99±0.69%Δ, 65±1 years, n=16). In the pooled sample, fasting plasma glucose was inversely related to FMD (r=−0.42, P<0.01) and was the strongest independent predictor of FMD (R2=0.32). Group differences in FMD were not affected by other subject characteristics or brachial artery properties, including brachial artery dilation to sublingual NTG (nitroglycerine, i.e. endothelium-independent dilation). IFG exacerbates age-associated vascular endothelial dysfunction and this adverse effect is completely prevented in MA/O adults who regularly perform aerobic exercise.
Role of Cation in Enhancing the Conversion of the Alzheimer’s Peptide into Amyloid Fibrils Using Protic Ionic Liquids
Authors: Debeljuh Natalie , Varghese Swapna , Barrow Colin J. , Byrne Nolene
Published: October 2012

We report on the impact of changes in the protic ionic liquid (pIL) cation on the fibrilisation kinetics and the conversion of the Aβ 16–22 from monomers to amyloid fibrils. When we compare the use of primary, secondary, and tertiary amines we find that the primary amine results in the greatest conversion into amyloid fibrils. We show that the pIL is directly interacting with the peptide and this likely drives the difference in conversion and kinetics observed.
Computer-Aided Molecular Design of Ionic Liquids: An Overview
Authors: Weis Derick C. , MacFarlane Douglas R.
Published: October 2012

Computer-aided molecular design (CAMD) is a technique that helps select potential target molecules that will have desired properties before synthesis and testing in the laboratory, and provides an excellent complement to the chemical intuition possessed by experimentalists. Property predictions are obtained from a quantitative structure–property relationship (QSPR) that links changes at the molecular structure level to differences in the macroscopic properties. Ionic liquids (ILs) offer an excellent opportunity for the application of CAMD because of the numerous possible combinations of cations and anions available to fine-tune physical properties. In addition, there are many innovative applications of ILs where CAMD could make an impact. In this overview, we present the general methodology for CAMD with QSPR, and describe recent progress in this area related to ILs.
Economics of nuclear power and climate change mitigation policies
Authors: Bauer Nico , Brecha Robert J. , Luderer Gunnar
Published: October 2012

The events of March 2011 at the nuclear power complex in Fukushima, Japan, raised questions about the safe operation of nuclear power plants, with early retirement of existing nuclear power plants being debated in the policy arena and considered by regulators. Also, the future of building new nuclear power plants is highly uncertain. Should nuclear power policies become more restrictive, one potential option for climate change mitigation will be less available. However, a systematic analysis of nuclear power policies, including early retirement, has been missing in the climate change mitigation literature. We apply an energy economy model framework to derive scenarios and analyze the interactions and tradeoffs between these two policy fields. Our results indicate that early retirement of nuclear power plants leads to discounted cumulative global GDP losses of 0.07% by 2020. If, in addition, new nuclear investments are excluded, total losses will double. The effect of climate policies imposed by an intertemporal carbon budget on incremental costs of policies restricting nuclear power use is small. However, climate policies have much larger impacts than policies restricting the use of nuclear power. The carbon budget leads to cumulative discounted near term reductions of global GDP of 0.64% until 2020. Intertemporal flexibility of the carbon budget approach enables higher near-term emissions as a result of increased power generation from natural gas to fill the emerging gap in electricity supply, while still remaining within the overall carbon budget. Demand reductions and efficiency improvements are the second major response strategy.
Analysis of human samples reveals impaired SHH-dependent cerebellar development in Joubert syndrome/Meckel syndrome
Authors: Aguilar Andrea , Meunier Alice , Strehl Laetitia , Martinovic Jelena , Bonniere Maryse , Attie-Bitach Tania , Encha-Razavi Féréchté , Spassky Nathalie
Published: October 2012

Joubert syndrome (JS) and Meckel syndrome (MKS) are pleiotropic ciliopathies characterized by severe defects of the cerebellar vermis, ranging from hypoplasia to aplasia. Interestingly, ciliary conditional mutant mice have a hypoplastic cerebellum in which the proliferation of cerebellar granule cell progenitors (GCPs) in response to Sonic hedgehog (SHH) is severely reduced. This suggests that Shh signaling defects could contribute to the vermis hypoplasia observed in the human syndromes. As existing JS/MKS mutant mouse models suggest apparently contradictory hypotheses on JS/MKS etiology, we investigated Shh signaling directly on human fetal samples. First, in an examination of human cerebellar development, we linked the rates of GCP proliferation to the different levels and localizations of active Shh signaling and showed that the GCP possessed a primary cilium with CEP290 at its base. Second, we found that the proliferation of GCPs and their response to SHH were severely impaired in the cerebellum of subjects with JS/MKS and Jeune syndrome. Finally, we showed that the defect in GCP proliferation was similar in the cerebellar vermis and hemispheres in all patients with ciliopathy analyzed, suggesting that the specific cause of vermal hypo-/aplasia precedes this defect. Our results, obtained from the analysis of human samples, show that the hemispheres and the vermis are affected in JS/MKS and provide evidence of a defective cellular mechanism in these pathologic processes.
Noncoding transcription within the
Igh
distal V
H
region at PAIR elements affects the 3D structure of the
Igh
locus in pro-B cells
Authors: Verma-Gaur Jiyoti , Torkamani Ali , Schaffer Lana , Head Steven R. , Schork Nicholas J. , Feeney Ann J.
Published: October 2012

Noncoding sense and antisense germ-line transcription within the Ig heavy chain locus precedes V(D)J recombination and has been proposed to be associated with
Igh
locus accessibility, although its precise role remains elusive. However, no global analysis of germ-line transcription throughout the
Igh
locus has been done. Therefore, we performed directional RNA-seq, demonstrating the locations and extent of both sense and antisense transcription throughout the
Igh
locus. Surprisingly, the majority of antisense transcripts are localized around two Pax5-activated intergenic repeat (PAIR) elements in the distal
IghV
region. Importantly, long-distance loops measured by chromosome conformation capture (3C) are observed between these two active PAIR promoters and Eμ, the start site of Iμ germ-line transcription, in a lineage- and stage-specific manner, even though this antisense transcription is Eμ-independent.
YY1

−/−

pro-B cells are greatly impaired in distal V
H
gene rearrangement and
Igh
locus compaction, and we demonstrate that YY1 deficiency greatly reduces antisense transcription and PAIR-Eμ interactions. ChIP-seq shows high level YY1 binding only at Eμ, but low levels near some antisense promoters. PAIR–Eμ interactions are not disrupted by DRB, which blocks transcription elongation without disrupting transcription factories once they are established, but the looping is reduced after heat-shock treatment, which disrupts transcription factories. We propose that transcription-mediated interactions, most likely at transcription factories, initially compact the
Igh
locus, bringing distal V
H
genes close to the DJ
H
rearrangement which is adjacent to Eμ. Therefore, we hypothesize that one key role of noncoding germ-line transcription is to facilitate locus compaction, allowing distal V
H
genes to undergo efficient rearrangement.
CIRCADIAN CLOCK-ASSOCIATED 1
regulates ROS homeostasis and oxidative stress responses
Authors: Lai Alvina Grace , Doherty Colleen J. , Mueller-Roeber Bernd , Kay Steve A. , Schippers Jos H. M. , Dijkwel Paul P.
Published: October 2012

Organisms have evolved endogenous biological clocks as internal timekeepers to coordinate metabolic processes with the external environment. Here, we seek to understand the mechanism of synchrony between the oscillator and products of metabolism known as Reactive Oxygen Species (ROS) in
Arabidopsis thaliana
. ROS-responsive genes exhibit a time-of-day–specific phase of expression under diurnal and circadian conditions, implying a role of the circadian clock in transcriptional regulation of these genes. Hydrogen peroxide production and scavenging also display time-of-day phases. Mutations in the core-clock regulator,
CIRCADIAN CLOCK ASSOCIATED 1
(
CCA1
), affect the transcriptional regulation of ROS-responsive genes, ROS homeostasis, and tolerance to oxidative stress. Mis-expression of
EARLY FLOWERING 3
,
LUX ARRHYTHMO
, and
TIMING OF CAB EXPRESSION 1
affect ROS production and transcription, indicating a global effect of the clock on the ROS network. We propose CCA1 as a master regulator of ROS homeostasis through association with the Evening Element in promoters of ROS genes in vivo to coordinate time-dependent responses to oxidative stress. We also find that ROS functions as an input signal that affects the transcriptional output of the clock, revealing an important link between ROS signaling and circadian output. Temporal coordination of ROS signaling by
CCA1
and the reciprocal control of circadian output by ROS reveal a mechanistic link that allows plants to master oxidative stress responses.
Identification of cation-binding sites on actin that drive polymerization and modulate bending stiffness
Authors: Kang Hyeran , Bradley Michael J. , McCullough Brannon R. , Pierre Anaëlle , Grintsevich Elena E. , Reisler Emil , De La Cruz Enrique M.
Published: October 2012

The assembly of actin monomers into filaments and networks plays vital roles throughout eukaryotic biology, including intracellular transport, cell motility, cell division, determining cellular shape, and providing cells with mechanical strength. The regulation of actin assembly and modulation of filament mechanical properties are critical for proper actin function. It is well established that physiological salt concentrations promote actin assembly and alter the overall bending mechanics of assembled filaments and networks. However, the molecular origins of these salt-dependent effects, particularly if they involve nonspecific ionic strength effects or specific ion-binding interactions, are unknown. Here, we demonstrate that specific cation binding at two discrete sites situated between adjacent subunits along the long-pitch helix drive actin polymerization and determine the filament bending rigidity. We classify the two sites as “polymerization” and “stiffness” sites based on the effects that mutations at the sites have on salt-dependent filament assembly and bending mechanics, respectively. These results establish the existence and location of the cation-binding sites that confer salt dependence to the assembly and mechanics of actin filaments.
Efficient TALEN-mediated gene knockout in livestock
Authors: Carlson Daniel F. , Tan Wenfang , Lillico Simon G. , Stverakova Dana , Proudfoot Chris , Christian Michelle , Voytas Daniel F. , Long Charles R. , Whitelaw C. Bruce A. , Fahrenkrug Scott C.
Published: October 2012

Transcription activator-like effector nucleases (TALENs) are programmable nucleases that join FokI endonuclease with the modular DNA-binding domain of TALEs. Although zinc-finger nucleases enable a variety of genome modifications, their application to genetic engineering of livestock has been slowed by technical limitations of embryo-injection, culture of primary cells, and difficulty in producing reliable reagents with a limited budget. In contrast, we found that TALENs could easily be manufactured and that over half (23/36, 64%) demonstrate high activity in primary cells. Cytoplasmic injections of TALEN mRNAs into livestock zygotes were capable of inducing gene KO in up to 75% of embryos analyzed, a portion of which harbored biallelic modification. We also developed a simple transposon coselection strategy for TALEN-mediated gene modification in primary fibroblasts that enabled both enrichment for modified cells and efficient isolation of modified colonies. Coselection after treatment with a single TALEN-pair enabled isolation of colonies with mono- and biallelic modification in up to 54% and 17% of colonies, respectively. Coselection after treatment with two TALEN-pairs directed against the same chromosome enabled the isolation of colonies harboring large chromosomal deletions and inversions (10% and 4% of colonies, respectively). TALEN-modified Ossabaw swine fetal fibroblasts were effective nuclear donors for cloning, resulting in the creation of miniature swine containing mono- and biallelic mutations of the LDL receptor gene as models of familial hypercholesterolemia. TALENs thus appear to represent a highly facile platform for the modification of livestock genomes for both biomedical and agricultural applications.
Counselling young people: Counsellors' perspectives on ‘what works’ – An exploratory study
Authors: Westergaard Jane
Published: October 2012

Aim: Counsellors who work with young people in a range of contexts know that they are not engaging with ‘mini‐adults’. The issues young people bring to counselling are often complex, challenging and wide‐ranging, as adolescents are experiencing times of turbulence and change in their physical, emotional, social and psychological development. This paper focuses on a research project undertaken with five counsellors who work with young people, and asks the question: ‘What works?’ Method: The research project is an in‐depth qualitative study into the counsellor's experience of counselling young people, using a narrative approach. Findings: Four key shared themes emerged: the significance of ‘safety’ in the relationship; building the therapeutic alliance; flexibility and integration relating to theoretical orientation; and the use of creativity. Outcomes: This paper offers counsellors the opportunity to reflect on ‘what works’ and consider the professional knowledge, which underpins their own counselling practice with young people.
Plasmonics: visit the past to know the future
Authors: Hayashi Shinji , Okamoto Takayuki
Published: October 2012

Surface plasmons are collective oscillations of free electrons localized at surfaces of structures made of metals. Since the surface plasmons induce fluctuations of electric charge at surfaces, they are accompanied by electromagnetic oscillations. Electromagnetic fields associated with surface plasmons are localized at surfaces of metallic structures and significantly enhanced compared with the excitation field. These two characteristics are ingredients for making good use of surface plasmons in plasmonics. Plasmonics is a rapidly growing and well-established research field, which covers various aspects of surface plasmons towards realization of a variety of surface-plasmon-based devices. In this paper, after summarizing the fundamental aspects of surface plasmons propagating on planar metallic surfaces and localized at metallic nanoparticles, recent progress in plasmonic waveguides, plasmonic light-emitting devices and plasmonic solar cells is reviewed.
Off-diagonal particle and toroidal momentum transport: a survey of experimental, theoretical and modelling aspects
Authors: Angioni C. , Camenen Y. , Casson F.J. , Fable E. , McDermott R.M. , Peeters A.G. , Rice J.E.
Published: October 2012

In tokamaks, turbulent particle and toroidal momentum transport are both characterized by the presence of off-diagonal contributions which play an essential role in establishing the profile shapes of the density and the toroidal rotation under most conditions. In this paper similarities and differences between the two turbulent transport channels are pointed out and, thereby, interesting physical aspects which connect the two channels are identified. The main contributions to off-diagonal particle and toroidal momentum transport are reviewed by means of a rather simplified description, which aims at providing, when possible, a direct connection between theoretical, modelling and experimental research.
Characterization of broadband MHD fluctuations during type-II edge localized modes as measured in 2D with ECE-imaging at ASDEX Upgrade
Authors: Boom J.E. , Wolfrum E. , Classen I.G.J. , de Vries P.C. , Maraschek M. , Suttrop W. , von Thun C.P. Pérez , Donné A.J.H. , Tobias B.J. , Domier C.W. , Luhmann N.C. , Park H.K.
Published: October 2012

The characterization of a broadband fluctuation that is typical for the type-II ELM regime at ASDEX Upgrade has been improved using the 2D capabilities of ECE-imaging. During the transition from the type-I to type-II ELMy phase, it has been found that electron temperature fluctuations form a broadband peak in the 19–65 kHz range. In the type-II phase, this broadband fluctuation reaches a maximum relative amplitude of almost 20% just inside the top of the pedestal. Simultaneously, the electron temperature profile is completely flattened at this location. The 2D distribution of the amplitude of this broadband fluctuation is such that, when averaged over time, a minimum occurs around the mid-plane. From the measurements of the nearby magnetic pickup coils, a similar broadband fluctuation seems visible in the same frequency range. However, this is peaked at a slightly lower frequency and does not show a similar minimum. From the analysis of the fluctuations on small timescales, the poloidal and toroidal mode numbers are estimated to be m ∼ 100 and n ∼ 21. Furthermore, activity reminiscent of beat waves has been observed, which might partially account for the fluctuation's broadband nature and the seeming velocity variation of single fluctuation passages. Overall, similarities between the characteristics of this broadband fluctuation and various precursors to type-I ELMs suggest that this fluctuation can play an important role in regulating the ELM cycle.
Magnetohydrodynamic simulations of edge poloidal flows
Authors: Guazzotto L. , Betti R.
Published: October 2012

Edge poloidal flows exceeding the poloidal sound speed lead to the formation of a pedestal structure (Guazzotto and Betti 2011 Phys. Rev. Lett.
107 125002). This result is based on the existence of ‘transonic’ equilibria, in which the edge region of the plasma flows supersonically with respect to the poloidal sound speed (i.e. the sound speed reduced by a factor B

θ
/B), while the plasma core is rotating with subsonic poloidal velocities. The ideal-MHD equilibrium force balance shows that radial discontinuities must be present at equilibrium in the presence of transonic flows. The formation of the transonic discontinuity was proven with time-dependent simulations. In this work, we prove that the transonic discontinuity can be formed with poloidal velocities no larger than a few tens of km s−1. Such relatively slow velocities are supersonic at the bottom of the pedestal where the temperature is a few tens of eVs. We also show how realistic toroidal velocity profiles can be obtained in transonic equilibria if the appropriate choice is made for the input free functions.
Features of spontaneous and pellet-induced ELMs on the HL-2A tokamak
Authors: Huang Y. , Liu C.H. , Nie L. , Feng Z. , Ji X.Q. , Yao K. , Zhu G.L. , Liu Yi , Cui Z.Y. , Yan L.W. , Wang Q.M. , Yang Q.W. , Ding X.T. , Dong J.Q. , Duan X.R.
Published: October 2012

The pellet pacing ELM mitigation concept is being tested in some tokamaks such as ASDEX Upgrade, DIII-D and JET. By increasing the ELM frequency, the ELM size can be reduced and eventually suppressed to meet the lifetime requirements on ITER target plates. In the HL-2A tokamak, ELMy H-mode operation is routinely performed and small type-III ELMs with a high repetition rate and some type-I (or possibly large type-III) ELM events are observed. Large ELMs are often preceded by strong coherent magnetic oscillations, and produce obvious perturbations on plasma current I

p
, electron density

at the edge, stored energy W
E, etc. The coherent magnetic oscillations before an ELM crash or during the ELM are measured by toroidal and poloidal Mirnov coils and analysed by the wavelet technique to study the spectral characteristics of the short time ELM events. Pellet injection experiments are performed in type-III ELMy H-mode plasmas and ELM-free H-mode plasmas to study the physics of pellet triggering ELM. The analyses of pellet-induced ELMs and spontaneous ELMs are presented. Because the pellet size is relatively large, it induces magnetic oscillations lasting longer than that of a natural ELM.
ELM control experiments in the KSTAR device
Authors: Kim Jayhyun , Jeon Y.-M. , Xiao W.W. , Yoon S.-W. , Park J.-K. , Yun G.S. , Ahn J.-W. , Kim H.S. , Yang H.-L. , Kim H.K. , Park S. , Jeong J.H. , Jung M. , Choe G.H. , Ko W.H. , Lee S.-G. , Nam Y.U. , Bak J.G. , Lee K.D. , Na H.K. , Hahn S.-H. , Diamond P.H. , Rhee T. , Kwon J.M. , Sabbagh S.A. , Park Y.S. , Park H.K. , Na Y.S. , Kim W.C. , Kwak J.G.
Published: October 2012

The fourth KSTAR campaign in 2011 concentrated on active edge-localized mode (ELM) control by various methods such as non-axisymmetric magnetic perturbations, supersonic molecular beam injection (SMBI), vertical jogs of the plasma column and edge electron heating. The segmented in-vessel control coil (IVCC) system is capable of applying n ⩽ 2 perturbed field with different phasing among top, middle and bottom coils. Application of an n = 1 perturbed field showed a desirable ELM suppression result. Fast vertical jogs of the plasma column achieved ELM pace-making and ELMs locked to 50 Hz vertical jogs were observed with a high probability of phase locking. A newly installed SMBI system was used for ELM control and the state of mitigated ELMs was sustained by the optimized repetitive SMBI pulse for a few tens of ELM periods. A change in ELM behaviour was seen due to edge electron heating although the effect of ECH launch needs supplementary analyses. The ECEI images of suppressed/mitigated ELM states showed apparent differences when compared with natural ELMy states. Further analyses are ongoing to explain the observed ELM control results.
Temporally resolved analysis of the response of density and temperature to modulated central electron heating on ASDEX Upgrade
Authors: Mlynek A. , Angioni C. , Fable E. , Fischer R. , Ryter F. , Stober J. , Suttrop W. , Zohm H.
Published: October 2012

In recent years, it has been found that the application of local heat sources in a fusion plasma can influence the shape of the density profile. This shows that a coupling between heat and particle transport exists, which is taken into account in transport models by introducing off-diagonal transport coefficients. In existing studies, the focus of analysis is mostly on the density profile that occurs after a sufficiently long settling time after altering the heating power level. In this paper, the transient behaviour of temperature and density in response to steps in the applied heating power is analysed, which leads to the observation of hysteresis loops in the local density–temperature diagram. Based on numerical transport simulations, it is shown that the occurrence of hysteresis curves can be reproduced on the basis of today's physics understanding, where the shape of the curve provides additional information on the transport coefficients and their interdependences.
Effects of local toroidal field ripples due to test blanket modules for ITER on radial transport of thermal ions
Authors: Oyama N. , Urano H. , Shinohara K. , Honda M. , Takizuka T. , Hayashi N. , Kamada Y.
Published: October 2012

The effects of local toroidal field (TF) ripples due to ferromagnetic steels used in test blanket modules (TBMs) in ITER on the radial transport of thermal ions located near the top of the pedestal are investigated using a fully three-dimensional magnetic field orbit following Monte Carlo (F3D-OFMC) code. In the simulation, the three-dimensional motion of 20 000 test particles, distributed near the top of the pedestal (Ψ
N
 = 0.91) with the same Maxwellian velocity distribution as the thermal ions at this location, is traced for 1.9 s. In comparison with the number of lost particles in the case without a TBM, the additional loss with three TBM ports expected in ITER is evaluated to be less than 1% of the test particles. The additional losses increase linearly with the number of TBM ports and with the square of the amplitude of the local TF ripple. The poloidal structure of the TF ripple without ferritic inserts and a case with 18 TBM ports are also compared. It is found that cases having the same ripple amplitude at a certain point can have substantially different additional loss rates if the poloidal ripple structure is not the same. The ripple amplitude near the banana tip seems to be the most important factor in determining the radial diffusion of thermal ions.
L–H transition in the presence of magnetic perturbations in ASDEX Upgrade
Authors: Ryter F. , Rathgeber S.K. , Viezzer E. , Suttrop W. , Burckhart A. , Fischer R. , Kurzan B. , Potzel S. , Pütterich T.
Published: October 2012

The L–H transition and the H-mode behaviour in the presence of non-axisymmetric n = 2 magnetic perturbations have been investigated. At low density no effect on the L–H transition is observed. Within a rather narrow density window around 50% of the Greenwald density limit, a transition to H-mode with small ELMs only and good confinement can be achieved. However, a strong density dependence of the L–H threshold power in the presence of magnetic perturbations forces the plasmas to remain in L-mode when the density is above 60% of the Greenwald value. The H-mode confinement time is not affected by the presence of the magnetic perturbations. All of these H-modes, with and without ELM mitigation, exhibit a common confinement degradation with increasing recycling.
Particle transport in density gradient driven TE mode turbulence
Authors: Skyman A. , Nordman H. , Strand P.I.
Published: October 2012

The turbulent transport of main ion and trace impurities in a tokamak device in the presence of steep electron density gradients has been studied. The parameters are chosen for trapped electron mode turbulence, driven primarily by steep electron density gradients relevant to H-mode physics. Results obtained through nonlinear and quasilinear gyrokinetic simulations using the GENE code are compared with results obtained from a fluid model. Impurity transport is studied by examining the balance of convective and diffusive transport, as quantified by the density gradient corresponding to zero particle flux (impurity peaking factor). Scalings are obtained for the impurity peaking with the background electron density gradient and the impurity charge number. It is shown that the impurity peaking factor is weakly dependent on impurity charge and significantly smaller than the driving electron density gradient.
H-mode characterization for dominant ECRH and comparison to dominant NBI and ICRF heating at ASDEX Upgrade
Authors: Sommer F. , Stober J. , Angioni C. , Bernert M. , Burckhart A. , Bobkov V. , Fischer R. , Fuchs C. , McDermott R.M. , Suttrop W. , Viezzer E.
Published: October 2012

The influence of pure electron heating versus combined electron and ion heating on a high collisionality H-mode plasma has been investigated in ASDEX Upgrade. This was done by replacing both neutral beam injection (NBI) and ion cyclotron resonance frequency (ICRF) heating in small steps with electron cyclotron resonance heating (ECRH) while keeping the total heating power constant. The stability of the global plasma parameters and the response of the kinetic profiles on the changed heating mix and torque input is shown. The differences in edge localized mode behaviour between the different heating mixes is reported. The data were analysed with an interpretative transport model and linear gyrokinetic simulations were performed to evaluate the underlying transport mechanism.
A model for the reversal of the toroidal rotation in tokamak
Authors: Spineanu Florin , Vlad Madalina
Published: October 2012

The transition from toroidal counter- to co-rotation in the core plasma has been observed at L to H transition in several tokamaks. Spontaneous reversal has also been observed in TCV beyond a threshold in the density. We develop a model based on the following phenomenology: (1) the increase in the gradient of the pressure triggers formation on a fast time scale of cells of convection (similar to Rayleigh–Benard, but with a single sign of vorticity); (2) poloidal rotation is induced by the envelope of the peripheric velocity of the convection cells; via the baroclinic term the gradients of temperature and density sustain the poloidal rotation against the decay due to the parallel viscosity; (3) the fast increase in poloidal flow induces a high-time derivative of the radial electric field; (4) the neoclassical polarization creates a series of parallel accelerations (kicks on each bounce) of the trapped ions, leading to an increase in the toroidal precession or to its reversal; the source of energy is the work done by the radial electric field. (5) the diffusion transfers on resistive scale the toroidal momentum from the trapped ions to the untrapped ones. The correlated interactions are examined and the estimated time scales are found to be compatible with the observations.
H-mode access by pellet fuelling in the MAST tokamak
Authors: Valovič M. , Garzotti L. , Gurl C. , Akers R. , Harrison J. , Michael C. , Naylor G. , Scannell R.
Published: October 2012

Access into H-mode is studied in the MAST tokamak when plasma is fuelled by cryogenic pellets. It is shown that pellet fuelling from the high-field side allows access to H-mode in plasmas heated by neutral beams. Simple and two-stage L–H transitions are identified. The results of comparison of the L–H transitions with pellet injection with transitions where plasmas are fuelled solely by gas puffing depend on the gas puff geometry: fuelling by high-field side gas leads to an L–H transition at the density comparable to the transition with pellet injection. In contrast low-field gas can completely prevent the L–H transition.
Magnetohydrodynamic tokamak plasma edge stability
Authors: Webster Anthony J.
Published: October 2012

The edge of a tokamak plasma is interesting due to its geometrical structure that is difficult to model mathematically and computationally, its tendency to form ‘transport barriers’ with increased confinement of energy and momentum, and the edge-localized instabilities associated with transport barriers that threaten the lifetime of components in large tokamaks. Ideal magnetohydrodynamics (MHD) is generally well understood, but only in the past decade has a good theoretical understanding emerged of MHD stability near the plasmas' separatrix when one or more X-points are present. By reviewing and discussing our theoretical understanding of ideal MHD stability of the plasma's edge, a clear picture emerges for its ideal stability. Conclusions are: ideal MHD will limit the width of strong transport barriers at the plasma's edge, a strong edge transport barrier will be associated with ELMs, ELMs will have a maximum toroidal mode number, will be preceded by smaller precursor instabilities, and can be triggered by sufficient changes to either the edge or the core plasma. Observations are made for the mechanisms responsible for edge transport barriers and ELMs, some leading to experimental predictions, others highlighting important open questions.
Ubiquity of non-diffusive momentum transport in JET H-modes
Authors: Weisen H. , Camenen Y. , Salmi A. , Versloot T.W. , deVries P.C. , Maslov M. , Tala T. , Beurskens M. , Giroud C.
Published: October 2012

A broad survey of the experimental database of neutral beam heated baseline H-modes and hybrid scenarios in the JET tokamak has established the ubiquity of non-diffusive momentum transport mechanisms in rotating plasmas. As a result of their presence, the normalized angular frequency gradient R∇ω/ω is higher than expected from momentum diffusion alone, by about unity in the core (r/a ∼ 0.3), rising to near 5 close to the edge, where its contribution to the total gradient is comparable to the gradient associated with the diffusive flux. The magnitude and parameter dependences of the non-diffusive contribution to the gradient are consistent with a theoretically expected pinch, which has its origin in the vertical particle drift resulting from the Coriolis force. Linear gyrokinetic calculations of the pinch number RV/χ

φ
and the Prandtl number χ

φ
/χ
i are in good agreement with the experimental observations, with similar dependences on R/L

n
, q and ε = r/R. A contribution due to residual stresses may also be present, but could not be identified with certainty.
Solitary magnetic perturbations at the ELM onset
Authors: Wenninger R.P. , Zohm H. , Boom J.E. , Burckhart A. , Dunne M.G. , Dux R. , Eich T. , Fischer R. , Fuchs C. , Garcia-Munoz M. , Igochine V. , Hölzl M. , N.C. Luhmann , Lunt T. , Maraschek M. , Müller H.W. , Park H.K. , Schneider P.A. , Sommer F. , Suttrop W. , Viezzer E.
Published: October 2012

Tokamak H-mode plasmas frequently exhibit edge-localized modes (ELMs). ELMs allow maintaining sufficient plasma purity and thus enable stationary H-mode. On the other hand in a future device ELMs may cause divertor power flux densities far in excess of tolerable material limits. The size of the energy loss per ELM is determined by saturation effects in the non-linear phase of the ELM, which at present is hardly understood. ASDEX Upgrade is now equipped with a set of fast sampling diagnostics, which is well suited to investigate the chain of events around the ELM crash with appropriate temporal resolution (⩽10 µs).

Solitary magnetic perturbations (SMPs) are identified as dominant features in the radial magnetic fluctuations below 100 kHz. They are typically observed close (±100 µs) to the onset of pedestal erosion. SMPs are field aligned structures rotating in the electron diamagnetic drift direction with perpendicular velocities of about 10 km s−1. A comparison of perpendicular velocities suggests that the perturbation evoking SMPs is located at or inside the separatrix. Analysis of very pronounced examples showed that the number of peaks per toroidal turn is 1 or 2, which is clearly lower than the corresponding numbers in linear stability calculations. In combination with strong peaking of the magnetic signals this results in a solitary appearance resembling modes like palm tree modes, edge snakes or outer modes. This behaviour has been quantified as solitariness and correlated with main plasma parameters.

SMPs may be considered as a signature of the non-linear ELM phase originating at the separatrix or further inside. Thus they provide a handle to investigate the transition from linear to non-linear ELM phase. By comparison with data from gas puff imaging processes in the non-linear phase at or inside the separatrix and in the scrape-off layer (SOL) can be correlated. A connection between the passing of an SMP and the onset of radial filament propagation has been found. Eventually the findings related to SMPs may contribute to a future quantitative understanding of the non-linear ELM evolution.
Electron density evolution after L–H transitions and the L–H/H–L cycle in ASDEX Upgrade
Authors: Willensdorfer M. , Wolfrum E. , Scarabosio A. , Aumayr F. , Fischer R. , Kurzan B. , McDermott R.M. , Mlynek A. , Nold B. , Rathgeber S.K. , Rohde V. , Ryter F. , Sauter P. , Viezzer E.
Published: October 2012

The development of the electron density profile and its dependences after the L–H transition have been investigated. Only electron cyclotron resonance heated H-modes have been analysed to exclude core particle fuelling. While the density gradient in the edge transport barrier increases significantly after the L–H transition, the pedestal top temperature rises continuously with the applied heating power and shows no pronounced change at the transition. The H-mode density saturates at a level which correlates with the neutral gas density in the divertor prior to the L–H transition. Although the density build-up varies with the available deuterium inventory, the initial increase in the edge density gradient is similar. This has been observed independent of the L-mode plasma collisionality (ν
* ≈ 2.8–5.5). The analysis of electron density and temperature profiles reveals that L–H and H–L transitions occur at similar pedestal top pressures, but the pedestal top densities are always higher at the time of the H–L back transition.
The sonic line as a free boundary
Authors: Keyfitz Barbara , Tesdall Allen , Payne Kevin , Popivanov Nedyu
Published: October 2012

We consider the steady transonic small disturbance equations on a domain and with data that lead to a solution that depends on a single variable. After writing down the solution, we show that it can also be found by using a hodograph transformation followed by a partial Fourier transform. This motivates considering perturbed problems that can be solved with the same technique. We identify a class of such problems.
Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer
Authors: Liang Han , Cheung Lydia W.T. , Li Jie , Ju Zhenlin , Yu Shuangxing , Stemke-Hale Katherine , Dogruluk Turgut , Lu Yiling , Liu Xiuping , Gu Chao , Guo Wei , Scherer Steven E. , Carter Hannah , Westin Shannon N. , Dyer Mary D. , Verhaak Roeland G.W. , Zhang Fan , Karchin Rachel , Liu Chang-Gong , Lu Karen H. , Broaddus Russell R. , Scott Kenneth L. , Hennessy Bryan T. , Mills Gordon B.
Published: October 2012

Endometrial cancer is the most common gynecological malignancy, with more than 280,000 cases occurring annually worldwide. Although previous studies have identified important common somatic mutations in endometrial cancer, they have primarily focused on a small set of known cancer genes and have thus provided a limited view of the molecular basis underlying this disease. Here we have developed an integrated systems-biology approach to identifying novel cancer genes contributing to endometrial tumorigenesis. We first performed whole-exome sequencing on 13 endometrial cancers and matched normal samples, systematically identifying somatic alterations with high precision and sensitivity. We then combined bioinformatics prioritization with high-throughput screening (including both shRNA-mediated knockdown and expression of wild-type and mutant constructs) in a highly sensitive cell viability assay. Our results revealed 12 potential driver cancer genes including 10 tumor-suppressor candidates (ARID1A,INHBA,KMO,TTLL5,GRM8,IGFBP3,AKTIP, PHKA2,TRPS1, andWNT11) and two oncogene candidates (ERBB3andRPS6KC1). The results in the “sensor” cell line were recapitulated by siRNA-mediated knockdown in endometrial cancer cell lines. Focusing onARID1A, we integrated mutation profiles with functional proteomics in 222 endometrial cancer samples, demonstrating thatARID1Amutations frequently co-occur with mutations in the phosphatidylinositol 3-kinase (PI3K) pathway and are associated with PI3K pathway activation. siRNA knockdown in endometrial cancer cell lines increased AKT phosphorylation supportingARID1Aas a novel regulator of PI3K pathway activity. Our study presents the first unbiased view of somatic coding mutations in endometrial cancer and provides functional evidence for diverse driver genes and mutations in this disease.
Buffering Capacity Explains Signal Variation in Symbiotic Calcium Oscillations
Authors: Granqvist Emma , Wysham Derin , Hazledine Saul , Kozlowski Wojciech , Sun Jongho , Charpentier Myriam , Martins Teresa Vaz , Haleux Pauline , Tsaneva-Atanasova Krasimira , Downie J. Allan , Oldroyd Giles E.D. , Morris Richard J.
Published: October 2012

Legumes form symbioses with rhizobial bacteria and arbuscular mycorrhizal fungi that aid plant nutrition. A critical component in the establishment of these symbioses is nuclear-localized calcium (Ca2+) oscillations. Different components on the nuclear envelope have been identified as being required for the generation of the Ca2+ oscillations. Among these an ion channel, Doesn't Make Infections1, is preferentially localized on the inner nuclear envelope and a Ca2+ ATPase is localized on both the inner and outer nuclear envelopes. Doesn't Make Infections1 is conserved across plants and has a weak but broad similarity to bacterial potassium channels. A possible role for this cation channel could be hyperpolarization of the nuclear envelope to counterbalance the charge caused by the influx of Ca2+ into the nucleus. Ca2+ channels and Ca2+ pumps are needed for the release and reuptake of Ca2+ from the internal store, which is hypothesized to be the nuclear envelope lumen and endoplasmic reticulum, but the release mechanism of Ca2+ remains to be identified and characterized. Here, we develop a mathematical model based on these components to describe the observed symbiotic Ca2+ oscillations. This model can recapitulate Ca2+ oscillations, and with the inclusion of Ca2+-binding proteins it offers a simple explanation for several previously unexplained phenomena. These include long periods of frequency variation, changes in spike shape, and the initiation and termination of oscillations. The model also predicts that an increase in buffering capacity in the nucleoplasm would cause a period of rapid oscillations. This phenomenon was observed experimentally by adding more of the inducing signal.
Organ Sales: Exploitative at Any Price?
Authors: Lawlor Rob
Published: October 2012

In many cases, claims that a transaction is exploitative will focus on the details of the transaction, such as the price paid or conditions. For example, in a claim that a worker is exploited, the grounds for the claim are usually that the pay is not sufficient or the working conditions too dangerous. In some cases, however, the claim that a transaction is exploitative is not seen to rely on these finer details. Many, for example, claim that organ sales would be exploitative, in a way that doesn't seem to depend on the details. This article considers, but ultimately rejects, a number of arguments which could be used to defend this sort of claim.
Species loss of stoneflies (Plecoptera) in the Czech Republic during the 20th century
Authors: BOJKOVÁ JINDŘIŠKA , KOMPRDOVÁ KLÁRA , SOLDÁN TOMÁŠ , ZAHRÁDKOVÁ SVĚTLANA
Published: October 2012

1. Rapid expansion and intensification of anthropogenic activities in the 20th century has caused profound changes in freshwater assemblages. Unfortunately, knowledge of the extent and causes of species loss (SL) is limited due to the lack of reliable historical data. An unusual data set allows us to compare changes in the most sensitive of aquatic insect orders, the Plecoptera, at some 170 locations in the Czech Republic between two time periods, 1955–1960 and 2006–2010. Historical data (1890–1911) on assemblages of six lowland rivers allow us to infer even earlier changes.

2. Regional stonefly diversity decreased in the first half of the 20th century. Streams at lower altitudes lost a substantial number of species, which were never recovered. In the second half of the century, large‐scale anthropogenic pressure caused SL in all habitats, leading to a dissimilarity of contemporary and previous assemblages. The greatest changes were found at sites affected by organic pollution and a mixture of organic pollution and channelisation or impoundment. Colonisation of new habitats was observed in only three of the 80 species evaluated.

3. Species of moderate habitat specialisation and tolerance to organic pollution were most likely to be lost. Those with narrow specialisations in protected habitats were present in both historical and contemporary collections.

4. Contemporary assemblages are the consequence of more than a 100 years of anthropogenic impacts. In particular, streams at lower altitude and draining intensively exploited landscapes host a mere fragment of the original species complement. Most stonefly species are less frequently present than before, although their assemblages remain almost intact in near‐natural mountain streams. Our analyses demonstrate dramatic restriction of species ranges and, in some cases, apparent changes in altitudinal preference throughout the area.
A cassette system for systematic cryostorage of low‐temperature scanning electron microscopy stubs
Authors: Lawton D. M. , Oswald W. B.
Published: October 2012

A system is described for the storage of cylindrical (10 × 3.5 mm) stubs for low‐temperature scanning electron microscopy. The system facilitates rapid retrieval of mounted specimens, maximizes the capacity of the low‐temperature (liquid nitrogen) specimen store, locates each stub exactly in a protected well, and eliminates the possibility of specimen damage from conventional hazards during transport between the storage facility and microscope.
Automated microdensitometry of nucleolar organizer regions using microspectrophoto‐microscopy
Authors: Zhang C. Z. , Young W. G. , Basford K. E.
Published: October 2012

Nucleolar organizer regions (NORs) are major sites of ribosomal RNA synthesis, providing an index of transcriptional activity and possibly determining the malignant status of cells. Difficulties lie in quantifying them. This study reports a methodology to assist in the standardization of the assessment of interphase NORs. Regenerating hepatocytes, which have increased rRNA synthesis, were chosen as a model to test automated microdensitometry for silver‐stained NORs. Quantification employed a microspectrophoto‐microscope as a microdensitometer. Significant differences in silver‐stained NORs in hepatocytes were recorded among treatment/fixative groups. As the quantitative method avoids subjective observer error and thus improves the accuracy of measurement, it would potentially have routine application to diagnostic pathology.