bluuebunny/crossref_metadata_2025 huggingface dataset:
Time evolution of mixing in heterogeneous porous media
Authors: de Dreuzy J.‐R. , Carrera J. , Dentz M. , Le Borgne T.
Published: May 2012

Mixing in heterogeneous media results from the competition between velocity fluctuations and local scale diffusion. Velocity fluctuations create a potential for mixing by generating disorder and large interfacial areas between resident and invading waters. Local scale diffusion smoothes out the disorder while transforming this potential into effective mixing. The effective mixing state is quantified by the integral of concentration squared over the spatial domain. Because it emerges from dispersion, the potential mixing is defined as the mixing state of a Gaussian plume that has the same longitudinal dispersion as the real plume. The difference γ between effective and potential mixing normalized by the latter traduces the lag of diffusion to homogenize the concentration structure generated by the dispersion processes. This new decomposition of effective mixing into potential mixing and departure rate γ makes a full use of dispersion for quantifying mixing and restricts the analysis of mixing to γ. For cases where the mean concentration can be assumed Gaussian, we use the concentration variance equation of Kapoor and Gelhar (1994) to show that γ depends solely on the macrodispersion coefficient (spreading rate) and the recently developed mixing scale defined as the smallest scale over which concentration can be considered uniform, and which quantifies the internal plume disorder. We use numerical simulations to show that γ turns out to follow a simple scaling form that depends on neither the heterogeneity level or the Peclet number. A very similar scaling form is recovered for Taylor dispersion. Both derivations of γ reinforce its relevance to characterize mixing. This generic characterization of mixing can offer new ways to set up transport equations that honor not only advection and spreading but also mixing.
Cyberinfrastructure for isotope analysis and modeling
Authors: Bowen Gabriel J. , West Jason B. , Zhao Lan , Takahashi George , Miller Chris , Zhang Tonglin
Published: May 2012

As the quantity and complexity of scientific data expand, accessible interfaces for data manipulation and analysis are needed to support broad and efficient data use. The Isoscapes Modeling, Analysis, and Prediction (IsoMAP; http://isomap.org) Web‐based geographical information system (GIS) gateway is an example of such a resource. Recently launched with support from the U.S. National Science Foundation (NSF) Division of Biological Infrastructure, IsoMAP enables analysis and integration of diverse light stable isotope and environmental data by a broad‐based user community. It provides an intuitive, spatial interface that streamlines data analysis, modeling, and exploration in research ranging from greenhouse gas biogeochemistry to food science.
Higher concentrations of chlorides and other contaminants found in many U.S. well networks
Authors: Showstack Randy
Published: May 2012

Higher concentrations of chlorides and other contaminants found in many U.S. well networks A new analysis of 56 well networks that represent many major U.S. aquifers and urban and agricultural land use areas has found that in 66% of the networks there was a statistically significant increase in concentration of at least one of three indicators of water quality: chlorides, dissolved solids, and nitrates. The analysis, by the U.S. Geological Survey's (USGS) National Water Quality Assessment Program ( NAWQA), which was released on 30 April, compared samples of groundwater collected from wells during 1988–2000 with corresponding samples collected from 2001–2010. The analysis found statistically significant increases of chloride concentrations in 43% of the networks, with the largest median decadal increases in well networks in the upper Illinois River Basin and in the New England coastal basins, while the largest median decadal decrease was in the upper Snake River Basin in the Pacific Northwest. The analysis also found statistically significant increases of dissolved solids concentrations in 41% of the well networks and increases of nitrate concentrations in 23%.
Aiding in biodiversity and ecosystem science and policy interface gaps
Authors: Showstack Randy
Published: May 2012

Aiding in biodiversity and ecosystem science and policy interface gaps The final operational design of the Intergovernmental Platform on Biodiversity and Ecosystem Services ( IPBES), which addresses gaps in the science and policy interface on these issues, was agreed upon by representatives from 90 nations at a 23 April meeting in Panama City, Panama. Core functions of IPBES include performing regular assessments of knowledge on biodiversity and ecosystem services and their linkages and identifying and prioritizing key scientific information for policy makers. The IPBES secretariat will be based in Bonn, Germany, and a trust fund will be set up to receive voluntary contributions from governments and others. For more information, see http://www.ipbes.net.
Honors
Authors: Anonymous
Published: May 2012

A number of AGU members were honored during the European Geosciences Union's (EGU) General Assembly, held on 22–27 April in Vienna. EGU Union awards were presented to the following people: Vincent Courtillot, University of Paris Diderot, France, received the 2012 Arthur Holmes Medal and EGU honorary membership for seminal contributions to geomagnetism and the geodynamics of mantle hot spots.Michael Ghil, University of California, Los Angeles, and École Normale Supérieure, France, received the 2012 Alfred Wegener Medal and EGU honorary membership for his leading contributions to theoretical climate dynamics; his innovative observational studies involving model assimilation of satellite data in meteorology, oceanography, and space physics; the breadth of his interdisciplinary studies, including macroeconomics; and his extensive supervision and mentoring of scores of graduate and postdoctoral students. Robin Clarke, Universidade Federal do Rio Grande do Sul, Brazil, received the 2012 Alexander von Humboldt Medal for fundamental contributions in statistical analysis and modeling of hydrological processes.Angioletta Coradini, Istituto Nazionale di Astrofsica, Italy, received the 2012 Jean Dominique Cassini Medal and EGU honorary membership in recognition of her important and wide range of work in planetary sciences and solar system formation and for her leading role in the development of space infrared instrumentation for planetary exploration.
Predicting carbon cycle feedbacks to climate: Integrating the right tools for the job
Authors: Billings Sharon A. , Ziegler Susan E. , Schlesinger William H. , Benner Ronald , de B. Richter Daniel
Published: May 2012

Organic matter (OM) is a critical component of Earth's carbon cycle, with strong potential to provide positive feedbacks to a warmer climate via enhanced release of carbon dioxide. Investigations of the fate of OM typically focus on large reservoirs (e.g., soils) and on abundant, relatively long‐lived compounds (e.g., lignin, a compound derived from the cell walls of woody plants), and the products of its decay. Many of these investigations are challenged by issues of scale. The appropriate spatial scale of many carbon cycling questions requires infrastructure beyond the means of most projects and temporal scales often impossible to achieve in a human lifetime. We advocate coupling flux measurements, parameters that ecosystem scientists often quantify, with compositional characterization of sources, reservoirs, and sinks, data often generated by organic geochemists. Combined, the approaches of these disciplines offer powerful tools to understand OM dynamics.
Challenges in understanding past and present eolian dust dynamics
Authors: Stuut Jan‐Berend , Merkel Ute , Rousseau Denis‐Didier
Published: May 2012

Dust Workshop 2011: Processes and Quaternary History of Dust Dynamics; Bremen, Germany, 31 October to 3 November 2011 Mineral dust is now generally recognized as a key element in global climate. However, many open questions need to be addressed to reduce the large uncertainties that still exist regarding the global dust cycle. The Atmospheric Dust During the Last Glacial Cycle: Observations and Modeling initiative (ADOM; see http://www.pages‐igbp.org/workinggroups/adom) of the Past Global Changes (PAGES) tackles these questions from both modern and paleo perspectives. A 3‐day workshop funded by PAGES and the Center for Marine Environmental Sciences (MARUM) in Germany brought together 50 international experts on marine, terrestrial, and polar dust archives; meteorology; remote sensing; and climate modeling. The workshop aimed to bridge gaps between disciplines and to cover all temporal and spatial scales involved in dust processes.
Swenson receives 2011 Geodesy Section Award: Citation
Authors: Wahr John , Tamisiea Mark
Published: May 2012

Sean Claude Swenson received the 2011 Geodesy Section Award at the 2011 AGU Fall Meeting, held 5–9 December in San Francisco, Calif. The award is given in recognition of major advances in geodesy.
In calm seas, precipitation drives air‐sea gas exchange
Authors: Schultz Colin
Published: May 2012

In a series of experiments run in what resembles a heavily instrumented fish tank,Harrison et al. investigated the interwoven roles of wind and rain on air‐sea gas exchange rates. Working with a 42‐meterlong, 1‐meter‐wide, and 1.25‐meter‐tall experimental pool, the authors were able to control the wind speed, rainfall rate, water circulation speed, and other parameters, which they used to assess the effect of 24 different wind speed–rainfall rate combinations on the gas exchange rate of sulfur hexafuoride, a greenhouse gas. In trials that lasted up to 3 hours, the authors collected water samples from the tank at regular intervals, tracking the concentration of the dissolved gas.
Ecohydrological feedbacks confound peat‐based climate reconstructions
Authors: Swindles Graeme T. , Morris Paul J. , Baird Andy J. , Blaauw Maarten , Plunkett Gill
Published: May 2012

Water‐table reconstructions from Holocene peatlands are increasingly being used as indicators of terrestrial palaeoclimate in many regions of the world. However, the links between peatland water tables, climate, and long‐term peatland development are poorly understood. Here we use a combination of high‐resolution proxy climate data and a model of long‐term peatland development to examine the relationship between rapid hydrological fluctuations in peatlands and climatic forcing. We show that changes in water‐table depth can occur independently of climate forcing. Ecohydrological feedbacks inherent in peatland development can lead to a degree of homeostasis that partially disconnects peatland water‐table behaviour from external climatic influences. We conclude by suggesting that further work needs to be done before peat‐based climate reconstructions can be used to test climate models.
Nonlinear principal component analysis in the detection of ionospheric electron content anomalies related to a deep earthquake (>300 km, M 7.0) on 1 January 2012, Izu Islands, Japan
Authors: Lin Jyh‐Woei
Published: May 2012

Nonlinear principal component analysis (NLPCA) and image processing are used to detect an ionospheric total electron content (TEC) anomaly above Japan's Izu Islands relating to an earthquake on 1 January 2012 (UT) (Mw = 7.0). This earthquake was 348 km deep. The earthquake occurred at 05:27:54 UT; NLPCA is applied to the time period 06:40 to 12:00 UT. NLPCA shows that the TEC anomaly is highly localized and decreases in intensity with time. PCA was unable to detect the anomaly. This work discusses potential reasons for the TEC anomaly over the Izu Islands after this earthquake and possible reasons including acoustic‐gravity waves, radon gas release, and P‐type semiconductor effects.
Does eddy‐eddy interaction control surface phytoplankton distribution and carbon export in the North Pacific Subtropical Gyre?
Authors: Guidi Lionel , Calil Paulo H. R. , Duhamel Solange , Björkman Karin M. , Doney Scott C. , Jackson George A. , Li Binglin , Church Matthew J. , Tozzi Sasha , Kolber Zbigniew S. , Richards Kelvin J. , Fong Allison A. , Letelier Ricardo M. , Gorsky Gabriel , Stemmann Lars , Karl David M.
Published: May 2012

In the North Pacific Subtropical Gyre (NPSG), the regular occurrence of summer phytoplankton blooms contributes to marine ecosystem productivity and the annual carbon export. The mechanisms underlying the formation, maintenance, and decay of these blooms remain largely unknown; nitrogen fixation, episodic vertical mixing of nutrients, and meso‐ (<100 km) and submesoscale (<10 km) physical processes are all hypothesized to contribute to bloom dynamics. In addition, zones of convergence in the ocean's surface layers are known to generate downwelling and/or converging currents that affect plankton distributions. It has been difficult to quantify the importance of these convergence zones in the export flux of particulate organic carbon (POC) in the open ocean. Here we use two high‐resolution ocean transects across a pair of mesoscale eddies in the vicinity of Station ALOHA (22° 45′N, 158° 00′W) to show that horizontal turbulent stirring may have been a dominant control on the spatial distribution of the nitrogen fixing cyanobacteriumTrichodesmium spp. Fast repetition rate fluorometry measurements suggested that this distribution stimulated new primary production; this conclusion was not confirmed by 14C‐based measurements, possibly because of different sampling scales for the two methods. Our observations of particle size distributions along the two transects showed that stretching by the mesoscale eddy field produced submesoscale features that mediated POC export via frontogenetically generated downwelling currents. This study highlights the need to combine high‐resolution biogeochemical and physical data sets to understand the links betweenTrichodesmium spp. surface distribution and POC export in the NPSG at the submesoscale level.
Global‐scale attribution of anthropogenic and natural dust sources and their emission rates based on MODIS Deep Blue aerosol products
Authors: Ginoux Paul , Prospero Joseph M. , Gill Thomas E. , Hsu N. Christina , Zhao Ming
Published: May 2012

Our understanding of the global dust cycle is limited by a dearth of information about dust sources, especially small‐scale features which could account for a large fraction of global emissions. Here we present a global‐scale high‐resolution (0.1°) mapping of sources based on Moderate Resolution Imaging Spectroradiometer (MODIS) Deep Blue estimates of dust optical depth in conjunction with other data sets including land use. We ascribe dust sources to natural and anthropogenic (primarily agricultural) origins, calculate their respective contributions to emissions, and extensively compare these products against literature. Natural dust sources globally account for 75% of emissions; anthropogenic sources account for 25%. North Africa accounts for 55% of global dust emissions with only 8% being anthropogenic, mostly from the Sahel. Elsewhere, anthropogenic dust emissions can be much higher (75% in Australia). Hydrologic dust sources (e.g., ephemeral water bodies) account for 31% worldwide; 15% of them are natural while 85% are anthropogenic. Globally, 20% of emissions are from vegetated surfaces, primarily desert shrublands and agricultural lands. Since anthropogenic dust sources are associated with land use and ephemeral water bodies, both in turn linked to the hydrological cycle, their emissions are affected by climate variability. Such changes in dust emissions can impact climate, air quality, and human health. Improved dust emission estimates will require a better mapping of threshold wind velocities, vegetation dynamics, and surface conditions (soil moisture and land use) especially in the sensitive regions identified here, as well as improved ability to address small‐scale convective processes producing dust via cold pool (haboob) events frequent in monsoon regimes.
Heterogeneity of Cholinergic Denervation in Parkinson's Disease without Dementia
Authors: Bohnen Nicolaas I , Müller Martijn L T M , Kotagal Vikas , Koeppe Robert A , Kilbourn Michael R , Gilman Sid , Albin Roger L , Frey Kirk A
Published: May 2012

Parkinson's disease (PD) is a multisystem neurodegenerative disorder. Heterogeneous clinical features may reflect heterogeneous changes in different brain regions. In contrast to the pronounced nigrostriatal denervation characteristic of PD, cholinergic changes are less marked. We investigated cholinergic innervation activity in PD subjects relative to normal subjects. Nondemented PD subjects ( n=101, age 65.3±7.2 years) and normal subjects ( n=29, age 66.8±10.9 years) underwent clinical assessment and [11C]methyl-4-piperidinyl propionate acetylcholinesterase and [11C]dihydrotetrabenazine monoaminergic positron emission tomography (PET) imaging. Cholinergic projection changes were heterogeneous for 65 out of 101 PD subjects who had neocortical and thalamic acetylcholinesterase activity within the normal range. The remainder had combined neocortical and thalamic (13/101), isolated neocortical (18/101), or isolated thalamic (5/101) acetylcholinesterase activity below the normal range. The low neocortical acetylcholinesterase activity subgroup had significantly lower global cognitive performance compared with the normal range subgroup (F=7.64, P=0.0069) with an independent effect for nigrostriatal denervation (F=7.60, P=0.0074). The low thalamic acetylcholinesterase activity subgroup did not differ from the normal thalamic acetylcholinesterase activity subgroup in cognitive performance or motor impairments except for a history of falls ( P=0.0023). Cholinergic denervation is heterogeneous with reduced neocortical and/or thalamic acetylcholinesterase activity in 36% of nondemented PD subjects with corresponding clinical phenotypic variation. Results also show independent cognitive effects for both cholinergic and dopaminergic system changes in nondemented PD subjects.
Cerebral Blood Volume Changes during Brain Activation
Authors: Krieger Steffen Norbert , Streicher Markus Nikolar , Trampel Robert , Turner Robert
Published: May 2012

Cerebral blood volume (CBV) changes significantly with brain activation, whether measured using positron emission tomography, functional magnetic resonance imaging (fMRI), or optical microscopy. If cerebral vessels are considered to be impermeable, the contents of the skull incompressible, and the skull itself inextensible, task- and hypercapnia-related changes of CBV could produce intolerable changes of intracranial pressure. Because it is becoming clear that CBV may be useful as a well-localized marker of neural activity changes, a resolution of this apparent paradox is needed. We have explored the idea that much of the change in CBV is facilitated by exchange of water between capillaries and surrounding tissue. To this end, we developed a novel hemodynamic boundary-value model and found approximate solutions using a numerical algorithm. We also constructed a macroscopic experimental model of a single capillary to provide biophysical insight. Both experiment and theory model capillary membranes as elastic and permeable. For a realistic change of input pressure, a relative pipe volume change of 21±5% was observed when using the experimental setup, compared with the value of approximately 17±1% when this quantity was calculated from the mathematical model. Volume, axial flow, and pressure changes are in the expected range.
Mitochondrial glutathione in toxicology and disease of the kidneys
Authors: Lash Lawrence H.
Published: May 2012

The tripeptide glutathione (GSH), comprised of the amino acids l-cysteine, glycine, and l-glutamate, is found in all cells of aerobic organisms and plays numerous, critical roles as an antioxidant and nucleophile in regulating cellular homeostasis and drug metabolism. GSH is synthesized exclusively in the cytoplasm of most cells by two ATP-dependent reactions. Despite this compartmentation, GSH is found in other subcellular compartments, including mitochondria. As the GSH molecule has a net negative charge at physiological pH, it cannot cross cellular membranes by diffusion. Rather, GSH is a substrate for a variety of anion and amino acid transporters. Two organic anion carriers in the inner membrane of renal mitochondria, the dicarboxylate carrier (DIC; Slc25a10) and the 2-oxoglutarate carrier (OGC; Slc25a11), are responsible for most of the transport of GSH from cytoplasm into mitochondrial matrix. Genetic manipulation of DIC and/or OGC expression in renal cell lines demonstrated the ability to produce sustained increases in mitochondrial GSH content, which then protected these cells from cytotoxicity due to several oxidants and mitochondrial toxicants. Several diseases and pathological states are associated with mitochondrial dysfunction and oxidative stress, suggesting that the mitochondrial GSH pool may be a therapeutic target. One such disease that is of particular concern for public health is diabetic nephropathy. Another chronic, pathological state that is associated with bioenergetic and redox changes is compensatory renal hypertrophy that results from reductions in functional renal mass. This review summarizes pathways of mitochondrial GSH transport and discusses studies on its manipulation in toxicological and pathological states.
Architecture of the catalytic HPN motif is conserved in all E2 conjugating enzymes
Authors: Cook Benjamin W. , Shaw Gary S.
Published: May 2012

E2 conjugating enzymes are the central enzymes in the ubiquitination pathway and are responsible for the transfer of ubiquitin and ubiquitin-like proteins on to target substrates. The secondary structural elements of the catalytic domain of these enzymes is highly conserved, including the sequence conservation of a three-residue HPN (His–Pro–Asn) motif located upstream of the active-site cysteine residue used for ubiquitin conjugation. Despite the vast structural knowledge of E2 enzymes, the catalytic mechanism of these enzymes remains poorly understood, in large part due to variation in the arrangements of the residues in the HPN motif in existing E2 structures. In the present study, we used the E2 enzyme HIP2 to probe the structures of the HPN motif in several other E2 enzymes. A combination of chemical-shift analysis, determination of the histidine protonation states and amide temperature coefficients were used to determine the orientation of the histidine ring and hydrogen-bonding arrangements within the HPN motif. Unlike many three-dimensional structures, we found that a conserved hydrogen bond between the histidine imidazole ring and the asparagine backbone amide proton, a common histidine protonation state, and a common histidine orientation exists for all E2 enzymes examined. These results indicate that the histidine within the HPN motif is orientated to structurally stabilize a tight turn motif in all E2 enzymes and is not orientated to interact with the asparagine side chain as proposed in some mechanisms. These results suggest that a common catalysis mechanism probably exists for all E2 conjugating enzymes to facilitate ubiquitin transfer.
Mechanotransduction in cells1
Authors: Goldmann Wolfgang H
Published: May 2012

Cell—matrix and cell—cell adhesions critically influence cell metabolism, protein synthesis, cell survival, cytoskeletal architecture and consequently cell mechanical properties such as migration, spreading and contraction. An important group of adhesive transmembrane receptors that mechanically link the ECM (extracellular matrix) with the internal cytoskeleton are integrins which are intimately connected with the FAs (focal adhesions) which consists of many proteins. The transient formation of FAs is greatly augmented either through externally applied tension to the cell or internally through myosin II‐driven cell contractility. Exactly which protein(s) within FAs sense, transmit and respond to mechanical stress is currently debated and numerous candidates have been proposed.
Magnocellular and Parvocellular Pathway Influences on Location-Based Inhibition-Of-Return
Authors: Brown James M , Guenther Benjamin A
Published: May 2012

The roles of the parvocellular (P) and magnocellular (M) retino-geniculo-cortical pathways during shifts of visual attention were investigated by creating M/dorsal-biased (eg low spatial frequency target, no objects present) and P/ventral-biased (ie high spatial frequency target, the perception of 3-D objects) stimulus conditions and measuring location-based inhibition-of-return (IOR). P/ventral-biased conditions produced the greatest IOR. M/dorsal-biased conditions produced the least IOR, in one instance eliminating it altogether. The results indicate a close relationship between IOR magnitude and relative P/ventral and M/dorsal activity with location-based IOR related more to P/ventral than to M/dorsal activity.
You Can Take the Eyes Out of the Doll, But…
Authors: Balas Benjamin , Horski Joseph
Published: May 2012

The perceived animacy of a face is well-predicted by the perceived animacy of the eyes presented in isolation. This is not true for other facial features (eg having a highly life-like nose does not appear to be crucial), suggesting that the eyes are a critical feature for perceiving life in a face. Here, we asked whether it was therefore possible to ‘transplant’ animacy into a face by transplanting the eyes into a face image. We conducted digital eye surgery on a series of morphed human/doll faces and found that while doll eyes make a morphed face look less alive, human eyes do not make you look more so. Thus, we cannot so easily transplant animacy into a face, but we can take it away.
Close, and a Cigar!—Why Size Perception Relates to Performance
Authors: Cañal-Bruland Rouwen , Pijpers J R (Rob) , Oudejans Raôul R D
Published: May 2012

In baseball batting, golf putting, and dart throwing, successful players estimate the size of the target object to be bigger than their less successful counterparts. While more and more empirical evidence is accumulated supporting the existence of this intriguing phenomenon, an explanation of the processes underpinning this effect remains to be provided. Here, we re-analysed data from a dart throwing experiment to examine the proposal—recently put forward by Proffitt and Linkenauger (in press)—that the variability in target-related performance may serve as a scaling metric for perceived target size which may explain why actors who perform consistently close to the target perceive the target to be bigger. Our results confirm that less variability in target-related performance in darts relates to perceiving the target as being bigger, thereby providing initial support for Proffitt and Linkenauger's proposal.
Activation of 5′-3′ exoribonuclease Xrn1 by cofactor Dcs1 is essential for mitochondrial function in yeast
Authors: Sinturel Flore , Bréchemier-Baey Dominique , Kiledjian Megerditch , Condon Ciarán , Bénard Lionel
Published: May 2012

The scavenger decapping enzyme Dcs1 has been shown to facilitate the activity of the cytoplasmic 5′-3′ exoribonuclease Xrn1 in eukaryotes. Dcs1 has also been shown to be required for growth in glycerol medium. We therefore wondered whether the capacity to activate RNA degradation could account for its requirement for growth on this carbon source. Indeed, a catalytic mutant of Xrn1 is also unable to grow in glycerol medium, and removal of the nuclear localization signal of Rat1, the nuclear homolog of Xrn1, restores glycerol growth. A cytoplasmic 5′-3′ exoribonuclease activity is therefore essential for yeast growth on glycerol, suggesting that Xrn1 activation by Dcs1 is physiologically important. In fact, Xrn1 is essentially inactive in the absence of Dcs1 in vivo. We analyzed the role of Dcs1 in the control of exoribonuclease activity in vitro and propose that Dcs1 is a specific cofactor of Xrn1. Dcs1 does not stimulate the activity of other 5′-3′ exoribonucleases, such as Rat1, in vitro. We demonstrate that Dcs1 improves the apparent affinity of Xrn1 for RNA and that Xrn1 and Dcs1 can form a complex in vitro. We examined the biological significance of this regulation by performing 2D protein gel analysis. We observed that a set of proteins showing decreased levels in a
DCS
deletion strain, some essential for respiration, are also systematically decreased in an
XRN1
deletion mutant. Therefore, we propose that the activation of Xrn1 by Dcs1 is important for respiration.
Control of neuronal differentiation by sumoylation of BRAF35, a subunit of the LSD1-CoREST histone demethylase complex
Authors: Ceballos-Chávez María , Rivero Sabrina , García-Gutiérrez Pablo , Rodríguez-Paredes Manuel , García-Domínguez Mario , Bhattacharya Shomi , Reyes José C.
Published: May 2012

The LSD1–CoREST histone demethylase complex is required to repress neuronal genes in nonneuronal tissues. Here we show that sumoylation of Braf35, one of the subunits of the complex, is required to maintain full repression of neuron-specific genes and for occupancy of the LSD1–CoREST complex at its gene targets. Interestingly, expression of Braf35 was sufficient to prevent neuronal differentiation induced by bHLH neurogenic transcription factors in P19 cells and in neuronal progenitors of the chicken embryo neural tube. Sumoylation of Braf35 is required for this antineurogenic activity. We also show that iBraf, a paralogue of Braf35, forms heterodimers with Braf35. Braf35–iBraf heterodimerization impairs Braf35 interaction with the LSD1–CoREST complex and inhibits Braf35 sumoylation. Consistent with these results, iBraf prevents the antineurogenic activity of Braf35 in vivo. Our data uncover a mechanism of regulation of the LSD1–CoREST complex and provide a molecular explanation for the antagonism between Braf35 and iBraf in neuronal differentiation.
Enhancing nonvolatile write-once-read-many-times memory effects with SiO2 nanoparticles sandwiched by poly(N-vinylcarbazole) layers
Authors: Xia Xianhai , Liu Xiangmei , Yi Mingdong , Fan Quli , Wang Lianhui , Tai Qiang , Shi Weiwei , Xie Linghai , Huang Wei
Published: May 2012

A nonvolatile write-once-read-many-times (WORM) memory device based on the ITO/poly(N-vinylcarbazole) (PVK)/SiO2 nanoparticles (SiO2 NPs)/PVK/Al structure is demonstrated. By employing SiO2 NPs, the ON/OFF current ratio of the device is enlarged from 20 to 7 × 102 at a low voltage, and the device shows obvious negative differential resistance (NDR) phenomenon at a high electric field. Compared with the ITO/PVK/Al and ITO/PVK/PVK/Al devices, it is found that the size of the SiO2 NPs sandwiched between two PVK layers plays an important role in enhancing the reproducibility and the ON state retention time of the WORM memory device. The WORM memory mechanisms of the device are investigated on the basis of the current–voltage (I–V) characteristics and scanning electron microscopy image. Here, the strength of the NDR effect in our devices is only related to the charge defects and traps of PVK films, and it can be enlarged by embedding charge traps into the PVK films.
Study of phase transformation behaviour of alumina through precipitation method
Authors: Shen Lu , Hu Chunfeng , Sakka Yoshio , Huang Qing
Published: May 2012

Alumina hydrates were prepared by the wet chemical method under different pH values and subsequently calcined through both conventional and microwave heating approaches. After calcination at 500 °C for 2 h, amorphous precursor was partially transformed to α-alumina. NH4NO3 remaining in the dried precursor without further washing after precipitation reaction was found to increase the transformation temperature, which is different from previous published results. Microwave calcination was also employed and can dramatically enhance the phase transformation rate in comparison with the conventional method. A combination of microwave heating and amorphous precursor may be a viable strategy to fabricate α-alumina at low temperatures rapidly.
Structural depth profile and nanoscale piezoelectric properties of randomly oriented Pb(Zr0.50Ti0.50)O3 thin films
Authors: Lima E C , Araújo E B , Souza Filho A G , Paschoal A R , Bdikin I K , Kholkin A L
Published: May 2012

The structural properties of Pb(Zr0.50Ti0.50)O3 thin films with no preferential orientation were studied throughout the film thickness. An analysis on depth profile shows the existence of a significant (1 0 0) alignment near the film–electrode interface. Nanoscale piezoelectric measurements demonstrate the existence of a self-polarization effect in the studied films. An increase in this effect with film thickness increasing from 200 to 710 nm suggests that Schottky barriers and/or mechanical coupling near the film–electrode interface cannot be the main mechanisms responsible for the self-polarization effect in the studied films.
The Fifth Workshop on Stochasticity in Fusion Plasmas (Jülich, Germany, 11–14 April 2011)
Authors: Oliver Schmitz
Published: May 2012

'Fusion meets chaotic dynamics'—this was the headline for the Fifth International Workshop on Stochasticity in Fusion Plasmas (SFP) held in Jülich, Germany from 11–14 April 2011. This headline reflects a landmark as the generic topic of chaotic dynamical systems has emerged a prominent application by controlling the plasma stability and transport. The workshop facilitated once more gathering of expertise from basic research in the field of non-linear dynamic systems and experts on plasma stability and transport from magnetically confined high temperature plasmas.

Resonant magnetic perturbations are used in most large-scale fusion experiments for control of the cyclic high heat flux pulses caused by edge-localized modes in high performance plasmas. This is one of the most prominent applications of non-linear perturbation schemes in modern plasma physics. It was experimentally shown that the edge transport in toroidal magnetic confinement systems as tokamaks and stellarators can be improved towards elimination of transient events, reduction of steady state heat flux densities and reduction of impurity inflow with improvement of the particle confinement. These results sketch the versatile application space of small-scale perturbations for optimization of the rigid magnetic cages used in magnetic confinement of fusion plasmas.

At the same time, these experimental observations represent a challenge to theory. The understanding of the experimental observations for extrapolation to future devices is a root requirement in this field of research. Two aspects were dominant in the workshop. First, the question of how the high temperature plasma as highly conductive media with potentially high rotation and plasma drift speeds reacts to a stationary external perturbation was central in all discussions on structural formation, related transport effects and interaction to plasma stability. Second, the topic was highlighted in how far the perturbed system and the final plasma stage is optimized in view of plasma–wall interaction.

The papers published in this special issue represent an overview of key aspects discussed at the workshop. This selection is a vital mixture taken out of the following four topical sessions: (1) Formation of stochastic magnetic layers and plasma response to external, non-axisymmetric magnetic perturbations; (2) Energy and particle transport in stochastic magnetic fields; (3) Exhaust in helical and island divertors; (4) Application of resonant magnetic perturbations for ELM control and implications for ITER. Each topical session was concluded with an appended discussion session. An overview of the key points identified in these discussion sessions is given in the workshop summary.

The next workshop is planned for early 2013. For details please see www.fz-juelich.de/sfp/. We hope this special issue of Nuclear Fusion will give a stimulating overview of the newest results in this field and highlights key aspects for application in next step fusion devices.
Screening of resonant magnetic perturbations by flows in tokamaks
Authors: Becoulet M. , Orain F. , Maget P. , Mellet N. , Garbet X. , Nardon E. , Huysmans G.T.A. , Casper T. , Loarte A. , Cahyna P. , Smolyakov A. , Waelbroeck F.L. , Schaffer M. , Evans T. , Liang Y. , Schmitz O. , Beurskens M. , Rozhansky V. , Kaveeva E.
Published: May 2012

The non-linear reduced four-field RMHD model in cylindrical geometry was extended to include plasma rotation, neoclassical poloidal viscosity and two fluid diamagnetic effects. Interaction of the static resonant magnetic perturbations (RMPs) with the rotating plasmas in tokamaks was studied. The self-consistent evolution of equilibrium electric field due to RMP penetration is taken into account in the model. It is demonstrated that in the pedestal region with steep pressure gradients, mean flows perpendicular to the magnetic field, which includes

and electron diamagnetic components plays an essential role in RMP screening by plasma. Generally, the screening effect increases for lower resistivity, stronger rotation and smaller RMP amplitude. Strong screening of central islands was observed limiting RMP penetration to the narrow region near the separatrix. However, at certain plasma parameters and due to the non-linear evolution of the radial electric field produced by RMPs, the

rotation can be compensated by electron diamagnetic rotation locally. In this case, RMPs can penetrate and form magnetic islands. Typical plasma parameters and RMPs spectra on DIII-D, JET and ITER were used in modelling examples presented in the paper.
First use of three-dimensional equilibrium, stability and transport calculations for interpretation of ELM triggering with magnetic perturbations in NSTX
Authors: Canik J.M. , Hirshman S.P. , Sanchez R. , Maingi R. , Ahn J.-W. , Bell R.E. , Diallo A. , Gerhardt S.P. , LeBlanc B.P. , Menard J.E. , Park J.-K. , Podesta M. , Sabbagh S.A.
Published: May 2012

The application of non-axisymmetric magnetic perturbations has been demonstrated to destabilize edge-localized modes (ELMs) in the National Spherical Torus Experiment. A model 3D equilibrium has been calculated for these experiments using the VMEC code, which assumes nested flux surfaces and therefore that resonant perturbations are shielded. First, a free-boundary equilibrium is calculated using the NSTX coil set, with pressure and current profiles matched to a standard 2D reconstruction, but with up–down symmetry enforced. A new equilibrium is then calculated with the n = 3 field applied at a level consistent with experiment. This equilibrium is then used as the basis of further calculations using codes developed for analysis of stellarator plasmas. The neoclassical transport due to the 3D fields is calculated to be small compared with the experimental transport rates. Initial stability analysis has been performed, and indicates a modest degradation in ballooning stability with 3D fields applied. A new 3D equilibrium is also calculated using the SIESTA code, which allows for the formation of islands and stochastic regions. A comparison of the field structure between the SIESTA calculation and the assumption of fully penetrated vacuum perturbation indicates smaller island sizes and very small stochastic transport in the SIESTA case.
Modifying locally the safety profile to improve the confinement of magnetic field lines in tokamak plasmas
Authors: Constantinescu D. , Firpo M.-C.
Published: May 2012

Using Hamiltonian models for the magnetic field lines, we propose a methodology to improve their confinement through the creation of transport barriers. A local modification of the safety profile creating a low-shear zone is shown to be sufficient to locally enhance drastically the regularity of the magnetic field lines without requesting a reversed shear. The optimal benefits of low-shear are obtained when the value q
0 of the safety profile in the low-shear zone is sufficiently far from the main resonance values m/n with low m and n, in the case of large enough values of those (m, n) mode amplitudes. A practical implementation in tokamak plasmas should involve electron cyclotron current drive to locally modify the magnetic shear.
Analysis of stochastic magnetic fields formed by the application of resonant magnetic perturbations on MAST and comparison with experiment
Authors: Denner P. , Liu Yueqiang , Nardon E. , Kirk A.
Published: May 2012

In MAST experiments with applied resonant magnetic perturbations (RMPs), clear reduction in line-averaged density has been observed in a wide range of L-mode plasmas when there is an alignment between the perturbation and the equilibrium magnetic field that maximizes the size of the resonant components of the applied magnetic field, as well as in a few H-mode plasmas but with a much stronger sensitivity to this alignment. This density pump-out is the result of increased particle transport, which is thought to be caused by the formation of a stochastic magnetic field in the plasma edge. This paper presents an analysis of the magnetic field structures formed by the application of n = 3 RMPs on MAST, including various parameters characterizing the degree of stochasticity in the plasma edge. Values for these parameters are calculated and compared with the amount of density pump-out observed in MAST experiments. It is found that density pump-out is fairly well correlated with some of the parameters calculated using vacuum modelling, but none of them provides a single threshold value for pump-out that applies to both L- and H-mode plasmas. Plasma response modelling provides a robust criterion for density pump-out that applies both to L- and H-mode plasmas.
Strike point splitting in the heat and particle flux profiles compared with the edge magnetic topology in a n = 2 resonant magnetic perturbation field at JET
Authors: Harting D.M. , Liang Y. , Jachmich S. , Koslowski R. , Arnoux G. , Devaux S. , Eich T. , Nardon E. , Reiter D. , Thomsen H.
Published: May 2012

At JET the error field correction coils can be used to generate an n = 1 or n = 2 magnetic perturbation field (Liang et al 2007 Plasma Phys. Control. Fusion
49 B581). Various experiments at JET have already been carried out to investigate the mitigation of ELMs by resonant magnetic perturbations (RMPs) (Liang et al 2010 Nucl. Fusion
50 025013, Liang et al 2011 Nucl. Fusion
51 073001). However, the typical formation of a secondary strike point (strike point splitting) by RMPs observed in other machines (Jakubowski et al 2010 Contrib. Plasma Phys.
50 701–7, Jakubowski et al 2004 Nucl. Fusion
44 S1–11, Nardon et al 2011 J. Nucl. Mater.

415 S914–7, Eich et al 2003 Phys. Rev. Lett.
91 195003, Evans et al 2007 J. Nucl. Mater.
363–365 570–4, Evans et al 2005 J. Phys.: Conf. Ser.
7 174–90, Watkins et al 2009 J. Nucl. Mater.
390–391 839–42) has never been observed at JET before. In this work we will present discharges where for the first time a strike point splitting by RMPs at JET has been observed. We will show that in these particular cases the strike point splitting matches the vacuum edge magnetic field topology. This is done by comparing heat and particle flux profiles on the outer divertor plate with the magnetic footprint pattern obtained by field line tracing. Further the evolution of the strike point splitting during the ramp up phase of the perturbation field and during a q
95-scan is investigated, and it will be shown that the spontaneous appearance of the strike point splitting is only related to some geometrical effects of the toroidal asymmetric magnetic topology.
First EMC3-Eirene simulations of the impact of the edge magnetic perturbations at ASDEX Upgrade compared with the experiment
Authors: Lunt T. , Feng Y. , Bernert M. , Herrmann A. , de Marné P. , McDermott R. , Müller H.W. , Potzel S. , Pütterich T. , Rathgeber S. , Suttrop W. , Viezzer E. , Wolfrum E. , Willensdorfer M.
Published: May 2012

The EMC3-Eirene code package was applied for the first time to simulate the edge plasma in an ASDEX Upgrade discharge, in which the newly installed magnetic perturbation (MP) coils were used to mitigate edge-localized modes (ELMs). Two different points in time during this discharge were simulated, the ELM-mitigated phase after turning-on of the MP coils and, as a reference, the ELMy H-mode phase before. The results were compared with the measurements of various edge and divertor diagnostics. Assuming the main chamber profiles to be shifted by 15 mm with respect to their calibrated positions, an agreement within a factor of 2 was found between the main chamber profiles outside the separatrix and those at the outer divertor target. The most important result is the observation of several maxima and minima in the particle flux and in particular in the power deposition pattern of both the simulation and the experiment for the case with MPs, an effect also known as strike-point splitting.
Impact of magnetic islands on turbulent transport in the WEGA stellarator
Authors: Marsen S. , Otte M. , Wolf R.
Published: May 2012

The role of the magnetic field topology for the complex interplay between turbulence and zonal flows (ZFs) leading to the formation of transport barriers is a recent topic in fusion research. Gaining knowledge on their relation in experiments requires a flexible magnetic configuration and a good diagnostic access with high temporal and spatial resolution. WEGA as a small classical stellarator with moderate plasma parameters is well suited for such experiments. Stationary n = 1 islands can be modified in size by external error field compensation coils. Configurations with m/n = 5/1 islands at the plasma edge are compared with configurations showing no major resonances (i.e. no islands). The spatio-temporal structure of fluctuations was studied with Langmuir-probe arrays at different toroidal and poloidal positions.

In low density discharges ZF-like patterns were observed in potential fluctuations. A characteristic feature of these oscillations is a long range correlation (LRC) with fluctuations being symmetric on a flux surface. It was shown for the first time that the presence of magnetic islands alters the structure of these low frequency fluctuations. At r < r
island the LRCs were still observed. Inside the islands the fluctuations showed up more like meso-scale structures with finite poloidal wave number. The poloidal correlation length was shown to be decreased with increasing islands width. Frequency resolved measurements of the turbulent transport across the island's X-point showed that these structures do not significantly contribute to the transport due to their nearly symmetric character. However, their decorrelation goes together with an increase in transport in the frequency range of the ambient turbulence.