bluuebunny/crossref_metadata_2025 huggingface dataset:
The importance of websites
Authors: MacFarlane Heather , Bultitude Matthew
Published: March 2012

The authors emphasise the importance of maintaining up‐to‐date and comprehensive information for patients on both general practice and hospital‐based websites. Copyright © 2012 John Wiley & Sons
ASH
Authors: Sandford Amanda
Published: March 2012

Action on Smoking and Health is a health campaigning charity working to reduce and ultimately eliminate the harm caused by tobacco use. The charity was founded by the Royal College of Physicians in 1971 and continues to work with the medical establishment on tobacco matters. The charity receives funding from the British Heart Foundation and Cancer Research UK. Copyright © 2012 John Wiley & Sons
How emergence and death assumptions affect count‐based estimates of butterfly abundance and lifespan
Authors: Calabrese Justin M.
Published: March 2012

Transect count data form the basis of many butterfly and other insect monitoring programs worldwide. A clear understanding of the limitations of such datasets, including the potential for biases in the statistical methods used to analyze them, is therefore crucial. The classical Zonneveld model (CZ) can extract estimates of a suite of demographic parameters from transect count datasets, and has also been used in theoretical analyses of protandry and reproductive asynchrony. The CZ relies on strong assumptions about the emergence and death processes underlying observed transect count datasets. Though reasonable as a starting place, a growing body of empirical evidence suggests these assumptions will, in many cases, not hold. Here, I explore how violations of these assumptions bias CZ‐based estimates of two key population parameters: total population size and mean individual lifespan. To do this, I generalize the Zonneveld model by relaxing the symmetrical emergence distribution and constant death rate assumptions such that the generalized models contain the CZ as a special case. Using the generalized models as data generating processes, I then show that the CZ is able to closely mimic the shape of the abundance time course produced by either variant of the generalized model under a wide range of conditions, but produces highly biased estimates of population size and mean lifespan in doing so. My analysis therefore demonstrates both that the CZ is not robust to violations of its emergence and death assumptions, and that a good observed fit to transect count data does not mean these assumptions are satisfied.
Cloning, expression, and characterization of an alkaline thermostable GH11 xylanase from Thermobifida halotolerans YIM 90462T
Authors: Zhang Feng , Chen Jiu-Jiu , Ren Wan-Zeng , Lin Lian-Bing , Zhou Yu , Zhi Xiao-Yang , Tang Shu-Kun , Li Wen-Jun
Published: March 2012

A xylanase gene (thxyn11A) from the Thermobifida halotolerans strain YIM 90462T was cloned and expressed in Escherichia coli. The open reading frame (ORF) of thxyn11A has 1,008 bp encoding a mature xylanase with a high degree of similarity (80 %) to the xylanase from Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111. This enzyme (Thxyn11A) also possesses a glycosyl hydrolases family 11 (GH11) domain and a high isoelectric point (pI = 9.1). However, Thxyn11A varies from most GH11 xylanases, due to its large molecular mass (34 kDa). Recombinant Thxyn11A demonstrated a strong pH and temperature tolerance with a maximum activity at pH 9.0 and 70 °C. Xylotriose, the end-product of xylan hydrolysis by Thxyn11A, serves as a catalyst for hemicellulose pretreatment in industrial applications and can also function as a food source or supplement for enterobacteria. Due to its attractive biochemical properties, Thxyn11A may have potential value in many commercial applications.
A Two-Step Bayesian Approach for Propensity Score Analysis: Simulations and Case Study
Authors: Kaplan David , Chen Jianshen
Published: March 2012

A two-step Bayesian propensity score approach is introduced that incorporates prior information in the propensity score equation and outcome equation without the problems associated with simultaneous Bayesian propensity score approaches. The corresponding variance estimators are also provided. The two-step Bayesian propensity score is provided for three methods of implementation: propensity score stratification, weighting, and optimal full matching. Three simulation studies and one case study are presented to elaborate the proposed two-step Bayesian propensity score approach. Results of the simulation studies reveal that greater precision in the propensity score equation yields better recovery of the frequentist-based treatment effect. A slight advantage is shown for the Bayesian approach in small samples. Results also reveal that greater precision around the wrong treatment effect can lead to seriously distorted results. However, greater precision around the correct treatment effect parameter yields quite good results, with slight improvement seen with greater precision in the propensity score equation. A comparison of coverage rates for the conventional frequentist approach and proposed Bayesian approach is also provided. The case study reveals that credible intervals are wider than frequentist confidence intervals when priors are non-informative.
Magical thinking in narratives of adolescent cutters
Authors: Gregory Robert J. , Mustata Georgian T.
Published: March 2012

Adolescents sometimes cut themselves to relieve distress; however, the mechanism is unknown. Previous studies have linked self‐injury to deficits in processing emotions symbolically through language. To investigate expressive language of adolescent cutters, the authors analyzed 100 narratives posted on the Internet. Most narratives (n = 66) displayed idiosyncratic use of language indicating poor differentiation between the real and the symbolic, such as blood substituting for negative emotions, which can then be released from the self; or emotional pain magically transforming into physical pain, which can then be managed. This kind of magical thinking correlated with cutting to relieve distress, to see blood, and to feel pain, but negatively correlated with complex representation of people, understanding social causality, and self‐esteem. The results suggest that magical thinking represents a pre‐symbolic mental state that processes and organizes distressing emotions through body schema. Magical thinking thus provides a plausible mechanism for why cutting works.
Hölder continuity for a drift-diffusion equation with pressure
Authors: Silvestre Luis , Vicol Vlad
Published: March 2012

We address the persistence of Hölder continuity for weak solutions of the linear drift-diffusion equation with nonlocal pressure

u_{t} + b \cdot \mathrm{∇}u− \bigtriangleup u = \mathrm{∇}p,\:\mathrm{∇} \cdot u = 0

on

[0,\infty) \times \mathbb{R}^{n}

, with

n \geq 2

. The drift velocity

b

is assumed to be at the critical regularity level, with respect to the natural scaling of the equations. The proof draws on Campanatoʼs characterization of Hölder spaces, and uses a maximum-principle-type argument by which we control the growth in time of certain local averages of

u

. We provide an estimate that does not depend on any local smallness condition on the vector field

b

, but only on scale invariant quantities.

Nous abordons la question de la persistance de la continuité Hölder pour les solutions faibles de lʼéquation linéaire de dérive-diffusion avec une pression non-locale

u_{t} + b \cdot \mathrm{∇}u− \bigtriangleup u = \mathrm{∇}p,\:\mathrm{∇} \cdot u = 0

sur

[0,\infty) \times \mathbb{R}^{n}

, avec

n \geq 2

. On suppose que la vitesse de dérive

b

est au niveau critique de régularité par rapport au changement dʼéchelle de lʼéquation. La démonstration sʼappuie sur la définition des espaces Hölder de Campanato, et elle utilise un argument de principe du maximum par lequel nous contrôlons la croissance en temps de certaines moyennes locales de

u

. Nous fournissons une estimation qui ne dépend dʼaucune condition de petitesse locale sur le champ de vecteur

b

, mais seulement sur des quantités invariantes par changement dʼéchelle.
Determination of the insolation function in the nonlinear Sellers climate model
Authors: Tort J. , Vancostenoble J.
Published: March 2012

We are interested in the climate model introduced by Sellers in 1969 which takes the form of some nonlinear parabolic equation with a degenerate diffusion coefficient. We investigate here some inverse problem issue that consists in recovering the so-called insolation function. We not only solve the uniqueness question but also provide some strong stability result, more precisely unconditional Lipschitz stability in the spirit of the well-known result by Imanuvilov and Yamamoto (1998) [22]. The main novelties rely in the fact that the considered model is degenerate and above all nonlinear. Indeed we provide here one of the first result of Lipschitz stability in a nonlinear case.
Mitochondrial fission proteins Fis1 and Mdv1, but not Dnm1, play a role in maintenance of heteroplasmy in budding yeast
Authors: Bradshaw Elliot , Yoshida Minoru , Ling Feng
Published: March 2012

In budding yeast, the mitochondrial DNA (mtDNA) replication pathway involving the homologous DNA pairing protein Mhr1 promotes mitochondrial allele segregation. Mitochondrial fusion facilitates the recombination‐mediated replication pathway; however, the role of fission remains largely unknown. By monitoring mitochondrial allele segregation during zygotic division, we found that the absence of fission proteins Fis1 or Mdv1, but not Dnm1, resulted in increased initial homoplasmy levels and decreased mtDNA copy number. However, decreases in mtDNA copy number alone were not sufficient for rapid establishment of homoplasmy, suggesting that inhibiting the activities of certain fission proteins promotes homoplasmy by reducing the number of mtDNA segregation units.
InTERTesting association between telomerase, mTOR and phytochemicals
Authors: Sundin Tabetha , Hentosh Patricia
Published: March 2012

Telomeres are stretches of repeated DNA sequences located at the ends of chromosomes that are necessary to prevent loss of gene-coding DNA regions during replication. Telomerase – the enzyme responsible for immortalising cancer cells through the addition of telomeric repeats – is active in ~90% of human cancers. Telomerase activity is inhibited by various phytochemicals such as isoprenoids, genistein, curcumin, epigallocatechin-3-gallate, resveratrol and others. Human TERT (telomerase reverse transcriptase – the rate-limiting component of telomerase), heat shock protein 90, Akt, p70 S6 kinase (S6K) and mammalian target of rapamycin (mTOR) form a physical and functional complex with one another. The inclusion of Akt, mTOR and S6K in the TERT complex is compelling evidence to support mTOR-mediated control of telomerase activity. This review will define the role of mTOR, the master regulator of protein translation, in telomerase regulation and provide additional insights into the numerous ways in which telomerase activity is hindered by phytochemicals.
EXTENSION OF AUTOMORPHISMS OF SUBGROUPS
Authors: BASTOS G. G. , JESPERS E. , JURIAANS S. O. , E SILVA A. DE A.
Published: March 2012

Let G be a group such that, for any subgroup H of G, every automorphism of H can be extended to an automorphism of G. Such a group G is said to be of injective type. The finite abelian groups of injective type are precisely the quasi-injective groups. We prove that a finite non-abelian group G of injective type has even order. If, furthermore, G is also quasi-injective, then we prove that G = K × B, with B a quasi-injective abelian group of odd order and either K = Q8 (the quaternion group of order 8) or K = Dih(A), a dihedral group on a quasi-injective abelian group A of odd order coprime with the order of B. We give a description of the supersoluble finite groups of injective type whose Sylow 2-subgroup are abelian showing that these groups are, in general, not quasi-injective. In particular, the characterisation of such groups is reduced to that of finite 2-groups that are of injective type. We give several restrictions on the latter. We also show that the alternating group A5 is of injective type but that the binary icosahedral group SL(2, 5) is not.
CONSISTENCY CONDITIONS FOR DIMER MODELS
Authors: BOCKLANDT RAF
Published: March 2012

Dimer models are a combinatorial tool to describe certain algebras that appear as noncommutative crepant resolutions of toric Gorenstein singularities. Unfortunately, not every dimer model gives rise to a noncommutative crepant resolution. Several notions of consistency have been introduced to deal with this problem. In this paper, we study the major different notions in detail and show that for dimer models on a torus, they are all equivalent.
Genotypic analysis of the foliose lichen Parmotrema tinctorum using microsatellite markers: association of mycobiont and photobiont, and their reproductive modes
Authors: MANSOURNIA Mohammad Reza , WU Bingyun , MATSUSHITA Norihisa , HOGETSU Taizo
Published: March 2012

To investigate the association between, and the reproductive modes of, mycobiont and photobiont in the lichen Parmotrema tinctorum, microsatellite markers (SSR markers) were developed for both bionts and genotypic analysis was performed for thalli in a Pinus thunbergii forest. In a within-thallus analysis, tissue pieces were sampled from many portions within each of five thalli. Within-thallus variation for both mycobiont and photobiont differed among the thalli investigated, suggesting that a single thallus can be derived from either a single mycobiont origin with or without occasional changes in the photobiont, or fusion of several independent thalli. In the within-tree analysis, thalli with the same genotypes were found on individual trees, suggesting the presence of short-distance isidium dispersal. In the within-stand analysis, genotypically similar photobionts tended to be associated with the same mycobiont genotype, suggesting the participation of local dispersal via isidia. The overall index of association (IA) for the mycobiont in the stand probably indicates the dominance of sexual reproduction, in contrast to that of the photobiont, where dominance of asexual reproduction is suggested. IA's of mycobiont and photobiont were also calculated for thalli collected from larger areas, where there is a signature for sexual reproduction for photobiont.
Fear for Manufacturing? China and the Future of Industry in Brazil and Latin America
Authors: Jenkins Rhys , Barbosa Alexandre de Freitas
Published: March 2012

There has been considerable concern in Latin America over the implications of increased competition from China for local industry. These concerns include the possibility of “deindustrialization,” the increased “primarization” of the region's exports and the difficulties of upgrading manufactured exports into higher technology products. This article examines the impact of Chinese competition both in the domestic market and in export markets on Brazilian industry. It documents the increased penetration of Chinese manufactures in the Brazilian market and the way in which Brazilian exports have lost market share to China in the US, European Union and four Latin American countries. Brazil, because of its more developed and locally integrated industrial sector, is not typical of other Latin American countries and the article also discusses the relevance of the Brazilian experience for the region as a whole.
Harnessing the Dragon: Overseas Chinese Entrepreneurs in Mexico and Cuba
Authors: Hearn Adrian H.
Published: March 2012

Chinese communities resident in Mexico and Cuba face a common problem: their dealings with business partners in China are perceived as a threat to national interests. In Mexico this concern emanates from manufacturers unable to compete with Chinese imports, and is evident in antagonistic news media and acts of hostility against Chinese businesses. In Cuba it stems from the state's stewardship over economic sovereignty, and is evident in efforts to assimilate Havana's Chinatown and its entrenched informal sector into a centralized scheme of commercial regulation. Interviews with policy makers, local officials and Chinese entrepreneurs indicate that the “rationalization” of Chinese ethnic allegiances for the greater public good is a critical step towards alleviating tensions. I conclude that both countries can leverage benefits from overseas Chinese communities, but to do so they must support their entrepreneurial activities, harness their networks to promote targeted imports and exports, and develop more culturally sensitive regulations.
Once and for all: The encounter between Stalinism and Nazism. Critical remarks on Timothy Snyder'sBloodlands
Authors: BABEROWSKI JÖRG
Published: March 2012

Twenty years ago it would have been unthinkable for a historian to combine the National Socialists’ murderous excesses and programme of extermination with Bolshevik atrocities in a single history. He would have been accused of ‘relativising’ one set of murderous crimes by relating it to the other. The comparison does indeed have a relativising effect in that it puts the events in a new light and so makes them, for the first time, comprehensible. But at that time, when historians still treated all historical questions as moral ones, nobody wanted to anything to do with that comparison because it ran counter to the political will. You could compare anything with anything, except the Holocaust, which had to remain unique. Nobody could write about the excesses of Stalinist violence without acknowledging that the Nazi murder programme was unique. Nonetheless everybody knew, even then, that uniqueness cannot be established without comparisons and contrasts.1Since then, a view that used to be considered shocking has become a self-evident: no examination of state atrocities is now possible without a comparative element. But this change can also serve political ends: the Holocaust has become the sole yardstick for measuring state-organised crimes of violence. It seems that such crimes can only be taken seriously if they are comparable to Nazi atrocities.2
National Heritage and Economic Policies in Free and Sovereign Poland after 1918
Authors: DADAK CASIMIR
Published: March 2012

Poland, whenever free and sovereign, has since 1918 implemented economic policies that emphasise free markets. This approach has failed to produce a rapid rate of economic growth, so the country is still substantially underdeveloped. Although significant government investment in 1936–9 resulted in strong economic growth and a higher standard of living, today's Poland continues to pursue neo-liberal economic policies. This paper links these policies to the nation's heritage, which stresses limited government. Such beliefs ruled the actions of the nation's ruling class before partitions in the eighteenth century and during the inter-war period, and continue to dominate economic policy now.
The Cost of Geography: Europe's International History Between the Wars, 1918–1939
Authors: REYNOLDS DAVID
Published: March 2012

‘Geography costs – why does the map of Europe never stay put?’ The American poet Carl Sandburg posed that question in 1940 as the European continent was engulfed by another great conflict, the second in a generation. The course and conduct of the two world wars continue to dominate publishers’ lists but several recent volumes offer stimulating interpretations of Europe's international history during the intervening twenty years. They shed a sobering light on the cost of geography and on the challenges of statecraft, because what moved the map were not only the tectonic forces of socio-economic change but also the decision-making of political leaders.
‘Farmers on notice’: the threat faced by Weimar Berlin's garden colonies in the face of the city'sNeues Bauenhousing programme
Authors: HOBBS MARK
Published: March 2012

TheNeues Bauenprogramme of urban development in Weimar Germany is best known amongst English-speaking historians for its modern housing estates, including those built by Bruno Taut in Berlin. Less well known are the negative impacts of this programme, particularly the displacement of thousands of garden colonies from the outskirts of towns and cities, which were cleared to make way for new developments. This article focuses on the historical development of the garden colonies in Berlin, and the threat they faced from urban expansion during the Weimar era.
Decision-making under duress: the treatment of churches in the City of London during and after World War II
Authors: LARKHAM PETER J. , NASR JOE L.
Published: March 2012

The process of making decisions about cities during the bombing of World War II, in its immediate aftermath and in the early post-war years remains a phenomenon that is only partly understood. The bombing left many church buildings damaged or destroyed across the UK. The Church of England's churches within the City of London, subject to a complex progression of deliberations, debates and decisions involving several committees and commissions set up by the bishop of London and others, are used to review the process and product of decision-making in the crisis of war. Church authorities are shown to have responded to the immediate problem of what to do with these sites in order most effectively to provide for the needs of the church as an organization, while simultaneously considering other factors including morale, culture and heritage. The beginnings of processes of consulting multiple experts, if not stakeholders, can be seen in this example of an institution making decisions under the pressures of a major crisis.
TRANSFINITE CARDINALS IN PARACONSISTENT SET THEORY
Authors: WEBER ZACH
Published: March 2012

This paper develops a (nontrivial) theory of cardinal numbers from a naive set comprehension principle, in a suitable paraconsistent logic. To underwrite cardinal arithmetic, the axiom of choice is proved. A new proof of Cantor’s theorem is provided, as well as a method for demonstrating the existence of large cardinals by way of a reflection theorem.
Dissolved zinc in the subarctic North Pacific and Bering Sea: Its distribution, speciation, and importance to primary producers
Authors: Jakuba Rachel Wisniewski , Saito Mak A. , Moffett James W. , Xu Yan
Published: March 2012

The eastern subarctic North Pacific, an area of high nutrients and low chlorophyll, has been studied with respect to the potential for iron to control primary production. The geochemistry of zinc, a critical micronutrient for diatoms, is less well characterized. Total zinc concentrations and zinc speciation were measured in near‐surface waters on transects across the subarctic North Pacific and across the Bering Sea. Total dissolved zinc concentrations in the near‐surface ranged from 0.10 nmol L−1 to 1.15 nmol L−1 with lowest concentrations in the eastern portions of both the North Pacific and Bering Sea. Dissolved zinc speciation was dominated by complexation to strong organic ligands whose concentration ranged from 1.1 to 3.6 nmol L−1 with conditional stability constants (K′ZnL/Zn′) ranging from 109.3 to 1011.0. The importance of zinc to primary producers was evaluated by comparison to phytoplankton pigment concentrations and by performing a shipboard incubation. Zinc concentrations were positively correlated with two pigments that are characteristic of diatoms. At one station in the North Pacific, the addition of 0.75 nmol L−1 zinc resulted in a doubling of chlorophyll after 4 days.
Entropy theory‐based criterion for hydrometric network evaluation and design: Maximum information minimum redundancy
Authors: Li Chao , Singh Vijay P. , Mishra Ashok K.
Published: March 2012

Hydrometric information constitutes the fundamental input for planning, design, operation, and management of water resources systems. How to optimally site monitoring gauges such that they are effective and efficient in gathering the hydrometric information or data has received considerable attention. This paper presents a generic approach for the design (or evaluation) of hydrometric networks. First, an entropy theory‐based criterion, named as maximum information minimum redundancy (MIMR), is proposed. The MIMR criterion maximizes the joint entropy of stations within the optimal set, and the transinformation between stations within and outside of the optimal set. Meanwhile, it insures that the optimal set contains minimum duplicated information. An easy‐to‐implement greedy ranking algorithm is developed to accomplish the MIMR selection. Two case studies are presented to illustrate the applicability of MIMR in hydrometric network evaluation and design. We also compare the MIMR selection with another entropy‐based approach. Results illustrate that MIMR is apt at finding stations with high information content, and locating independent stations. The proposed approach is suitable for design (or evaluation) of any type of hydrometric network.
Competitive and mutualistic dependencies in multispecies vegetation dynamics enabled by hydraulic redistribution
Authors: Quijano Juan C. , Kumar Praveen , Drewry Darren T. , Goldstein Allen , Misson Laurent
Published: March 2012

The goal of this study is to understand the interaction between belowground and aboveground ecohydrologic dynamics as facilitated by hydraulic redistribution. We analyze the partitioning of moisture and energy between tall and understory vegetation, and soil evaporation. Both the competitive and facilitative dependencies are examined using a shared resource model where the soil serves as a common reservoir for the interaction between the different vegetation species. The moisture state of the reservoir is altered by the addition and withdrawal by vegetation roots in conjunction with soil‐moisture transport. Vertical patterns of soil moisture state and uptake reflect the nonlinear interactions between vegetation species. The study is performed using data from the Blodgett Forest Ameriflux site in the Sierra Nevada Mountains of California. The Mediterranean climate of the region, with wet winters and long dry summers, offers an ideal environment for the study. The results indicate that deep layer uptake of water by the tall vegetation and its release in the shallow layers enhances the productivity of the understory vegetation during the summer. The presence of understory vegetation reduces direct soil‐evaporative loss making more moisture available for vegetation which enhances the total ecosystem productivity. The litter layer is also found to play an important role in the partitioning of the water and energy fluxes by damping the radiation reaching the soil and thereby reducing water loss due to soil evaporation.
Eddy contributions to the meridional transport of salt in the North Atlantic
Authors: Treguier A. M. , Deshayes J. , Lique C. , Dussin R. , Molines J. M.
Published: March 2012

The meridional transport of salt in the Atlantic ocean is an important process for climate, controlling the stability of the meridional overturning circulation. The contribution of transient eddies to this transport is quantified in an eddy resolving North Atlantic model at 1/12° resolution (NATL12), and compared with lower resolution North‐Atlantic and global 1/4° models. In NATL12 between 10°N and 40°N, there is a volume loss by evaporation of 0.6 Sverdrups (Sv). The divergence of the eddy flux of salt (normalized by a reference salinity of 34.8) is 0.2 Sv over the region, a significant fraction of the total air‐seawater exchange, but it is compensated by an opposite convergent transport of salt by the mean flow, so that the total transport of salt is small. The compensation between eddy and mean salt transport is almost complete in a multicentury long global model experiment, but less effective in NATL12 because the short integration time does not allow the salt content to equilibrate and the model drift is large. Eddies arising from baroclinic instability contribute to the meridional salt transports at the northern and southern boundary of the subtropical gyre, where they appear consistent with a lateral diffusion acting on the mean salinity gradient. However, the eddy transport of salt is the sum of two terms: an advective contribution (arising from the correlations of velocity and isopycnal thicknesses) and a diffusion along isopycnals. Both components have the same amplitude at the southern boundary of the subtropical gyre, while diffusion is dominant at the northern boundary.
Nodularin, a cyanobacterial toxin, is synthesized in planta by symbiotic Nostoc sp.
Authors: Gehringer Michelle M , Adler Lewis , Roberts Alexandra A , Moffitt Michelle C , Mihali Troco K , Mills Toby J T , Fieker Claus , Neilan Brett A
Published: March 2012

The nitrogen-fixing bacterium, Nostoc, is a commonly occurring cyanobacterium often found in symbiotic associations. We investigated the potential of cycad cyanobacterial endosymbionts to synthesize microcystin/nodularin. Endosymbiont DNA was screened for the aminotransferase domain of the toxin biosynthesis gene clusters. Five endosymbionts carrying the gene were screened for bioactivity. Extracts of two isolates inhibited protein phosphatase 2A and were further analyzed using electrospray ionization mass spectrometry (ESI-MS)/MS. Nostoc sp. ‘Macrozamia riedlei 65.1’ and Nostoc sp. ‘Macrozamia serpentina 73.1’ both contained nodularin. High performance liquid chromatography (HPLC) HESI-MS/MS analysis confirmed the presence of nodularin at 9.55±2.4 ng μg−1 chlorophyll a in Nostoc sp. ‘Macrozamia riedlei 65.1’ and 12.5±8.4 ng μg−1 Chl a in Nostoc sp. ‘Macrozamia serpentina 73.1’ extracts. Further scans indicated the presence of the rare isoform [L-Har2] nodularin, which contains l-homoarginine instead of l-arginine. Nodularin was also present at 1.34±0.74 ng ml−1 (approximately 3 pmol per g plant ww) in the methanol root extracts of M. riedlei MZ65, while the presence of [L-Har2] nodularin in the roots of M. serpentina MZ73 was suggested by HPLC HESI-MS/MS analysis. The ndaA-B and ndaF genomic regions were sequenced to confirm the presence of the hybrid polyketide/non-ribosomal gene cluster. A seven amino-acid insertion into the NdaA-C1 domain of N. spumigena NSOR10 protein was observed in all endosymbiont-derived sequences, suggesting the transfer of the nda cluster from N. spumigena to terrestrial Nostoc species. This study demonstrates the synthesis of nodularin and [L-Har2] nodularin in a non-Nodularia species and the production of cyanobacterial hepatotoxin by a symbiont in planta.
DNA binding by the plant-specific NAC transcription factors in crystal and solution: a firm link to WRKY and GCM transcription factors
Authors: Welner Ditte H. , Lindemose Søren , Grossmann J. Günter , Møllegaard Niels Erik , Olsen Addie N. , Helgstrand Charlotte , Skriver Karen , Lo Leggio Leila
Published: March 2012

NAC (NAM/ATAF/CUC) plant transcription factors regulate essential processes in development, stress responses and nutrient distribution in important crop and model plants (rice, Populus, Arabidopsis), which makes them highly relevant in the context of crop optimization and bioenergy production. The structure of the DNA-binding NAC domain of ANAC019 has previously been determined by X-ray crystallography, revealing a dimeric and predominantly β-fold structure, but the mode of binding to cognate DNA has remained elusive. In the present study, information from low resolution X-ray structures and small angle X-ray scattering on complexes with oligonucleotides, mutagenesis and (DNase I and uranyl photo-) footprinting, is combined to form a structural view of DNA-binding, and for the first time provide experimental evidence for the speculated relationship between plant-specific NAC proteins, WRKY transcription factors and the mammalian GCM (Glial cell missing) transcription factors, which all use a β-strand motif for DNA-binding. The structure shows that the NAC domain inserts the edge of its core β-sheet into the major groove, while leaving the DNA largely undistorted. The structure of the NAC–DNA complex and a new crystal form of the unbound NAC also indicate limited flexibility of the NAC dimer arrangement, which could be important in recognizing suboptimal binding sites.
Solution structure of the natively assembled yeast ribosomal stalk determined by small-angle X-ray scattering
Authors: Grela Przemysław , Gajda Michal J. , Armache Jean-Paul , Beckmann Roland , Krokowski Dawid , Svergun Dmitri I. , Grankowski Nikodem , Tchórzewski Marek
Published: March 2012

The ribosomal stalk of the 60S subunit has been shown to play a crucial role in all steps of protein synthesis, but its structure and exact molecular function remain an unanswered question. In the present study, we show the low-resolution models of the solution structure of the yeast ribosomal stalk, composed of five proteins, P0–(P1–P2)2. The model of the pentameric stalk complex determined by small-angle X-ray scattering reveals an elongated shape with a maximum length of 13 nm. The model displays three distinct lobes, which may correspond to the individual P1–P2 heterodimers anchored to the C-terminal domain of the P0 protein.
Epitaxial graphene
Authors: de Heer Walt A , Berger Claire
Published: March 2012

Graphene is widely regarded as an important new electronic material with interesting two-dimensional electron gas properties. Not only that, but graphene is widely considered to be an important new material for large-scale integrated electronic devices that may eventually even succeed silicon. In fact, there are countless publications that demonstrate the amazing applications potential of graphene.

In order to realize graphene electronics, a platform is required that is compatible with large-scale electronics processing methods. It was clear from the outset that graphene grown epitaxially on silicon carbide substrates was exceptionally well suited as a platform for graphene-based electronics, not only because the graphene sheets are grown directly on electronics-grade silicon carbide (an important semiconductor in its own right), but also because these sheets are oriented with respect to the semiconductor. Moreover, the extremely high temperatures involved in production assure essentially defect-free and contamination-free materials with well-defined interfaces.

Epitaxial graphene on silicon carbide is not a unique material, but actually a class of materials. It is a complex structure consisting of a reconstructed silicon carbide surface, which, for planar hexagonal silicon carbide, is either the silicon- or the carbon-terminated face, an interfacial carbon rich layer, followed by one or more graphene layers. Consequently, the structure of graphene films on silicon carbide turns out to be a rich surface-science puzzle that has been intensively studied and systematically unravelled with a wide variety of surface science probes. Moreover, the graphene films produced on the carbon-terminated face turn out to be rotationally stacked, resulting in unique and important structural and electronic properties.

Finally, in contrast to essentially all other graphene production methods, epitaxial graphene can be grown on structured silicon carbide surfaces to produce graphene nanostructured without patterning the graphene itself. This method produces graphene nanostructures with atomically smooth edges that ultimately determine the transport properties of these structures.

The coherent collection of papers in this special issue of Journal of Physics D: Applied Physics provides a snapshot of the current state of the art, presented by leading experts, highlighting various aspects of the science and technology of epitaxial graphene. This collection systematically addresses the production of epitaxial graphene on the two polar faces of silicon carbide, as well as the structural and electronic properties of the graphene films. Special attention is paid to the rapidly emerging field of chemically modified graphene, which promises to introduce a bandgap into the electronic structure of graphene, which is critical for many electronic applications. Also presented are methods to incorporate properties of the silicon carbide itself, as well as advanced methods to produce high-quality graphene and graphene nanostructures using structured growth methods.
Implanted bottom gate for epitaxial graphene on silicon carbide
Authors: Waldmann D , Jobst J , Fromm F , Speck F , Seyller T , Krieger M , Weber H B
Published: March 2012

We present a technique to tune the charge density of epitaxial graphene via an electrostatic gate that is buried in the silicon carbide substrate. The result is a device in which graphene remains accessible for further manipulation or investigation. Via nitrogen or phosphor implantation into a silicon carbide wafer and subsequent graphene growth, devices can routinely be fabricated using standard semiconductor technology. We have optimized samples for room temperature as well as for cryogenic temperature operation. Depending on implantation dose and temperature we operate in two gating regimes. In the first, the gating mechanism is similar to a MOSFET, the second is based on a tuned space charge region of the silicon carbide semiconductor. We present a detailed model that describes the two gating regimes and the transition in between.
Growth and electronic transport properties of epitaxial graphene on SiC
Authors: Hibino H , Tanabe S , Mizuno S , Kageshima H
Published: March 2012

With the aim of developing a single-crystal graphene substrate indispensable to graphene's practical applications, we are investigating the structural and physical properties of graphene epitaxially grown on SiC by thermal decomposition. We grow monolayer and bilayer graphene uniformly on a micrometre scale on the Si face of SiC in an Ar environment and in ultra-high vacuum, respectively. Epitaxial bilayer graphene, even if uniform in thickness, contains two types of domains with different stacking orders. We compare the transport properties of monolayer and bilayer graphene using top-gate Hall bar devices. Quantum Hall effects are observed in monolayer graphene and a band gap is electrically detected in bilayer graphene. The monolayer and bilayer graphene show quite different transport properties, reflecting their electronic structures.
Message from the Editor
Authors: Paul Thomas
Published: March 2012

Whilst travelling to Vienna to hand over the Editorship of Nuclear Fusion to Ron Stambaugh, I jotted down a few ideas to put in a farewell message. Somewhat unsurprisingly, I find them almost identical to the remarks that Chris Schueller made in handing over to me five years ago. Both of us served in this role for five years, which seems like a good timescale to replace presidents and editors alike; just to allow a fresh approach. In addition, since I have been directly involved in ITER, I have found it increasingly difficult, due to time pressure, to give the journal the attention that it deserves. Therefore, I am very pleased that Ron Stambaugh has agreed to take over as Editor. Not only does he bring the experience as a leading figure in the US fusion programme but, in addition, he has all the contacts, worldwide, from his leadership of the ITPA. I am completely assured that the journal is in a highly competent pair of hands.

Such a farewell should not lack my heartfelt thanks to all of those who have made being Editor of Nuclear Fusion so enjoyable and stimulating; readership, authors, referees, the Editorial Board and the NF Office alike. I wish Ron all the best for his tenure and have offered such help and support as I am able to give.
Greetings from the new Editor-in-Chief, Ronald Stambaugh
Authors: Ronald Stambaugh
Published: March 2012

I am very pleased to join the outstanding leadership team for the journal Nuclear Fusion as Scientific Editor. The journal's high position in the field of fusion energy research derives in no small measure from the efforts of the IAEA team in Vienna, the production and marketing of IOP Publishing, the Board of Editors led by its chairman Mitsuru Kikuchi, the Associate Editor for Inertial Confinement Max Tabak and the outgoing Scientific Editor, Paul Thomas. During Paul's five year tenure submissions have grown by over 40%. The usage of the electronic journal has grown year by year with about 300 000 full text downloads of Nuclear Fusion articles in 2011, an impressive figure due in part to the launch of the full 50 year archive. High quality has been maintained while times for peer review and publishing have been reduced and the journal achieved some of the highest impact factors ever (as high as 4.27).

The journal has contributed greatly to building the international scientific basis for fusion. I was privileged to serve from 2003 to 2010 as chairman of the Coordinating Committee for the International Tokamak Physics Activity (ITPA) which published in Nuclear Fusion the first ITER Physics Basis (1999) and its later update (2007). The scientific basis that has been developed to date for fusion has led to the construction of major facilities to demonstrate the production of power-plant relevant levels of fusion reactions. We look forward to the journal continuing to play a key role in the international effort toward fusion energy as these exciting major facilities and the various approaches to fusion continue to be developed.

It is clear that Nuclear Fusion maintains its position in the field because of the perceived high quality of the submissions, the refereeing and the editorial processes, and the availability and utility of the online journal. The creation of the Nuclear Fusion Prize, led by the Board of Editors chairman Mitsuru Kikuchi, for the most outstanding paper published in the journal each year has furthered the submission and recognition of papers of the highest quality. The accomplishments of the journal's team over the last five years will be a tough act to follow but I look forward to working with this competent and dedicated group to continue the journal's high standards and ensure that Nuclear Fusion remains the journal of choice for authors and readers alike.
Linear properties of reversed shear Alfvén eigenmodes in the DIII-D tokamak
Authors: Deng W. , Lin Z. , Holod I. , Wang Z. , Xiao Y. , Zhang H.
Published: March 2012

Linear properties of the reverse shear Alfvén eigenmode (RSAE) in a well-diagnosed DIII-D tokamak experiment (discharge #142111) are studied in gyrokinetic particle simulations. Simulations find that a weakly damped RSAE exists due to toroidal coupling and other geometric effects. The mode is driven unstable by density gradients of fast ions from neutral beam injection. Various damping and driving mechanisms are identified and measured in the simulations. Accurate damping and growth rate calculation requires a non-perturbative, fully self-consistent simulation to calculate the true mode structure. The mode structure has no up–down symmetry mainly due to the radial symmetry breaking by the density gradients of the fast ions, as measured in the experiment by electron cyclotron emission imaging. The RSAE frequency up-sweeping and the mode transition from RSAE to TAE (toroidal Alfvén eigenmode) are in good agreement with the experimental results when the values of the minimum safety factor are scanned in gyrokinetic simulations.
Yogi Berra, Forrest Gump, and the discovery ofListeriaactin comet tails
Authors: Portnoy Daniel A.
Published: March 2012

In 1988, eminent cell biologist Lew Tilney and newly appointed Assistant Professor of Microbiology Dan Portnoy met at a picnic and initiated a collaboration that led to a groundbreaking paper published in Journal of Cell Biology entitled “Actin filaments and the growth, movement, and spread of the intracellular bacterial parasite, Listeria monocytogenes.” The paper has been cited more than 800 times, the most of any publication in the careers of both investigators. Using an electron microscope from the Sputnik era, they assembled a stunning collection of micrographs that illustrated how L. monocytogenes enters the host cell and exploits a host system of actin-based motility to move within cells and into neighboring cells without leaving the host cell cytosol. This research captured the imagination of cell biologists and microbiologists alike and led to novel insights into cytoskeletal dynamics. Here, Portnoy provides a retrospective that shares text from the original submission that was deleted at the time of publication, along with reviewers' comments ranging from “It is really just a show and tell paper and doesn';t have any meat” to “the finding will have major impact in cell biology and in medicine. Potentially, the paper will be a classic.”
Endosomal maturation by Rab conversion in Aspergillus nidulans is coupled to dynein-mediated basipetal movement
Authors: Abenza Juan F. , Galindo Antonio , Pinar Mario , Pantazopoulou Areti , de los Ríos Vivian , Peñalva Miguel A.
Published: March 2012

We exploit the ease with which highly motile early endosomes are distinguished from static late endosomes in order to study Aspergillus nidulans endosomal traffic. RabSRab7 mediates homotypic fusion of late endosomes/vacuoles in a homotypic fusion- and vacuole protein sorting/Vps41–dependent manner. Progression across the endocytic pathway involves endosomal maturation because the end products of the pathway in the absence of RabSRab7 are minivacuoles that are competent in multivesicular body sorting and cargo degradation but retain early endosomal features, such as the ability to undergo long-distance movement and propensity to accumulate in the tip region if dynein function is impaired. Without RabSRab7, early endosomal Rab5s—RabA and RabB—reach minivacuoles, in agreement with the view that Rab7 homologues facilitate the release of Rab5 homologues from endosomes. RabSRab7 is recruited to membranes already at the stage of late endosomes still lacking vacuolar morphology, but the transition between early and late endosomes is sharp, as only in a minor proportion of examples are RabA/RabB and RabSRab7 detectable in the same—frequently the less motile—structures. This early-to-late endosome/vacuole transition is coupled to dynein-dependent movement away from the tip, resembling the periphery-to-center traffic of endosomes accompanying mammalian cell endosomal maturation. Genetic studies establish that endosomal maturation is essential, whereas homotypic vacuolar fusion is not.
Polo-like kinase 4 controls centriole duplication but does not directly regulate cytokinesis
Authors: Holland Andrew J. , Fachinetti Daniele , Da Cruz Sandrine , Zhu Quan , Vitre Benjamin , Lince-Faria Mariana , Chen Denaly , Parish Nicole , Verma Inder M. , Bettencourt-Dias Monica , Cleveland Don W.
Published: March 2012

Centrioles organize the centrosome, and accurate control of their number is critical for the maintenance of genomic integrity. Centrioles duplicate once per cell cycle, and duplication is coordinated by Polo-like kinase 4 (Plk4). We previously demonstrated that Plk4 accumulation is autoregulated by its own kinase activity. However, loss of heterozygosity of Plk4 in mouse embryonic fibroblasts has been proposed to cause cytokinesis failure as a primary event, leading to centrosome amplification and gross chromosomal abnormalities. Using targeted gene disruption, we show that human epithelial cells with one inactivated Plk4 allele undergo neither cytokinesis failure nor increase in centrosome amplification. Plk4 is shown to localize exclusively at the centrosome, with none in the spindle midbody. Substantial depletion of Plk4 by small interfering RNA leads to loss of centrioles and subsequent spindle defects that lead to a modest increase in the rate of cytokinesis failure. Therefore, Plk4 is a centriole-localized kinase that does not directly regulate cytokinesis.