bluuebunny/crossref_metadata_2025 huggingface dataset:
Analytic model for coaxial helicity injection in tokamak plasmas
Authors: Weening R. H.
Published: December 2011

Using a partial differential equation for the time evolution of the mean-field poloidal magnetic flux that incorporates resistivity η and hyper-resistivity Λ terms, an exact analytic solution is obtained for steady-state coaxial helicity injection (CHI) in force-free large aspect ratio tokamaks. The analytic mean-field Ohm’s law model allows for calculation of the tokamak CHI current drive efficiency and the plasma inductances at arbitrary levels of magnetic fluctuations, or dynamo activity. The results of the mean-field model suggest that CHI approaching Ohmic efficiency is only possible in tokamaks when the size of the effective current drive boundary layer, δ≡(Λ/η)1/2, becomes greater than half the size of the plasma, δ>a/2, with a the plasma minor radius. The electron thermal diffusivity due to magnetic fluctuation induced transport is obtained from the expression χe=Λ/μ0de2, with μ0 the permeability of free space and de the electron skin depth, which for typical tokamak fusion plasma parameters is on the order of a millimeter. Thus, the ratio of the energy confinement time to the resistive diffusion time in a tokamak plasma driven by steady-state CHI approaching Ohmic efficiency is shown to be constrained by the relation τE/τη<(de/a)2≈10-6. The mean-field model suggests that steady-state CHI can be viewed most simply as a boundary layer of stochastically wandering magnetic field lines.
Positive magnetoresistance in granular magnetic films with perpendicular anisotropy
Authors: Kalita V. M. , Timopheev A. A. , Lozenko A. F. , Ryabchenko S. M. , Los A. V. , Stognei O. V. , Sitnikov A. V.
Published: December 2011

Magnetic and magneto-transport properties of granular ferromagnetic Cox-(Al2O3)1-x films with a large range of cobalt concentrations x are investigated. The films with x below the percolation threshold xp demonstrate the presence of oriented uniaxial anisotropy of the granules with the anisotropy field Ha ∼ 2 kOe and easy anisotropy axis perpendicular to the film plane. It is shown that for the values of x close but below xp, field dependencies of the magnetoresistance in the magnetic fields applied in the film plane, possess an anomalous field dependence with a positive magnetoresistance and a maximum in the range of field magnitudes 0 < H < Ha. The positive magnetoresistance effect is isotropic in the film plane and reduces as the field direction is rotated out of the film plane up to the complete quenching for the field perpendicular to the film plane. The effect is not related to an anisotropic magnetoresistance manifestation and is temperature-dependent. We propose a model, which explains the phenomenon and bases on an accounting of thermal fluctuations of uniaxial particle magnetic moments in the fields perpendicular to the particle easy anisotropy axis in the presence of the ferromagnetic interaction between the particles.
Rotational coherence imaging and control for CN molecules through time-frequency resolved coherent anti-Stokes Raman scattering
Authors: Lindgren Johan , Hulkko Eero , Pettersson Mika , Kiljunen Toni
Published: December 2011

Numerical wave packet simulations are performed for studying coherent anti-Stokes Raman scattering (CARS) for CN radicals. Electronic coherence is created by femtosecond laser pulses between the X 2Σ and B 2Σ states. Due to the large energy separation of vibrational states, the wave packets are superpositions of rotational states only. This allows for a specially detailed inspection of the second- and third-order coherences by a two-dimensional imaging approach. We present the time-frequency domain images to illustrate the intra- and intermolecular interferences, and discuss the procedure to rationally control and experimentally detect the interferograms in solid Xe environment.
Thermodynamic integration from classical to quantum mechanics
Authors: Habershon Scott , Manolopoulos David E.
Published: December 2011

We present a new method for calculating quantum mechanical corrections to classical free energies, based on thermodynamic integration from classical to quantum mechanics. In contrast to previous methods, our method is numerically stable even in the presence of strong quantum delocalization. We first illustrate the method and its relationship to a well-established method with an analysis of a one-dimensional harmonic oscillator. We then show that our method can be used to calculate the quantum mechanical contributions to the free energies of ice and water for a flexible water model, a problem for which the established method is unstable.
Quasi-splitting subspaces and Foulis-Randall subspaces
Authors: Buhagiar D. , Chetcuti E. , Dvurečenskij A.
Published: December 2011

For a pre-Hilbert space S, let F(S) denote the orthogonally closed subspaces, Eq(S) the quasi-splitting subspaces, E(S) the splitting subspaces, D(S) the Foulis-Randall subspaces, and R(S) the maximal Foulis-Randall subspaces, of S. It was an open problem whether the equalities D(S) = F(S) and E(S) = R(S) hold in general [Cattaneo, G. and Marino, G., “Spectral decomposition of pre-Hilbert spaces as regard to suitable classes of normal closed operators,” Boll. Unione Mat. Ital. 6 1-B, 451–466 (1982); Cattaneo, G., Franco, G., and Marino, G., “Ordering of families of subspaces of pre-Hilbert spaces and Dacey pre-Hilbert spaces,” Boll. Unione Mat. Ital. 71-B, 167–183 (1987); Dvurečenskij, A., Gleason's Theorem and Its Applications (Kluwer, Dordrecht, 1992), p. 243.]. We prove that the first equality is true and exhibit a pre-Hilbert space S for which the second equality fails. In addition, we characterize complete pre-Hilbert spaces as follows: S is a Hilbert space if, and only if, S has an orthonormal basis and Eq(S) admits a non-free charge.
Differential shrinkage of mesophyll cells in transpiring cotton leaves: implications for static and dynamic pools of water, and for water transport pathways
Authors: Canny Martin , Wong Suan Chin , Huang Cheng , Miller Celia
Published: December 2011

Shrinkage of palisade cells during transpiration, previously measured for sclerophyllous leaves of Eucalyptus where cells shrank equally, was compared with shrinkage in thin mesophytic leaves of cotton (Gossypium hirsutum L.). Selected vapour pressure differences (Δe) from 0.6 to 2.7 kPa were imposed during steady-state photosynthesis and transpiration. Leaves were then cryo-fixed and cryo-planed paradermally, and images obtained with a cryo-scanning electron microscope (CSEM). Diameters of palisade ‘cavity cells’ within sub-stomatal cavities, and surrounding palisade ‘matrix cells’ were measured on CSEM images. Cavity and spongy mesophyll cells shrank progressively down to Δe = 2.7 kPa, while matrix cells remained at the same diameter at all Δe. Diameters were also measured of cavity and matrix cells quasi-equilibrated with relative humidities (RHs) from 100% to 86%. In leaves quasi-equilibrated with 95% RH, the cavity cells shrank so much as to be almost unmeasurable, while matrix cells shrank by only 6%. These data suggest that there are two distinct pools of water in cotton leaves: cavity plus spongy mesophyll cells (two-thirds of leaf volume) which easily lose water; and matrix cells (one-third of leaf volume), which retain turgor down to relative water loss = 0.4, providing structural rigidity to prevent wilting. This phenomenon is probably widespread among mesophytic leaves.
Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells
Authors: Coufal Nicole G. , Garcia-Perez Josè Luis , Peng Grace E. , Marchetto Maria C. N. , Muotri Alysson R. , Mu Yangling , Carson Christian T. , Macia Angela , Moran John V. , Gage Fred H.
Published: December 2011

Long interspersed element-1 (L1) retrotransposons compose ∼20% of the mammalian genome, and ongoing L1 retrotransposition events can impact genetic diversity by various mechanisms. Previous studies have demonstrated that endogenous L1 retrotransposition can occur in the germ line and during early embryonic development. In addition, recent data indicate that engineered human L1s can undergo somatic retrotransposition in human neural progenitor cells and that an increase in human-specific L1 DNA content can be detected in the brains of normal controls, as well as in Rett syndrome patients. Here, we demonstrate an increase in the retrotransposition efficiency of engineered human L1s in cells that lack or contain severely reduced levels of ataxia telangiectasia mutated, a serine/threonine kinase involved in DNA damage signaling and neurodegenerative disease. We demonstrate that the increase in L1 retrotransposition in ataxia telangiectasia mutated-deficient cells most likely occurs by conventional target-site primed reverse transcription and generate either longer, or perhaps more, L1 retrotransposition events per cell. Finally, we provide evidence suggesting an increase in human-specific L1 DNA copy number in postmortem brain tissue derived from ataxia telangiectasia patients compared with healthy controls. Together, these data suggest that cellular proteins involved in the DNA damage response may modulate L1 retrotransposition.
Inhibition of eye blinking reveals subjective perceptions of stimulus salience
Authors: Shultz Sarah , Klin Ami , Jones Warren
Published: December 2011

Spontaneous eye blinking serves a critical physiological function, but it also interrupts incoming visual information. This tradeoff suggests that the inhibition of eye blinks might constitute an adaptive reaction to minimize the loss of visual information, particularly information that a viewer perceives to be important. To test this hypothesis, we examined whether the timing of blink inhibition, during natural viewing, is modulated between as well as within tasks, and also whether the timing of blink inhibition varies as a function of viewer engagement and stimulus event type. While viewing video scenes, we measured the timing of blinks and blink inhibition, as well as visual scanning, in a group of typical two-year-olds, and in a group of two-year-olds known for attenuated reactivity to affective stimuli: toddlers with Autism Spectrum Disorders (ASD). Although both groups dynamically adjusted the timing of their blink inhibition at levels greater than expected by chance, they inhibited their blinking and shifted visual fixation differentially with respect to salient onscreen events. Moreover, typical toddlers inhibited their blinking earlier than toddlers with ASD, indicating active anticipation of the unfolding of those events. These findings indicate that measures of blink inhibition can serve as temporally precise markers of perceived stimulus salience and are useful quantifiers of atypical processing of social affective signals in toddlers with ASD.
Avoidance of overheating and selection for both hair loss and bipedality in hominins
Authors: Ruxton Graeme D. , Wilkinson David M.
Published: December 2011

Two frequently debated aspects of hominin evolution are the development of upright bipedal stance and reduction in body hair. It has long been argued, on the basis of heat-balance models, that thermoregulation might have been important in the evolution of both of these traits. Previous models were based on a stationary individual standing in direct sunlight; here we extend this approach to consider a walking hominin, having argued that walking is more thermally challenging than remaining still. Further, stationary activities may be more compatible with shade seeking than activities (such as foraging) involving travel across the landscape. Our model predictions suggest that upright stance probably evolved for nonthermoregulatory reasons. However, the thermoregulatory explanation for hair loss was supported. Specifically, we postulate progressive hair loss being selected and this allowing individuals to be active in hot, open environments initially around dusk and dawn without overheating. Then, as our ancestors’ hair loss increased and sweating ability improved over evolutionary time, the fraction of the day when they could remain active in such environments extended. Our model suggests that only when hair loss and sweating ability reach near-modern human levels could hominins have been active in the heat of the day in hot, open environments.
Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis
Authors: Chaikuad Apirat , Froese D. Sean , Berridge Georgina , von Delft Frank , Oppermann Udo , Yue Wyatt W.
Published: December 2011

Glycogenin initiates the synthesis of a maltosaccharide chain covalently attached to itself on Tyr195 via a stepwise glucosylation reaction, priming glycogen synthesis. We have captured crystallographic snapshots of human glycogenin during its reaction cycle, revealing a dynamic conformational switch between ground and active states mediated by the sugar donor UDP-glucose. This switch includes the ordering of a polypeptide stretch containing Tyr195, and major movement of an approximately 30-residue “lid” segment covering the active site. The rearranged lid guides the nascent maltosaccharide chain into the active site in either an intra- or intersubunit mode dependent upon chain length and steric factors and positions the donor and acceptor sugar groups for catalysis. The Thr83Met mutation, which causes glycogen storage disease XV, is conformationally locked in the ground state and catalytically inactive. Our data highlight the conformational plasticity of glycogenin and coexistence of two modes of glucosylation as integral to its catalytic mechanism.
Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (
Gossypium
)
Authors: Bao Ying , Hu Guanjing , Flagel Lex E. , Salmon Armel , Bezanilla Magdalena , Paterson Andrew H. , Wang Zining , Wendel Jonathan F.
Published: December 2011

Cotton is remarkable among our major crops in that four species were independently domesticated, two allopolyploids and two diploids. In each case thousands of years of human selection transformed sparsely flowering, perennial shrubs into highly productive crops with seeds bearing the vastly elongated and abundant single-celled hairs that comprise modern cotton fiber. The genetic underpinnings of these transformations are largely unknown, but comparative gene expression profiling experiments have demonstrated up-regulation of profilin accompanying domestication in all three species for which wild forms are known. Profilins are actin monomer binding proteins that are important in cytoskeletal dynamics and in cotton fiber elongation. We show that
Gossypium
diploids contain six profilin genes (
GPRF
1–
GPRF
6), located on four different chromosomes (eight chromosomes in the allopolyploid). All but one profilin (
GPRF
6) are expressed during cotton fiber development, and both homeologs of
GPRF
1–
GPRF
5 are expressed in fibers of the allopolyploids. Remarkably, quantitative RT-PCR and RNAseq data demonstrate that
GPRF
1–
GPRF
5 are all up-regulated, in parallel, in the three independently domesticated cottons in comparison with their wild counterparts. This result was additionally supported by iTRAQ proteomic data. In the allopolyploids, there This usage of novel should be fine, since it refers to a novel evolutionary process, not a novel discovery has been novel recruitment of the sixth profilin gene (
GPRF
6) as a result of domestication. This parallel up-regulation of an entire gene family in multiple species in response to strong directional selection is without precedent and suggests unwitting selection on one or more upstream transcription factors or other proteins that coordinately exercise control over profilin expression.
Spontaneous generation of anchorless prions in transgenic mice
Authors: Stöhr Jan , Watts Joel C. , Legname Giuseppe , Oehler Abby , Lemus Azucena , Nguyen Hoang-Oanh B. , Sussman Joshua , Wille Holger , DeArmond Stephen J. , Prusiner Stanley B. , Giles Kurt
Published: December 2011

Some prion protein mutations create anchorless molecules that cause Gerstmann–Sträussler–Scheinker (GSS) disease. To model GSS, we generated transgenic mice expressing cellular prion protein (PrP
C
) lacking the glycosylphosphatidyl inositol (GPI) anchor, denoted PrP(ΔGPI). Mice overexpressing PrP(ΔGPI) developed a late-onset, spontaneous neurologic dysfunction characterized by widespread amyloid deposition in the brain and the presence of a short protease-resistant PrP fragment similar to those found in GSS patients. In Tg(PrP,ΔGPI) mice, disease onset could be accelerated either by inoculation with brain homogenate prepared from spontaneously ill animals or by coexpression of membrane-anchored, full-length PrP
C
. In contrast, coexpression of N-terminally truncated PrP(Δ23–88) did not affect disease progression. Remarkably, disease from ill Tg(PrP,ΔGPI) mice transmitted to mice expressing wild-type PrP
C
, indicating the spontaneous generation of prions.
Histone deacetylase inhibitors prevent the degradation and restore the activity of glucocerebrosidase in Gaucher disease
Authors: Lu Jie , Yang Chunzhang , Chen Masako , Ye Donald Y. , Lonser Russell R. , Brady Roscoe O. , Zhuang Zhengping
Published: December 2011

Gaucher disease (GD) is caused by a spectrum of genetic mutations within the gene encoding the lysosomal enzyme glucocerebrosidase (GCase). These mutations often lead to misfolded proteins that are recognized by the unfolded protein response system and are degraded through the ubiquitin–proteasome pathway. Modulating this pathway with histone deacetylase inhibitors (HDACis) has been shown to improve protein stability in other disease settings. To identify the mechanisms involved in the regulation of GCase and determine the effects of HDACis on protein stability, we investigated the most prevalent mutations for nonneuronopathic (N370S) and neuronopathic (L444P) GD in cultured fibroblasts derived from GD patients and HeLa cells transfected with these mutations. The half-lives of mutant GCase proteins correspond to decreases in protein levels and enzymatic activity. GCase was found to bind to Hsp70, which directed the protein to TCP1 for proper folding, and to Hsp90, which directed the protein to the ubiquitin–proteasome pathway. Using a known HDACi (SAHA) and a unique small-molecule HDACi (LB-205), GCase levels increased rescuing enzymatic activity in mutant cells. The increase in the quantity of protein can be attributed to increases in protein half-life that correspond primarily with a decrease in degradation rather than an increase in chaperoned folding. HDACis reduce binding to Hsp90 and prevent subsequent ubiquitination and proteasomal degradation without affecting binding to Hsp70 or TCP1. These findings provide insight into the pathogenesis of GD and indicate a potent therapeutic potential of HDAC inhibitors for the treatment of GD and other human protein misfolding disorders.
Typographical Translations: Spanish Refashioning of Lipsius'sPoliticorum libri sex*
Authors: Peraita Carmen
Published: December 2011

The typographical language of Justus Lipsius'sPoliticorum libri sex(1589) is a crucial element for understanding itscompositio. The page layout, designed by Lipsius (1547–1606) probably in collaboration with his printer, displayed the author's inventive methods and writing strategies. All Latin editions of thePoliticafollowed the precise typographic design of the editio princeps. The work was disseminated across seventeenth-century Europe by different printers without changes to its fundamental material features, including its typography. Something different happened, however, with the various vernacular editions of thePolitica. All of them redesigned Lipsius's typography. These editions refashioned the display ofsententiaeand provided visual uniformity to the page, transforming the text from a compendium of interrelated commonplaces into a dense treatise. In this article I focus on the changes and accommodations evidenced in Bernardino de Mendoza's Spanish translation. In this case, an exceptional document survived that allows one to examine the different interventions in the process of accommodation of thePolitica:the printer's copy and the manuscript supervised by Mendoza, approved and licensed by the Council of Castile, and used by the Imprenta Real in Madrid to printLos seis libros de las Políticas(1604).
M3: an improved SNP calling algorithm for Illumina BeadArray data
Authors: Li Gengxin , Gelernter Joel , Kranzler Henry R. , Zhao Hongyu
Published: December 2011

Summary: Genotype calling from high-throughput platforms such as Illumina and Affymetrix is a critical step in data processing, so that accurate information on genetic variants can be obtained for phenotype–genotype association studies. A number of algorithms have been developed to infer genotypes from data generated through the Illumina BeadStation platform, including GenCall, GenoSNP, Illuminus and CRLMM. Most of these algorithms are built on population-based statistical models to genotype every SNP in turn, such as GenCall with the GenTrain clustering algorithm, and require a large reference population to perform well. These approaches may not work well for rare variants where only a small proportion of the individuals carry the variant. A fundamentally different approach, implemented in GenoSNP, adopts a single nucleotide polymorphism (SNP)-based model to infer genotypes of all the SNPs in one individual, making it an appealing alternative to call rare variants. However, compared to the population-based strategies, more SNPs in GenoSNP may fail the Hardy–Weinberg Equilibrium test. To take advantage of both strategies, we propose a two-stage SNP calling procedure, named the modified mixture model (M3), to improve call accuracy for both common and rare variants. The effectiveness of our approach is demonstrated through applications to genotype calling on a set of HapMap samples used for quality control purpose in a large case–control study of cocaine dependence. The increase in power with M3 is greater for rare variants than for common variants depending on the model.

Availability: M3 algorithm: http://bioinformatics.med.yale.edu/group.

Contact:  name@bio.com; hongyu.zhao@yale.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
How to do (or not to do) … Tracking data on development assistance for health
Authors: Grépin Karen A , Leach-Kemon Katherine , Schneider Matthew , Sridhar Devi
Published: December 2011

Development assistance for health (DAH) has increased substantially in recent years and is seen as important to the improvement of health and health systems in developing countries. As a result, there has been increasing interest in tracking and understanding these resource flows from the global health community. A number of datasets, each with its own strengths and weaknesses, are available to track DAH. In this article we review the available datasets on DAH and summarize the strengths and weaknesses of each of these datasets to help researchers make the best choice of which to use to inform their analysis. Finally, we also provide recommendations about how each of these datasets could be improved.
Within-Field Variation of Fusarium graminearum Isolates for Aggressiveness and Deoxynivalenol Production in Wheat Head Blight
Authors: Talas Firas , Kalih Rasha , Miedaner Thomas
Published: December 2011

Fusarium head blight (FHB), caused by Fusarium graminearum sensu stricto (s.s.), causes tremendous annual yield losses in wheat worldwide. Variation of aggressiveness of isolates from individual field populations in terms of FHB infection and deoxynivalenol (DON) concentration in the host are important population parameters reflecting parasitic ability. Our main objective was to estimate the variation of both traits within three populations of F. graminearum s.s., each consisting of 30 single-spore isolates collected from small wheat fields in Germany, and to compare it with 11 isolates of a collection (F. graminearum collection) from four countries. The same isolates were characterized using 19 single-sequence repeat markers. All isolates were spray inoculated on a moderately resistant spring wheat cultivar at two field locations over 2 years (i.e., in four environments). The genotypic proportion of phenotypic variance (σ2G) within populations was significant (P < 0.01) for both traits, and the σ2G × environment interaction was even more important for mean FHB severity. Ranges in mean FHB severity and DON concentration in the host were only slightly smaller for the field populations than for the F. graminearum collection. Both traits were significantly (P < 0.05) correlated within and across populations. A further partitioning of σ2G revealed 72% of σ2G within and 28% of σ2G across populations for both traits. Molecular variance of the three populations was similarly distributed (73.6% within versus 26.4% between populations). In view of this high within-field variation for traits of parasitic ability and selection, neutral molecular markers, multiple resistance genes of different origin should be employed in wheat breeding programs to obtain a long-term stable FHB resistance.
Microbulbifer taiwanensis sp. nov., isolated from coastal soil
Authors: Kämpfer P. , Arun A. B. , Young Chiu-Chung , Rekha P. D. , Martin K. , Busse H.-J. , Chen Wen-Ming
Published: December 2011

A Gram-negative, non-spore-forming rod (CC-LN1-12T) was isolated from coastal soil samples of Lutao Island (Green Island), Taiwan, and its taxonomic position was studied. 16S rRNA gene sequence analysis showed that isolate CC-LN1-12T was grouped into the

Microbulbifer

cluster, with the highest similarities to

Microbulbifer okinawensis

ABABA23T (97.9 %),

Microbulbifer maritimus

TF-17T (97.7 %) and

Microbulbifer donghaiensis

CN85T (97.7 %), similarities to all other species of the genus

Microbulbifer

were lower than 96.8 %. The polyamine pattern contained the major compounds spermidine and cadaverine. The fatty acid profile, comprising the major fatty acids iso-C15 : 0, iso-C17 : 1ω9c, C18 : 1ω7c and iso-C11 : 0 3-OH as the major hydroxylated fatty acid, supported the affiliation of strain CC-LN1-12T to the genus

Microbulbifer

. DNA–DNA hybridizations between strain CC-LN1-12T and

Microbulbifer okinawensis

ABABA23T,

M. donghaiensis

CN85T and

M. maritimus

JCM 12187T resulted in relatedness values of 21.5 % (14.3 %, reciprocal analysis), 35.9 % (48.5 %, reciprocal analysis) and 48.1 % (52.1 %, reciprocal analysis), respectively. From these data, as well as from physiological and biochemical tests, strain CC-LN1-12T could be clearly differentiated from the most closely related species of the genus

Microbulbifer

. It is concluded that strain CC-LN1-12T represents a novel species, for which the name Microbulbifer taiwanensis sp. nov. is proposed. The type strain is CC-LN1-12T ( = LMG 26125T = CCM 7856T).
Oceanitalea nanhaiensis gen. nov., sp. nov., an actinobacterium isolated from seawater
Authors: Fu Yingnan , Li Qipei , Liu Keshao , Xu Yongle , Wang Yanan , Jiao Nianzhi
Published: December 2011

A Gram-positive, motile, short-rod-shaped bacterium, designated strain JLT1488T, was isolated from the South China Sea and investigated in a taxonomic study using a polyphasic approach. The peptidoglycan type determined for strain JLT1488T was A4α with lysine as the diagnostic cell-wall diamino acid and an interpeptide bridge of l-Lys–l-Glu. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unknown glycolipid and an unknown phospholipid. The only detected menaquinone was MK-8(H4), and the major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) , C16 : 0 and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c); significant amounts of C12 : 0 3-OH, C10 : 0 and C19 : 0 cyclo ω8c were also present. The G+C content of the genomic DNA was 62.3 mol%. Comparison of the 16S rRNA gene sequence of strain JLT1488T with those of related type strains demonstrated that it represented a novel lineage within the family

Bogoriellaceae

, suborder

Micrococcineae

, being closely related to species of the genera

Georgenia

,

Bogoriella

and

Cellulomonas

(94.6–96.8 % sequence similarity). These results demonstrate that strain JLT1488T is a member of a new genus, for which the name Oceanitalea nanhaiensis gen. nov., sp. nov. is proposed. The type strain of the type species is JLT1488T ( = JCM 17755T = CGMCC 1.10826T).
Taxonomy of the family Halobacteriaceae: a paradigm for changing concepts in prokaryote systematics
Authors: Oren Aharon
Published: December 2011

The halophilic Archaea of the familyHalobacteriaceae(36 genera with 129 species with standing in nomenclature as of November 2011) provide an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods have influenced the way in which the taxonomy of a single group of prokaryotes is treated. This review gives an overview of the taxonomy of the familyHalobacteriaceae, showing the impact that methods of phenotypic characterization, numerical taxonomy, chemotaxonomy and especially polar lipid analysis, 16S rRNA gene sequence comparisons, multilocus type analysis and comparative genomics have had on their classification.
Syringyl Lignin Is Unaltered by Severe Sinapyl Alcohol Dehydrogenase Suppression in Tobacco
Authors: Barakate Abdellah , Stephens Jennifer , Goldie Alison , Hunter William N. , Marshall David , Hancock Robert D. , Lapierre Catherine , Morreel Kris , Boerjan Wout , Halpin Claire
Published: December 2011

The manipulation of lignin could, in principle, facilitate efficient biofuel production from plant biomass. Despite intensive study of the lignin pathway, uncertainty exists about the enzyme catalyzing the last step in syringyl (S) monolignol biosynthesis, the reduction of sinapaldehyde to sinapyl alcohol. Traditional schemes of the pathway suggested that both guaiacyl (G) and S monolignols are produced by a single substrate-versatile enzyme, cinnamyl alcohol dehydrogenase (CAD). This was challenged by the discovery of a novel sinapyl alcohol dehydrogenase (SAD) that preferentially uses sinapaldehyde as a substrate and that was claimed to regulate S lignin biosynthesis in angiosperms. Consequently, most pathway schemes now show SAD (or SAD and CAD) at the sinapaldehyde reduction step, although functional evidence is lacking. We cloned SAD from tobacco (Nicotiana tabacum) and suppressed it in transgenic plants using RNA interference–inducing vectors. Characterization of lignin in the woody stems shows no change to content, composition, or structure, and S lignin is normal. By contrast, plants additionally suppressed in CAD have changes to lignin structure and S:G ratio and have increased sinapaldehyde in lignin, similar to plants suppressed in CAD alone. These data demonstrate that CAD, not SAD, is the enzyme responsible for S lignin biosynthesis in woody angiosperm xylem.
Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage
Authors: Jeong Dong-Hoon , Park Sunhee , Zhai Jixian , Gurazada Sai Guna Ranjan , De Paoli Emanuele , Meyers Blake C. , Green Pamela J.
Published: December 2011

Small RNAs have a variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify previously unknown rice (Oryza sativa) microRNAs (miRNAs) and those regulated by environmental stress, 62 small RNA libraries were constructed from rice plants and used for deep sequencing with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. More than 94 million genome-matched reads were obtained, resulting in more than 16 million distinct small RNA sequences. This allowed an evaluation of ~400 annotated miRNAs with current criteria and the finding that among these, ~150 had small interfering RNA–like characteristics. Seventy-six new miRNAs were found, and miRNAs regulated in response to water stress, nutrient stress, or temperature stress were identified. Among the new examples of miRNA regulation were members of the same miRNA family that were differentially regulated in different organs and had distinct sequences Some of these distinct family members result in differential target cleavage and provide new insight about how an agriculturally important rice phenotype could be regulated in the panicle. This high-resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae.
POPCORNFunctions in the Auxin Pathway to Regulate Embryonic Body Plan and Meristem Organization inArabidopsis
Authors: Xiang Daoquan , Yang Hui , Venglat Prakash , Cao Yongguo , Wen Rui , Ren Maozhi , Stone Sandra , Wang Edwin , Wang Hong , Xiao Wei , Weijers Dolf , Berleth Thomas , Laux Thomas , Selvaraj Gopalan , Datla Raju
Published: December 2011

The shoot and root apical meristems (SAM and RAM) formed during embryogenesis are crucial for postembryonic plant development. We report the identification of POPCORN (PCN), a gene required for embryo development and meristem organization in Arabidopsis thaliana. Map-based cloning revealed that PCN encodes a WD-40 protein expressed both during embryo development and postembryonically in the SAM and RAM. The two pcn alleles identified in this study are temperature sensitive, showing defective embryo development when grown at 22°C that is rescued when grown at 29°C. In pcn mutants, meristem-specific expression of WUSCHEL (WUS), CLAVATA3, and WUSCHEL-RELATED HOMEOBOX5 is not maintained; SHOOTMERISTEMLESS, BODENLOS (BDL) and MONOPTEROS (MP) are misexpressed. Several findings link PCN to auxin signaling and meristem function: ectopic expression of DR5rev:green fluorescent protein (GFP), pBDL:BDL-GFP, and pMP:MP-β-glucuronidase in the meristem; altered polarity and expression of pPIN1:PIN1-GFP in the apical domain of the developing embryo; and resistance to auxin in the pcn mutants. The bdl mutation rescued embryo lethality of pcn, suggesting that improper auxin response is involved in pcn defects. Furthermore, WUS, PINFORMED1, PINOID, and TOPLESS are dosage sensitive in pcn, suggesting functional interaction. Together, our results suggest that PCN functions in the auxin pathway, integrating auxin signaling in the organization and maintenance of the SAM and RAM.
ArabidopsisATM and ATR Kinases Prevent Propagation of Genome Damage Caused by Telomere Dysfunction
Authors: Amiard Simon , Depeiges Annie , Allain Elisabeth , White Charles I. , Gallego Maria Eugenia
Published: December 2011

The ends of linear eukaryotic chromosomes are hidden in nucleoprotein structures called telomeres, and loss of the telomere structure causes inappropriate repair, leading to severe karyotypic and genomic instability. Although it has been shown that DNA damaging agents activate a DNA damage response (DDR), little is known about the signaling of dysfunctional plant telomeres. We show that absence of telomerase in Arabidopsis thaliana elicits an ATAXIA-TELANGIECTASIA MUTATED (ATM) and ATM AND RAD3-RELATED (ATR)-dependent DDR at telomeres, principally through ATM. By contrast, telomere dysfunction induces an ATR-dependent response in telomeric Conserved telomere maintenance component1 (Ctc1)-Suppressor of cdc thirteen (Stn1)-Telomeric pathways in association with Stn1 (CST)–complex mutants. These results uncover a new role for the CST complex in repressing the ATR-dependent DDR pathway in plant cells and show that plant cells use two different DNA damage surveillance pathways to signal telomere dysfunction. The absence of either ATM or ATR in ctc1 and stn1 mutants significantly enhances developmental and genome instability while reducing stem cell death. These data thus give a clear illustration of the action of ATM/ATR-dependent programmed cell death in maintaining genomic integrity through elimination of genetically unstable cells.
12‐hydroxy‐eicosatetraenoic acid (12‐HETE): a biomarker of Churg‐Strauss syndrome
Authors: Szczeklik W. , Sanak M. , Mastalerz L. , Sokołowska B. M. , Gielicz A. , Soja J. , Kumik J. , Musiał J. , Szczeklik A.
Published: December 2011

Background

Churg‐Strauss syndrome (CSS) shares similarities with asthma and hypereosinophilic syndrome (HES). Eicosanoids – important inflammatory and signaling molecules – are present in exhaled breath condensate (EBC) and broncho‐alveolar lavage fluid (BALF).

Objectives

To assess eicosanoid profile both in EBC and BALF of CSS subjects searching for a pattern characteristic of this syndrome.

Methods

EBCs from 23 CSS patients, 30 asthmatics, 12 HES patients and 54 healthy controls (HC) were assessed quantitatively for 19 eicosanoids by a high‐performance liquid chromatography ‐ tandem mass spectrometry (HPLC‐MS/MS). In addition, in 21 of 23 CSS subjects and in nine asthmatics, eicosanoids were determined in BALF.

Results

EBC from CSS patients showed markedly elevated levels of 12‐HETE as compared with other studied groups. BALF was characterized by a significant elevation of 12‐HETE and its metabolite 12‐tetranor HETE in CSS as compared with asthma. Clinical activity of CSS correlated with 12‐HETE and its metabolites levels in BALF, but not in EBC.

Conclusion and Clinical Relevance

CSS is clearly distinguished from bronchial asthma, and HES by a marked increase in 12‐HETE concentration in both EBC and BALF. This points to a possible new pathogenic mechanism in CSS and may help in future in establishing the diagnosis of CSS.
Changes in the surface of four calcium silicate‐containing endodontic materials and an epoxy resin‐based sealer after a solubility test
Authors: Borges R. P. , Sousa‐Neto M. D. , Versiani M. A. , Rached‐Júnior F. A. , De‐Deus G. , Miranda C. E. S. , Pécora J. D.
Published: December 2011

Borges RP, Sousa‐Neto MD, Versiani MA, Rached‐Júnior FA, De‐Deus G, Miranda CES, Pécora JD. Changes in the surface of four calcium silicate‐containing endodontic materials and an epoxy resin‐based sealer after a solubility test. International Endodontic Journal, 45, 419–428, 2012.

Aim  To compare the changes in the surface structure and elemental distribution, as well as the percentage of ion release, of four calcium silicate‐containing endodontic materials with a well‐established epoxy resin‐based sealer, submitted to a solubility test.

Methodology  Solubility of AH Plus, iRoot SP, MTA Fillapex, Sealapex and MTA‐Angelus (MTA‐A) was tested according to ANSI/ADA Specification 57. The deionized water used in the solubility test was submitted to atomic absorption spectrophotometry to determine and quantify Ca2+, Na+, K+, Zn2+, Ni2+ and Pb2+ ions release. In addition, the outer and inner surfaces of nonsubmitted and submitted samples of each material to the solubility test were analysed by means of scanning electron microscopy and energy‐dispersive spectroscopy (SEM/EDX). Statistical analysis was performed by using one‐way anova and Tukey’s post hoc tests (α = 0.05).

Results  Solubility results, in percentage, sorted in an increasing order were −1.24 ± 0.19 (MTA‐A), 0.28 ± 0.08 (AH Plus), 5.65 ± 0.80 (Sealapex), 14.89 ± 0.73 (MTA Fillapex) and 20.64 ± 1.42 (iRoot SP). AH Plus and MTA‐A were statistically similar (P > 0.05), but different from the other materials (P < 0.05). High levels of Ca2+ ion release were observed in all groups except AH Plus sealer. MTA‐A also had the highest release of Na2+ and K+ ions. Zn+2 ion release was observed only with AH Plus and Sealapex sealers. After the solubility test, all surfaces had morphological changes. The loss of matrix was evident and the filler particles were more distinguishable. EDX analysis displayed high levels of calcium and carbon at the surface of Sealapex, MTA Fillapex and iRoot SP.

Conclusions  AH Plus and MTA‐A were in accordance with ANSI/ADA’s requirements regarding solubility whilst iRoot SP, MTA Fillapex and Sealapex did not fulfil ANSI/ADA’s protocols. High levels of Ca2+ ion release were observed in all materials except AH Plus. SEM/EDX analysis revealed that all samples had morphological changes in both outer and inner surfaces after the solubility test. High levels of calcium and carbon were also observed at the surface of all materials except AH Plus and MTA‐A.
Modelling spread of British wind‐dispersed plants under future wind speeds in a changing climate
Authors: Bullock James M. , White Steven M. , Prudhomme Christel , Tansey Christine , Perea Ramón , Hooftman Danny A. P.
Published: December 2011

1. Climate change impacts on habitat suitability and demography are often studied, but direct effects on plant dispersal are rarely considered. To address this we analysed climate model projections of future wind speeds and modelled their possible impacts on dispersal and spread of wind‐dispersed plants.

2. Projections for 17 Global Climate Models and three emission scenarios suggested great uncertainty about wind speeds in southern England by the period 2070–99. Projections ranged from −90% to +100% change in the mean wind speed, although the average projection was for large falls in both summer and winter wind speeds.

3. Using a novel method for converting projected changes in mean wind speed to new seasonal wind speed distributions, we parameterized a mechanistic model of seed dispersal by wind using baseline and changes in mean wind speed from −80% to +80%.

4. The mechanistic seed dispersal model was combined with demographic data in an analytical model of plant spread. This was carried out for three British native and three non‐native species, which represented a range of life‐forms.

5. Dispersal kernels and population spread rates were affected disproportionately by changes in wind speed, demonstrating nonlinear propagation of uncertainty in wind speed projections through to modelled plant spread rates.

6. Sensitivity analyses showed differences among the plant species in which demographic transitions were most important in determining spread rates. By contrast, sensitivity of spread rates to dispersal parameters showed great consistency among species, with seed release height being more important than seed terminal velocity.

7. Synthesis. Plant populations will need to shift their geographic ranges to keep pace with climate change‐driven habitat loss. This study shows that climate change may affect that ability by decreasing the dispersal distances of wind‐dispersed plants and thus their potential spread rates. However, the modelling approach presented here illustrates that uncertainty in climate models leads to an even greater uncertainty about how dispersal and spread will change in future climates. Caution should therefore be exercised in making predictions as to how fast plant species may spread in response to climate change.
Quality improvement in medical education: current state and future directions
Authors: Wong Brian M , Levinson Wendy , Shojania Kaveh G
Published: December 2011

Medical Education 2012: 46: 107–119

Context  During the last decade, there has been a drive to improve the quality of patient care and prevent the occurrence of avoidable errors. This review describes current efforts to teach or engage trainees in patient safety and quality improvement (QI), summarises progress to date, as well as successes and challenges, and lists our recommendations for the next steps that will shape the future of patient safety and QI in medical education.

Current status  Trainees encounter patient safety and QI through three main groups of activity. First are formal curricula that teach concepts or methods intended to facilitate trainees’ participation in QI activities. These curricula increase learner knowledge and may improve clinical processes, but demonstrate limited capacity to modify learner behaviours. Second are educational activities that impart specific skills related to safety or quality which are considered to represent core doctor competencies (e.g. effective patient handover). These are frequently taught effectively, but without emphasis on the general safety or quality principles that inform the relevant skills. Third are real‐life QI initiatives that involve trainees as active or passive participants. These innovative approaches expose trainees to safety and quality by integrating QI activities into trainees’ day‐to‐day work. However, this integration can be challenging and can sometimes result in tension with broader educational goals.

Future directions  To prepare the next generation of doctors to make meaningful contributions to the quality mission, we propose the following call to action. Firstly, a major effort to build faculty capacity, especially among teachers of QI, should be instigated. Secondly, accreditation standards and assessment methods, both during training and at end‐of‐training certification examinations, should explicitly target these competencies. Finally, and perhaps most importantly, we must refocus our attention at all levels of training and instil fundamental, collaborative, open‐minded behaviours so that future clinicians are primed to promote a culture of safer, higher‐quality care.
Making sense of work‐based assessment: ask the right questions, in the right way, about the right things, of the right people
Authors: Crossley Jim , Jolly Brian
Published: December 2011

Medical Education 2012: 46: 28–37

Context  Historically, assessments have often measured the measurable rather than the important. Over the last 30 years, however, we have witnessed a gradual shift of focus in medical education. We now attempt to teach and assess what matters most. In addition, the component parts of a competence must be marshalled together and integrated to deal with real workplace problems. Workplace‐based assessment (WBA) is complex, and has relied on a number of recently developed methods and instruments, of which some involve checklists and others use judgements made on rating scales. Given that judgements are subjective, how can we optimise their validity and reliability?

Methods  This paper gleans psychometric data from a range of evaluations in order to highlight features of judgement‐based assessments that are associated with better validity and reliability. It offers some issues for discussion and research around WBA. It refers to literature in a selective way. It does not purport to represent a systematic review, but it does attempt to offer some serious analyses of why some observations occur in studies of WBA and what we need to do about them.

Results and Discussion  Four general principles emerge: the response scale should be aligned to the reality map of the judges; judgements rather than objective observations should be sought; the assessment should focus on competencies that are central to the activity observed, and the assessors who are best‐placed to judge performance should be asked to participate.