bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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.
Regulation of Plasmodesmatal Permeability and Stomatal Patterning by the Glycosyltransferase-Like Protein KOBITO1
Authors: Kong Danyu , Karve Rucha , Willet Alaina , Chen Ming-Kun , Oden Jennifer , Shpak Elena D. 
Published: March 2012

AbstractThe differentiation of stomata provides a convenient model for studying pattern formation in plant tissues. Stomata formation is induced by a set of basic helix-loop-helix transcription factors and inhibited by a signal transduction pathway initiated by TOO MANY MOUTHS (TMM) and ERECTA family (ERf) receptors. The formation of a proper stomata pattern is also dependent upon the restriction of symplastic movement of basic helix-loop-helix transcription factors into neighboring cells, especially in the backgrounds where the function of the TMM/ERf signaling pathway is compromised. Here, we describe a novel mutant of KOBITO1 in Arabidopsis (Arabidopsis thaliana). The kob1-3 mutation leads to the formation of stomata clusters in the erl1 erl2 background but not in the wild type. Cell-to-cell mobility assays demonstrated an increase in intercellular protein trafficking in kob1-3, including increased diffusion of SPEECHLESS, suggesting that the formation of stomata clusters is due to an escape of cell fate-specifying factors from stomatal lineage cells. While plasmodesmatal permeability is increased in kob1-3, we did not detect drastic changes in callose accumulation at the neck regions of the plasmodesmata. Previously, KOBITO1 has been proposed to function in cellulose biosynthesis. Our data demonstrate that disruption of cellulose biosynthesis in the erl1 erl2 background does not lead to the formation of stomata clusters, indicating that cellulose biosynthesis is not a major determining factor for regulating plasmodesmatal permeability. Analysis of KOBITO1 structure suggests that it is a glycosyltransferase-like protein. KOBITO1 might be involved in a carbohydrate metabolic pathway that is essential for both cellulose biosynthesis and the regulation of plasmodesmatal permeability.
Evolution of a Complex Disease Resistance Gene Cluster in DiploidPhaseolusand TetraploidGlycine
Authors: Ashfield Tom , Egan Ashley N. , Pfeil Bernard E. , Chen Nicolas W.G. , Podicheti Ram , Ratnaparkhe Milind B. , Ameline-Torregrosa Carine , Denny Roxanne , Cannon Steven , Doyle Jeff J. , Geffroy Valérie , Roe Bruce A. , Saghai Maroof M.A. , Young Nevin D. , Innes Roger W. 
Published: March 2012

AbstractWe used a comparative genomics approach to investigate the evolution of a complex nucleotide-binding (NB)-leucine-rich repeat (LRR) gene cluster found in soybean (Glycine max) and common bean (Phaseolus vulgaris) that is associated with several disease resistance (R) genes of known function, including Rpg1b (for Resistance to Pseudomonas glycinea1b), an R gene effective against specific races of bacterial blight. Analysis of domains revealed that the amino-terminal coiled-coil (CC) domain, central nucleotide-binding domain (NB-ARC [for APAF1, Resistance genes, and CED4]), and carboxyl-terminal LRR domain have undergone distinct evolutionary paths. Sequence exchanges within the NB-ARC domain were rare. In contrast, interparalogue exchanges involving the CC and LRR domains were common, consistent with both of these regions coevolving with pathogens. Residues under positive selection were overrepresented within the predicted solvent-exposed face of the LRR domain, although several also were detected within the CC and NB-ARC domains. Superimposition of these latter residues onto predicted tertiary structures revealed that the majority are located on the surface, suggestive of a role in interactions with other domains or proteins. Following polyploidy in the Glycine lineage, NB-LRR genes have been preferentially lost from one of the duplicated chromosomes (homeologues found in soybean), and there has been partitioning of NB-LRR clades between the two homeologues. The single orthologous region in common bean contains approximately the same number of paralogues as found in the two soybean homeologues combined. We conclude that while polyploidization in Glycine has not driven a stable increase in family size for NB-LRR genes, it has generated two recombinationally isolated clusters, one of which appears to be in the process of decay.
Seasonal wing colour plasticity varies dramatically between buckeye butterfly populations in different climatic zones
Authors: DANIELS EMILY V. , MOONEY KAILEN A. , REED ROBERT D. 
Published: March 2012

1. In the present study, how seasonal wing colour plasticity in buckeye butterflies (Junonia coenia Hübner) differs between populations in different climatic regions, and whether these differences are explained by regional environmental differences or reflect genetic divergences in plasticity is addressed.2. Using museum specimen data, it is shown that buckeye wing colour variation is much greater in populations from the humid and subtropical climates of the eastern U.S.A. than in populations from the desert and mediterranean climates of the western U.S.A.3. Museum specimen data further show that wing colour in eastern populations is strongly correlated with seasonal variation in day length and temperature, whereas wing colour in western populations is only weakly associated with these cues.4. Controlled incubator experiments comparing Southern California and North Carolina populations suggest that regional differences in wing pattern variation are attributable to dramatically increased robustness to environmental variation in western populations.5. Together these experiments show that while phenotypic variation can be influenced by environmental cues, the range of this variation can genetically diverge between populations in different regions.
Sharing the same space: foraging behaviour of saproxylic beetles in relation to dietary components of morphologically similar larvae
Authors: PŘIKRYL ZDENĚK B. , TURČÁNI MAREK , HORÁK JAKUB 
Published: March 2012

1. Saproxylic beetles (Coleoptera) have particular requirements for dead wood. Little is known about their larval development, especially within intermediate and late stages of dead wood decay.2. We studied the natural foraging behaviour of three saproxylic beetles with morphologically similar (i.e. convergent) larvae and similar habitat requirements –Cucujus cinnaberinus Scopoli (Cucujidae), Pyrochroa coccinea L., and Schizotus pectinicornis L. (Pyrochroidae) – examining dietary components using visual gut content analysis.3. There were few significant differences in diet among the study species, but there were significant differences for the different dietary components in individual species. Guts of all three species included more plant and fungal material than animal. We also observed that with increasing body size larvae foraged significantly less on fungal material. We observed significant differences among species and selection with respect to body size during the overwintering period. Larvae swallowed more animal and less fungal material with increasing body size.4. The study species seem to be opportunistic foragers, varying their foraging capability according to seasonality and age. They probably generally foraged woody material infested by filamentous fungi (i.e. xylomycetophagy), swallowing other material that is in their way while foraging, including animal parts and small arthropods.5. We found that morphologically similar larvae do not differ much in their foraging behaviour even when sharing the same habitat. Larval size seems to be a useful predictor for foraging behaviour of saproxylic beetles within the same guild. The study species are probably occasional predators with less ability to forage on other animals than previously suggested.
First evidence that marine protected areas can work for marine mammals
Authors: Gormley Andrew M. , Slooten Elisabeth , Dawson Steve , Barker Richard J. , Rayment Will , du Fresne Sam , Bräger Stefan 
Published: March 2012

Summary1. Marine protected areas (MPAs) have been advocated for the protection of threatened marine mammals, but there is no empirical evidence that they are effective. In 1988, the Banks Peninsula Marine Mammal Sanctuary was established to reduce gillnet mortalities of Hector’s dolphin Cephalorhynchus hectori, an endangered dolphin species endemic to New Zealand. This study assesses the effectiveness of the MPA in improving the survival rate of Hector’s dolphin at Banks Peninsula.2. Over 21 years, we undertook photo‐identification surveys of Hector’s dolphins along standardized transects from small outboard‐powered boats. From 1986 to 2006, we photographically captured 462 reliably marked individuals. We estimated mean annual survival during the pre‐sanctuary and post‐sanctuary periods by applying a Bayesian random effects capture‐recapture model to the data. Population growth was estimated from population simulations using a stage‐structured matrix model.3. We estimate a 90% probability that survival has improved between the pre‐sanctuary and post‐sanctuary periods, with estimates of mean survival probability increasing by 5·4% (from 0·863 to 0·917). This improvement in survival corresponds to a 6% increase in mean annual population growth (from 0·939 to 0·995).4. Synthesis and applications. Our study demonstrates improvement in a demographic parameter of an endangered marine mammal species following conservation action. Our results provide evidence that area‐based protection measures can be effective for marine mammals. We note that estimating demographic parameters in marine mammals requires many years of data to achieve sufficient precision to detect biologically meaningful change. MPAs should be established with a commitment to long‐term monitoring.
Obtaining the mean relative weights of the cost of care in Catalonia (Spain): retrospective application of the adjusted clinical groups case‐mix system in primary health care
Authors: Sicras‐Mainar Antoni , Velasco‐Velasco Soledad , Navarro‐Artieda Ruth , Jodar Alba Aguado , Plana‐Ripoll Oleguer , Hermosilla‐Pérez Eduardo , Bolibar‐Ribas Bonaventura , Prados‐Torres Alejandra , Violan‐Fors Concepción 
Published: March 2012

AbstractObjective  The study aims to obtain the mean relative weights (MRWs) of the cost of care through the retrospective application of the adjusted clinical groups (ACGs) in several primary health care (PHC) centres in Catalonia (Spain) in routine clinical practice.Methods  This is a retrospective study based on computerized medical records. All patients attended by 13 PHC teams in 2008 were included. The principle measurements were: demographic variables (age and sex), dependent variables (number of diagnoses and total costs), and case‐mix or co‐morbidity variables (International Classification of Primary Care). The costs model for each patient was established by differentiating the fix costs from the variable costs. In the bivariate analysis, the Student's t, analysis of variance, chi‐squared, Pearson's linear correlation and Mann–Whitney–Wilcoxon tests were used. In order to compare the MRW of the present study with those of the United States (US), the concordance [intraclass correlation coefficient (ICC) and concordance correlation coefficient (CCC)] and the correlation (coefficient of determination: R2) were measured.Results  The total number of patients studied was 227 235, and the frequentation was 5.9 visits/habitant/year) and with a mean diagnoses number of 4.5 (3.2). The distribution of costs was €148.7 million, of which 29.1% were fixed costs. The mean total cost per patient/year was €654.2 (851.7), which was considered to be the reference MRW. Relationship between study‐MRW and US‐MRW: ICC was 0.40 [confidential interval (CI) 95%: 0.21–0.60] and the CCC was 0.42 (CI 95%: 0.35–0.49). The correlation between the US MRW and the MRW of the present study can be seen; the adjusted R2 value is 0.691. The explanatory power of the ACG classification was 36.9% for the total costs. The R2 of the total cost without considering outliers was 56.9%.Conclusions  The methodology has been shown appropriate for promoting the calculation of the MRW for each category of the classification. The results provide a possible practical application in PHC clinical management.
First trimester Down syndrome screening is less effective and the number of invasive procedures is increased in women younger than 35 years of age
Authors: Peuhkurinen Sini , Laitinen Paivi , Ryynanen Markku , Marttala Jaana 
Published: March 2012

AbstractObjectives  We evaluated the performance of first trimester screening for Down syndrome in women less than 35 years of age (study group) and in women aged 35 years or more (control group) in an unselected low‐risk population.Methods  The study group comprised a total of 63 945 women who participated in the first trimester combined screening in public health care in Finland during the study period of 1 May 2002 to 31 December 2008. Women at the age of 35 or more (n = 13 004) were controls. Prevalence of Down syndrome, detection rate, false positive rate and number of invasive procedures needed to detect a single case of Down syndrome were analyzed in both groups.Results  The overall prevalence of Down syndrome (n = 73) in the study group was 1:876. The number of detected cases was 54. The detection rate was 74.0% with a false positive rate of 2.8%. Number of invasive procedures needed to detect a single case of Down syndrome was 33. In the control group, the detection rate was 87.0% with a false positive rate of 11.9%. The number of invasive procedures needed to detect a single case of Down syndrome was 15. The differences in detection rate and false positive rate were significant, P < 0.012, P < 0.001, respectively.Conclusion  The overall detection rate given for the entire population is an overestimate for a woman younger than the age of 35, which should be taken into consideration when counselling women of that age.
Development and testing of hyperbaric atomic force microscopy (AFM) and fluorescence microscopy for biological applications
Authors: D’AGOSTINO D.P. , MCNALLY H.A. , DEAN J.B. 
Published: March 2012

SummaryA commercially available atomic force microscopy and fluorescence microscope were installed and tested inside a custom‐designed hyperbaric chamber to provide the capability to study the effects of hyperbaric gases on biological preparations, including cellular mechanism of oxidative stress. In this report, we list details of installing and testing atomic force microscopy and fluorescence microscopy inside a hyperbaric chamber. The pressure vessel was designed to accommodate a variety of imaging equipment and ensures full functionality at ambient and hyperbaric conditions (≤85 psi). Electrical, gas and fluid lines were installed to enable remote operation of instrumentation under hyperbaric conditions, and to maintain viable biological samples with gas‐equilibrated superfusate and/or drugs. Systems were installed for vibration isolation and temperature regulation to maintain atomic force microscopy performance during compression and decompression. Results of atomic force microscopy testing demonstrate sub‐nanometre resolution at hyperbaric pressure in dry scans and fluid scans, in both contact mode and tapping mode. Noise levels were less when measurements were taken under hyperbaric pressure with air, helium (He) and nitrogen (N2). Atomic force microscopy and fluorescence microscopy measurements were made on a variety of living cell cultures exposed to hyperbaric gases (He, N2, O2, air). In summary, atomic force microscopy and fluorescence microscopy were installed and tested for use at hyperbaric pressures and enables the study of cellular and molecular effects of hyperbaric gases and pressure per se in biological preparations.
Fire management and minesite rehabilitation in a frequently burnt tropical savanna
Authors: COOK GARRY DAVID 
Published: March 2012

AbstractThe interactions between vegetation dynamics, fuel dynamics and fire hazard in rehabilitation after bauxite mining at Gove, Northern Territory, Australia were investigated. It was found that a policy of fire exclusion had led to fuel loads of the oldest rehabilitation being three to four times greater than those of frequently burnt adjoining unmined landscapes. Consequently, the potential fire intensities are beyond those experienced elsewhere in the region. Where occasional fires have occurred in the rehabilitated areas, the proportion of tree death has varied, with the most severe cases having 43% to 70% mortality. In rehabilitated sites that have been burnt, the fuel loads are lower. These findings indicate that the fire hazard in the unburnt rehabilitation is extreme, but because not all sites had substantial tree death, there is potential to manage fuel loads with carefully planned fires. The paradigm of fire exclusion during the rehabilitation process is based on a long‐debunked forestry management paradigm which was applied to some Australian savanna landscapes and needs to be overturned to facilitate integration of the rehabilitation into the broader frequently burnt landscape.
Low local recurrence rates in young Asian patients with phyllodes tumours: less is more
Authors: Teo Jin Yao , Cheong Crystal Shuk‐Jin , Wong Chow Yin 
Published: March 2012

AbstractBackground:  Phyllodes tumours are increasingly being discovered incidentally in young patients after excision of a seemingly innocuous breast lump. The clinical course of this group of patients has not been well‐described, especially in the Asian population.Methods:  A retrospective review of 44 consecutive patients below 25 years of age undergoing surgery for phyllodes tumours at our institution from 1992 to 2010 was conducted. Clinico‐pathological data, local recurrence rates and margin involvement were recorded.Results:  The majority of the patients had benign lesions treated with simple enucleation, and there were no local recurrences documented after a mean and median length of follow‐up of 47.6 and 29.5 months, respectively.Conclusion:  We conclude that in young Asian patients who present with benign phyllodes tumours, simple excision, followed by close follow‐up is sufficient, regardless of surgical margin status.
Short‐term and working memory skills in primary school‐aged children with specific language impairment and children with pragmatic language impairment: phonological, linguistic and visuo‐spatial aspects
Authors: Freed Jenny , Lockton Elaine , Adams Catherine 
Published: March 2012

Abstract Background: Children with specific language impairment (CwSLI) are consistently reported to have short‐term memory (STM) and working memory (WM) difficulties.Aim: To compare STM and WM abilities in CwSLI with children with pragmatic language impairment (CwPLI).Methods & Procedures: Primary school‐aged CwSLI (n= 12) and CwPLI (n= 23) were assessed on measures of STM and WM.Outcomes & Results: CwPLI had significantly higher scores than CwSLI on STM tasks, and this difference could not be accounted for by differences in receptive language ability. There were no between‐group differences for WM tasks. The majority of CwSLI and a significant proportion of CwPLI scored in the impaired range on each of the memory measures. In contrast, some CwPLI scored within the normal range.Conclusions & Implications: CwPLI present with a different profile of STM but not WM ability to CwSLI. Clinical implications are discussed.