bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of electron backscatter diffraction to the study of phase transformations: present and possible future
Authors: GOURGUES‐LORENZON A.‐F. 
Published: February 2009

SummaryThis paper first underlines the main advantages, use and limitations of the electron backscatter diffraction technique from the viewpoint of phase transformations. To get a deeper understanding of physical mechanisms involved in phase transformations, several evolutions are now in progress to get an insight into both three‐dimensional and real‐time information. Two of them, in particular, improvement of data collection versus improvement of data processing are discussed in the second part of this paper.
Effect of annealing temperatures on the secondary re‐crystallization of extruded PM2000 steel bar
Authors: CHEN C.‐L. , TATLOCK G. J. , JONES A.R. 
Published: February 2009

SummaryThe ferritic oxide dispersion‐strengthened alloy PM2000 is an ideal candidate for high‐temperature applications as it contains uniform nano‐oxide dispersoids, which act as pinning points to obstruct dislocation and grain boundary motion and therefore impart excellent creep resistance. The development of the microstructure during re‐crystallization of oxide dispersion‐strengthened alloys has been discussed by a number of authors, but the precise mechanism of secondary re‐crystallization still remains uncertain. Hence, this work is aimed at investigating the re‐crystallization behaviour of extruded PM2000 bar for different annealing temperatures, using electron backscatter diffraction, in particular, to determine grain orientations, grain boundary misorientation angles, etc. The results show that the as‐extruded bar microstructure comprises both low‐angle grain boundaries pinned by oxide particles and high‐angle boundaries that will have inherent boundary mobility to allow boundary migration. In addition, dynamical re‐crystallization was found in the outer region of the non–heat‐treated PM2000 bar, which suggested that deformation heterogeneities can be introduced during thermo‐mechanical processing that enhance the nucleation of re‐crystallization. Subsequent heat treatments promote and stimulate secondary re‐crystallization, giving rise to large grains with few sub‐grain boundaries.
Characterization of cast Al86Mn3Be11 alloy
Authors: BONČINA T. , MARKOLI B. , ZUPANIČ F. 
Published: February 2009

SummaryAn Al86Mn3Be11 alloy cast into copper mould was subjected to metallographic investigation. The as‐cast microstructure consisted of a quasicrystalline icosahedral phase (i‐phase), Be4AlMn phase and, occasionally, a hexagonal phase. Al‐rich solid solution represented the dominant phase. The chemical compositions of phases were determined using AES. The composition of the Be4AlMn slightly deviated from the stoichiometric composition, whereas the composition of the i‐phase was approximately Al52Mn18Be30, containing an appreciable amount of Be. The average composition of the hexagonal phase was Al66Mn21Be13. Deep etching and particle extraction provided a deep insight into the three‐dimensional morphology of the i‐phase and the hexagonal phase, whereas Be4AlMn was slightly attacked by the etchant. The i‐phase was present predominantly in the form of dendrites and a rodlike eutectic phase. The hexagonal phase was primarily in the form of hexagonal platelets, whereas Be4AlMn was rather irregular in shape. The morphology of the i‐phase can be explained by predominant growth in 3‐fold directions and the lowest energy of the 5‐fold planes, leading to the faceting and adopting a pentagonal dodecahedron shape. The brightnesses of phases in the backscattered electron images were rationalized by determining their backscattering coefficients. TEM investigation showed considerable phason strain in the i‐phase, and the polycrystalline nature of the Be4AlMn phase.
Estimating contrast transfer function and associated parameters by constrained non‐linear optimization
Authors: YANG C. , JIANG W. , CHEN D.‐H. , ADIGA U. , NG E.G. , CHIU W. 
Published: February 2009

SummaryThe three‐dimensional reconstruction of macromolecules from two‐dimensional single‐particle electron images requires determination and correction of the contrast transfer function (CTF) and envelope function. A computational algorithm based on constrained non‐linear optimization is developed to estimate the essential parameters in the CTF and envelope function model simultaneously and automatically. The application of this estimation method is demonstrated with focal series images of amorphous carbon film as well as images of ice‐embedded icosahedral virus particles suspended across holes.
Combined EBSD/EDS tomography in a dual‐beam FIB/FEG–SEM
Authors: WEST G.D. , THOMSON R.C. 
Published: February 2009

SummaryAn automated method for collecting combined three‐dimensional (3D) electron backscatter diffraction (EBSD)/energy dispersive spectroscopy (EDS) data sets on a dual‐beam focused ion beam (FIB)/field emission gun scanning electron microscope (FEG–SEM) microscope is described. The method uses simple scripting files on the dual beam to move between the EBSD collection and the FIB slicing positions, which are linked to a commercial EBSD data collection programme. The EDS data are collected simultaneously with the EBSD patterns analogous to combined two‐dimensional (2D) EBSD/EDS. The technique has been successfully applied to study both the interdiffusion zone between a coating and a substrate and a complex multi‐phase coating on a nickel‐based superalloy sample. This analysis is shown to enable the complex grain shapes, location of precipitates and phase interconnectivity within these samples to be determined without the ambiguities associated with 2D stereographic analysis.
Advantages of indium–tin oxide‐coated glass slides in correlative scanning electron microscopy applications of uncoated cultured cells
Authors: PLUK H. , STOKES D.J. , LICH B. , WIERINGA B. , FRANSEN J. 
Published: February 2009

SummaryA method of direct visualization by correlative scanning electron microscopy (SEM) and fluorescence light microscopy of cell structures of tissue cultured cells grown on conductive glass slides is described. We show that by growing cells on indium–tin oxide (ITO)‐coated glass slides, secondary electron (SE) and backscatter electron (BSE) images of uncoated cells can be obtained in high‐vacuum SEM without charging artefacts. Interestingly, we observed that BSE imaging is influenced by both accelerating voltage and ITO coating thickness. By combining SE and BSE imaging with fluorescence light microscopy imaging, we were able to reveal detailed features of actin cytoskeletal and mitochondrial structures in mouse embryonic fibroblasts. We propose that the application of ITO glass as a substrate for cell culture can easily be extended and offers new opportunities for correlative light and electron microscopy studies of adherently growing cells.
Texture heterogeneities in αp/αs titanium forging analysed by EBSD‐Relation to fatigue crack propagation
Authors: UTA E. , GEY N. , BOCHER P. , HUMBERT M. , GILGERT J. 
Published: February 2009

SummaryThe microstructure and the local texture of a large IMI 834 forging were characterized using the Electron Back Scattered Diffraction (EBSD) technique. Crystallographic domains called macrozones and formed by a majority of primary αp grains with their axes in nearly the same direction were found. They had a band‐like structure, parallel to the axial direction of the forging. The influence of these macrozones on the cold dwell‐fatigue properties was studied. Several samples were tested under cold dwell‐fatigue conditions. The crack initiation and the short‐distance propagation region optically matched a bright region that contained numerous quasi‐cleavage facets. The analysis of the EBSD measurements showed that this bright region was enclosed within a sharp textured region with axes at less than 30° from the loading axis. The crystallographic features of the crack nucleation site and the crack propagation path were also analysed.
Host‐associated speciation in the coral barnacleWanella milleporae(Cirripedia: Pyrgomatidae) inhabiting theMilleporacoral
Authors: TSANG LING MING , CHAN BENNY KWOK KAN , SHIH FU‐LONG , CHU KA HOU , ALLEN CHEN CHAOLUN 
Published: February 2009

AbstractSpeciation by host shift is a common phenomenon observed in many symbiotic animals. The symbiont–host interaction is highly dynamic, but it is poorly documented in the marine realm. In the present study, we examined the genetic and morphological differentiation of the coral barnacleWanella milleporae(obligate to fire corals) collected from four differentMilleporahost species in Taiwan to investigate the host specificity of this barnacle. Phylogenetic analysis of mitochondrial COI gene for 241 individuals ofWanellarevealed five distinct clades, whose sequence divergences are comparable to values between other cogeneric barnacle species. The five clades also differ in shell and opercular plate morphology and colour. Genetic and morphological differentiations together strongly suggest the presence of cryptic species. Although the five clades do not display species‐level host specificity, they showed a significant difference in preference on host growth form. Clades 1 and 2 were predominantly found on encrustingMillepora exaesaandMillepora platyphylla, while clades 3, 4 and 5 live exclusively on branching‐form fire coralsMillepora dichotomaandMillepora tenella. Phylogeny inferred from the combined mitochondrial COI, 16S and 12S (2182 bp) analysis suggests the division of the five clades into two major lineages congruent with the morphology of the host coral. Multiple independent invasions to the same form of host and subsequent speciation are evident in the Red Sea and Taiwan. Our results indicate that ecological/sympatric speciation could occur in marine symbiotic invertebrates through host shift and specialization. It appears that, as in their terrestrial counterparts, host–symbiont radiations in the marine realm are more prevalent than we expected and thus warrant further investigation.
Pedigrees and microsatellites among endangered ungulates: what do they tell us?
Authors: RUIZ‐LÓPEZ MARÍA JOSÉ , ROLDÁN EDUARDO R. S. , ESPESO GERARDO , GOMENDIO MONTSERRAT 
Published: February 2009

AbstractRelationships between pedigree coefficients of inbreeding and molecular metrics are generally weak, suggesting that measures of heterozygosity estimated using microsatellites may be poor surrogates of genome‐wide inbreeding. We compare three endangered species of gazelles (Gazella) with different degrees of threat in their natural habitats, for which captive breeding programmes exist. For G. dorcas, the species with the largest founding population, the highest and most recent number of founding events, the correlation between pedigree coefficient of inbreeding and molecular metrics was higher than for outbred populations of mammals, probably because it has both higher mean f and variance. For the two species with smaller founding populations, conventional assumptions about founders, i.e. outbred and unrelated, are unrealistic. When realistic assumptions about the founders were made, clear relationships between pedigree coefficients of inbreeding and molecular metrics were revealed for G. cuvieri. This population had a small founding population, but it did experience admixture years later; thus, the relationship between inbreeding and molecular metrics in G. cuvieri is very similar to the expected values but lower than in G. dorcas. In contrast, no relationship was found for G. dama mhorr which had a much smaller founding population than had been previously assumed, which probably had high levels of inbreeding and low levels of genetic variability, and no admixture. In conclusion, the strength of the association between pedigree coefficient of inbreeding and molecular metrics among endangered species depends on the level of inbreeding and genetic variability present in the founding population, its size and its history.
Landscape genetics and least‐cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense)
Authors: WANG IAN J. , SAVAGE WESLEY K. , BRADLEY SHAFFER H. 
Published: February 2009

AbstractA major goal of landscape genetics is to understand how landscapes structure genetic variation in natural populations. However, landscape genetics still lacks a framework for quantifying the effects of landscape features, such as habitat type, on realized gene flow. Here, we present a methodology for identifying the costs of dispersal through different habitats for the California tiger salamander (Ambystoma californiense), an endangered species restricted to grassland/vernal pool habitat mosaics. We sampled larvae from all 16 breeding ponds in a geographically restricted area of vernal pool habitat at the Fort Ord Natural Reserve, Monterey County, California. We estimated between‐pond gene flow using 13 polymorphic microsatellite loci and constructed GIS data layers of habitat types in our study area. We then used least‐cost path analysis to determine the relative costs of movement through each habitat that best match rates of gene flow measured by our genetic data. We identified four measurable rates of gene flow between pairs of ponds, with between 10.5% and 19.9% of larvae having immigrant ancestry. Although A. californiense is typically associated with breeding ponds in grassland habitat, we found that dispersal through grassland is nearly twice as costly as dispersal through chaparral and that oak woodland is by far the most costly habitat to traverse. With the increasing availability of molecular resources and GIS data, we anticipate that these methods could be applied to a broad range of study systems, particularly those with cryptic life histories that make direct observation of movement challenging.
Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase
Authors: Zimmer Sarah L. , Schein Aleks , Zipor Gadi , Stern David B. , Schuster Gadi 
Published: February 2009

SummaryThe polyadenylation‐stimulated RNA degradation pathway takes place in plant and algal organelles, yet the identities of the enzymes that catalyze the addition of the tails remain to be clarified. In a search for the enzymes responsible for adding poly(A) tails in Chlamydomonas and Arabidopsis organelles, reverse genetic and biochemical approaches were employed. The involvement of candidate enzymes including members of the nucleotidyltransferase (Ntr) family and polynucleotide phosphorylase (PNPase) was examined. For several of the analyzed nuclear‐encoded proteins, mitochondrial localization was established and possible dual targeting to mitochondria and chloroplasts could be predicted. We found that certain members of the Ntr family, when expressed in bacteria, displayed poly(A) polymerase (PAP) activity and partially complemented an Escherichia coli strain lacking the endogenous PAP1 enzyme. Other Ntr proteins appeared to be specific for tRNA maturation. When the expression of PNPase was down‐regulated by RNAi in Chlamydomonas, very few poly(A) tails were detected in chloroplasts for the atpB transcript, suggesting that this enzyme may be solely responsible for chloroplast polyadenylation activity in this species. Depletion of PNPase did not affect the number or sequence of mitochondrial mRNA poly(A) tails, where unexpectedly we found, in addition to polyadenylation, poly(U)‐rich tails. Together, our results identify several Ntr‐PAPs and PNPase in organelle polyadenylation, and reveal novel poly(U)‐rich sequences in Chlamydomonas mitochondria.
Characterization of selenocysteine methyltransferases from Astragalus species with contrasting selenium accumulation capacity
Authors: Sors Thomas G. , Martin Catherine P. , Salt David E. 
Published: February 2009

SummaryA group of selenium (Se)‐hyperaccumulating species belonging to the genus Astragalus are known for their capacity to accumulate up to 0.6% of their foliar dry weight as Se, with most of this Se being in the form of Se‐methylselenocysteine (MeSeCys). Here, we report the isolation and molecular characterization of the gene that encodes a putative selenocysteine methyltransferase (SMT) enzyme from the non‐accumulator Astragalus drummondii and biochemically compare it with an authentic SMT enzyme from the Se‐hyperaccumulator Astragalus bisulcatus, a related species that lives within the same native habitat. The non‐accumulator enzyme (AdSMT) shows a high degree of homology with the accumulator enzyme (AbSMT) but lacks the selenocysteine methyltransferase activity in vitro, explaining why little or no detectable levels of MeSeCys accumulation are observed in the non‐accumulator plant. The insertion of mutations on the coding region of the non‐accumulator AdSMT enzyme to better resemble enzymes that originate from Se accumulator species results in increased selenocysteine methyltransferase activity, but these mutations were not sufficient to fully gain the activity observed in the AbSMT accumulator enzyme. We demonstrate that SMT is localized predominantly within the chloroplast in Astragalus, the principal site of Se assimilation in plants. By using a site‐directed mutagenesis approach, we show that an Ala to Thr amino acid mutation at the predicted active site of AbSMT results in a new enzymatic capacity to methylate homocysteine. The mutated AbSMT enzyme exhibited a sixfold higher capacity to methylate selenocysteine, thereby establishing the evolutionary relationship of SMT and homocysteine methyltransferase enzymes in plants.
Functional expression and characterization of Arabidopsis ABCB, AUX 1 and PIN auxin transporters in Schizosaccharomyces pombe
Authors: Yang Haibing , Murphy Angus S. 
Published: February 2009

SummaryHeterologous expression systems based on tobacco BY‐2 cells, Arabidopsis cell cultures, Xenopus oocytes, Saccharomyces cerevisiae, and human HeLa cells have been used to express and characterize PIN, ABCB (PGP), and AUX/LAX auxin transporters from Arabidopsis. However, no single system has been identified that can be used for effective comparative analyses of these proteins. We have developed an accessible Schizosaccharomyces pombe system for comparative studies of plant transport proteins. The system includes knockout mutants in all ABC and putative auxin transport genes and Gateway®‐compatible expression vectors for functional analysis and subcellular localization of recombinant proteins. We expressed Arabidopsis ABCB1 and ABCB19 in mam1pdr1 host lines under the inducible nmt41 promoter. ABCB19 showed a higher 3H‐IAA export activity than ABCB1. Arabidopsis PIN proteins were expressed in a mutant lacking the auxin effluxer like 1 (AEL1) gene. PIN1 showed higher activity than PIN2 with similar protein expression levels. Expression of AUX1 in a permease‐deficient vat3 mutant resulted in increased net auxin uptake activity. Finally, ABCB4 expressed in mam1pdr1 displayed a concentration‐dependent reversal of 3H‐IAA transport that is consistent with its observed activity in planta. Structural modelling suggests that ABCB4 has three substrate interaction sites rather than the two found in ABCB19, thus providing a rationale for the observed substrate activation. Taken together, these results suggest that the S. pombe system described here can be employed for comparative analyses and subsequent structural characterizations of plant transport proteins.
Colorectal cancer patients’ attitudes towards involvement in decision making
Authors: Beaver Kinta , Campbell Malcolm , Craven Olive , Jones David , Luker Karen A. , Susnerwala Shabbir S. 
Published: February 2009

AbstractObjectives  To design and administer an attitude rating scale, exploring colorectal cancer patients’ views of involvement in decision making. To examine the impact of socio‐demographic and/or treatment‐related factors on decision making. To conduct principal components analysis to determine if the scale could be simplified into a number of factors for future clinical utility.Methods  An attitude rating scale was constructed based on previous qualitative work and administered to colorectal cancer patients using a cross‐sectional survey approach.Results  375 questionnaires were returned (81.7% response). For patients it was important to be informed and involved in the decision‐making process. Information was not always used to make decisions as patients placed their trust in medical expertise. Women had more positive opinions on decision making and were more likely to want to make decisions. Written information was understood to a greater degree than verbal information. The scale could be simplified to a number of factors, indicating clinical utility.Conclusion  Few studies have explored the attitudes of colorectal cancer patients towards involvement in decision making. This study presents new insights into how patients view the concept of participation; important when considering current policy imperatives in the UK of involving service users in all aspects of care and treatment.
Choosing between CT colonography and colonoscopy in the diagnostic context: a qualitative study of influences on patient preferences
Authors: Von Wagner Christian , Halligan Steve , Atkin Wendy S. , Lilford Richard J. , Morton Dion , Wardle Jane 
Published: February 2009

AbstractObjective  To explore information needs and preferences on diagnostic bowel tests and elicit preferences for CT colonography (CTC) vs. colonoscopy (CC).Background  CTC is a new technology for large‐bowel imaging that has been widely assumed to be more acceptable than CC because it is non‐invasive.Design  Semi‐structured focus groups discussing information choices and procedure preferences.Setting and participants  Non‐patient sample of 26 asymptomatic volunteers (mean age 64 years).Main outcome measures  Information choices and CC‐vs.‐CTC preferences were recorded following stepwise presentation of different test attributes. Qualitative thematic analysis was used to examine transcripts of group discussions.Results  On the basis of minimal information about the two tests, a majority of participants preferred CTC to CC (65% vs. 11%), while 24% had no preference. However, once they had received information on all aspects, this was reversed, with 80% of participants preferring CC compared with 8% preferring CTC. Thematic analysis of the discussion showed that participants almost unanimously considered information about test sensitivity to be the most important feature, and perceived relatively modest differences in test sensitivity to be highly significant. Information about risks and side‐effects was considered to be the second most important aspect and attracted questions about risks of bowel perforation and health consequences following exposure to radiation.Conclusions  Patients place high value on quality rather than comfort for medical investigations. This has important implications for the development of educational materials supporting informed choice as well as future directions in refinement of CTC technology.