bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural characterization of an endoglucanase from Serpula lacrymans var. lacrymans S7.9
Authors: Kibedi Szabo Csaba Zoltan , Galicza Judit , Weyda Istvan , Andras Csaba Dezso
Published: November 2011

Lately cellulase enzymes from fungi and also bacteria, have received much attention due to their application in bioethanol production from lignocellulosic feedstock. Dry rot fungus (Serpula lacrymans) is known to be the most damaging destroyer of indoor wood construction materials in temperate regions. Therefore the very recent sequencing of this fungus genome has opened new possibilities. We describe here the analysis of the primary, secondary and tertiary structure of a 255 amino acid sequence endoglucanase, from S. lacrymans var. lacrymans S7.9, having a molecular weight of 26746. We also provide the amino acids from the active site.
Improved Imputation of Common and Uncommon Single Nucleotide Polymorphisms (SNPs) with a New Reference Set
Authors: Albanes Demetrius , Teras Lauren , Tucker Margaret , Berndt Sonja , Haiman Christopher , Chanock Stephen , Chung Charles , Henderson Brian , Diver W. Ryan , Stram Daniel , Deng Xiang , Wang Zhaoming , Hsing Ann , Jacobs Kevin , Virtamo Jarmo , Yeager Meredith , Eberle Michael , Hutchinson Amy , Stone Jennifer , Purdue Mark , Sampson Joshua , Gabstur Susan , Taylor Phil , Chatterjee Nilanjan
Published: November 2011

Statistical imputation of genotype data is an important technique for analysis of genome-wide association studies (GWAS). We have built a reference dataset to improve imputation accuracy for studies of individuals of primarily European descent using genotype data from the Hap1, Omni1, and Omni2.5 human SNP arrays (Illumina). Our dataset contains 2.5-3.1 million variants for 930 European, 157 Asian, and 162 African/African-American individuals. Imputation accuracy of European data from Hap660 or OmniExpress array content, measured by the proportion of variants imputed with R^2^>0.8, improved by 34%, 23% and 12% for variants with MAF of 3%, 5% and 10%, respectively, compared to imputation using publicly available data from 1,000 Genomes and International HapMap projects. The improved accuracy with the use of the new dataset could increase the power for GWAS by as much as 8% relative to genotyping all variants. This reference dataset is available to the scientific community through the NCBI dbGaP portal. Future versions will include additional genotype data as well as non-European populations.
Fundamental Aspects of Salts and Co-crystals
Authors: Bond Andrew D.
Published: November 2011

The chapter provides background information about fundamental aspects of salts and co-crystals and describes some of the approaches that have been taken to prepare strategic co-crystal or salts. Definitions of co-crystals and salts are considered and a flexible approach is encouraged, without application of arbitrary borderlines. The supramolecular synthon is presented as the basis for rational co-crystal or salt design strategies and the essential supporting role of the Cambridge Structural Database is noted. It is stressed that the synthon approach is probabilistic in its nature and therefore that co-crystal design strategies must also be probabilistic. However, it is possible to exert a significant degree of control over specific chemical systems by considering a synthon hierarchy. Examples of successful targeted realisation of co-crystals and salts are given, including binary and ternary examples. Finally, the expectation of obtaining a salt rather than a co-crystal is discussed in the specific context of proton transfer from an acid to a base and it is shown that the ionisation states of the molecules in a multi-component crystal can be difficult to predict.
Polymorph Prediction of Small Organic Molecules, Co-crystals and Salts
Authors: Leusen Frank J. J. , Kendrick John
Published: November 2011

Crystal structure prediction is regarded by some as the holy grail of crystal engineering because reliable and accurate prediction of the polymorphs that a compound can crystallise in would allow the design of organic materials with specific properties from first principles. This contribution provides an overview of the current status of crystal structure prediction of small organic molecules in general and focuses on the specific issues encountered in the prediction of co-crystal and salt structures. Both the global optimisation problem of searching for all possible crystal structures of a compound and the problem of calculating accurate lattice energies in order to rank potential crystal structures according to stability are discussed. A number of illustrative examples are presented, including an overview of the Cambridge Crystallographic Data Centre's blind tests in crystal structure prediction, as well as some examples of co-crystals, solvates and salts.
Shape and Polarity in Co-crystal Formation: Database Analysis and Experimental Validation
Authors: Fábián L. , Friščić T.
Published: November 2011

Supramolecular synthons provide the most important and successful approach to the rational design of co-crystals. Yet, the relatively low success rate of co-crystal screening experiments demonstrates that the availability of appropriate synthons is only one of many factors that influence co-crystallisation. The aim of our work was to identify other factors and to use them in developing design strategies that are complementary to supramolecular synthons.

Co-crystal structures were extracted from the Cambridge Structural Database and molecular descriptors were calculated for each molecule in this data set. Statistical analysis of the resulting database revealed that co-crystals are usually formed by molecules that have similar shapes and polarities. Observed distributions of the corresponding descriptors were used to derive criteria for likely co-crystal formation. Screening experiments on more than 200 compound pairs were analysed to test the usefulness of these criteria. The results show that performing only the experiments that match the criteria can significantly increase the success rate of screening.

The relative influence of supramolecular synthons and shape similarity was investigated by screening experiments in which both the shapes of the molecules and the strength of the supramolecular heterosynthons were varied systematically. Co-crystals were obtained reliably if both strong synthons and similar molecular shapes favoured their formation. Molecules of dissimilar shapes co-crystallised only when extremely strong synthons could be formed. Mismatch between expected co-crystallisation behaviour and experimental results for four steroids led to the recognition of a new specific interaction between the steroid α-face and the π-electron density of aromatic co-formers.
Solid Forms and Pharmacokinetics
Authors: Biswas N.
Published: November 2011

In the world of pharmaceutics, a very close relationship exists between ADMET, pharmacokinetic parameters and the physicochemical properties of a drug. They are decisive factors dictating the therapeutic performance of the drug in vivo. Physicochemical parameters (such as dissolution properties and solubility) act as “chauffeurs” guiding the drug through the different barriers in the body which significantly affect its absorption. During early development, these parameters are optimized to some extent by structural modifications in the molecule, but in most cases this approach is limited, as they result in the loss of efficacy.

Solid state modifications either by electrostatic interactions (such as in salts) or non-covalent interactions (such as in co-crystals) have evolved as an excellent alternative that can efficiently alter the dissolution rate and affect its pharmacokinetics. They can be custom designed, not only to alter the mode of administration, but can also optimize the release-action profiles of a drug for more patient-friendly dosages. In addition to the bountiful merits, solid state alterations can also prove to be life threatening. An altered form in a specific lot/generic batch can lead to varied concentrations of the drug in plasma which can potentially cross the therapeutic window leading to no efficacy or toxicity. Again, unanticipated co-crystallization amongst the formulation components during manufacture or storage can lead the formation of a form with unacceptable physicochemical and pharmacokinetic properties that is detrimental to the health of the patient. Therefore, detailed solid state screening during drug development is seminal in every discovery program.
Co-crystal Solubility and Thermodynamic Stability
Authors: Roy L. , Lipert M.P. , Rodríguez-Hornedo N.
Published: November 2011

Co-crystals play a significant role in solving bioavailability problems because they have the ability to fine tune solubility and delivery of drugs. Understanding the link between the structure/composition of co-crystals and their solution properties is important, so that co-crystal and formulation conditions can be selected on a rational basis. This chapter presents the thermodynamic factors that influence co-crystal solubility, the parameters that determine co-crystal stability, and experimental methods that overcome the difficulties of co-crystal conversion to less soluble phases.
Concluding Remarks using Piracetam as a Learning Model
Authors: Wouters Johan , Tilborg Anaelle , Quéré Luc
Published: November 2011

Selected structures of co-crystals involving Piracetam illustrate the possibility of formation of co-crystals of an API using both hydrogen bonds and/or metal coordination. Distinct patterns of interactions (supramolecular synthons) within the crystal packing are discussed. Synthesis of an original co-crystal between Brivaracetam, a structurally related analog of Piracetam, and MgCl2 paves the way for the development of a pharmaceutically acceptable ionic co-crystal drug candidate.

On this basis, and with the many examples that have been provided throughout the different chapters of the book, it is suggested that most (if not all) APIs contain in their structure the functional group(s) that could lead to co-crystallisation, and hence to the expansion of their pharmaceutical space. This exciting perspective fully justifies both academic and industrial interest in these systems.
New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory
Authors: Roszak Aleksander W. , Moulisová Vladimíra , Reksodipuro Adhie D. P. , Gardiner Alastair T. , Fujii Ritsuko , Hashimoto Hideki , Isaacs Neil W. , Cogdell Richard J.
Published: November 2011

Newly determined crystal structures of the photosynthetic RC (reaction centre) from two substrains of the non-sulfur purple bacterium Blastochloris viridis strain DSM 133, together with analysis of their gene sequences, has revealed intraspecies evolutionary changes over a period of 14 years. Over 100 point mutations were identified between these two substrains in the four genes encoding the protein subunits of the RC, of which approximately one-fifth resulted in a total of 16 amino acid changes. The most interesting difference was in the M subunit where the change from a leucine residue to glycine in the carotenoid-binding pocket allowed NS5 (1,2-dihydroneurosporene) to adopt a more sterically favoured conformation, similar to the carotenoid conformation found in other related RCs. The results of the present study, together with a high rate of mutations in laboratory bacterial cultures described recently, suggest that bacteria evolve faster than has been generally recognized. The possibility that amino acid changes occur within protein sequences, without exhibiting any immediately observable phenotype, should be taken into account in studies that involve long-term continuous growth of pure bacterial cultures. The Blc. viridis RC is often studied with sophisticated biophysical techniques and changes such as those described here may well affect their outcome. In other words, there is a danger that laboratory-to-laboratory variation could well be due to different groups not realising that they are actually working with slightly different proteins. A way around this problem is suggested.
Blogging Solo: New Media, ‘Old’ Politics
Authors: Taylor Anthea
Published: November 2011

This article focuses on the blogosphere as an oppositional field where the meanings around contemporary Western women's singlehood are contested, negotiated and rewritten. In contrast to dominant narratives in which single women are pathologised, in the blogs by, for, and about single women analysed here, writers aim to refigure women's singleness as well as providing resources, support and a textual community where others can intervene and contribute to the re-valuation of single women. These blogs also function as alternative forms of knowledge, seeking to (re)legitimise women's singleness and to trouble their aberrance and social liminality. Rather than only considering the form in isolation from its content, this article analyses the discourses deployed by bloggers and within blogs and how women bloggers publicly perform their very singleness as part of a personal and political strategy of re-signification. In this way, while cautious not to overestimate the democratic potentialities of the so-called blogosphere, it underscores the important cultural – and indeed political – work being undertaken by single women therein. Moreover, by demonstrating how these blogs use discursive tactics commonly associated with feminism's second-wave – women's consciousness-raising; identity politics; deploying and reiterating the famous feminist dictum: ‘the personal is political’; naming discrimination; and empathy and community-building – it argues that they are using so-called ‘new’ media for what is now problematically believed to be ‘old’ (feminist) politics.
Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics
Authors: Sobhy M. A. , Elshenawy M. M. , Takahashi M. , Whitman B. H. , Walter N. G. , Hamdan S. M.
Published: November 2011

Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy transfer (FRET) and a technically challenging four-color FRET experiments on doubly labeled duplex DNA and quadruple-labeled Holliday junction, respectively.
Production of vacancy-oxygen defect in electron irradiated silicon in the presence of self-interstitial-trapping impurities
Authors: Voronkov V. V. , Falster R. , Londos C. A. , Sgourou E. N. , Andrianakis A. , Ohyama H.
Published: November 2011

The enhancement by carbon of vacancy-oxygen (VO) defect formation in electron irradiated silicon was investigated using many samples of various carbon contents. The effect of carbon is well described by a simple analytical model of competing trapping of self-interstitials by VO and by carbon (and by emerging carbon-related defects like CiOi and ICiOi). The trapping ratio by Cs and by VO was determined to be about 0.9, and the optical calibration coefficients for CiOi and ICiOi were deduced. In crystals containing a high concentration of Ge, germanium also acts as a self-interstitial trapping impurity and, thus, enhances VO production. The trapping efficiency of Ge is 1000 times less than that of carbon.
Influence of magnetic field on the electric breakdown in penning ion source
Authors: Mahjour-Shafiei M. , Noori H. , Ranjbar A. H.
Published: November 2011

A cold-cathode penning-type ion source has been developed in our laboratory to study the electric breakdown in this type of sources. The breakdown voltage was measured as a function of axial magnetic field, in the range of 440–600 G, and anode length, in steps of 14, 20, and 24 mm. The measurement was performed with stainless steel cathodes in argon gas at pressure of 4 × 10−2 mbar. Furthermore, a model was developed to explain the breakdown voltage data. In the construction of the model, the first Townsend coefficient was not directly used to avoid difficulties originating from the non-uniformity of the electric field. The empirical parameters of the model were obtained using the experimental data. The equation γ = c × (Ez/N)n, expressing the effective secondary emission coefficient in terms of reduced electric field, which was needed in the modeling process, was inspired from previous works. The parameters c and n were then calculated from the empirical parameters of the model. The n parameter turned out to be 0.59, which differs from the value reported by other authors merely by 1.6%. Three values, 0.010, 0.013, and 0.017 corresponding to the three anodes were obtained for the c parameter. These numbers are in good agreement with 0.01, which has been reported in the previous works. It was also found that the value of n has a decisive impact on the breakdown voltage curve in the high breakdown voltage region.
Unexpected short- and medium-range atomic structure of sputtered amorphous silicon upon thermal annealing
Authors: Haberl B. , Bogle S. N. , Li T. , McKerracher I. , Ruffell S. , Munroe P. , Williams J. S. , Abelson J. R. , Bradby J. E.
Published: November 2011

We investigate the structure of magnetron-sputtered (MS) amorphous silicon (a-Si) prepared under standard deposition conditions and compare this to pure ion-implanted (II) a-Si. The structure of both films is characterized in their as-prepared and thermally annealed states. Significant differences are observed in short- and medium-range order following thermal annealing. Whereas II a-Si undergoes structural relaxation toward a continuous random network, MS a-Si exhibits little change. Cross-sectional transmission electron microscopy reveals the presence of nanopores in the MS film consistent with reduced mass-density. Therefore, the short- and medium-range order of annealed, MS a-Si is tentatively attributed to these pores.
Electrical characteristics and operating mechanisms of nonvolatile memory devices fabricated utilizing core-shell CuInS2-ZnS quantum dots embedded in a poly(methyl methacrylate) layer
Authors: Wan Han Kyu , Ho Lee Min , Whan Kim Tae , Yeol Yun Dong , Woo Kim Sung , Wook Kim Sang
Published: November 2011

Nonvolatile memory devices were fabricated with core-shell CuInS2-ZnS quantum dots (QDs) embedded in poly(methyl methacrylate) (PMMA). Capacitance-voltage (C-V) measurements at 300 K on the Al/CuInS2-ZnS QDs embedded in PMMA layer/p-Si device showed capacitance hysteresis behaviors with a flatband voltage shift. The memory window of the device increased with increasing applied sweep voltage and saturated at high electric fields due to the current leakage. Capacitance-time measurements showed that the retention time was larger than 1 × 105 s that was more than 10 years. The operating mechanisms for the devices are described on the basis of the C-V curves.
Fast-response signal upconversion by the use of a “time-space conversion” method
Authors: Saito Mitsunori , Nakamura Shingo , Kita Teppei
Published: November 2011

Lanthanide-doped phosphors achieve signal wavelength conversion between visible and infrared communication systems. A long lifetime of their excited states is advantageous for inducing two-photon absorption that realizes upconversion. The long lifetime, however, restricts the conversion rate to ∼500 bit/s because of the afterglow. This contradiction was solved by embedding a phosphor (YbEr:Gd2O2S) in a rotating disk. When an infrared (940 nm) pulse train of 1 Mbit/s (time domain) was focused on the disk, a fluorescent dot array (space domain) was created and moved with the disk rotation. Consequently, a visible (∼550 nm) pulse train was detected on the dot trajectory.
Adaptation behaviour of local and rangeland cattle relocated to a temperate agricultural pasture
Authors: Thomas D. T. , Wilmot M. G. , Kelly R. W. , Revell D. K.
Published: November 2011

Relocating cattle from rangeland properties to agricultural pastures in southern Western Australia allows producers to improve year-round continuity of feed supply in their beef cattle businesses, and can reduce substantially the time taken to grow animals to meet market specifications. In this study the behaviour and growth of two groups of young cattle that were sourced from different locations was evaluated after they were transferred to a new extensive grazing system. In Experiment 1, 122 Limousin-cross heifers that were raised in the agricultural region of Western Australia (AR cattle) were transferred to the experimental site from a neighbouring property (~10 km away). In Experiment 2, 95 Brahman-cross heifers that were raised in the rangelands of Western Australia (RR cattle) were transferred to the experimental site. Animal growth and behaviour were analysed across time and differences in the time-course of behavioural changes between the groups were compared. Rate of liveweight gain in the AR cattle remained consistent (~1.2 kg/day) during the experiment. There was an increase in horizontal (16%; P < 0.001) and vertical (12%; P = 0.002) head movement in AR cattle over the first several weeks after relocation, indicative of increased grazing activity, but there was little change in other behaviours over the duration of the experiment. In contrast, the RR cattle had reduced growth during the first 4 weeks after relocation (P < 0.001). From weeks 2–4 weight gain in RR cattle was 0.31 kg/day, approximately one-quarter of their average daily gain attained 4 weeks later. During the first 6 weeks, RR cattle showed behavioural changes indicative of adaptation, including a 61% increase in horizontal head movements, suggesting more grazing activity. The paddock area utilised daily by RR cattle was 32% higher in week 6 compared with week 1, and during daylight hours (0600–1900 hours) they began to travel more (23%) and spent more time active (16%). We conclude that rangeland-raised Bos indicus heifers take from 4 to 6 weeks to adapt from their previous large paddocks/natural plant environment to a new temperate agricultural environment. Our results suggest that the cause of lost productivity in rangeland cattle when they are relocated to a temperate pasture is at least in part due to initial lower grazing activity as they become familiar with the new environment.
Crop improvement in the era of climate change: an integrated, multi-disciplinary approach for common bean (Phaseolus vulgaris)
Authors: McClean Phillip E. , Burridge Jimmy , Beebe Stephen , Rao Idupulapati M. , Porch Timothy G.
Published: November 2011

Climate change and global population increase are two converging forces that will jointly challenge researchers to design programs that ensure crop production systems meet the world’s food demand. Climate change will potentially reduce productivity while a global population increase will require more food. If productivity is not improved for future climatic conditions, food insecurity may foster major economic and political uncertainty. Given the importance of grain legumes in general – common bean (Phaseolus vulgaris L.) in particular – a workshop entitled ‘Improving Tolerance of Common Bean to Abiotic Stresses’ was held with the goal of developing an interdisciplinary research agenda designed to take advantage of modern genotyping and breeding approaches that are coupled with large scale phenotyping efforts to improve common bean. Features of the program included a multinational phenotyping effort to evaluate the major common bean core germplasm collections and appropriate genetic populations. The phenotyping effort will emphasise the response of root and shoot traits to individual and combined stress conditions. These populations would also be genotyped using newly emerging high density single nucleotide polymorphism (SNP) marker arrays or next generation sequencing technology. Association analysis of the core collections aims to identify key loci associated with the response to the stress conditions. Companion bi-parental quantitative trait loci (QTL) experiments will act as confirmation experiments for the association analysis. The upcoming release of the genome sequence of common bean will be leveraged by utilising population genomic approaches to discover genomic regions that differentiate stress-responsive and non-responsive genotypes. The genome sequence will also enable global gene expression studies that will highlight specific molecular-based stress responses. This collective knowledge will inform the selection of parental lines to improve the efficiency of common bean improvement programs.
Physiological consequences of parasite infection in the burrowing mud shrimp, Upogebia pugettensis, a widespread ecosystem engineer
Authors: Repetto Michele , Griffen Blaine D.
Published: November 2011

The burrowing mud shrimp, Upogebia pugettensis, is an important ecosystem engineer throughout bays and estuaries along the Pacific coast of North America. Populations of U. pugettensis have recently declined throughout its range. A likely reason for this decline is the arrival of an invasive bopyrid isopod parasite, Orthione griffenis, which has colonised the system and increased in prevalence. We tested the following three hypotheses regarding this host–parasite system: (1) parasite infection is correlated with the volume of water processed by the host; (2) infection negatively affects host’s energetic state; and (3) infection causes feminisation in male hosts. We used several physiological and morphological measures to quantify the effects of this parasite infection on U. pugettensis. The parasite appears to have different physiological effects on male and female hosts. Our study provides mixed support for the previous theory that predicted the mechanistic interactions between this host and its new parasite. Recent examples from other systems have demonstrated that invasive parasites can have far-reaching influences when they infect ecosystem engineers. Given the negative effects of O. griffenis on U. pugettensis, this invasive parasite may have similarly large impacts on Pacific North-west estuaries throughout its invaded range.
Criteria for the translation and assessment of Qur’anic metaphor
Authors: El-Zeiny Iman
Published: November 2011

This paper discusses different approaches to the translation of Qur’anic metaphor, as one of the semantic problematic areas in translating the Qur’an, with a view to recommending principled criteria for translating Qur’anic metaphor. An attempt has been made to analyze, compare and assess six different approaches to the translation of Qur’anic metaphor and a blueprint is provided. The six selected translations are those by Sale (first published in1734), Ali (first published in 1937), Arberry (first published in 1955), Dawood (first published in 1956), Khatib (first published in 1986) and Khān–Hilālī (1996 edition). These translatons represent different orientations in translating the Muslim’s holy Book. Moreover, their translations are regularly reprinted.
Translating English modal expressions
Authors: Eades Domenyk
Published: November 2011

Modals are a source of difficulty in translation due to the subtle and complex nature of the meanings they convey, as well as the diversity of formal means by which modal meaning is coded from one language to another. The present study sheds light on difficulties associated with the translation of modal expressions by exploring errors in the translations of a group of native Arabic-speaking translator trainees, and identifies difficulties they experienced in transferring modal meaning from an English source text (ST) to an Arabic target text (TT). Shortcomings in the skills and training of the participants are discussed in the light of these findings, and suggestions are given as to how these may be remedied.
The results of the study show that while the students generally exhibit a sound knowledge of the dictionary meanings of the modal expressions in the ST, the precise sense of a given modal was often misconstrued and in many cases the modal meaning was missing entirely from the translations. These problems suggest that the participants tended to process the meanings of the ST at the word and sentence level while neglecting broader macro-level meanings conveyed in the text (e.g. cohesion, text type, relationship between author and audience).
The study reveals that in addition to the need for students to develop greater awareness of the nature of modality and its expression in both English and Arabic, greater emphasis is needed in the training of the students on the improvement of topdown text processing skills.
La subtitulación al servicio del aprendizaje de lenguas: el entorno LvS
Authors: Romero Lupe , Torres-Hostench Olga , Sokoli Stavroula
Published: November 2011

LvS (Learning via Subtitling) is a subtitling tool for language teaching. The main objective of LvS is to provide educational material for the active learning of foreign languages through subtitled video clips. Using this tool and the specific activities created by the teacher, students can add subtitles to video clips, thus participating in active writing and listening comprehension activities. LvS is a subtitle simulator for specific purposes.
This paper presents the possibilities offered by an environment such as LvS for learning languages through subtitling and the effectiveness of the use of news videos in L2 teaching. It describes the different stages of a LvS activity involving teaching Italian for translators.
Traduire la culture poétique du français en anglais
Authors: Owoeye Tuesday
Published: November 2011

That literary texts appear to be more difficult to translate than technical ones is no longer a subject of debate. This truth is fundamentally as a result of obvious challenges the literary translator has to face, since he is under the obligation to translate not only the literal meaning of his source text, but also its literary style. Even within the literary field of translation, if the translator of prose or drama rarely has an easy task, the translator of poetry is likely to meet harder obstacles in the course of his exercise. Poetry — especially when it has to do with traditional poems – appears, thus, the most dreaded terrain for the translator.
This article presents a comparative study of the poetic culture of French and English with the principal objective of demystifying the theoretical and practical problems associated with poetic translation. Supported by a critical analysis of an English translation of a French sonnet, the paper argues that the work of the poetic translator would be made more simplified if priority is given to the culture of the target language. The article thus recommends faithfulness to the poetic culture of the target language in order to produce a translation that will be acceptable to the reader of that language.
Discursive control and persuasion in early modern news discourse
Authors: Chaemsaithong Krisda
Published: November 2011

As an early form of news discourse, witchcraft pamphlets were one of the primary sites in which and through which ideologies about witchcraft and witches were articulated and disseminated in Early Modern England. Recognizing the pivotal position of language in constructing and perpetuating ideologies, this paper adopts a discourse analytic perspective (Van Dijk 2001, 2008; Halmari and Virtanen 2005) and uses insights from the study of stance and evaluation (Hunston and Thompson 2000; Hyland 2005, 2008) to examine the ways in which the prefatory materials of those pamphlets construct and (re)produce ideologies about witchcraft through linguistic and rhetorical choices, and the ways in which such a process may affect the audience’s perceptions, notions, and beliefs about witchcraft and witches. The findings reveal that the pamphleteers seek to manipulate linguistic choices and, in doing so, naturalize the ideologies about witchcraft which promote an image of Otherness that is inimical to the community. Persuasive strategies used include the negative depiction of the accused individuals as threats to society to prioritize the urgency of persecuting witches in the community; the pamphleteers’ construction of a positive self-image to establish itself as a source that can be trusted; and reader involvement to invite the reader to engage in the argumentation. Such strategies work in concert to reinforce the beliefs about witchcraft of those believers, and/or to persuade those who might still be in doubt.
Parametric dependences of momentum pinch and Prandtl number in JET
Authors: Tala T. , Salmi A. , Angioni C. , Casson F.J. , Corrigan G. , Ferreira J. , Giroud C. , Mantica P. , Naulin V. , Peeters A.G. , Solomon W.M. , Strintzi D. , Tsalas M. , Versloot T.W. , de Vries P.C. , Zastrow K.-D.
Published: November 2011

Several parametric scans have been performed to study momentum transport on JET. A neutral beam injection modulation technique has been applied to separate the diffusive and convective momentum transport terms. The magnitude of the inward momentum pinch depends strongly on the inverse density gradient length, with an experimental scaling for the pinch number being -Rv
pinch/χϕ = 1.2R/L
n + 1.4. There is no dependence of the pinch number on collisionality, whereas the pinch seems to depend weakly on q-profile, the pinch number decreasing with increasing q. The Prandtl number was not found to depend either on R/L
n, collisionality or on q. The gyro-kinetic simulations show qualitatively similar dependence of the pinch number on R/L
n, but the dependence is weaker in the simulations. Gyro-kinetic simulations do not find any clear parametric dependence in the Prandtl number, in agreement with experiments, but the experimental values are larger than the simulated ones, in particular in L-mode plasmas. The extrapolation of these results to ITER illustrates that at large enough R/L
n > 2 the pinch number becomes large enough (>3–4) to make the rotation profile peaked, provided that the edge rotation is non-zero. And this rotation peaking can be achieved with small or even with no core torque source. The absolute value of the core rotation is still very challenging to predict partly due to the lack of the present knowledge of the rotation at the plasma edge, partly due to insufficient understanding of 3D effects like braking and partly due to the uncertainties in the extrapolation of the present momentum transport results to a larger device.
Gene therapy for haemophilia: prospects and challenges to prevent or reverse inhibitor formation
Authors: Scott David W. , Lozier Jay N.
Published: November 2011

Monogenic hereditary diseases, such as haemophilia A and B, are ideal targets for gene therapeutic approaches. While these diseases can be treated with protein therapeutics, such as factor VIII (FVIII) or IX (FIX), the notion that permanent transfer of the genes encoding these factors can cure haemophilia is very attractive. An underlying problem with a gene therapy approach, however, is the patient’s immune response to the therapeutic protein (as well as to the transmission vector), leading to the formation of inhibitory antibodies. Even more daunting is reversing an existing immune response in patients with pre‐existing inhibitors. In this review, we will describe the laboratory and clinical progress, and the challenges met thus far, in achieving the goal of gene therapy efficacy, with a focus on the goal of tolerance induction.
Autoantibodies against apolipoprotein A‐1 and phosphorylcholine for diagnosis of non‐ST‐segment elevation myocardial infarction
Authors: Keller P.‐F. , Pagano S. , Roux‐Lombard P. , Sigaud P. , Rutschmann O. T. , Mach F. , Hochstrasser D. , Vuilleumier N.
Published: November 2011

Abstract.  Keller P‐F, Pagano S, Roux‐Lombard P, Sigaud P, Rutschmann OT, Mach F, Hochstrasser D Vuilleumier N (Geneva University Hospitals, Geneva). Autoantibodies against apolipoprotein A‐1 and phosphorylcholine for diagnosis of non‐ST‐segment elevation myocardial infarction. J Intern Med 2012; 271: 451–462.

Objectives.  To explore the diagnostic accuracies of anti‐apolipoproteinA‐1 (anti‐ApoA‐1) IgG and anti‐phosphorylcholine (anti‐PC) IgM alone, expressed as a ratio (anti‐ApoA‐1 IgG/anti‐PC IgM), and combined with the Thrombolysis In Myocardial Infarction (TIMI) score for non‐ST‐segment elevation myocardial infarction (NSTEMI) (NSTEMI‐TIMI score) to create a new diagnostic algorithm – the Clinical Autoantibody Ratio (CABR) score – for the diagnosis of NSTEMI and subsequent cardiac troponin I (cTnI) elevation in patients with acute chest pain (ACP).

Methods.  In this single‐centre prospective study, 138 patients presented at the emergency department with ACP without ST‐segment elevation myocardial infarction. Anti‐ApoA‐1 IgG and anti‐PC IgM were assessed by enzyme‐linked immunosorbent assay on admission. Post hoc determination of the CABR score cut‐off was performed by receiver operating characteristics analyses.

Results.  The adjudicated final diagnosis was NSTEMI in 17% (24/138) of patients. Both autoantibodies alone were found to be significant predictors of NSTEMI diagnosis, but the CABR score had the best diagnostic accuracy [area under the curve (AUC): 0.88; 95% confidence interval (CI): 0.82–0.95]. At the optimal cut‐off of 3.3, the CABR score negative predictive value (NPV) was 97% (95% CI: 90–99). Logistic regression analysis showed that a CABR score >3.3 increased the risk of subsequent NSTEMI diagnosis 19‐fold (odds ratio: 18.7; 95% CI: 5.2–67.3). For subsequent cTnI positivity, only anti‐ApoA‐1 IgG and CABR score displayed adequate predictive accuracies with AUCs of 0.80 (95% CI: 0.68–0.91) and 0.82 (95% CI: 0.70–0.94), respectively; the NPVs were 95% (95% CI: 90–98) and 99% (95% CI: 94–100), respectively.

Conclusion.  The CABR score, derived from adding the anti‐ApoA‐1 IgG/anti‐PC IgM ratio to the NSTEMI‐TIMI score, could be a useful measure to rule out NSTEMI in patients presenting with ACP at the emergency department without electrocardiographic changes.
Low‐grade systolic murmurs in healthy middle‐aged individuals: innocent or clinically significant? A 35‐year follow‐up study of 2014 Norwegian men
Authors: Bodegard J. , Skretteberg P. T. , Gjesdal K. , Pyörälä K. , Kjeldsen S. E. , Liestøl K. , Erikssen G. , Erikssen J.
Published: November 2011

Abstract.  Bodegard J, Skretteberg PT, Gjesdal K, Pyörälä K, Kjeldsen SE, Liestøl K, Erikssen G, Erikssen J (Oslo University Hospital, Oslo; University of Oslo, Oslo; University of Eastern Finland, Kuopio; University of Oslo, Oslo; Oslo University Hospital, Oslo). Low‐grade systolic murmurs in healthy middle‐aged individuals: innocent or clinically significant? A 35‐year follow‐up study of 2014 Norwegian men. J Intern Med 2012; 271: 581–588.

Objective.  To determine whether a low‐grade systolic murmur, found at heart auscultation, in middle‐aged healthy men influences the long‐term risk of aortic valve replacement (AVR) and death from cardiovascular disease (CVD).

Setting and subjects.  During 1972–1975, 2014 apparently healthy men aged 40–59 years underwent an examination programme including case history, clinical examination, blood tests and a symptom‐limited exercise ECG test. Heart auscultation was performed under standardized conditions, and murmurs were graded on a scale from I to VI. No men were found to have grade V/VI murmurs. Participants were followed for up to 35 years.

Results.  A total of 1541 men had no systolic murmur; 441 had low‐grade murmurs (grade I/II) and 32 had moderate‐grade murmurs (grade III/IV). Men with low‐grade murmurs had a 4.7‐fold [95% confidence interval (CI) 2.1–11.1] increased age‐adjusted risk of AVR, but no increase in risk of CVD death. Men with moderate‐grade murmurs had an 89.3‐fold (95% CI 39.2–211.2) age‐adjusted risk of AVR and a 1.5‐fold (95% CI 0.8–2.5) age‐adjusted increased risk of CVD death.

Conclusions.  Low‐grade systolic murmur was detected at heart auscultation in 21.9% of apparently healthy middle‐aged men. Men with low‐grade murmur had an increased risk of AVR, but no increase in risk of CVD death. Only 1.6% of men had moderate‐grade murmur; these men had a very high risk of AVR and a 1.5‐fold albeit non‐significant increase in risk of CVD death.
Enhanced Expression of Heme Oxygenase‐1 and Carbon Monoxide Excitatory Effects in Oxytocin and Vasopressin Neurones During Water Deprivation
Authors: Reis W. L. , Biancardi V. C. , Son S. , Antunes‐Rodrigues J. , Stern J. E.
Published: November 2011

A growing body of evidence indiates that carbon monoxide (CO) acts as a gas neurotransmitter within the central nervous system. Although CO has been shown to affect neurohypophyseal hormone release in response to osmotic stimuli, the precise sources, targets and mechanisms underlying the actions of CO within the magnocellular neurosecretory system remain largely unknown. In the present study, we combined immunohistochemistry and patch‐clamp electrophysiology to study the cellular distribution of the CO‐synthase enzyme heme oxygenase type 1 (HO‐1), as well as the actions of CO on oxytocin (OT) and vasopressin (VP) magnocellular neurosecretory cells (MNCs), in euhydrated (EU) and 48‐h water‐deprived rats (48WD). Our results show the expression of HO‐1 immunoreactivity both in OT and VP neurones, as well as in a small proportion of astrocytes, both in supraoptic (SON) and paraventricular (PVN) nuclei. HO‐1 expression, and its colocalisation with OT and VP neurones within the SON and PVN, was significantly enhanced in 48WD rats. Inhibition of HO activity with chromium mesoporphyrin IX chloride (CrMP; 20 μm) resulted in a slight membrane hyperpolarisation in SON neurones from EU rats, without significantly affecting their firing activity. In 48WD rats, on the other hand, CrMP resulted in a more robust membrane hyperpolarisation, significantly decreasing neuronal firing discharge. Taken together, our results indicate that magnocellular SON and PVN neurones express HO‐1, and that CO acts as an excitatory gas neurotransmitter in this system. Moreover, we found that the expression and actions of CO were enhanced in water‐deprived rats, suggesting that the state‐dependent up‐regulation of the HO‐1/CO signalling pathway contributes to enhance MNCs firing activity during an osmotic challenge.
Identification of three oligo‐/polysaccharide‐specific ligases in Yersinia enterocolitica
Authors: Pinta Elise , Li Zhilin , Batzilla Julia , Pajunen Maria , Kasanen Tiina , Rabsztyn Kamila , Rakin Alexander , Skurnik Mikael
Published: November 2011

In lipopolysaccharide (LPS) biosynthesis of Gram‐negative bacteria the lipid A‐core oligosaccharide (LA‐core) and O‐polysaccharide (O‐PS) biosynthesis pathways proceed separately and converge in periplasmic space where the waaL‐encoded ligase joins O‐PS onto LA‐core. Enterobacterial common antigen (ECA) biosynthesis follows that of O‐PS except that ECA is usually ligated to phosphatidylglycerol (PG) and only rarely to LA‐core. In Yersinia enterocolitica serotype O:3 LPS is composed of LA‐inner core (IC) onto which a homopolymeric O‐PS, a hexasaccharide called outer core (OC), and/or ECA are ligated. We found that an individual O:3 LPS molecule carries either OC or O‐PS substitution but not both. Related to this, we identified three genes in Y. enterocolitica O:3 that all expressed O‐PS ligase activity in the Escherichia coliΔwaaL mutant. The LPS phenotypes of Y. enterocolitica O:3 single, double and triple ligase mutants indicated that two of ligases, named as WaaLos and WaaLps, had a preferred substrate specificity for OC and O‐PS, respectively, although with some promiscuity between the ligases; the third ligase named as WaaLxs was not involved in LPS or ECA biosynthesis. In Y. enterocolitica O:8 the WaaLos homologue (Ye1727) ligated a single pentasaccharide O‐unit to LA‐IC suggesting that in both Y. enterocolitica O:3 and O:8 WaaLos is an oligosaccharide (OS)‐specific ligase. Finally, Yersinia pestis and Y. pseudotuberculosis carry only the waaLps gene, while either waaLos or waaLxs or both are additionally present in other Yersinia species. This is the first report on the presence of three different oligo‐/polysaccharide‐specific ligases in a single bacterium.
The crystal structure of AphB, a virulence gene activator from Vibrio cholerae, reveals residues that influence its response to oxygen and pH
Authors: Taylor Jennifer L. , De Silva Rukman S. , Kovacikova Gabriela , Lin Wei , Taylor Ronald K. , Skorupski Karen , Kull F. Jon
Published: November 2011

Expression of the two critical virulence factors of Vibrio cholerae, toxin‐coregulated pilus and cholera toxin, is initiated at the tcpPH promoter by the regulators AphA and AphB. AphA is a winged helix DNA‐binding protein that enhances the ability of AphB, a LysR‐type transcriptional regulator, to activate tcpPH expression. We present here the 2.2 Å X‐ray crystal structure of full‐length AphB. As reported for other LysR‐type proteins, AphB is a tetramer with two distinct subunit conformations. Unlike other family members, AphB must undergo a significant conformational change in order to bind to DNA. We have found five independent mutations in the putative ligand‐binding pocket region that allow AphB to constitutively activate tcpPH expression at the non‐permissive pH of 8.5 and in the presence of oxygen. These findings indicate that AphB is responsive to intracellular pH as well as to anaerobiosis and that residues in the ligand‐binding pocket of the protein influence its ability to respond to both of these signals. We have solved the structure of one of the constitutive mutants, and observe conformational changes that would allow DNA binding. Taken together, these results describe a pathway of conformational changes allowing communication between the ligand and DNA binding regions of AphB.