bluuebunny/crossref_metadata_2025 huggingface dataset:
“Yes, we can” — framing political events in terms of change
Authors: Sing Christine S.
Published: January 2011

This paper discusses the importance of change in American presidential discourse. Taking the inaugural address as its data, the study proposes a corpus-based analysis of the change frame in American presidential rhetoric. Change will be shown to relate to two levels of analysis using a combined approach of quantitative and qualitative methods. Firstly, its occurrence as a lexical concept in the corpus at hand will be examined. Secondly, the study of extended portions of discourse will demonstrate that meaning representation largely occurs on the basis of motion concepts, including the conceptual metaphor CHANGE IS MOTION as the central mapping of the event structure metaphor system (ESM). As will be shown, the knowledge in the change frame is suggestive of ideological discourse structures, which attach opposing value judgements to the presence vs. absence of change, respectively.
Causal framing for medical instrumentality
Authors: Sambre Paul , Wermuth Cornelia
Published: January 2011

This paper explores the linguistic patterns of instrumentality in the titles of English medical research papers, at the interface between conceptual and linguistic structure, and offers a contribution to the little studied interrelationships between static and dynamic conceptual relations in medical ontology and LSP terminology. It is demonstrated how causal cues constitute the conceptual background against which instrumentals are profiled in the causal chain of the medical model. Taking inspiration from Talmy, frame semantics and construction grammar, the linguistic patterns in which causal and instrumental frame elements are co-activated are transcribed as complex patterns with partial morphological, syntactic and lexical marking of the conceptual relations under study. The paper offers an exploratory typology of causal cues for instrumentals and describes how multiple instruments can appear in medical LSP. The findings are relevant for those interested in the nexus between ontology, constructional aspects of expert language and frame semantics
The re-imagined West in Chinese television
Authors: Cao Qing
Published: January 2011

This paper examines television portrayals of the West in contemporary China, focusing on an emerging non-victimistic media discourse on modern Western history. The analysis is contextualized within the wider sociopolitical dynamics of a rising nationalism and increased space for negotiation among the different groupings of Chinese elites. The paper falls into three parts. The first investigates the discursive features of a television documentary text that constructs a fresh, positive image of the West. The second discusses critiques of the series from the perspectives of a liberal, pro-market right and anti-capitalist new left. The third part extends the analysis to the social context of the mainstream pragmatic nationalism that has risen to prominence in recent decades. The paper concludes with a discussion on tensions within differing views of the West, and a critical assessment of the fresh, non-moralistic account of the Western road to modernity.
A neural network approach to compositionality and co-compositionality
Authors: Fortescue Michael
Published: January 2011

The issue of compositionality is applied to the modelling of the mental lexicon in terms of neural networks as described in Fortescue (2009). The approach is illustrated by applying it to the analysis of a semantically complex verb, conquer, illustrating the need to draw upon top-down (social, stylistic) as well as bottom-up (sensory) affordances in modelling such lexical items. Thereafter, a collocation that requires the mutual adjustment of the semantics of its individual components is analysed. Finally, adjectives of temperature crucially involving “limbic” affordances are treated. In all instances, the relevance of universal conceptual “primitives” to the processes of paraphrase and (co)composition will be seen to be highly restricted.
Automaticity and attentional control in spoken language processing
Authors: Shtyrov Yury
Published: January 2011

A long-standing debate in the science of language is whether our capacity to process language draws on attentional resources, or whether some stages or types of this processing may be automatic. I review a series of experiments in which this issue was addressed by modulating the level of attention on the auditory input while recording event-related brain activity elicited by spoken linguistic stimuli. The overall results of these studies show that the language function does possess a certain degree of automaticity, which seems to apply to different types of information. It can be explained, at least in part, by robustness of strongly connected linguistic memory circuits in the brain that can activate fully even when attentional resources are low. At the same time, this automaticity is limited to the very first stages of linguistic processing (<200 ms from the point in time when the relevant information is available in the auditory input). Later processing steps are, in turn, more affected by attention modulation. These later steps, which possibly reflect a more in-depth, secondary processing or re-analysis and repair of incoming speech, therefore appear dependant on the amount of resources allocated to language. Full processing of spoken language may thus not be possible without allocating attentional resources to it; this allocation in itself may be triggered by the early automatic stages in the first place.
The sensorimotor theory of cognition
Authors: Newton Natika
Published: January 2011

The sensorimotor theory of cognition holds that human cognition, along with that of other animals, is determined by sensorimotor structures rather than by uniquely human linguistic structures. The theory has been offered to explain the use of bodily terminology in nonphysical contexts, and to recognize the role of experienced embodiment in cognition. This paper defends a version of the theory which specifies that reasoning makes use of mental models constructed by means of action-planning mechanisms. Evidence is offered from cognitive psychology, the neurosciences, and work in primatology and evolutionary theory. Further scientific and philosophical advantages of the theory are discussed: the theory is more parsimonious than its rival, and it offers better accounts of intrinsic intentionality and consciousness. The paper concludes with observations concerning the role of language in thought.
Common-sense reasoning and everyday activities
Authors: Rogers Yvonne
Published: January 2011

This paper is concerned with the nature of common-sense reasoning and understanding in relation to practical behaviour. It examines the relationship between intuitive knowledge based on everyday experience and institutionalized theory and practice. An analysis of the types of knowledge that guide the selection of actions and understanding in the domain of cooking practice is presented. Verbal transcripts were elicited from participants, with varying levels of experience, of the cooking methods they followed and their underlying rationale. The results suggest that individuals utilize various high level knowledge primitives in combination with pragmatic utility principles in their reasoning. The findings are discussed in the light of recent theoretical approaches concerned with the relationship between knowledge and inference.
El efecto de la comunicación mediada por computadora en la adquisición de los registros del discurso académico en español
Authors: Clachar Arlene
Published: January 2011

Este artículo analiza la tendencia de transferir las características de los registros del discurso oral al discurso académico en español cuando se les enseña a los migrantes puertorriqueños de retorno (MPRR) las características de los registros del discurso académico a través de la Comunicación Mediada por Computadora (la CMC). Puesto que los sitios Web en la CMC tienen exigencias psicolingüísticas y lingüísticas inherentes a la exposición gráfica del discurso, el artículo examina cómo estas propiedades electrónicas e interactivas obligan a los estudiantes MPRR a: (a) considerar la coherencia textual al mismo tiempo que el impacto inmediato sobre los lectores; (b) variar constantemente de los registros típicos del discurso oral a los registros del discurso académico; (c) pensar en las estructuras de las cláusulas y en la forma que éstas dan al discurso; (d) crear cláusulas interactivas, claras y sucintas; y (e) emplear la estructura y el contenido conceptual del discurso académico en sus sitios Web personales.
The real distribution of the English “group genitive”
Authors: Denison David , Scott Alan K. , Börjars Kersti
Published: January 2011

The English possessive ’s (POSSLS) is widely regarded as a clitic which attaches at the right edge of noun phrases. The so-called “group genitive”, where POSSLS attaches after a postmodifier (the man in the corner’s hat), is crucial to theoretical accounts. We evaluate both theoretical and descriptive treatments.
We then describe the actual use of POSSLS in the spoken component of the British National Corpus, with particular attention to postmodified possessors, demonstrating that the crucial pattern is surprisingly marginal and that at least one other pattern has been missed entirely. This leads to discussions of grammaticality versus usage, of postmodification, and of the factors that condition the use of possLs and their relevance to theory.
The linguistics of weather
Authors: Eriksen Pål Kristian , Kittilä Seppo , Kolehmainen Leena
Published: January 2011

This paper is a cross-linguistic investigation of meteorological expressions (such as it is snowing or the wind blows). The paper proposes a three-fold typology of meteorological constructions according to the element primarily responsible for the coding of weather. In the predicate type, a predicate expresses the meteorological event, while an argument has other functions. In the argument type, an argument is responsible for expressing weather, while any eventual predicate is semantically rather vacuous. In the argument-predicate type, finally, both a predicate and an argument are involved. All types include subtypes, depending on the syntactic valency and the parts of speech of the elements involved. Building upon the typology of constructions, a typology of languages is also proposed based on the coding of precipitation and temperature.
Acceptability of sign manipulations
Authors: Arendsen Jeroen , Doorn Andrea J. van , Ridder Huib de
Published: January 2011

This study contains the results of an experiment in which signers were asked to judge the acceptability of a set of sign manipulations. Signs were recorded with variations in different categories, in the temporal and spatial dimension. Participants varied much in tolerance, i.e. in the percentage of movies they judged to be acceptable, but their rankings of the acceptability of sign manipulations correlated well. On the level of dimensionality, we found that temporal manipulations were highly acceptable while spatial (and spatiotemporal) manipulations were often judged unacceptable. Further division of the manipulations into categories, such as changes in hand orientation or movement direction, showed much variability and little regularity. The roles of phonology and iconicity in acceptability judgments were studied. Part of the variability in the acceptability of sign manipulations could be explained on the basis of the type of phonological error caused by each manipulation, and by considering a sign’s iconicity and classifying whether manipulations are compatible or incompatible with that iconicity. Finally, human judgments were compared to acceptability ratings by three automatic sign recognizers for three of the signs. With some exceptions, the rankings of the acceptability of sign manipulations as calculated by these sign recognizers did not correlate well with the rankings by humans.
Dissociative patterns of foreperiod effects in temporal discrimination and reaction time tasks
Authors: Los Sander A. , Horoufchin Himeh
Published: January 2011

This study examined whether the process of temporal preparation for a target stimulus is the same regardless of the task required by the target stimulus. To this end, the same variable-foreperiod design was used in a temporal discrimination task (Experiment 1) and a reaction time task (Experiment 2). In Experiment 1, both temporal sensitivity and perceived duration increased as a function of foreperiod, whereas in Experiment 2, foreperiod did not influence reaction time. Furthermore, both temporal sensitivity and perceived duration revealed an asymmetric sequential effect of foreperiod, but the pattern of this effect was opposite to the pattern observed in the reaction time task. Together these dissociative patterns of foreperiod effects suggest that the mechanism of temporal preparation depends on the task required by the target stimulus.
Rapid communication: Sex differences in artificial grammar learning: Evidence for different strategies in men and women
Authors: Lotz Anja , Kinder Annette
Published: January 2011

In this article we report an experiment that investigated differences in classification performance of women and men in artificial grammar learning (AGL). Women's and men's responses correspond to a large extent. Consistent differences, however, were found in a variable that codes overlaps between training and test items in terms of string fragments. The results are best explained by the assumption that women and men apply different cognitive strategies at test.
EPS Prize Lecture: Characterizing congenital amusia
Authors: Stewart Lauren
Published: January 2011

The ability to make sense of the music in our environment involves sophisticated cognitive mechanisms that, for most people, are acquired effortlessly and in early life. A special population of individuals, with a disorder termed congenital amusia, report lifelong difficulties in this regard. Exploring the nature of this developmental disorder provides a window onto the cognitive architecture of typical musical processing, as well as allowing a study of the relationship between processing of music and other domains, such as language. The present article considers findings concerning pitch discrimination, pitch memory, contour processing, experiential aspects of music listening in amusia, and emerging evidence concerning the neurobiology of the disorder. A simplified model of melodic processing is outlined, and possible loci of the cognitive deficit are discussed.
Modelling of atmospheric pressure plasmas for biomedical applications
Authors: Lee H W , Park G Y , Seo Y S , Im Y H , Shim S B , Lee H J
Published: January 2011

As interest has increased in the interaction between low-temperature plasmas and living cells or organic materials, the role of modelling and simulation of atmospheric pressure plasmas has become important in understanding the effects of charged particles and radicals in biomedical applications. This review paper introduces the general properties of low-temperature atmospheric pressure plasma devices for biomedical applications and explains recently reported simulation results. Control parameters of atmospheric pressure plasmas, such as gas mixture composition, driving frequency and voltage and the function shape of sinusoidal and pulsed power, are considered through both a review of previous findings and new simulation results in order to improve plasma properties for given purposes. Furthermore, the simulation or modelling techniques are explained along with surface interactions of the plasma for the future development of simulation codes to study the interaction of plasmas with living cells.
Nuclear Fusion Award 2010 speech
Authors: John Rice
Published: January 2011

Following the suggestion of Earl Marmar in 1995, I installed a compact von Hamos type x-ray spectrometer (originally built with Elisabeth Rachlew and Jan Kallne) on a tangentially viewing port on the Alcator C-Mod tokamak. The spectrometer views the plasma through a 2 cm diameter hole, and is tuned to H-like argon, suitable for passive measurement of the core toroidal rotation velocity from the Doppler shift. It soon became evident that the rotation in Ohmic L-mode discharges, while for the most part directed counter-current, depends in a very complicated fashion on plasma parameters, notably the electron density, current and magnetic configuration. The rotation can even flip sign for almost no apparent reason! In Ohmic and ion cyclotron range of frequencies (ICRF) heated H-mode plasmas the rotation is in the co-current direction and has a relatively simple dependence on plasma parameters, proportional to the stored energy normalized to the current. Rotation velocities as high as 130 km s-1 have been observed without external momentum input. In dimensionless terms this intrinsic (or spontaneous rotation) depends on the normalized plasma pressure. The association of toroidal rotation with plasma pressure in ICRF H-modes was first observed by Lars-Goran Eriksson in JET discharges. Similar results were subsequently reported for Tore Supra enhanced confinement plasmas.

In the early 2000s concerns began to surface about the lack of substantial neutral beam driven rotation in ITER, and intrinsic rotation became a topic of interest in the ITPA Transport Group. Through that connection, similar observations from DIII-D, TCV and JT-60U were added to the growing list. A database of intrinsic rotation observations was assembled with the goal of extrapolating to the expected values for ITER. Both dimensional and dimensionless scalings were developed and formed the backbone of the 2007 Nuclear Fusion paper. I gratefully acknowledge the important contributions to this paper from Alex Ince-Cushman, John deGrassie, Lars-Goran Eriksson, Yoshiteru Sakamoto, Andrea Scarabosio and Yuri Podpaly, as well as the other coauthors. I would like to express my sincere appreciation to Earl Marmar, Martin Greenwald and Miklos Porkolab at MIT for continued support of this work, as well as to the entire C-Mod team.
This award was made possible due to the insight of Mitsuru Kikuchi and the support of the IAEA through Werner Burkhart, and I am truly grateful to both of them. Many thanks as well to the outstanding staff at Nuclear Fusion. It is a distinct honor to be included in the group of previous winners: Tim Luce, Clemente Angioni, Todd Evans and Steve Sabbagh. It is also a great honor to be considered alongside the 2010 nominees: Phil Snyder, Sibylle Guenter, Maiko Yoshida, Hajime Urano, Fulvio Zonca, Erik Garcia, Costanza Maggi, Hartmut Zohm, Thierry Loarer and Bruce Lipschultz.

Finally, I would like to thank the readers of Nuclear Fusion for the many citations.

John Rice
2010 Nuclear Fusion Award winner
Plasma Science and Fusion Center, MIT, Cambridge, MA, USA
Characterization of MRP RNA–protein interactions within the perinucleolar compartment
Authors: Pollock Callie , Daily Kelly , Nguyen Van Trung , Wang Chen , Lewandowska Marzena Anna , Bensaude Olivier , Huang Sui
Published: January 2011

The perinucleolar compartment (PNC) forms in cancer cells and is highly enriched with a subset of polymerase III RNAs and RNA-binding proteins. Here we report that PNC components mitochondrial RNA–processing (MRP) RNA, pyrimidine tract–binding protein (PTB), and CUG-binding protein (CUGBP) interact in vivo, as demonstrated by coimmunoprecipitation and RNA pull-down experiments. Glycerol gradient analyses show that this complex is large and sediments at a different fraction from known MRP RNA–containing complexes, the MRP ribonucleoprotein ribozyme and human telomerase reverse transcriptase. Tethering PNC components to a LacO locus recruits other PNC components, further confirming the in vivo interactions. These interactions are present both in PNC-containing and -lacking cells. High-resolution localization analyses demonstrate that MRP RNA, CUGBP, and PTB colocalize at the PNC as a reticulated network, intertwining with newly synthesized RNA. Furthermore, green fluorescent protein (GFP)–PTB and GFP-CUGBP show a slower rate of fluorescence recovery after photobleaching at the PNC than in the nucleoplasm, illustrating the different molecular interaction of the complexes associated with the PNC. These findings support a working model in which the MRP RNA–protein complex becomes nucleated at the PNC in cancer cells and may play a role in gene expression regulation at the DNA locus that associates with the PNC.
The Ccr4a (CNOT6) and Ccr4b (CNOT6L) deadenylase subunits of the human Ccr4–Not complex contribute to the prevention of cell death and senescence
Authors: Mittal Saloni , Aslam Akhmed , Doidge Rachel , Medica Rachel , Winkler G. Sebastiaan
Published: January 2011

A key step in cytoplasmic mRNA degradation is the shortening of the poly(A) tail, which involves several deadenylase enzymes. Relatively little is known about the importance of these enzymes for the cellular physiology. Here we focused on the role of the highly similar Ccr4a (CNOT6) and Ccr4b (CNOT6L) deadenylase subunits of the Ccr4–Not complex. In addition to a role in cell proliferation, Ccr4a and Ccr4b play a role in cell survival, in contrast to the Caf1a (CNOT7) and Caf1b (CNOT8) deadenylase subunits or the CNOT1 and CNOT3 noncatalytic subunits of the Ccr4–Not complex. Underscoring the differential contributions of the deadenylase subunits, we found that knockdown of Caf1a/Caf1b or Ccr4a/Ccr4b differentially affects the formation of cytoplasmic foci by processing-body components. Furthermore, we demonstrated that the amino-terminal leucine-rich repeat (LRR) domain of Ccr4b influenced its subcellular localization but was not required for the deadenylase activity of Ccr4b. Moreover, overexpression of Ccr4b lacking the LRR domain interfered with cell cycle progression but not with cell viability. Finally, gene expression profiling indicated that distinct gene sets are regulated by Caf1a/Caf1b and Ccr4a/Ccr4b and identified Ccr4a/Ccr4b as a key regulator of insulin-like growth factor–binding protein 5, which mediates cell cycle arrest and senescence via a p53-dependent pathway.
ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration
Authors: Bottolo Leonardo , Chadeau-Hyam Marc , Hastie David I. , Langley Sarah R. , Petretto Enrico , Tiret Laurence , Tregouet David , Richardson Sylvia
Published: January 2011

Summary:  ESS++ is a C++ implementation of a fully Bayesian variable selection approach for single and multiple response linear regression. ESS++ works well both when the number of observations is larger than the number of predictors and in the ‘large p, small n’ case. In the current version, ESS++ can handle several hundred observations, thousands of predictors and a few responses simultaneously. The core engine of ESS++ for the selection of relevant predictors is based on Evolutionary Monte Carlo. Our implementation is open source, allowing community-based alterations and improvements.

Availability: C++ source code and documentation including compilation instructions are available under GNU licence at http://bgx.org.uk/software/ESS.html.

Contact:  l.bottolo@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
X-MATE: a flexible system for mapping short read data
Authors: Wood David L. A. , Xu Qinying , Pearson John V. , Cloonan Nicole , Grimmond Sean M.
Published: January 2011

Summary: Accurate and complete mapping of short-read sequencing to a reference genome greatly enhances the discovery of biological results and improves statistical predictions. We recently presented RNA-MATE, a pipeline for the recursive mapping of RNA-Seq datasets. With the rapid increase in genome re-sequencing projects, progression of available mapping software and the evolution of file formats, we now present X-MATE, an updated version of RNA-MATE, capable of mapping both RNA-Seq and DNA datasets and with improved performance, output file formats, configuration files, and flexibility in core mapping software.

Availability: Executables, source code, junction libraries, test data and results and the user manual are available from http://grimmond.imb.uq.edu.au/X-MATE/.

Contact:  n.cloonan@uq.edu.au; s.grimmond@uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics Online.
HiSpOD: probe design for functional DNA microarrays
Authors: Dugat-Bony Eric , Missaoui Mohieddine , Peyretaillade Eric , Biderre-Petit Corinne , Bouzid Ourdia , Gouinaud Christophe , Hill David , Peyret Pierre
Published: January 2011

Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays.

Results: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contaminated environmental sample proved the specificity and the sensitivity of probes designed with the HiSpOD program.

Availability:  http://fc.isima.fr/~g2im/hispod/.

Contact:  pierre.peyret@univ-bpclermont.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision
Authors: Abyzov Alexej , Gerstein Mark
Published: January 2011

Motivation: Defining the precise location of structural variations (SVs) at single-nucleotide breakpoint resolution is an important problem, as it is a prerequisite for classifying SVs, evaluating their functional impact and reconstructing personal genome sequences. Given approximate breakpoint locations and a bridging assembly or split read, the problem essentially reduces to finding a correct sequence alignment. Classical algorithms for alignment and their generalizations guarantee finding the optimal (in terms of scoring) global or local alignment of two sequences. However, they cannot generally be applied to finding the biologically correct alignment of genomic sequences containing SVs because of the need to simultaneously span the SV (e.g. make a large gap) and perform precise local alignments at the flanking ends.

Results: Here, we formulate the computations involved in this problem and describe a dynamic-programming algorithm for its solution. Specifically, our algorithm, called AGE for Alignment with Gap Excision, finds the optimal solution by simultaneously aligning the 5′ and 3′ ends of two given sequences and introducing a ‘large-gap jump’ between the local end alignments to maximize the total alignment score. We also describe extensions allowing the application of AGE to tandem duplications, inversions and complex events involving two large gaps. We develop a memory-efficient implementation of AGE (allowing application to long contigs) and make it available as a downloadable software package. Finally, we applied AGE for breakpoint determination and standardization in the 1000 Genomes Project by aligning locally assembled contigs to the human genome.

Availability and Implementation: AGE is freely available at http://sv.gersteinlab.org/age.

Contact:  pi@gersteinlab.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Physiome Model Repository 2
Authors: Yu Tommy , Lloyd Catherine M. , Nickerson David P. , Cooling Michael T. , Miller Andrew K. , Garny Alan , Terkildsen Jonna R. , Lawson James , Britten Randall D. , Hunter Peter J. , Nielsen Poul M. F.
Published: January 2011

Motivation: The Physiome Model Repository 2 (PMR2) software was created as part of the IUPS Physiome Project (Hunter and Borg, 2003), and today it serves as the foundation for the CellML model repository. Key advantages brought to the end user by PMR2 include: facilities for model exchange, enhanced collaboration and a detailed change history for each model.

Availability: PMR2 is available under an open source license at http://www.cellml.org/tools/pmr/; a fully functional instance of this software can be accessed at http://models.physiomeproject.org/.

Contact: tommy.yu@auckland.ac.nz
A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies
Authors: Ong Rick Twee-Hee , Liu Xuanyao , Poh Wan-Ting , Sim Xueling , Chia Kee-Seng , Teo Yik-Ying
Published: January 2011

Motivation: Methods for detecting positive selection relied on finding evidence of long haplotypes to identify candidate regions under selection. However, these methods generally do not identify the length and form of the selected haplotype.

Results: We present HapFinder, a method which can find the common longest haplotype under three different settings from a database, which is relevant in the analysis of positive selection in population genetics and also in medical genetics for finding the likely haplotype form carrying the causal allele at the functional polymorphism.

Availability: A java program, implementing the methods described in HapFinder, together with R scripts and datasets for producing the figures presented in this article are publicly available at http://www.nus-cme.org.sg/sgvp/software/hapfinder.html. The site also hosts an online browser for finding haplotypes from the International HapMap Project and the Singapore Genome Variation Project.

Contact:  g0801900@nus.edu.sg; statyy@nus.edu.sg
Sources of variability in prevalence and distribution of bitter crab disease in snow crab (Chionoecetes opilio) along the northeast coast of Newfoundland
Authors: Mullowney Darrell R. , Dawe Earl G. , Morado J. Frank , Cawthorn Richard J.
Published: January 2011

Mullowney, D. R., Dawe, E. G., Morado, J. F., and Cawthorn, R. J. 2011. Sources of variability in prevalence and distribution of bitter crab disease in snow crab (Chionoecetes opilio) along the northeast coast of Newfoundland. – ICES Journal of Marine Science, 68: . Bitter crab disease (BCD), caused by a parasitic dinoflagellate of the genus Hematodinium, is a source of mortality in Newfoundland and Labrador snow crab (Chionoecetes opilio). Prevalence and distribution patterns have been spatially and temporally variable since the discovery of BCD in 1990, and controlling factors are poorly understood. Data from a long-term trap survey in two bays along the northeast coast of Newfoundland are analysed, investigating the influences and interactions of various biotic and abiotic factors over BCD. Factors examined include host size and density, temperature, salinity, and depth. The density of small to medium-sized snow crabs was directly related to prevalence and distribution of BCD, whereas all other factors had either an indirect or no effect. Further, much of the spatio-temporal variability in disease expression is a function of variability in host productivity, growth, and movement. The study also considers the impacts BCD can exert on the commercial fishery, and the potential for predicting intermediate to long-term recruitment potential based on BCD prevalence levels.
Spinactinospora alkalitolerans gen. nov., sp. nov., an actinomycete isolated from marine sediment
Authors: Chang Xianbo , Liu Wenzheng , Zhang Xiao-Hua
Published: January 2011

A novel marine actinomycete, designated CXB654T, was isolated from marine sediment collected at a depth of 17.5 m near the Yellow Sea Cold Water Mass, China. Optimal growth occurred at 37.0 °C, at pH 7.0–8.0 and in 3–8 % (w/v) NaCl. Strain CXB654T formed branched substrate mycelium without fragmentation. Abundant aerial mycelium differentiated into long or short chains of spores and spores were elliptical and cylindrical with spiny surfaces. Strain CXB654T contained meso-diaminopimelic acid as the diagnostic diamino acid, and ribose and glucose as the major whole-cell components. Phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. MK-10(H8), MK-10(H6) and MK-9(H8) were the predominant menaquinones. The major fatty acids were i-C16 : 0 (24.46 %), ai-C17 : 0 (20.66 %) and C18 : 0 (20.14 %). The DNA G+C content was 71.1 mol%. Comparative analysis of 16S rRNA gene sequences showed that the novel strain was most closely related to genera within the family Nocardiopsaceae, but formed a separate lineage. Highest sequence similarities were to Murinocardiopsis flavida DSM 45312T (96.6 %), Thermobifida halotolerans YIM 90462T (96.5 %) and Marinactinospora thermotolerans DSM 45154T (96.1 %). On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain CXB654T was considered to represent a novel species in a new genus in the family Nocardiopsaceae, and the name Spinactinospora alkalitolerans gen. nov., sp. nov. is proposed; the type strain is CXB654T ( = DSM 45414T = LMG 25485T).
Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers
Authors: Sérandour Aurélien A. , Avner Stéphane , Percevault Frédéric , Demay Florence , Bizot Maud , Lucchetti-Miganeh Céline , Barloy-Hubler Frédérique , Brown Myles , Lupien Mathieu , Métivier Raphaël , Salbert Gilles , Eeckhoute Jérôme
Published: January 2011

Transcription factors (TFs) bind specifically to discrete regions of mammalian genomes called cis-regulatory elements. Among those are enhancers, which play key roles in regulation of gene expression during development and differentiation. Despite the recognized central regulatory role exerted by chromatin in control of TF functions, much remains to be learned regarding the chromatin structure of enhancers and how it is established. Here, we have analyzed on a genomic-scale enhancers that recruit FOXA1, a pioneer transcription factor that triggers transcriptional competency of these cis-regulatory sites. Importantly, we found that FOXA1 binds to genomic regions showing local DNA hypomethylation and that its cell-type-specific recruitment to chromatin is linked to differential DNA methylation levels of its binding sites. Using neural differentiation as a model, we showed that induction of FOXA1 expression and its subsequent recruitment to enhancers is associated with DNA demethylation. Concomitantly, histone H3 lysine 4 methylation is induced at these enhancers. These epigenetic changes may both stabilize FOXA1 binding and allow for subsequent recruitment of transcriptional regulatory effectors. Interestingly, when cloned into reporter constructs, FOXA1-dependent enhancers were able to recapitulate their cell type specificity. However, their activities were inhibited by DNA methylation. Hence, these enhancers are intrinsic cell-type-specific regulatory regions of which activities have to be potentiated by FOXA1 through induction of an epigenetic switch that includes notably DNA demethylation.
Multiplexed shotgun genotyping for rapid and efficient genetic mapping
Authors: Andolfatto Peter , Davison Dan , Erezyilmaz Deniz , Hu Tina T. , Mast Joshua , Sunayama-Morita Tomoko , Stern David L.
Published: January 2011

We present a new approach to genotyping based on multiplexed shotgun sequencing that can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. We first describe a simple library construction protocol that uses just 10 ng of genomic DNA per individual and makes the approach accessible to any laboratory with standard molecular biology equipment. Sequencing this library results in a large number of sequence reads widely distributed across the genomes of multiplexed bar-coded individuals. We develop a Hidden Markov Model to estimate ancestry at all genomic locations in all individuals using these data. We demonstrate the utility of the approach by mapping a dominant marker allele in D. simulans to within 105 kb of its true position using 96 F1-backcross individuals genotyped in a single lane on an Illumina Genome Analyzer. We further demonstrate the utility of our method by genetically mapping more than 400 previously unassembled D. simulans contigs to linkage groups and by evaluating the quality of targeted introgression lines. At this level of multiplexing and divergence between strains, our method allows estimation of recombination breakpoints to a median of 38-kb intervals. Our analysis suggests that higher levels of multiplexing and/or use of strains with lower levels of divergence are practicable.
Fibroblast growth factor-2 alters the nature of extinction
Authors: Graham Bronwyn M. , Richardson Rick
Published: January 2011

These experiments examined the effects of the NMDA-receptor (NMDAr) antagonist MK801 on reacquisition and re-extinction of a conditioned fear that had been previously extinguished before injection of fibroblast growth factor-2 (FGF2) or vehicle. Recent findings have shown that relearning and re-extinction, unlike initial learning and extinction, do not depend on NMDAr activation. Three experiments demonstrated that FGF2 prevents the switch from NMDAr-dependent to NMDAr-independent reacquisition and re-extinction, suggesting that FGF2 may lead to the partial erasure of the original fear memory. These findings add to a growing body of work suggesting that FGF2 may be a novel pharmacological enhancer of exposure therapy for humans with anxiety disorders.
The role of the nucleus accumbens in knowing when to respond
Authors: Singh Teghpal , McDannald Michael A. , Takahashi Yuji K. , Haney Richard Z. , Cooch Nisha K. , Lucantonio Federica , Schoenbaum Geoffrey
Published: January 2011

While knowing what to expect is important, it is equally important to know when to expect it and to respond accordingly. This is apparent even in simple Pavlovian training situations in which animals learn to respond more strongly closer to reward delivery. Here we report that the nucleus accumbens core, an area well-positioned to represent information about the timing of impending rewards, plays a critical role in this timing function.
The Folylpolyglutamate Synthetase Plastidial Isoform Is Required for Postembryonic Root Development in Arabidopsis
Authors: Srivastava Avinash C. , Ramos-Parra Perla A. , Bedair Mohamed , Robledo-Hernández Ana L. , Tang Yuhong , Sumner Lloyd W. , Díaz de la Garza Rocío I. , Blancaflor Elison B.
Published: January 2011

A recessive Arabidopsis (Arabidopsis thaliana) mutant with short primary roots and root hairs was identified from a forward genetic screen. The disrupted gene in the mutant encoded the plastidial isoform of folylpolyglutamate synthetase (FPGS), previously designated as AtDFB, an enzyme that catalyzes the addition of glutamate residues to the folate molecule to form folylpolyglutamates. The short primary root of atdfb was associated with a disorganized quiescent center, dissipated auxin gradient in the root cap, bundled actin cytoskeleton, and reduced cell division and expansion. The accumulation of monoglutamylated forms of some folate classes in atdfb was consistent with impaired FPGS function. The observed cellular defects in roots of atdfb underscore the essential role of folylpolyglutamates in the highly compartmentalized one-carbon transfer reactions (C1 metabolism) that lead to the biosynthesis of compounds required for metabolically active cells found in the growing root apex. Indeed, metabolic profiling uncovered a depletion of several amino acids and nucleotides in atdfb indicative of broad alterations in metabolism. Methionine and purines, which are synthesized de novo in plastids via C1 enzymatic reactions, were particularly depleted. The root growth and quiescent center defects of atdfb were rescued by exogenous application of 5-formyl-tetrahydrofolate, a stable folate that was readily converted to metabolically active folates. Collectively, our results indicate that AtDFB is the predominant FPGS isoform that generates polyglutamylated folate cofactors to support C1 metabolism required for meristem maintenance and cell expansion during postembryonic root development in Arabidopsis.
Poly(ethylene) oxide for small-molecule crystal growth in gelled organic solvents
Authors: Choquesillo-Lazarte Duane , García-Ruiz Juan Manuel
Published: January 2011

The use of poly(ethylene) oxide (PEO) as a gelator has been evaluated with a selected list of organic solvents. From the 26 solvents tested, eight formed gel matrices. This number was extended to 19 when poly(ethylene) oxide was used with a mixture of solvents. The procedure for the preparation of PEO organogels is described, and their application for the crystallization of small molecules using different crystallization techniques in the presence of organic solvents is discussed.
Modulated structure of nepheline
Authors: Friese Karen , Grzechnik Andrzej , Petříček Vaclav , Schönleber Andreas , van Smaalen Sander , Morgenroth Wolfgang
Published: January 2011

The incommensurately modulated structure of a natural nepheline of composition K0.54Na3.24Ca0.03Al3.84Si4.16O16has been determined in superspace. The compound crystallizes in the trigonal centered superspace groupX3(00γ)0 with γ = 0.2048 (10),X= (0, 0, 0, 0), (1/3, 2/3, 0, 2/3), (2/3, 1/3, 0, 1/3),a= 17.2889 (8) andc= 8.3622 (10) Å. The structure is characterized by a framework of corner-connected (Al,Si)O4tetrahedra. The additional cations are incorporated in two different types of channels of the framework. All atoms in the structure are displacively modulated with amplitudes below 0.1 Å. The modulation can be well described taking into account harmonics of first order only. Atomic positions in the smaller channels of the framework are fully occupied by Na+. Cationic positions in the larger channel are occupationally modulated, yet the variation of electron density as a function of the internal coordinatetis very small and indicates that the incorporation of different types of cations (K+, Na+, Ca2+) and vacancies is realised in a highly disordered way. AverageT—O distances indicate a nearly complete Al/Si ordering in the tetrahedral framework. A large part of the O atoms are approximated by split-atom positions, which are additionally affected by occupational modulation resulting in a high degree of disorder in the modulated structure. Occupational probabilities for the split-atom positions are complementary. Occupational modulations of the cations in the larger channels and the O atoms of the tetrahedral framework are coupled and correlations between occupational and displacive modulations exist.
R&D collaboration in 50 major Spanish companies
Authors: Perianes‐Rodríguez Antonio , Olmeda‐Gómez Carlos , Antonia Ovalle‐Perandones María , Chinchilla‐Rodríguez Zaida , Moya‐Anegón Felix
Published: January 2011

Purpose

Although the role of enterprise in R&D is broadly acknowledged, few attempts have been made to gather data for analyzing the nature and scope of private sector collaboration. This study aims to deliver empirical results based on quantitative data to gain insight into the role of private enterprise as an indispensable actor in scientific development and innovation.

Design/methodology/approach

The study aimed to deliver empirical results based on quantitative data to gain insight into the role of private enterprise as an indispensable actor in scientific development and innovation. To this end, an analysis was conducted of the contribution made by Spanish business, focusing on the 50 most active companies in terms of internationally visible scientific output, from three perspectives.

Findings

The findings provide insight into business involvement in the R&D system based on: research papers published; national, international and sectoral collaboration patterns; structural patterns; and the identification of the most prominent companies from a systematic comparison of their research results and their position in the resulting collaboration network.

Research limitations/implications

Bibliometric analyses do not measure all types of publications. Indicators are usually based on data in the Thomson Reuters databases, which are regarded as being representative of peer‐reviewed, publicly accessible papers with high international visibility and impact. The Thomson Reuters databases feature a series of advantages that make them indispensable for studies on scientific collaboration.

Originality/value

One of the core ideas of this study is the emphasis on the essential role of collaboration in improving scientific results, as borne out by the correlation between the clustering coefficient and the hybrid indicators. The findings also provide proof of the success of strategies for institutional collaboration. The foregoing shows that the application of hybrid indicators to institutional aggregates yields novel results not explored in preceding studies.
Development strategy in offshore markets: evidence from the Channel Islands
Authors: Hearn Bruce
Published: January 2011

Purpose

This paper aims to review the development of the Channel Islands exchange and assess the potential diversification benefits arising from the inclusion of this market in investment portfolios containing UK and French equity assets.

Design/methodology/approach

First this paper uses a simple stochastic drift, GARCH, and time‐varying parameter CAPM to model total returns indices. Second, it uses the unconditional and conditional means and variances from first stage as inputs into a mean‐variance portfolio quadratic optimisation problem: the solutions of which denote the optimal asset weights.

Findings

The evidence suggests that although there are serious difficulties in modelling time series from small illiquid equity markets owing to price‐rigidity, the limited benefits that do exist for the inclusion of Channel Islands assets in portfolios do so preferentially with Paris as opposed to London assets.

Originality/value

This paper extends the literature development policy options for small offshore markets and provides the first analysis of the Channel Islands.
Use of e‐journals among research scholars at Central Science Library, University of Delhi
Authors: Naushad Ali P.M. , Nisha Faizul
Published: January 2011

Purpose

The purpose of this paper is to determine the extent to which research scholars at Central Science Library, University of Delhi are aware and make use of e‐journals.

Design/methodology/approach

A survey was designed to collect basic information about the level of use of electronic journals as well as other factors contributing to and associated with their use. A well‐structured questionnaire was administered among research scholars to collect the necessary primary data, keeping in view the objectives of the study.

Findings

The findings clearly reveal that more than 60 per cent of users in the Central Science Library are using e‐journals weekly for the purpose of research. Printed journals are consulted by the majority of users compared with e‐journals. Keyword is the most popular search method for searching e‐journals among research scholars, whereas the date of publication carries the least percentage among all the options. However, if is found that slow downloading of PDF files is the major problem that would discourage users while using e‐journals.

Research limitations/implications

The present paper consists only of e‐journal users and the geographical area is restricted to the CSL at the University of Delhi. The scope of the paper could be extended to additional centrally funded universities. An intra‐comparative study could also be made between some select central and state universities for users of e‐journals.

Originality/value

There are a number of studies on the use of e‐journals, but this is the first of its kind within Delhi University. As such, it should pave the way for research in other Indian universities as well as elsewhere.