bluuebunny/crossref_metadata_2025 huggingface dataset:
A formal analysis of phonological contrast and iconicity in sign language handshapes
Authors: Eccarius Petra , Brentari Diane
Published: January 2011

This paper discusses the role of iconicity in sign language phonology by utilizing recently developed tools available in the areas of phonological contrast and feature distribution. In particular, we explain the degree to which iconic elements of handshape interact with the feature system of sign language handshapes in different components of the lexicon, by making specific reference to handshape features that specify joint position. We then discuss similarities and differences between signed languages and spoken languages and the implications for a theory of features that might adequately capture phenomena in both communication modalities. Although cross-linguistic data have been collected and analyzed in this regard, we focus on data from American Sign Language in this work.
Early acquisition of sign language
Authors: Malaia Evie , Wilbur Ronnie B.
Published: January 2011

Early acquisition of a natural language, signed or spoken, has been shown to fundamentally impact both one’s ability to use the first language, and the ability to learn subsequent languages later in life (Mayberry 2007, 2009). This review summarizes a number of recent neuroimaging studies in order to detail the neural bases of sign language acquisition. The logic of this review is to present research reports that contribute to the bigger picture showing that people who acquire a natural language, spoken or signed, in the normal way possess specialized linguistic abilities and brain functions that are missing or deficient in people whose exposure to natural language is delayed or absent. Comparing the function of each brain region with regards to the processing of spoken and sign languages, we attempt to clarify the role each region plays in language processing in general, and to outline the challenges and remaining questions in understanding language processing in the brain.
The Relations Between Translation and Material Text Transfer
Authors: Pym Anthony
Published: January 2011

The notion of text transfer, understood as the material moving of texts across space-time, makes it possible to see the relationships between transfer and translation as not only causal (texts are translated because they are transferred), but also economic (translation is one of several options for the distribution of textual resources), semiotic (translations represent acts of transfer), and epistemological (attention to transfer affects the way translations are perceived). Awareness of these relationships should open up new possibilities for strongly interdisciplinary research into the nature and history of translation.
Translation Policy and Literary/Cultural Changes in Early Modern Korea (1895-1921)
Authors: Hyun Theresa
Published: January 2011

This article gives an overview of the relationship between the establishment of translation policy and literary/cultural shifts during the first two decades of the twentieth century in Korea. During the Kae Hwa ("Enlightenment") period, 1895-1910, translations were undertaken primarily for didactic purposes. Next followed a period when foreign texts were imported with the aim of developing modern Korean literature. The concept of "translational norms", as proposed by Toury, is used to explain the changing practices of individual translators as well as the general evolution of translation within the Korean literary system.
On Two Style Markers of Modern Arabic-Hebrew Prose Translations
Authors: Sarig Lea
Published: January 2011

Following Enkvist's method for establishing style markers, one 'positive' and one 'negative' marker of modern Arabic-Hebrew prose translations are constituted through a comparison of the translations with their respective original texts. A complementary intra-language study of original Hebrew prose fiction, which revealed the same style markers, shows that the findings are not translation-specific, but rather a language-bound phenomenon. Although the findings for Hebrew translations from English and German concerning the 'negative' style marker do not concur with the findings in the translations from Arabic, they nonetheless indirectly support the conclusion that it is language-bound.
The Cloze Technique as A Pedagogical Tool for the Training of Translators and Interpreters
Authors: Lambert Sylvie
Published: January 2011

This article focuses on the versatility of the cloze technique, as a tool not only for measuring second-language proficiency, but also for selecting and training both translators (written cloze) and interpreters (aural cloze). When presented auditorily, the cloze test discriminates pass and fail interpreter students, given the external pacing and speed stress experienced by simultaneous interpreters in real life. The article offers several ways to administer the cloze technique as well as examples of such doctored material.
Coping with traumatic stress in journalism: A critical ethnographic study
Authors: Buchanan Marla , Keats Patrice
Published: January 2011

Journalists who witness trauma and disaster events are at risk for physical, emotional, and psychological injury. The purpose of this paper is to present the results of a critical ethnographic study among 31 Canadian journalists and photojournalists with regard to coping strategies used to buffer the effects of being exposed to trauma and disaster events and work‐related stress. The findings are the result of in‐depth individual interviews and six workplace observations with journalists across Canada. The most commonly reported coping strategies were: avoidance strategies at work, use of black humor, controlling one's emotions and memories, exercise and other physical activities, focusing on the technical aspects, and using substances. Recommendations for addressing the effects of work‐related stress within this population are provided.
The relationship between the need for closure and deviant bias: An investigation of generality and process
Authors: Rubin Mark , Paolini Stefania , Crisp Richard J.
Published: January 2011

The need for closure predicts an evaluative bias against people whose opinions or behaviors deviate from those of other members of their social groups. In the present study, we investigated whether the relationship between the need for closure and deviant bias generalized to nonsocial stimuli, and we examined the process underlying this relationship. Sixty‐one undergraduate students completed measures of the need for closure, the need for structure, intolerance for ambiguity, and the ability to be decisive and achieve cognitive structure. They then rated their liking for letters of the Latin alphabet (“A” & “B”) whose locations were consistent and inconsistent with relevant categories (“A circle” and “B circle”). Participants liked category‐inconsistent letters less than category‐consistent letters. Measures related to the need for structure and closed‐mindedness correlated positively with this deviant bias, whereas measures related to the ability to be decisive and achieve cognitive structure did not. These results imply that the relationship between the need for closure and deviant bias is a relatively basic and pervasive effect that is not unique to social deviance and is driven by the need for structure and closed‐mindedness. Implications for social and nonsocial stimuli are discussed.
Illusory correlations revisited: The role of pseudocontingencies and working-memory capacity
Authors: Eder Andreas B. , Fiedler Klaus , Hamm-Eder Silke
Published: January 2011

Three experiments investigate illusory correlations in a feedback learning paradigm. Diverging from a standard paradigm, in which stimuli consist of joint observations of group–behaviour pairs, participants were asked to guess the group reference of positive and negative stimulus behaviours. They only knew that one group was larger than the other, and the stimulus series soon revealed that positive (negative) behaviours appeared more frequently in the stimulus series than negative (positive) behaviours. Regardless of whether feedback of the actual group reference was provided or not, the predominant valence was more strongly associated with the large than the small group. This illusory-correlation effect was evident in memory-based measures at the end of the stimulus series as well as in the online predictions during stimulus presentation. The strength of illusory correlations increased with decreasing working-memory capacity, operationalized either by an interpersonal differences measure or a cognitive-load manipulation. The occurrence of illusory correlations in the absence of joint observations about group–valence pairs (in the no-feedback condition and in the early phase of the online prediction task) can be explained as a reflection of pseudocontingency inferences.
Gender dimorphic effects of voluntary running in laboratory rats depends on maturational status
Authors: Carrera Olaia , Cerrato Maria , Vazquez Reyes , Sineiro Clotilde , Gutierrez Emilio
Published: January 2011

This study examined the effect of 24 hr per day wheel access on running, body weight, and food intake for 30- or 50-day-old male and female rats under ad lib feeding conditions. Food intake and body weight were also monitored in a control group housed without access to running wheels. A dimorphic effect was observed after wheel introduction in 50-day-old but not 30-day-old rats: A temporary decline in food intake and a lasting decrease in body weight occurred for active male rats in comparison to their sedentary controls, and wheel access facilitated food intake and preserved body weight gain in female rats in comparison to their sedentary counterparts. Hyperphagia in adult females is interpreted in terms of the evolutionary acquired advantage linked to their reproductive function.
Explaining away the negative effects of evaluation on analogical transfer: The perils of premature evaluation
Authors: Bearman Christopher , Ormerod Thomas C. , Ball Linden J. , Deptula Daniel
Published: January 2011

Four experiments explored effects on analogical transfer of evaluating solutions to base problems. In contrast to reports of positive effects of explanation, evaluation consistently reduced transfer rates and impaired mental representations of base material. This effect was not ameliorated by encoding for a later memory test, summarizing, or engaging in similar processes at encoding and recall. However, providing a prior explanation task removed the inhibitory effect of evaluation. It appears that evaluation leads to encoding of extraneous material that interferes with access to solution-critical analogous information. Prior explanation inoculates against negative effects on transfer by ensuring that new information introduced via evaluation is organized around existing representations of relevant information of the base problem. The results suggest that the source of difficulty in analogical transfer may reside not only in retrieval and mapping but also in the initial encoding of problems.
Nuclear Fusion prize laudation
Authors: W. Burkart
Published: January 2011

Clean energy in abundance will be of critical importance to the pursuit of world peace and development. As part of the IAEA's activities to facilitate the dissemination of fusion related science and technology, the journal Nuclear Fusion is intended to contribute to the realization of such energy from fusion.

In 2010, we celebrated the 50th anniversary of the IAEA journal. The excellence of research published in the journal is attested to by its high citation index. The IAEA recognizes excellence by means of an annual prize awarded to the authors of papers judged to have made the greatest impact. On the occasion of the 2010 IAEA Fusion Energy Conference in Daejeon, Republic of Korea at the welcome dinner hosted by the city of Daejeon, we celebrated the achievements of the 2009 and 2010 Nuclear Fusion prize winners.

Steve Sabbagh, from the Department of Applied Physics and Applied Mathematics, Columbia University, New York is the winner of the 2009 award for his paper:

'Resistive wall stabilized operation in rotating high beta NSTX plasmas' [1].

This is a landmark paper which reports record parameters of beta in a large spherical torus plasma and presents a thorough investigation of the physics of resistive wall mode (RWM) instability. The paper makes a significant contribution to the critical topic of RWM stabilization.

John Rice, from the Plasma Science and Fusion Center, MIT, Cambridge is the winner of the 2010 award for his paper:

'Inter-machine comparison of intrinsic toroidal rotation in tokamaks' [2].

The 2010 award is for a seminal paper that analyzes results across a range of machines in order to develop a universal scaling that can be used to predict intrinsic rotation. This paper has already triggered a wealth of experimental and theoretical work.

I congratulate both authors and their colleagues on these exceptional papers.

W. Burkart
Deputy Director General
Department of Nuclear Sciences and Applications
International Atomic Energy Agency, Vienna, Austria

References

[1] Sabbagh S. et al 2006 Nucl. Fusion

46 635–44

[2] Rice J.E. et al 2007 Nucl. Fusion

47 1618–24
Integral torque balance in tokamaks
Authors: Pustovitov V.D.
Published: January 2011

The study is aimed at clarifying the balance between the sinks and sources in the problem of intrinsic plasma rotation in tokamaks reviewed recently by deGrassie (2009 Plasma Phys. Control. Fusion
51 124047). The integral torque on the toroidal plasma is calculated analytically using the most general magnetohydrodynamic (MHD) plasma model taking account of plasma anisotropy and viscosity. The contributions due to several mechanisms are separated and compared. It is shown that some of them, though, possibly, important in establishing the rotation velocity profile in the plasma, may give small input into the integral torque, but an important contribution can come from the magnetic field breaking the axial symmetry of the configuration. In tokamaks, this can be the error field, the toroidal field ripple or the magnetic perturbation created by the correction coils in the dedicated experiments. The estimates for the error-field-induced electromagnetic torque show that the amplitude of this torque is comparable to the typical values of torques introduced into the plasma by neutral beam injection. The obtained relations allow us to quantify the effect that can be produced by the existing correction coils in tokamaks on the plasma rotation, which can be used in experiments to study the origin and physics of intrinsic rotation in tokamaks. Several problems are proposed for theoretical studies and experimental tests.
The role of radial particle pinches in ELM suppression by resonant magnetic perturbations
Authors: Stacey W.M. , Evans T.E.
Published: January 2011

The force balance in the plasma edge in a matched pair of DIII-D (Luxon 2002 Nucl. Fusion
42 6149) tokamak discharges with and without resonant magnetic perturbations (RMPs) is evaluated in order to investigate the effects on particle transport of RMP applied for the purpose of suppressing edge-localized modes (ELMs). Experimental data are used to evaluate the radial and toroidal force balances, which may be written as a pinch–diffusion relation for the radial ion flux to facilitate investigation of transport effects. The radial electric field in the H-mode plasma had a sharp negative dip in the steep gradient region of the edge pedestal, associated with which was a large inward pinch velocity. The main effect of RMP was to make the edge electric field less negative or more positive, reducing this strong negative dip in the radial electric field (even reversing it from negative to positive over some regions), thereby reducing the strong inward particle pinch in the edge of an H-mode discharge, thus causing a reduction in edge density below the ELM threshold.
Hausdorff dimension of the limit set of conformal iterated function systems with overlaps
Authors: Mihailescu Eugen , Urbański Mariusz
Published: January 2011

We give a new approach to the study of conformal iterated function systems with arbitrary overlaps. We provide lower and upper estimates for the Hausdorff dimension of the limit sets of such systems; these are expressed in terms of the topological pressure and the function

d
d

, counting overlaps. In the case when the function

d
d

is constant, we get an exact formula for the Hausdorff dimension. We also prove that in certain cases this formula holds if and only if the function

d
d

is constant.
A novel protein kinase D phosphorylation site in the tumor suppressor Rab interactor 1 is critical for coordination of cell migration
Authors: Ziegler Susanne , Eiseler Tim , Scholz Rolf-Peter , Beck Alexander , Link Gisela , Hausser Angelika
Published: January 2011

The multifunctional signal adapter protein Ras and Rab interactor 1 (RIN1) is a Ras effector protein involved in the regulation of epithelial cell processes such as cell migration and endocytosis. RIN1 signals via two downstream pathways, namely the activation of Rab5 and Abl family kinases. Protein kinase D (PKD) phosphorylates RIN1 at serine 351 in vitro, thereby regulating interaction with 14–3-3 proteins. Here, we report the identification of serine 292 in RIN1 as an in vivo PKD phosphorylation site. PKD-mediated phosphorylation at this site was confirmed with a phospho-specific antibody and by mass spectrometry. We demonstrate that phosphorylation at serine 292 controls RIN1-mediated inhibition of cell migration by modulating the activation of Abl kinases. We further provide evidence that RIN1 in vivo phosphorylation at serine 351 occurs independently of PKD. Collectively, our data identify a novel PKD signaling pathway through RIN1 and Abl kinases that is involved in the regulation of actin remodeling and cell migration.
Myosin light chain kinase and Src control membrane dynamics in volume recovery from cell swelling
Authors: Barfod Elisabeth T. , Moore Ann L. , Van de Graaf Benjamin G. , Lidofsky Steven D.
Published: January 2011

The expansion of the plasma membrane, which occurs during osmotic swelling of epithelia, must be retrieved for volume recovery, but the mechanisms are unknown. Here we have identified myosin light chain kinase (MLCK) as a regulator of membrane internalization in response to osmotic swelling in a model liver cell line. On hypotonic exposure, we found that there was time-dependent phosphorylation of the MLCK substrate myosin II regulatory light chain. At the sides of the cell, MLCK and myosin II localized to swelling-induced membrane blebs with actin just before retraction, and MLCK inhibition led to persistent blebbing and attenuated cell volume recovery. At the base of the cell, MLCK also localized to dynamic actin-coated rings and patches upon swelling, which were associated with uptake of the membrane marker FM4-64X, consistent with sites of membrane internalization. Hypotonic exposure evoked increased biochemical association of the cell volume regulator Src with MLCK and with the endocytosis regulators cortactin and dynamin, which colocalized within these structures. Inhibition of either Src or MLCK led to altered patch and ring lifetimes, consistent with the concept that Src and MLCK form a swelling-induced protein complex that regulates volume recovery through membrane turnover and compensatory endocytosis under osmotic stress.
Identification of sumoylation targets, combined with inactivation ofSMT3, reveals the impact of sumoylation upon growth, morphology, and stress resistance in the pathogenCandida albicans
Authors: Leach Michelle D. , Stead David A. , Argo Evelyn , Brown Alistair J.P.
Published: January 2011

Posttranslational modifications of proteins play critical roles in the control of cellular differentiation, development, and environmental adaptation. In particular, the covalent attachment of the small ubiquitin-like modifier, SUMO, to target proteins (sumoylation) regulates cell cycle progression, transcription, nucleocytoplasmic transport, and stress responses. Here we combine proteomic, molecular, and cellular approaches to examine the roles of sumoylation in the major fungal pathogen of humans, Candida albicans. Using an N-terminally FLAG-tagged SUMO, 31 sumoylated proteins were identified in C. albicans with roles in stress responses (e.g., Hsp60, Hsp70 family members, Hsp104), the cytoskeleton and polarized growth (e.g., Tub1, Cct7, Mlc1), secretion, and endocytosis (e.g., Lsp1, Sec24, Sec7). The output from this proteomic screen was entirely consistent with the phenotypes of C. albicans mutants in which the single SUMO-encoding locus (SMT3) was inactivated or down-regulated. C. albicans smt3/smt3 cells displayed defects in growth, morphology, cell separation, nuclear segregation, and chitin deposition, suggesting important roles for sumoylation in cell cycle control. Smt3/smt3 cells also displayed sensitivity to thermal, oxidative, and cell wall stresses as well as to the antifungal drug caspofungin. Mutation of consensus sumoylation sites in Hsp60 and Hsp104 affected the resistance of C. albicans to thermal stress. Furthermore, signaling via the cell integrity pathway was defective in C. albicans smt3/smt3 cells. These observations provide mechanistic explanations for many of the observed phenotypic effects of Smt3 inactivation upon C. albicans growth and environmental adaptation. Clearly sumoylation plays key roles in fundamental cellular processes that underpin the pathogenicity of this medically important fungus.
MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets
Authors: Baron Daniel , Bihouée Audrey , Teusan Raluca , Dubois Emeric , Savagner Frédérique , Steenman Marja , Houlgatte Rémi , Ramstein Gérard
Published: January 2011

Summary: MADGene is a software environment comprising a web-based database and a java application. This platform aims at unifying gene identifiers (ids) and performing gene set analysis. MADGene allows the user to perform inter-conversion of clone and gene ids over a large range of nomenclatures relative to 17 species. We propose a set of 23 functions to facilitate the analysis of gene sets and we give two microarray applications to show how MADGene can be used to conduct meta-analyses.

Availability: The MADGene resources are freely available online from http://www.madtools.org, a website dedicated to the analysis and annotation of DNA microarray data.

Contact:  gerard.ramstein@univ-nantes.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
A Java API for working with PubChem datasets
Authors: Southern Mark R. , Griffin Patrick R.
Published: January 2011

Summary: PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP.

These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose–response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development.

Availability:  http://code.google.com/p/pubchemdb

Contact:  southern@scripps.edu
MIRACH: efficient model checker for quantitative biological pathway models
Authors: Koh Chuan Hock , Nagasaki Masao , Saito Ayumu , Li Chen , Wong Limsoon , Miyano Satoru
Published: January 2011

Summary: Model checking is playing an increasingly important role in systems biology as larger and more complex biological pathways are being modeled. In this article we report the release of an efficient model checker MIRACH 1.0, which supports any model written in popular formats such as CSML and SBML. MIRACH is integrated with a Petri-net-based simulation engine, enabling efficient online (on-the-fly) checking. In our experiment, by using Levchenko et al. model, we reveal that timesaving gains by using MIRACH easily surpass 400% compared with its offline-based counterpart.

Availability and implementation: MIRACH 1.0 was developed using Java and thus executable on any platform installed with JDK 6.0 (not JRE 6.0) or later. MIRACH 1.0, along with its source codes, documentation and examples are available at http://sourceforge.net/projects/mirach/ under the LGPLv3 license.

Contact:  masao@ims.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
A greedy, graph-based algorithm for the alignment of multiple homologous gene lists
Authors: Fostier Jan , Proost Sebastian , Dhoedt Bart , Saeys Yvan , Demeester Piet , Van de Peer Yves , Vandepoele Klaas
Published: January 2011

Motivation: Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed. However, such an approach is susceptible to the propagation of alignment errors in early pairwise alignment steps, especially when dealing with strongly diverged genomic regions. In this article, we present a novel accurate and efficient greedy, graph-based algorithm for the alignment of multiple homologous genomic segments, represented as ordered gene lists.

Results: Based on provable properties of the graph structure, several heuristics are developed to resolve local alignment conflicts that occur due to gene duplication and/or rearrangement events on the different genomic segments. The performance of the algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using both a progressive alignment method and an earlier graph-based implementation. Especially for datasets that contain strongly diverged segments, the proposed method achieves a substantially higher alignment accuracy, and proves to be sufficiently fast for large datasets including a few dozens of eukaryotic genomes.

Availability:  http://bioinformatics.psb.ugent.be/software. The algorithm is implemented as a part of the i-ADHoRe 3.0 package.

Contact:  yves.vandepeer@psb.vib-ugent.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation
Authors: Cao Yang , Song Lin , Miao Zhichao , Hu Yun , Tian Liqing , Jiang Taijiao
Published: January 2011

Motivation: Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy.

Results: We present a side-chain modeling method (CIS-RR), which couples a novel clash-detection guided iterative search (CIS) algorithm with continuous torsion space optimization of rotamers (RR). Benchmark testing shows that compared with the existing popular side-chain modeling methods, CIS-RR removes atomic clashes much more effectively and achieves comparable or even better prediction accuracy while having comparable computational cost. We believe that CIS-RR could be a useful method for accurate side-chain modeling.

Availability: CIS-RR is available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/cisrr/cisrr.html.

Contact:  taijiao@moon.ibp.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
A novel hybrid gene prediction method employing protein multiple sequence alignments
Authors: Keller Oliver , Kollmar Martin , Stanke Mario , Waack Stephan
Published: January 2011

Motivation: As improved DNA sequencing techniques have increased enormously the speed of producing new eukaryotic genome assemblies, the further development of automated gene prediction methods continues to be essential.

While the classification of proteins into families is a task heavily relying on correct gene predictions, it can at the same time provide a source of additional information for the prediction, complementary to those presently used.

Results: We extended the gene prediction software AUGUSTUS by a method that employs block profiles generated from multiple sequence alignments as a protein signature to improve the accuracy of the prediction. Equipped with profiles modelling human dynein heavy chain (DHC) proteins and other families, AUGUSTUS was run on the genomic sequences known to contain members of these families. Compared with AUGUSTUS' ab initio version, the rate of genes predicted with high accuracy showed a dramatic increase.

Availability: The AUGUSTUS project web page is located at http://augustus.gobics.de, with the executable program as well as the source code available for download.

Contact:  keller@cs.uni-goettingen.de; mario.stanke@uni-greifswald.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR
Authors: Chignola Francesca , Mari Silvia , Stevens Tim J. , Fogh Rasmus H. , Mannella Valeria , Boucher Wayne , Musco Giovanna
Published: January 2011

Summary: We present here the freely available Metabolomics Project resource specifically designed to work under the CcpNmr Analysis program produced by CCPN (Collaborative Computing Project for NMR) (Vranken et al., 2005, The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins, 59, 687–696). The project consists of a database of assigned 1D and 2D spectra of many common metabolites. The project aims to help the user to analyze and assign 1D and 2D NMR spectra of unknown metabolite mixtures. Spectra of unknown mixtures can be easily superimposed and compared with the database spectra, thus facilitating their assignment and identification.

Availability: The CCPN Metabolomics Project, together with an annotated example dataset, is freely available via: http://www.ccpn.ac.uk/metabolomics/.

Contact:  mari.silvia@hsr.it (experiments & protocol); tjs23@cam.ac.uk (software).

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Spatial structure of commercial marine fisheries in Northwest Mexico
Authors: Erisman Brad E. , Paredes Gustavo A. , Plomozo-Lugo Tomas , Cota-Nieto Juan J. , Hastings Philip A. , Aburto-Oropeza Octavio
Published: January 2011

Erisman, B. E., Paredes, G. A., Plomozo-Lugo, T., Cota-Nieto, J. J., Hastings, P. A., and Aburto-Oropeza, O. 2011. Spatial structure of commercial marine fisheries in Northwest Mexico. – ICES Journal of Marine Science, 68: . The spatial structure of commercial marine fisheries in Northwest (NW) Mexico was investigated using official landings data from 39 local fisheries offices in the region. Multivariate analyses revealed a clear spatial pattern in fishing activities, in which there was a positive linear relationship between the species composition of fisheries offices and both latitude and longitude. Fisheries offices formed eight distinct clusters organized by similarities in geographic location, species-group composition, and coastal habitat type. Five of the eight clusters comprised offices from the same geographic region and coastal ecosystem, and the other three clusters contained the largest industrial fishing ports in NW Mexico. The results of this study suggest that NW Mexico would benefit from an ecosystem-based management framework that focuses on the direct, spatial connection that exists between coastal habitats, harvested species groups, and fishing activities within each region. Subdivision into five separate regions is proposed, with management attention paid specially to the few industrialized ports whose fishing capacities and geographic ranges of fishing far exceed the other areas.
Low allozyme heterozygosity in North Pacific and Bering Sea populations of red king crab (Paralithodes camtschaticus): adaptive specialization, population bottleneck, or metapopulation structure?
Authors: Grant W. Stewart , Merkouris Susan E. , Kruse Gordon H. , Seeb Lisa W.
Published: January 2011

Grant, W. S., Merkouris, S. E., Kruse, G. H., and Seeb, L. W. 2011. Low allozyme heterozygosity in North Pacific and Bering Sea populations of red king crab (Paralithodes camtschaticus): adaptive specialization, population bottleneck, or metapopulation structure? – ICES Journal of Marine Science, 68: . Populations of red king crab in the North Pacific and Bering Sea have declined in response to ocean-climate shifts and to harvesting. An understanding of how populations are geographically structured is important to the management of these depressed resources. Here, the Mendelian variability at 38 enzyme-encoding loci was surveyed in 27 samples (n = 2427) from 18 general locations. Sample heterozygosities were low, averaging HE = 0.015 among samples. Weak genetic structure was detected among three groups of populations, the Bering Sea, central Gulf of Alaska, and Southeast Alaska, but without significant isolation by distance among populations. A sample from Adak Island in the western Aleutians was genetically different from the remaining samples. The lack of differentiation among populations within regions may, in part, be due to post-glacial expansions and a lack of migration-drift equilibrium and to limited statistical power imposed by low levels of polymorphism. Departures from neutrality may reflect the effects of both selective and historical factors. The low allozyme diversity in red king crab may, in part, be attributable to adaptive specialization, background selection, ice-age population bottlenecks, or metapopulation dynamics in a climatically unstable North Pacific.
HIV-1 Modulates the tRNA Pool to Improve Translation Efficiency
Authors: van Weringh Anna , Ragonnet-Cronin Manon , Pranckeviciene Erinija , Pavon-Eternod Mariana , Kleiman Lawrence , Xia Xuhua
Published: January 2011

Despite its poorly adapted codon usage, HIV-1 replicates and is expressed extremely well in human host cells. HIV-1 has recently been shown to package non-lysyl transfer RNAs (tRNAs) in addition to the tRNALys needed for priming reverse transcription and integration of the HIV-1 genome. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding codons that are highly used by HIV-1 but avoided by its host are overrepresented in HIV-1 virions. In particular, tRNAs decoding A-ending codons, required for the expression of HIV's A-rich genome, are highly enriched. Because the affinity of Gag-Pol for all tRNAs is nonspecific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Codon usage of HIV-1 early genes is similar to that of highly expressed host genes, but codon usage of HIV-1 late genes was better adapted to the selectively enriched tRNA pool, suggesting that alterations in the tRNA pool are induced late in viral infection. If HIV-1 genes are adapting to an altered tRNA pool, codon adaptation of HIV-1 may be better than previously thought.
The pathway to intelligent implants: osteoblast response to nano silicon-doped hydroxyapatite patterning
Authors: Munir G. , Koller G. , Di Silvio L. , Edirisinghe M. J. , Bonfield W. , Huang J.
Published: January 2011

Bioactive hydroxyapatite (HA) with addition of silicon (Si) in the crystal structure (silicon-doped hydroxyapatite (SiHA)) has become a highly attractive alternative to conventional HA in bone replacement owing to the significant improvement in the
in vivo
bioactivity and osteoconductivity. Nanometre-scaled SiHA (nanoSiHA), which closely resembles the size of bone mineral, has been synthesized in this study. Thus, the silicon addition provides an extra chemical cue to stimulate and enhance bone formation for new generation coatings, and the next stage in metallic implantation design is to further improve cellular adhesion and proliferation by control of cell alignment. Topography has been found to provide a powerful set of signals for cells and form contact guidance. Using the recently developed novel technique of template-assisted electrohydrodynamic atomization (TAEA), patterns of pillars and tracks of various dimensions of nanoSiHA were achieved. Modifying the parameters of TAEA, the resolution of pattern structures was controlled, enabling the topography of a substrate to be modified accordingly. Spray time, flow rate and distance between the needle and substrate were varied to improve the pattern formation of pillars and tracks. The 15 min deposition time provided the most consistent patterned topography with a distance of 50 mm and flow rate of 4 µl min
−1
. A titanium substrate was patterned with pillars and tracks of varying widths, line lengths and distances under the optimized TAEA processing condition. A fast bone-like apatite formation rate was found on nanoSiHA after immersion in simulated body fluid, thus demonstrating its high
in vitro
bioactivity. Primary human osteoblast (HOB) cells responded to SiHA patterns by stretching of the filopodia between track and pillar, attaching to the apex of the pillar pattern and stretching between two. HOB cells responded to the track pattern by elongating along and between the track, and the length of HOB cells was proportional to the gaps between track patterns, but this relationship was not observed on the pillar patterns. The study has therefore provided an insight for future design of next generation implant surfaces to control and guide cellular responses, while TAEA patterning provides a controllable technique to provide topography to medical implants.
The bizarre wing of the Jamaican flightless ibisXenicibis xympithecus: a unique vertebrate adaptation
Authors: Longrich Nicholas R. , Olson Storrs L.
Published: January 2011

Birds have frequently evolved to exploit insular environments by becoming adapted to a terrestrial lifestyle and losing the ability to fly, usually via reducing the wings and pectoral girdle. The enigmatic flightless ibisXenicibis xympithecus(Threskiornithidae) from the Quaternary of Jamaica provides a rare example of flight loss in ibises. We report on previously undescribed fossils ofXenicibis, and show that the wing differed radically from that of all other birds, flightless or volant. The metacarpus is elongate, grotesquely inflated and has extremely thick walls; phalanges are short and block-like; the radius is distally expanded; and the humerus is elongate. The furcula, coracoid and sternum are all well developed. We propose that the elongate forelimb and massive hand functioned in combat as a jointed club or flail. This hypothesis is supported by the morphology of the carpometacarpus, by features permitting rapid extension of the wing and by the presence of fractures in wing bones. Although other birds use the wings as weapons, none resembleXenicibis, which represents a unique and extraordinary morphological solution to this functional problem.Xenicibisstrikingly illustrates how similar selective pressures, acting on a similar starting point, can result in novel outcomes.
Brachybacterium saurashtrense sp. nov., a halotolerant root-associated bacterium with plant growth-promoting potential
Authors: Gontia Iti , Kavita Kumari , Schmid Michael , Hartmann Anton , Jha Bhavanath
Published: January 2011

A Gram-positive-staining, aerobic, non-motile, coccoid shaped, halotolerant bacterium (strain JG 06T) was isolated from the roots of Salicornia brachiata, an extreme halophyte. Phylogenetic analysis based on 16S rRNA gene sequence showed that the novel strain had sequence similarities of 99.2 % to Brachybacterium paraconglomeratum JCM 11608T, 99.0 % to Brachybacterium conglomeratum DSM 10241 and 98.2 % to Brachybacterium faecium DSM 4810T. DNA–DNA hybridization with B. paraconglomeratum DSM 46341T, B. conglomeratum DSM 10241T, B. faecium DSM 4810T, Brachybacterium tyrofermentans DSM 10673T, Brachybacterium alimentarium DSM 10672T, Brachybacterium fresconsis DSM 14564T, Brachybacterium sacelli DSM 14566T and Brachybacterium muris DSM 15460T resulted in reassociation values of 36.2 %, 36.5 %, 35.8 %, 27.6 %, 27.9 %, 28.2 %, 28.7 % and 11.2 %, respectively. The peptidoglycan type of strain JG 06T was variant A4γ. The menaquinone content was MK7 (100 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, monogalactosyl diglyceride, three unidentified phospholipids and three glycolipids. The predominant fatty acid was anteiso-C15 : 0 (52.07 %); significant amounts of iso-C16 : 0 (12.38 %), iso-C15 : 0 (8.59 %) and anteiso-C17 : 0 (10.03 %) were also present. The G+C content of the DNA was 73.0 mol%. The strain formed a growth pellicle in nitrogen-free semisolid NFb medium containing NaCl at levels of up to 4 % (w/v) and reduced acetylene to ethylene, a result indicative of N2 fixation. In nutrient broth medium the novel strain grew at NaCl concentrations up to 15 % (w/v). It also had the ability to produce indole-3-acetic acid (IAA) and siderophores, utilized 1-aminocyclopropane-1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. On the basis of physiological, biochemical data and phylogenetic analyses, strain JG 06T should be placed in the genus Brachybacterium. Strain JG 06T represents a novel species of the genus Brachybacterium for which the name Brachybacterium saurashtrense sp. nov. is proposed (type strain JG 06T = DSM 23186T = IMCC 252T).
Proposal that the arsenite-oxidizing organisms Thiomonas cuprina and ‘Thiomonas arsenivorans’ be reclassified as strains of Thiomonas delicata, and emended description of Thiomonas delicata
Authors: Battaglia-Brunet Fabienne , El Achbouni Hafida , Quemeneur Marianne , Hallberg Kevin B. , Kelly Donovan P. , Joulian Catherine
Published: January 2011

The three As(III)-oxidizing members of the class Betaproteobacteria Thiomonas delicata, Thiomonas cuprina and ‘Thiomonas arsenivorans’ were isolated from mining sites in geographically distinct areas, namely Japan, Germany and France, respectively. They are all able to oxidize As(III) but only ‘T. arsenivorans’ and T. cuprina show efficient autotrophic growth with As(III) and are able to grow on a sole carbon source. These two organisms are also motile, whereas T. delicata is not. Only T. cuprina can grow autotrophically on chalcopyrite. The three strains share >99 % gene sequence similarity with each other based on their 16S rRNA genes and 16S–23S ITS regions. DNA–DNA hybridization results are above, or close to, the threshold value of 70 % recommended for the definition of bacterial species. The three taxa show very similar fatty acid profiles with differences only in five minor fatty acid components. They possess phylogenetic and chemotaxonomic similarities supporting the reclassification of these taxa as a single species. We propose that ‘T. arsenivorans’ and T. cuprina be reassigned as strains of T. delicata (type strain DSM 17897T).
Paenibacillus wooponensis sp. nov., isolated from wetland freshwater
Authors: Baik Keun Sik , Choe Han Na , Park Seong Chan , Kim Eun Mi , Seong Chi Nam
Published: January 2011

A rod-shaped, endospore-forming, Gram-reaction-positive bacterium, designated strain WPCB018T, was isolated from a fresh water sample collected from Woopo wetland, Korea. The isolate was identified as a member of the genus Paenibacillus on the basis of phenotypic characteristics and phylogenetic inference based on 16S rRNA gene sequence analysis. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and unknown aminophospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 (32.2 %), C16 : 0 (20.1 %) and C18 : 0 (18.1 %). The DNA G+C content was 56.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WPCB018T belongs to a cluster comprising species of the genus Paenibacillus, its closest neighbours being Paenibacillus humicus PC-147T (97.5 %) and Paenibcillus pasadenensis SAFN-007T (96.2 %). Genomic DNA–DNA hybridizations performed with strain WPCB018T and type strains of the species P. humicus, P. pinihumi, P. phyllosphaerae, P. pasadenensis and P. tarimensis showed relatedness values of only 10, 17, 18, 19 and 20 %, respectively. On the basis of phenotypic, molecular and genetic evidence, strain WPCB018T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus wooponensis sp. nov. is proposed. The type strain of the novel species is WPCB018T ( = KCTC 13280T  = JCM 16350T).
Weissella ceti sp. nov., isolated from beaked whales (Mesoplodon bidens)
Authors: Vela A. I. , Fernández A. , Bernaldo de Quirós Y. , Herráez P. , Domínguez L. , Fernández-Garayzábal J. F.
Published: January 2011

During an investigation into the microbiota of beaked whales (Mesoplodon bidens), nine isolates were obtained from different organs of four animals. The isolates were Gram-positive-staining, catalase-negative, short rod-shaped or coccoid organisms. A phylogenetic analysis based on 16S rRNA gene sequences of these isolates allocated them to the genus Weissella, showing 96.3 % and 96.0 % 16S rRNA gene sequence similarity with Weissella viridescens NRIC 1536Tand Weissella minor NRIC 1625T, respectively. On the basis of phenotypic, physiological and phylogenetic evidence, it is proposed that the new isolates from whales represent a novel species of the genus Weissella, Weissella ceti sp. nov. The type strain of Weissella ceti is 1119-1A-09T ( = CECT 7719T = CCUG 59653T).
Enterobacter mori sp. nov., associated with bacterial wilt on Morus alba L.
Authors: Zhu Bo , Lou Miao-Miao , Xie Guan-Lin , Wang Guo-Fen , Zhou Qin , Wang Fang , Fang Yuan , Su Ting , Li Bin , Duan Yong-Pin
Published: January 2011

Two isolates of mulberry-pathogenic bacteria isolated from diseased mulberry roots were investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated strains R18-2T and R3-3 to the genus Enterobacter, with Enterobacter asburiae, E. amnigenus, E. cancerogenus, E. cloacae subsp. cloacae, E. cloacae subsp. dissolvens and E. nimipressuralis as their closest relatives. Cells of the isolates were Gram-negative, facultatively anaerobic rods, 0.3–1.0 µm wide and 0.8–2.0 µm long, with peritrichous flagella, showing a DNA G+C content of 55.1±0.5 mol%. Calculation of a similarity index based on phenotypic features and fatty acid methyl ester (FAME) analysis suggested that these isolates are members of E. cancerogenus or E. asburiae or a closely related species. Biochemical data revealed that the isolates could be differentiated from their nearest neighbours by the presence of lysine decarboxylase activity and their ability to utilize d-arabitol. DNA–DNA relatedness also distinguished the two isolates from phylogenetically closely related Enterobacter strains. Based on these data, it is proposed that the isolates represent a novel species of the genus Enterobacter, named Enterobacter mori sp. nov. The type strain is R18-2T ( = CGMCC 1.10322T  = LMG 25706T).