bluuebunny/crossref_metadata_2025 huggingface dataset:
“But I first… and then he kept picking”
Authors: Tsai Wanyu , Chang Chien-ju
Published: February 2014

This study investigates the narrative skill of school-aged children with language impairment in Taiwan. Twelve children, 6 children with language impairment (LI) and 6 children with typical language development (TLD), aged from 8;0 to 9;5 participated in this study. They were asked to tell three personally experienced stories and the longest one was selected and coded along four dimensions, i.e., narrative structure, conjunction, referential strategies, and discourse context. The revision of the Chinese Narrative Assessment Profile (NAP) was also used to score children’s narrative performance. Results show that the children with LI had more difficulties in producing clear, coherent narratives. In comparison with the stories narrated by children with TLD, the stories produced by children with LI exhibited fewer narrative components, evaluation devices, and connectives, but more ambiguous referencing information was evident in their narratives. The narrative profile of each child with LI, however, varied. Limitations of this study and suggestions for further research on narrative skill in children with LI were provided.
Troubled, troublesome, troubling mothers
Authors: Austin Helena , Carpenter Lorelei
Published: February 2014

Motherhood is under review. What counts as a ‘good mother’ is receiving attention in both popular and academic contexts (Arendell, 2000; Hays, 1996). The mothers we spoke with are judged not to be ‘good’ mothers by medical professionals, teachers, friends and family, because they do not have ‘good’ children. Their children are disorderly, disorganised and disruptive, they have ADHD. We extend current debates to explore these mothers’ ransoming to the narrative of ‘the way things should be’ in terms of Bourdieu’s (1990) concepts of habitus, misrecognition and symbolic violence. Importantly, we examine how these women talk back to the cultural narratives that malign and disregard them and their children. They trouble those narratives. However, in speaking out, in being always vigilant to their child’s interests, women often find they are considered not only troublesome, but themselves troubled. Rather than hearing them this way, we hear their stories as challenges to the cultural narratives that constrain them. We hear their voices as important activism in reformulating motherhood.
Introduction
Authors: Enfield N.J. , Wierzbicka Anna
Published: February 2014

Anthropologists and linguists have long been aware that the body is explicitly referred to in conventional description of emotion
in languages around the world. There is abundant linguistic data showing expression of emotions in terms of their imagined ‘locus’
in the physical body. The most important methodological issue in the study of emotions is language, for the ways people talk give
us access to ‘folk descriptions’ of the emotions. ‘Technical terminology’, whether based on English or otherwise, is not excluded
from this ‘folk’ status. It may appear to be safely ‘scientific’ and thus culturally neutral, but in fact it is not: technical
English is a variety of English and reflects, to some extent, culture-specific ways of thinking (and categorising) associated with
the English language. People — as researchers studying other people, or as people in real-life social association — cannot
directly access the emotional experience of others, and language is the usual mode of ‘packaging’ one’s experience so it may be
accessible to others. Careful description of linguistic data from as broad as possible a cross-linguistic base is thus an
important part of emotion research. All people experience biological events and processes associated with certain thoughts (or, as
psychologists say, ‘appraisals’), but there is more to ‘emotion’ than just these physiological phenomena. Speakers of some
languages talk about their emotional experiences as if they are located in some internal organ such as ‘the liver’, yet they
cannot localise feeling in this physical organ. This phenomenon needs to be understood better, and one of the problems is finding
a method of comparison that allows us to compare descriptions from different languages which show apparently great formal and
semantic variation. Some simple concepts including feel and body are universal or near-universal, and as such are good candidates
for terms of description which may help to eradicate confusion and exoticism from cross-linguistic comparison and semantic
typology. Semantic analysis reveals great variation in concepts of emotion across languages and cultures — but such analysis
requires a sound and well-founded methodology. While leaving room for different approaches to the task, we suggest that such a
methodology can be based on empirically established linguistic universal (or near-universal) concepts, and on ‘cognitive
scenarios’ articulated in terms of these concepts. Also, we warn against the danger of exoticism involved in taking all body part
references ‘literally’. Above all, we argue that what is needed is a combination of empirical cross-linguistic investigations and
a theoretical and methodological awareness, recognising the impossibility of exploring other people’s emotions without keeping
language in focus: both as an object and as a tool of study.
Cultural scripting of body parts for emotions
Authors: Ameka Felix K.
Published: February 2014

Different languages present a variety of ways of talking about emotional experience. Very commonly, feelings are described through
the use of ‘body image constructions’ in which they are associated with processes in, or states of, specific body parts. The
emotions and the body parts that are thought to be their locus and the kind of activity associated with these body parts vary
cross-culturally. This study focuses on the meaning of three ‘body image constructions’ used to describe feelings similar to, but
also different from, English ‘jealousy’, ‘envy’, and ‘covetousness’ in the West African language Ewe. It is demonstrated that a
‘moving body’, a pychologised eye, and red eyes are scripted for these feelings. It is argued that the expressions are not
figurative and that their semantics provide good clues to understanding the cultural construction of emotions both emotions and
the body.
The body in expressions of emotion: Kuot
Authors: Lindström Eva
Published: February 2014

This contribution examines the use of body terms in expressions of emotion in Kuot, a non-Austronesian language of New Ireland,
Papua New Guinea. It is found that expressions involving the word for ‘stomach’, daləp, correspond mainly to what
we would consider to be psychological states, while expressions making use of neip ‘skin; body’ are largely
concerned with physical states. Some other body parts also form part of emotive expressions.
Emotions and the body in Russian and English
Authors: Pavlenko Aneta
Published: February 2014

The goal of the present paper is to examine Wierzbicka’s (1992, 1998a, 1999) claims that the connection between emotions and the
body is encoded and emphasized in Russian to a higher degree than it is in English, and that English favors the adjectival pattern
in emotion discourse, while Russian prefers the verbal one. The study analyzes oral narratives elicited through the same visual
stimuli from 40 monolingual Russians and 40 monolingual Americans. The results of the quantitative and qualitative analyses of the
narrative corpus support Wierzbicka’s claims, suggesting that ‘the reading of the body’ is not a culture- and language-free
experience, but is shaped by cultural, social, and linguistic forces, as well as by individual differences. At the same time,
neither quantitative nor qualitative differences have been identified with regard to gendered use of emotion discourse.
Insides and emotion in Koromu
Authors: Priestley Carol
Published: February 2014

This paper describes several emotion expressions in Koromu, a language of Papua New Guinea. As in other languages, emotions can be
expressed by reference to body events and processes. Bodily images are used for common and pertinent emotion expressions in Koromu
and the alternative grammatical constructions in which some of these expressions occur enable speakers to express varying emotions
while still indicating that there are shared semantic components between the expressions. In addition, as the emotion expressions
are examined and their meanings explicated, a number of universal concepts and components of meaning can be observed. A study of
these language specific expressions therefore contributes to a cross-linguistic understanding of the relationship between emotion
and the body.
Body part terms in Kaytetye feeling expressions
Authors: Turpin Myfany
Published: February 2014

This paper addresses the question of how feelings are expressed in Kaytetye, a Central Australian language of the Pama-Nyugan
family. It identifies three different formal constructions for expressing feelings, and explores the extent to which specific body
part terms are associated with types of feelings, based on linguistic evidence in the form of lexical compounds, collocations and
the way people talk about feelings. It is suggested that particular body part terms collocate with different feeling expressions
for different reasons: either because the body part is the perceived locus of the feeling, or because of a lexicalised polysemy of
a body part term, or because of a metonymic association between a body part, a behaviour and a feeling.
Enhancing in automatic recognition and extraction of term variants with linguistic features
Authors: Ville-Ometz Fabienne , Royauté Jean , Zasadzinski Alain
Published: February 2014

The recognition and extraction of terms and their variants in texts are crucial processes in text mining. We use the ILC platform, an automatic controlled indexing platform, to perform these linguistic processes. We present a methodology for enhancing the recognition of syntactic term variation in English, using syntactic and morpho-syntactic features. Principal spurious variants of terms are ascribed to incorrect word dependencies. To overcome these problems, we consider each term variant as a window on the sentence and introduce two criteria: an internal syntactic criterion which checks that the dependencies between words in the window are respected, and an external criterion which defines boundaries, making it possible to ensure that the window is well positioned in the sentence. The use of these criteria improves filtering of the variants and assists the expert in validating the indexing.
Recent advances in automatic term recognition
Authors: Kageura Kyo , Yoshioka Masaharu , Takeuchi Koichi , Koyama Teruo , Tsuji Keita , Yoshikane Fuyuki
Published: February 2014

This article provides basic background information on the articles included in this special issue on Japanese term extraction, by (i) clarifying the basic background of research into automatic term recognition, (ii) explaining briefly the ‘contest’-style workshop we organised in 1999, and (iii) briefly summarising the ATR methodologies proposed in the articles, and positioning their ideas, philosophies and methodologies within ATR from a unified perspective. Through this information, we intend to consolidate the contributions of the NTCIR TMREC workshop, and, hopefully, clarify a basic framework for discussion which different researchers can use to constructively communicate with each other about automatic term extraction and beyond.
Automatic term recognition based on statistics of compound nouns
Authors: Nakagawa Hiroshi
Published: February 2014

The NTCIR1 TMREC group called for participation of the term recognition task which is a part of NTCIR1 held in 1999. As an activity of TMREC, they have provided us with the test collection of the term recognition task. The goal of this task is to automatically recognize and extract terms from the text corpus which consists of 1,870 abstracts gathered from the NACSIS Academic Conference Database. This article describes the term extraction method we have proposed to extract terms consisting of simple and compound nouns and the experimental evaluation of the proposed method with this NTCIR TMREC test collection. The basic idea of scoring a simple noun N of our term extraction method is to count how many nouns are conjoined with N to make compound nouns. Then we extend this score to measure the score of compound nouns because most of technical terms are compound nouns. Our method has a parameter to tune the degree of preference either for longer compound nouns or for shorter compound nouns. As for term candidates, in addition to noun sequences, we may add variations such as patterns of "A no B" that roughly means "B of A" or "A’ś B" and/or "A na B" where "A na" is an adjective. Experimental results of our method are promising, namely recall of 0.83, precision of 0.46 and F-value of 0.59 for exactly matched extracted terms when we take into account top scoring 16,000 extracted terms.
Extracting terms by a combination of term frequency and a measure of term representativeness
Authors: Hisamitsu Toru , Niwa Yoshiki , Nishioka Shingo , Sakurai Hirofumi , Imaichi Osamu , Iwayama Makoto , Takano Akihiko
Published: February 2014

This article describes a method for extracting terms that combines term frequency with a novel measure of term representativeness (i.e., informativeness or domain specificity). The measure is defined as the normalized distance between the word distribution in the documents which contain the term and the word distribution in the whole corpus. The measure is particularly effective in discarding uninformative terms that frequently appear and has a well-defined threshold value for judging the representativeness of a term. We combined the new measure with term frequency and applied it to the extraction of terms from abstracts of artificial intelligence papers. This article introduces the measure and reports on its effectiveness in term extraction.
Statistical and linguistic approaches to automatic term recognition
Authors: Fukushige Yoshio , Noguchi Naohiko
Published: February 2014

In this article we describe our approaches and the results to the Term Recognition (TMREC) task in the first NTCIR Workshop on Research in Japanese Text. Retrieval and Term Recognition, held 30 August-1 September 1999. Our first approach aims to collect words that appear distinctively in documents of the target domain through statistical method. Our second approach aims to collect terms that have a particular inner structure by applying several diagnostic tests using the collocational information in the corpus. Section 1 describes the outline of the term recognition task. Section 2 briefly describes the two approaches, details of which are described in Sections 3 and 4. In Section 6, we offer a short discussion based on the comparison between the candidates.
Using author keywords for automatic term recognition
Authors: Utiyama Masao , Murata Masaki , Isahara Hitoshi
Published: February 2014

This paper proposes a method which regards the keywords provided by the authors of technical papers as terms and learns the statistics which distinguish terms from non-terms. Since it uses keywords as training data, it requires no hand-labeled training corpora manually annotated with terms. The proposed method was used to extract terms from the NTCIR morphologically tagged corpus and achieved 0.800 recall and 0.431 precision. The effectiveness of the proposed method has thus been demonstrated.
Metaphorical radiodiagnostic terms
Authors: Méndez-Cendón Beatriz , Chang Leslie-Ann
Published: February 2014

The purpose of this article is to identify and classify metaphorical sign terms in the field of abdominal radiodiagnostic imaging. A 1,000,000 word electronic corpus of English and Spanish medical texts was used to compile an extensive list of metaphorical designations for signs detected on radiological images. These terms were classified thematically and structurally and analyzed from the terminological perspective of logical motivation. The fundamental premise behind this research is the belief that a better knowledge of this type of terminology (both English and Spanish) can lead to a better understanding of the specialist’s perception of the prototypical image conjured by the metaphor.
Translation Studies and academic allies
Authors: Gentzler Edwin
Published: February 2014

While a critical mass of scholarship may have been reached to launch a journal such as TIS, much work needs to be done in developing allies and growing the field of translation and interpreting studies in the United States. This paper attempts to outline a few natural academic allies—programs in creative writing, area studies, com-parative literature, and anthropology. While looking at the respective strengths of the translation scholarship in these allied fields, I also offer a critique of some of those pro-grams. The goal is to point out areas of interest that will mutually benefit both translation studies and other fields. The paper is divided into five parts: (1) The 2004 ATSA Confer-ence; (2) The First US Translation Studies Scholar; (3) The Present State of Translation Studies in the United States; (4) Connections with Emerging Area Studies Programs; and (5) Connections with Comparative Literature and Anthropology. I conclude by suggesting that, while a critical mass may have been reached to start a journal, much work needs to be done in broadening the scope of our organization to include potential partners. The goal is to build a truly open and inclusive discipline, one that reflects the true range of ongoing translation studies investigations in the country.
Minding the Gaps: New directions in Interpreting Studies
Authors: Angelelli Claudia V.
Published: February 2014

This article presents an overview of the state of interpreting studies from the origins of the profession to the current state of the field. It explores the in-terconnection between interpreting and translation studies and the evolution of inter-preting into a field of study in its own right. Since interpreting is an interdisciplinary endeavor, this article argues for the need to continue to expand perspectives, paying special consideration to perspectives from related fields. It takes a closer look at interpreting as a situated practice, as it unfolds in courts of law, health care organi-zations, and business environments. It suggests the need for a deeper dialogue among all related disciplines and suggests a research agenda for the future.
Translation and the nationalist/migrant double bind
Authors: Robinson Douglas
Published: February 2014

Using an expanded version of Gregory Bateson’s model of the double-bind, the article explores conflicting ideological norms governing the translator’s loyalties to countries, cultures, and languages through a series of doubly-bound commands.
Translating maman and papa: A corpus-based survey
Authors: Cummins Sarah , Parent Geneviève
Published: February 2014

This study examines the translation of the French terms maman and papa by English-language translators from the nineteenth century to the present. Following a comparative analysis of the semantics of the French terms and of their most typical English translations, the authors of the study isolate trends in the translation of these terms through analysis of corpora of French and Quebecois literary texts and their translations.
"Translational thinking" among foreign scholars writing discipline-specific English
Authors: Raymond Patricia M. , Williams Donna A.
Published: February 2014

This article reports on a study which is a small step toward the exploration of translational exchange of ideas and practices among academic disciplines and across languages and cultures. It presents results of an ongoing longitudinal study auditing the cultural performance of resources made available to foreign scholars at universities in Canada and concludes by discussing implications for future study of the intersection between academic self-translation and cross-cultural communication.
Translating "America's most nuclear family" into Italian: Dubbing and cultural adaptation in The Simpsons
Authors: Tomaiuolo Saverio
Published: February 2014

The Simpsons is one of the most successful cartoons and one of the most famous (and widely quoted) sitcoms in TV history, a mass-media phenomenon and the longest-running prime-time animated show in television history. As a typical postmodern creation, it oscillates between a work of art and a consumer good to be exported and sold. Translators and dubbing teams attempting to reproduce it in another language (and culture) must deal confidently with an enormous amount of textual material. This article analyzes the practical strategies adopted by Italian translators using selected episodes from Season Five (with references to other seasons and episodes). As this analysis of the Italian edition will try to demonstrate that, while The Simpsons undoubtedly remains an American ‘product’, many of its themes and references are part of a global cultural background whose adaptation for a ‘local’ audience, such as the Italian one, can still be possible.
The application of text type in non-literary translation teaching
Authors: Qiujin Chen
Published: February 2014

Despite the relevance of text type to translation practice, especially to Chinese-English non-literary translation in which the two languages display remarkable textual differences, there has been a general lack of attention to the text type-related issues in translation teaching in Chinese universities. Centered upon translation of literary works, the teaching has long focused on techniques at the lexical and syntactic level, and a text-based approach has yet to be adopted. This coincides with the clear tendency in the assignment of non-literary translation that students are quite active in making adaptation at the lexical and syntactic level, but much more reluctant to make decisions at the textual level. Despite their intuitive awareness of the textual differences between the two languages, they are not well trained to effectively deal with such differences so that the translated text can fulfill its communicative function. This article is an attempt to pinpoint this problem and highlight the necessity of including text type in translation pedagogy. It also experimentally proposes a new teaching framework within which text type is taught in a systematic manner.
A Fock space model for addition and multiplication of c-free random variables
Authors: Popa Mihai
Published: February 2014

The paper presents a Fock space model suitable for construction of c-free algebras. Immediate applications are direct proofs for the properties of the c-free

R
R

- and

S
S

-transforms.
Evaluating Igusa functions
Authors: Bröker Reinier , Lauter Kristin
Published: February 2014

The moduli space of principally polarized abelian surfaces is parametrized by three Igusa functions. In this article we investigate a new way to evaluate these functions by using the Siegel Eisenstein series. We explain how to compute the Fourier coefficients of certain Siegel modular forms using classical modular forms of half-integral weight. One of the results in this paper is an explicit algorithm to evaluate the Igusa functions to a prescribed precision.
FAP20 is an inner junction protein of doublet microtubules essential for both the planar asymmetrical waveform and stability of flagella inChlamydomonas
Authors: Yanagisawa Haru-aki , Mathis Garrison , Oda Toshiyuki , Hirono Masafumi , Richey Elizabeth A. , Ishikawa Hiroaki , Marshall Wallace F. , Kikkawa Masahide , Qin Hongmin
Published: February 2014

The axoneme—the conserved core of eukaryotic cilia and flagella—contains highly specialized doublet microtubules (DMTs). A long-standing question is what protein(s) compose the junctions between two tubules in DMT. Here we identify a highly conserved flagellar-associated protein (FAP), FAP20, as an inner junction (IJ) component. The flagella of Chlamydomonas FAP20 mutants have normal length but beat with an abnormal symmetrical three-dimensional pattern. In addition, the mutant axonemes are liable to disintegrate during beating, implying that interdoublet connections may be weakened. Conventional electron microscopy shows that the mutant axonemes lack the IJ, and cryo–electron tomography combined with a structural labeling method reveals that the labeled FAP20 localizes at the IJ. The mutant axonemes also lack doublet-specific beak structures, which are localized in the proximal portion of the axoneme and may be involved in planar asymmetric flagellar bending. FAP20 itself, however, may not be a beak component, because uniform localization of FAP20 along the entire length of all nine DMTs is inconsistent with the beak's localization. FAP20 is the first confirmed component of the IJ. Our data also suggest that the IJ is important for both stabilizing the axoneme and scaffolding intra–B-tubular substructures required for a planar asymmetrical waveform.
The stoichiometry of the nucleoporin 62 subcomplex of the nuclear pore in solution
Authors: Ulrich Alexander , Partridge James R. , Schwartz Thomas U.
Published: February 2014

The nuclear pore complex (NPC) regulates transport between the nucleus and cytoplasm. Soluble cargo-protein complexes navigate through the pore by binding to phenylalanine-glycine (FG)-repeat proteins attached to the channel walls. The Nup62 complex contains the FG-repeat proteins Nup62, Nup54, and Nup58 and is located in the center of the NPC. The three proteins bind each other via conserved coiled-coil segments. To determine the stoichiometry of the Nup62 complex, we undertook an in vitro study using gel filtration and analytical ultracentrifugation. Our results reveal a 1:1:1 stoichiometry of the Nup62 complex, where Nup54 is central with direct binding to Nup62 and Nup58. At high protein concentration, the complex forms larger assemblies while maintaining the Nup62:Nup54:Nup58 ratio. For the homologous Nsp1 complex from Saccharomyces cerevisiae, we determine the same stoichiometry, indicating evolutionary conservation. Furthermore, we observe that eliminating one binding partner can result in the formation of complexes with noncanonical stoichiometry, presumably because unpaired coiled-coil elements tend to find a promiscuous binding partner. We suggest that these noncanonical stoichiometries observed in vitro are unlikely to be physiologically relevant.
Kinetochore-driven outgrowth of microtubules is a central contributor to kinetochore fiber maturation in crane-fly spermatocytes
Authors: LaFountain James R. , Oldenbourg Rudolf
Published: February 2014

We use liquid crystal polarized light imaging to record the life histories of single kinetochore (K-) fibers in living crane-fly spermatocytes, from their origins as nascent K-fibers in early prometaphase to their fully matured form at metaphase, just before anaphase onset. Increased image brightness due to increased retardance reveals where microtubules are added during K-fiber formation. Analysis of experimentally generated bipolar spindles with only one centrosome, as well as of regular, bicentrosomal spindles, reveals that microtubule addition occurs at the kinetochore-proximal ends of K-fibers, and added polymer expands poleward, giving rise to the robust K-fibers of metaphase cells. These results are not compatible with a model for K-fiber formation in which microtubules are added to nascent fibers solely by repetitive “search and capture” of centrosomal microtubule plus ends. Our interpretation is that capture of centrosomal microtubules—when deployed—is limited to early stages in establishment of nascent K-fibers, which then mature through kinetochore-driven outgrowth. When kinetochore capture of centrosomal microtubules is not used, the polar ends of K-fibers grow outward from their kinetochores and usually converge to make a centrosome-free pole.
Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures
Authors: Nagata Ken , Randall Arlo , Baldi Pierre
Published: February 2014

Motivation: Accurately predicting protein side-chain conformations is an important subproblem of the broader protein structure prediction problem. Several methods exist for generating fairly accurate models for moderate-size proteins in seconds or less. However, a major limitation of these methods is their inability to model post-translational modifications (PTMs) and unnatural amino acids. In natural living systems, the chemical groups added following translation are often critical for the function of the protein. In engineered systems, unnatural amino acids are incorporated into proteins to explore structure–function relationships and create novel proteins.

Results: We present a new version of SIDEpro to predict the side chains of proteins containing non-standard amino acids, including 15 of the most frequently observed PTMs in the Protein Data Bank and all types of phosphorylation. SIDEpro uses energy functions that are parameterized by neural networks trained from available data. For PTMs, the and accuracies are comparable with those obtained for the precursor amino acid, and so are the RMSD values for the atoms shared with the precursor amino acid. In addition, SIDEpro can accommodate any PTM or unnatural amino acid, thus providing a flexible prediction system for high-throughput modeling of proteins beyond the standard amino acids.

Availability and implementation: SIDEpro programs and Web server, rotamer libraries and data are available through the SCRATCH suite of protein structure predictors at http://scratch.proteomics.ics.uci.edu/

Contact:  pfbaldi@uci.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes
Authors: Huerta Mario , Munyi Marc , Expósito David , Querol Enric , Cedano Juan
Published: February 2014

Summary: The microarrays performed by scientific teams grow exponentially. These microarray data could be useful for researchers around the world, but unfortunately they are underused. To fully exploit these data, it is necessary (i) to extract these data from a repository of the high-throughput gene expression data like Gene Expression Omnibus (GEO) and (ii) to make the data from different microarrays comparable with tools easy to use for scientists. We have developed these two solutions in our server, implementing a database of microarray marker genes (Marker Genes Data Base). This database contains the marker genes of all GEO microarray datasets and it is updated monthly with the new microarrays from GEO. Thus, researchers can see whether the marker genes of their microarray are marker genes in other microarrays in the database, expanding the analysis of their microarray to the rest of the public microarrays. This solution helps not only to corroborate the conclusions regarding a researcher's microarray but also to identify the phenotype of different subsets of individuals under investigation, to frame the results with microarray experiments from other species, pathologies or tissues, to search for drugs that promote the transition between the studied phenotypes, to detect undesirable side effects of the treatment applied, etc. Thus, the researcher can quickly add relevant information to his/her studies from all of the previous analyses performed in other studies as long as they have been deposited in public repositories.

Availability: Marker-gene database tool: http://ibb.uab.es/mgdb

Contact:  jcedano@unorte.edu.uy
Optimization of gene set annotations via entropy minimization over variable clusters (EMVC)
Authors: Frost H. Robert , Moore Jason H.
Published: February 2014

Motivation: Gene set enrichment has become a critical tool for interpreting the results of high-throughput genomic experiments. Inconsistent annotation quality and lack of annotation specificity, however, limit the statistical power of enrichment methods and make it difficult to replicate enrichment results across biologically similar datasets.

Results: We propose a novel algorithm for optimizing gene set annotations to best match the structure of specific empirical data sources. Our proposed method, entropy minimization over variable clusters (EMVC), filters the annotations for each gene set to minimize a measure of entropy across disjoint gene clusters computed for a range of cluster sizes over multiple bootstrap resampled datasets. As shown using simulated gene sets with simulated data and Molecular Signatures Database collections with microarray gene expression data, the EMVC algorithm accurately filters annotations unrelated to the experimental outcome resulting in increased gene set enrichment power and better replication of enrichment results.

Availability and implementation:  http://cran.r-project.org/web/packages/EMVC/index.html.

Contact:  jason.h.moore@dartmouth.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Complex assessments or simple management procedures for efficient fisheries management: a comparative study
Authors: Geromont H. F. , Butterworth D. S.
Published: February 2014

Complex stock assessment methods are data- and expertise-hungry, with the annual updates of catch-at-age data and models typically seen as an essential requirement for sound management. But are the heavy commitments of resources required for this level of annual intervention really necessary to achieve efficient long-term fishery management? This question is addressed through a retrospective analysis of management performance over the last 20 years for four North Atlantic fish stocks. The assessments for two of these stocks have exhibited fairly strong retrospective patterns. The actual assessment advice for these stocks was provided based on complex assessment methods making use of age data. The outcomes are compared with what could have been achieved with much simpler catch control rules based upon age-aggregated survey indices alone. Even for the stocks whose assessments exhibit retrospective patterns, these simple rules can achieve virtually equivalent catch and risk performance, with much less interannual TAC variability, compared with what actually occurred over the past 20 years.
Fishing for revenue: how leasing quota can be hazardous to your health
Authors: Emery Timothy J. , Hartmann Klaas , Green Bridget S. , Gardner Caleb , Tisdell John
Published: February 2014

Fisheries management decisions have the potential to influence the safety of fishers by affecting how and when they fish. This implies a responsibility of government agencies to consider how fishers may behave under different policies and regulations in order to reduce the incidence of undesirable operational health and safety outcomes. In the Tasmanian southern rock lobster fishery, Australia, the expansion of the quota lease market under individual transferable quota (ITQ) management coincided with a rise in the number of commercial fishing fatalities, with five between 2008 and 2012. A discrete choice model of daily participation was fitted to compare whether physical risk tolerance varied between fishers who owned the majority of their quota units (quota owners) and those who mainly leased (lease quota fishers). In general, fishers were averse to physical risk (wave height), however this was offset by increases in expected revenue. Lease quota fishers were more responsive to changes in expected revenue than quota owners, which contributed to risk tolerance levels that were significantly higher than those of quota owners in some areas. This pattern in behaviour appeared to be related to the cost of leasing quota. Although ITQs have often been considered to reduce the incentive for fishers to operate in hazardous weather conditions, this assumes fishing by quota owners. This analysis indicated that this doesn't hold true for lease quota fishers in an ITQ system, where in some instances there remains an economic incentive to fish in conditions with high levels of physical risk.
Epigenetics of Human Myometrium: DNA Methylation of Genes Encoding Contraction-Associated Proteins in Term and Preterm Labor
Authors: Mitsuya Kohzoh , Singh Natasha , Sooranna Suren R. , Johnson Mark R. , Myatt Leslie
Published: February 2014

Preterm birth involves the interaction of societal and environmental factors potentially modulating the length of gestation via the epigenome. An established form of epigenetic regulation is DNA methylation where promoter hypermethylation is associated with gene repression. We hypothesized we would find differences in DNA methylation in the myometrium of women with preterm labor of different phenotypes versus normal term labor. Myometrial tissue was obtained at cesarean section at term with or without labor, preterm without labor, idiopathic preterm labor, and twin gestations with labor. Genomic DNA was isolated, and samples in each group were combined and analyzed on a NimbleGen 2.1M human DNA methylation array. Differences in methylation from −8 to +3 kb of transcription start sites of 22 contraction-associated genes were determined. Cytosine methylation was not present in CpG islands of any gene but was present outside of CpG islands in shores and shelves in 19 genes. No differential methylation was found across the tissue groups for six genes (PTGES3L, PTGER2, PTGER4, PTGFRN, ESR2, and GJA1). For 13 genes, differential methylation occurred in several patterns between tissue groups. We find a correlation between hypomethylation and increased mRNA expression of PTGES/mPGES-1, indicating potential functional relevance of methylation, but no such correlation for PTGS2/COX-2, suggesting other regulatory mechanisms for PTGS2 at labor. The majority of differential DNA methylation of myometrial contraction-associated genes with different labor phenotypes occurs outside of CpG islands in gene promoters, suggesting that the entirety of DNA methylation across the genome should be considered.
Fast-spiking Cell to Pyramidal Cell Connections Are the Most Sensitive to Propofol-induced Facilitation of GABAergic Currents in Rat Insular Cortex
Authors: Koyanagi Yuko , Oi Yoshiyuki , Yamamoto Kiyofumi , Koshikawa Noriaki , Kobayashi Masayuki
Published: February 2014

Background:

Propofol facilitates γ-aminobutyric acid–mediated inhibitory synaptic transmission. In the cerebral cortex, γ-aminobutyric acidergic interneurons target both excitatory pyramidal cells (Pyr) and fast-spiking (FS) and non-FS interneurons. Therefore, the propofol-induced facilitation of inhibitory transmission results in a change in the balance of excitatory and inhibitory inputs to Pyr. However, it is still unknown how propofol modulates γ-aminobutyric acidergic synaptic transmission in each combination of Pyr and interneurons.

Methods:

The authors examined whether propofol differentially regulates inhibitory postsynaptic currents (IPSCs) depending on the presynaptic and postsynaptic cell subtypes using multiple whole cell patch clamp recording from γ-aminobutyric acidergic interneurons and Pyr in rat insular cortex.

Results:

Propofol (10 μM) consistently prolonged decay kinetics of unitary IPSCs (uIPSCs) in all types of inhibitory connections without changing paired-pulse ratio of the second to first uIPSC amplitude or failure rate. The FS→Pyr connections exhibited greater enhancement of uIPSC charge transfer (2.2 ± 0.5 pC, n = 36) compared with that of FS→FS/non-FS connections (0.9 ± 0.2 pC, n = 37), whereas the enhancement of charge transfer in non-FS→Pyr (0.3 ± 0.1 pC, n = 15) and non-FS→FS/non-FS connections (0.2 ± 0.1 pC, n = 36) was smaller to those in FS→Pyr/FS/non-FS. Electrical synapses between FS pairs were not affected by propofol.

Conclusions:

The principal inhibitory connections (FS→Pyr) are the most sensitive to propofol-induced facilitation of uIPSCs, which is likely mediated by postsynaptic mechanisms. This preferential uIPSC enhancement in FS→Pyr connections may result in suppressed neural activities of projection neurons, which in turn reduces excitatory outputs from cortical local circuits.
A partial proteome reference map of the wine lactic acid bacterium
Oenococcus oeni
ATCC BAA-1163
Authors: Mohedano María de la Luz , Russo Pasquale , de los Ríos Vivian , Capozzi Vittorio , Fernández de Palencia Pilar , Spano Giuseppe , López Paloma
Published: February 2014

Oenococcus oeni
is the main lactic acid bacterium that carries out the malolactic fermentation in virtually all red wines and in some white and sparkling wines.
Oenococcus oeni
possesses an array of metabolic activities that can modify the taste and aromatic properties of wine. There is, therefore, industrial interest in the proteins involved in these metabolic pathways and related transport systems of this bacterium. In this work, we report the characterization of the
O. oeni
ATCC BAA-1163 proteome. Total and membrane protein preparations from
O. oeni
were standardized and analysed by two-dimensional gel electrophoresis. Using tandem mass spectrometry, we identified 224 different spots corresponding to 152 unique proteins, which have been classified by their putative function and subjected to bioinformatics analysis.
Pseudopedobacter beijingensis gen. nov., sp. nov., isolated from coking wastewater activated sludge, and reclassification of Pedobacter saltans as Pseudopedobacter saltans comb. nov.
Authors: Cao Junwei , Lai Qiliang , Li Guizhen , Shao Zongze
Published: February 2014

A taxonomic study was carried out on strain GCS-AE-31T, which was isolated from a phenol-degrading consortium, enriched from coking wastewater activated sludge of the Beijing Shougang Company Limited during the screening of phenol-degrading bacteria. Cells of strain GCS-AE-31T were Gram-stain-negative, short rods, motile by gliding, oxidase- and catalase-positive. Growth was observed at salinities of 0–3 % and at temperatures of 10–37 °C. On the basis of 16S rRNA gene sequence similarity, strain GCS-AE-31T was most closely related to

Pedobacter saltans

LMG 10337T (96.17 %), but it showed low similarity to all other species of the genus

Pedobacter

(89.28–92.45 %). It also showed low 16S rRNA gene similarity to all other species of the family

Sphingobacteriaceae

(87.25–92.45 %) examined. The dominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), anteiso-C15 : 0 and iso-C17 : 0 3-OH. The menaquinones were MK-7 (95.5 %) and MK-6 (4.5 %). The polar lipids were phosphatidylethanolamine, three aminolipids and three unknown phospholipids. Sphingolipid was present. The G+C content of the chromosomal DNA was 36.2 mol%. According to its phylogenetic position and phenotypic traits, the novel strain could not be assigned to the genus

Pedobacter

; it should be classified as representing a novel species of a novel genus in the family

Sphingobacteriaceae

, for which the name Pseudopedobacter beijingensis gen. nov., sp. nov. is proposed (type strain GCS-AE-31T = MCCC 1A01299T = CGMCC 1.12329T = LMG 27180T). The misclassified species

Pedobacter saltans

is transferred to the novel genus as Pseudopedobacter saltans comb. nov. (type strain LMG 10337T = MCCC 1A06472T = DSM 12145T = CCUG 39354T = CIP 105500T = JCM 21818T = NBRC 100064T).
Metschnikowia laotica f.a., sp. nov., a dimorphic, pigment-producing yeast species isolated from fruit
Authors: Sipiczki Matthias
Published: February 2014

Eight strains with identical sequences of the D1/D2 domains of the large subunit rRNA genes were isolated from fallen fruits in two distant localities in Laos. These strains represent a novel dimorphic budding yeast species producing invasive pseudohyphae and a brown pigment when growing on media containing quinic acid as the sole carbon source or tryptophan as the sole nitrogen source. Phylogenetic analysis of the sequences of the D1/D2 domains, the internal transcribed spacer (ITS) regions and the 18S rRNA genes placed the novel species in theMetschnikowiaclade close toCandida torresii,Metschnikowia drosophilaeandCandida danieliae. The taxonomic nameMetschnikowia laoticaf.a., sp. nov., reflecting the geographical origin of the isolates, is proposed for the novel species. The type strain is 11-524T( = CBS 12961T = NCAIM Y.02124T = CCY 64-4-1T). The Mycobank number is MB 807383.
Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi
Authors: Sorokin Dimitry Y. , Vejmelkova Dana , Lücker Sebastian , Streshinskaya Galina M. , Rijpstra W. Irene C. , Sinninghe Damsté Jaap S. , Kleerbezem Robbert , van Loosdrecht Mark , Muyzer Gerard , Daims Holger
Published: February 2014

A novel nitrite-oxidizing bacterium (NOB), strain LbT, was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain LbTwas an obligately aerobic, chemolitoautotrophic NOB, utilizing nitrite or formate as the energy source and CO2as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with nitrite was optimal at pH 6.8–7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20alkyl 1,2-diols with the dominant fatty acids being 10MeC18and C18 : 1ω9. The peptidoglycan lackedmeso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain LbTinto the classThermomicrobiaof the phylumChloroflexiwithSphaerobacter thermophilusas the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain LbTrepresents a novel species of a new genus, with the suggested nameNitrolancea hollandicagen. nov., sp. nov. The type strain of the type species is LbT( = DSM 23161T = UNIQEM U798T).
The Escherichia coli datA site promotes proper regulation of cell division
Authors: Morigen Morigen , Flåtten Ingvild , Skarstad Kirsten
Published: February 2014

InEscherichia coliinhibition of replication leads to a block of cell division. This checkpoint mechanism ensures that no cell divides without having two complete copies of the genome to pass on to the two daughter cells. The chromosomaldatAsite is a 1 kb region that contains binding sites for the DnaA replication initiator protein, and which contributes to the inactivation of DnaA. An excess ofdatAsites provided on plasmids has been found to lead to both a delay in initiation of replication and in cell division during exponential growth. Here we have investigated the effect ofdatAon the cell division block that occurs upon inhibition of replication initiation in adnaC2mutant. We found that this checkpoint mechanism was aided by the presence ofdatA. In cells wheredatAwas deleted or an excess of DnaA was provided, cell division occurred in the absence of replication and anucleate cells were formed. This finding indicates that loss ofdatAand/or excess of DnaA protein promote cell division. This conclusion was supported by the finding that the lethality of the division-compromised mutantsftsZ84 andftsI23 was suppressed by deletion ofdatA, at the lowest non-permissive temperature. We propose that the cell division block that occurs upon inhibition of DNA replication is, at least in part, due to a drop in the concentration of the ATP–DnaA protein.