bluuebunny/crossref_metadata_2025 huggingface dataset:
Discursive democratization in Mainland China
Authors: Huang Ying , Chen Jian-ping
Published: August 2009

From the perspective of critical discourse analysis, the present study reveals, both qualitatively and quantitatively, that there has emerged a trend of discursive democratization in the New Year’s editorials in the People’s Daily. This emerging trend is signaled by the reduction of explicit power markers such as the modalities, the negative linguistic items of Judgment and by the increase of implicit power markers of positive linguistic items of Appreciation in Appraisal system. We suggest that discursive democratization in these editorials is the result of the restructuring of both institutional and societal orders of discourse in mainland China; however, the trend of discursive democratization is only conditional and rather limited under the current political system.
Reconstructing Taiwanese and Taiwan Guoyu on the Taiwan-based Internet
Authors: Su Hsi-Yao
Published: August 2009

This study investigates a type of online language play popularized on the Taiwan-based Internet, including the rendering in Chinese characters of the sounds of Taiwanese and Taiwan Guoyu (Taiwanese-accented Mandarin), which are defined as Stylized Taiwanese and Stylized Taiwanese-accented Mandarin, respectively. The playfulness inherent in these stylized practices has multiple sources. First, they manipulate the Chinese writing system and create an incongruity between sound and meaning. Second, they call attention simultaneously to a number of functions of language (Jakobson, 1960). Third, the two stylized practices bring into play the respective social meanings and stereotypes associated with their spoken counterparts. Thus the superficially similar forms of language play may be interpreted differently and further serve subtly different interactional functions in face-threatening situations. Two cases of stylized practices are examined in detail to illustrate how stylized language play is used to mitigate potential tension, to show positive affect, and to regulate appropriate group behaviors simultaneously.
Tense marking in the nominal domain
Authors: Alexiadou Artemis
Published: August 2009

The aim of this paper is to argue that temporal marking in the nominal domain should not be taken as evidence for the existence of a syntactic category TP within the extended projection of the noun phrase. On the basis of two unrelated languages, Somali and Halkomelem, the paper re-interprets the role of temporal morphology as being linked to specificity in the former case and as being adverbial in the latter. Building on an analysis of Halkomelem, according to which the language lacks a syntactic category TP (Wiltschko 2003), the paper derives from this property the lack of a categorial distinction between nouns and verbs in Halkomelem. This is based on the proposal that becoming verbal necessarily requires a combination between some primitive predicative head and an Agreeing T in the syntax.
Copy-reflexive and copy-control constructions
Authors: Boeckx Cedric , Hornstein Norbert , Nunes Jairo
Published: August 2009

This paper discusses reflexive and control constructions in San Lucas Quiaviní Zapotec (Lee 2003) and Hmong (Mortensen 2003), where instead of a reflexive in the former and a null category in the latter, one may find a copy of the antecedent. The paper argues that these constructions provide compelling evidence for a movement analysis of control (Hornstein 2001, 2003; Boeckx & Hornstein 2003, 2004) and reflexivization (Hornstein 2001), as well as the proposal that the phonetic realization of copies generated by movement is regulated by linearization and morphological requirements (Nunes 1999, 2004).
Sequence of tense in (French) child language
Authors: Demirdache Hamida , Lungu Oana
Published: August 2009

We discuss the results of an L1 French comprehension study of the construal of present and imperfective past in (non) subordinate contexts. Our findings reveal that children accept (sometimes enforce) non-indexical simultaneous construals of both present and past under a matrix past — though present is utterance-indexical in adult French. Extending Kratzer’s (1998) zero-tense analysis of English past under past simultaneous construals to Japanese present under past simultaneous construals, we argue that zero-tenses in L1 French surface either as past (adult French) or as present (adult Japanese). That children allow multi-valued parameter settings is expected on the Multiple Grammars hypothesis where language acquisition involves grammar competition. We extend our zero-tense analysis of non-adult tense construals in subordinate contexts to non-subordinate contexts, by arguing that the binder of a zero-tense in child grammar can be a temporal adverb denoting the ‘now’ of the speaker or some salient time implicit in the context.
Preposition stranding, passivisation, and extraction from adjuncts in Germanic
Authors: Truswell Robert
Published: August 2009

The crosslinguistic distribution of preposition stranding by A movement in pseudopassive constructions matches that of a marked A' phenomenon, namely extraction from Bare Present Participial Adjuncts. Moreover, both constructions show sensitivity to external factors of a sort that reanalysis-based theories of P-stranding are designed to capture, but which is not immediately predicted by P-stranding theories based on parametrisation of PP’s status as a bounding node or phase. However, an expanded version of Abels’ (2003) phase-based account of P-stranding, according to which the sensitivity of P-stranding under A- and A'-movement to PP-external factors is due to general constraints on movement and passivisation, captures the relevant data without resorting to a reanalysis operation.
Variation in the expression of universal quantification and free choice
Authors: Zimmermann Malte
Published: August 2009

I argue that the interpretation of expressions consisting of disjunction marker and wh-element (wh-disj expressions), which varies across languages, constitutes a case of semantic variation. In Hausa, these expressions denote universal generalized quantifiers, which give rise to free choice effects in intensional contexts (Giannakidou 2001). The universal meaning is derived in compositional fashion, where the disjunction marker expresses set union over the wh-domain. The free choice effects follow from the scopal interaction of universal quantifier and intensional operator. The account relates to Giannakidou & Cheng’s (2006) analysis of (quasi)universal FCIs, but it does not extend to Japanese and Malayalam wh-disj expressions, which are interpreted with existential force and should be analyzed as indeterminate pronouns (Jayaseelan 2001; Kratzer & Shimoyama 2002). Motivated by the analysis of FCIs in Menendéz-Benito (2005), we finally consider an alternative analysis of koo-wh expressions as selective indeterminate pronouns, which is rejected on conceptual and empirical grounds.
Collective numeral constructions in Dutch
Authors: Corver Norbert , Kranendonk Huib
Published: August 2009

In this paper, we discuss some collective numeral constructions from Dutch, which display a remarkable plural morpheme -en: wij vieren “the four of us”, met ons vieren “with four” and met z’n vieren “with four”. We argue that these at first sight idiosyncratic constructs are formed in syntax by application of the regular syntactic rules: Merge and Move. A central claim we make is that these collective numeral constructions contain a silent noun PERSOON/PERSON (cf. Kayne 2002, 2003, 2007). Although the noun itself is silent, its plurality is realized as -en. The silent noun is licensed by a local (i.e., DP-internal) antecedent. Dialectal variation in the realization of these constructions is analyzed in terms of “externalization”. It is argued that the basic syntactic make-up is similar in all variants. It is the (morpho-) phonological realization of heads, which causes the differences at the surface.
Beyond preferred argument structure
Authors: Huang Huei-ju , Huang Shuanfan
Published: August 2009

This paper investigates the preferred argument structure in Tsou, and the extent to which such a preference pattern is shaped by the interaction among mention type, valency role and activation status. Two significant findings emerge from the data. Strikingly, Ss and Os in discourse are not the most preferred loci for introducing new information. In addition, lexical NPs in Tsou are not a dispreferred form for encoding given information, and pronominals are restricted to occurring only with specific valency roles. Since lexical As are shown to occur with a higher proportion than those in other languages, they cannot strictly be said to be avoided in Tsou discourse. The morphosyntactic properties in Tsou are argued to add a critical fourth dimension to the three-way interaction of mention type, valency role and activation status to shape the final form of preferred argument structure in discourse.
Hiberno-English medial-object perfects reconsidered
Authors: Pietsch Lukas
Published: August 2009

Perfects of the type I have my dinner eaten are a well-known feature of Irish English dialects. They can be linked to a functionally similar construction in Irish, of the type tá mo dhinneár ite agam (literally “is my dinner eaten at-me”), but also to earlier constructions in Standard English. The issue has sometimes been treated as a competition between two seemingly mutually exclusive explanations, a “substrate” and a “retentionist” hypothesis. This dichotomy can be overcome on the basis of a model of “contact-induced grammaticalisation” (Heine/Kuteva 2005): an existing source structure in the receiving language (English) expands along normal paths, but under a triggering effect of a contact language (Irish), ultimately leading to an apparent duplication of a foreign model. Empirical data comes from historical 18th/19th century corpus material. It provides evidence about the chronology and sociolinguistic setting in which the relevant changes took place. It supports a scenario where both Irish-English bilingualism and exposure to the English source constructions played crucial roles.
The grammatical versatility of taboo terms
Authors: Napoli Donna Jo , Hoeksema Jack
Published: August 2009

Taboo terms in certain English expressions and constructions are intensifiers, which have spread as a unit over time to various syntactic positions (Hoeksema & Napoli 2008). Here we look at the pragmatic coherence that has allowed such semantically disparate terms to be grammaticalized as a unit. We examine language using taboo terms in English with comparisons to Dutch, Italian, and other languages. The terms studied here regard religion, disease, sex, and bodily excretions. They exhibit common characteristics with cross-linguistic variation.
The origin of serialization
Authors: Rose Françoise
Published: August 2009

This paper gives clear synchronic evidence for the origin of serial verb constructions (SVCs) in Emerillon, a Tupi-Guarani language. SVCs in that language result from a gerundive construction after the loss of both a subordinator and an indexation pattern specific to dependent clauses. After a short review of the general literature on the origins of SVCs and their similarity to converbs (of which Tupi-Guarani gerundives may be considered a subtype), the author gives a detailed account of the Emerillon SVCs. Strong arguments then show that Emerillon serial verbs (superficially comparable to independent verbs) originate from a ‘deranked’ dependent clause. The paper ends with some discussions on clause linkage, comparing more specifically SVCs and converbs on the morphological, syntactic and functional levels.
From topic to subject
Authors: Ahland Michael
Published: August 2009

The predicative possessive construction in Amharic exhibits a mismatch in grammatical coding: the possessor receives object marking on the verb while the overt NP exhibits phenomena associated with nominative case in Amharic. This article investigates the mismatch in light of its historical development as attested in archaisms found in proverbs and old Biblical texts, examines both overt and covert syntactic properties of the possessor today, and also considers evidence from other related constructions. The possessive construction developed from the existential construction where the possessor corresponded to a locative/recipient and today shows evidence of developing subject status.
Anton Popovič’s contribution to translation studies
Authors: Špirk Jaroslav
Published: August 2009

The present paper explores the contribution of the Slovak scholar Anton Popovič (1933–1984) to translation studies from the end of the 1960s until the beginning of the 1980s. It mentions the theoretical and methodological underpinnings of Popovič’s work (particularly Jiří Levý and František Miko), briefly analyzes Popovič’s most important publications within the field of translation studies, and discusses criticisms as well as inspirations of his conception of translation. The paper concludes with an evaluation of Popovič’s role in developing the field of Czechoslovak and international translation studies, most importantly ofdescriptive translation studiesandthe manipulation school.
Polish metaphorical perceptions of the translator and translation
Authors: Skibińska Elżbieta , Blumczyński Piotr
Published: August 2009

The paper offers a comprehensive overview of the Polish metaphorics of translation. It starts by examining the Polish linguistic image of translating, followed by a survey of metaphorical descriptions of the translator and translation from the 18th century, representing the pre-scientific era in reflection on translation. Most attention is devoted to metaphors found in contemporary Polish discourse on translation, centered around: (1) the nature of translation; (2) the relationship between the source and target text, and between the author and translator; and (3) the role of the translator. It is demonstrated that the Polish context offers a rich repertoire of metaphorical depictions of translating, which reflects its distinctive historical and cultural setup.
Philosophy of translation meets translation studies
Authors: Weissbrod Rachel
Published: August 2009

Though there are no clear-cut boundaries between the philosophy of translation and translation studies, they are obviously not the same. They differ not only in how they address their subject matter but also in that they occupy different “niches” in the culture. In the terminology of Bourdieu, they partake in different, though possibly partly overlapping cultural fields. This article attempts to create a meeting place for two representatives of these disciplines: Paul Ricœur, a leading figure in French hermeneutics of the 20th century, and Gideon Toury, a prominent researcher in the field of translation studies. Ricœur’s concept of the (non-existing) “third text” is compared with Toury’s concept of “the adequate translation as a hypothetical construct”, which was proposed in the 1980s and negated in the 1990s; and Ricœur’s view of translation as “equivalence without adequacy” is compared with Toury’s stand on this issue. The possibility of working with both and reading each of them in light of the other is examined by applying their ideas to a test case—three Hebrew translations of Kipling’s “If ”. The underlying assumption is that establishing links between translation studies and the philosophy of translation can contribute to the understanding of the phenomenon, which is the subject matter of both.
Modal particles explained
Authors: Winters Marion
Published: August 2009

The present paper comprises a corpus-based study of translator style, comparing two German translations of the novel The Beautiful and Damned by Francis Scott Fitzgerald. The translations, by Hans-Christian Oeser and Renate Orth-Guttmann, were both published in 1998. The study isolates the linguistic feature of modal particles in which the individual styles of the translators manifest themselves on the textual level and investigates the influence the translators’ microlevel linguistic choices have on the macrolevel of the novel. An electronic corpus was compiled, comprising The Beautiful and Damned and its two translations, both entitled Die Schönen und Verdammten. A quantitative analysis was carried out to discover potential patterns of the use of modal particles by the translators, and the results showed that while both translators use modal particles to the extent and in the general context one would expect, they differ considerably in their choice and use of individual modal particles. The subsequent qualitative analysis takes a pragmatic approach, and discusses the selected modal particle wohl according to its communicative function, its role in speech and thought acts and in the narrative, and in the context of the respective narrative points of view. Finally it is argued that the two translators differ in their translation styles to an extent that affects the novel’s macrolevel in that one translator provides a character study while the other focuses on societal issues.
Translating asyndeton from French literary texts into English
Authors: Rossette Fiona
Published: August 2009

While asyndeton between finite clauses within the sentence may be considered a marginal construction, compared for example to coordination or subordination, it is more frequent in French than in English, in which it is limited with respect to genre. Particularly interesting examples, both quantitively and qualitively, can be found in French literature, notably in the fiction of Marguerite Duras, who made asyndeton her hallmark. This study documents the choices made by English translators of Duras, and of three other French writers who exploit asyndeton. Literature aside, asyndeton in French texts is not carried over into English, in what can be qualified as norm-governed translation. However, asyndeton in literary texts is carried over into English in up to fifty percent of cases, reflecting a certain compromise between norms in the source language and those in the target language. Apart from describing Duras’ specific use of asyndeton, and illustrating the difficulty of translating any element that is an essential ingredient of a writer’s style, which, by definition, represents a departure from an accepted norm, this study brings to light certain aspects governing clause combining in English. Certain linguistic parameters that favour the exploitation of asyndeton in English are systematised, specifically concision, rhythm and isotopy. Semantic, temporal and/or aspectual constraints are also highlighted.
Reciprocal Efficiency of RNQ1 and Polyglutamine Detoxification in the Cytosol and Nucleus
Authors: Douglas Peter M. , Summers Daniel W. , Ren Hong-Yu , Cyr Douglas M.
Published: August 2009

Onset of proteotoxicity is linked to change in the subcellular location of proteins that cause misfolding diseases. Yet, factors that drive changes in disease protein localization and the impact of residence in new surroundings on proteotoxicity are not entirely clear. To address these issues, we examined aspects of proteotoxicity caused by Rnq1-green fluorescent protein (GFP) and a huntingtin's protein exon-1 fragment with an expanded polyglutamine tract (Htt-103Q), which is dependent upon the intracellular presence of [RNQ+] prions. Increasing heat-shock protein 40 chaperone activity before Rnq1-GFP expression, shifted Rnq1-GFP aggregation from the cytosol to the nucleus. Assembly of Rnq1-GFP into benign amyloid-like aggregates was more efficient in the nucleus than cytosol and nuclear accumulation of Rnq1-GFP correlated with reduced toxicity. [RNQ+] prions were found to form stable complexes with Htt-103Q, and nuclear Rnq1-GFP aggregates were capable of sequestering Htt-103Q in the nucleus. On accumulation in the nucleus, conversion of Htt-103Q into SDS-resistant aggregates was dramatically reduced and Htt-103Q toxicity was exacerbated. Alterations in activity of molecular chaperones, the localization of intracellular interaction partners, or both can impact the cellular location of disease proteins. This, in turn, impacts proteotoxicity because the assembly of proteins to a benign state occurs with different efficiencies in the cytosol and nucleus.
Glycogen Synthase Kinase-3 and Omi/HtrA2 Induce Annexin A2 Cleavage followed by Cell Cycle Inhibition and Apoptosis
Authors: Wang Chi-Yun , Lin Yee-Shin , Su Wu-Chou , Chen Chia-Ling , Lin Chiou-Feng
Published: August 2009

Annexin A2 is involved in multiple cellular processes, including cell survival, growth, division, and differentiation. A lack of annexin A2 makes cells more sensitive to apoptotic stimuli. Here, we demonstrate a potential mechanism for apoptotic stimuli-induced annexin A2 cleavage, which contributes to cell cycle inhibition and apoptosis. Annexin A2 was persistently expressed around the proliferative but not the necrotic region in BALB/c nude mice with human lung epithelial carcinoma cell A549-derived tumors. Knockdown expression of annexin A2 made cells susceptible to either serum withdrawal-induced cell cycle inhibition or cisplatin-induced apoptosis. Under apoptotic stimuli, annexin A2 was time-dependently cleaved. Mechanistic studies have shown that protein phosphatase 2A (PP2A)-activated glycogen synthase kinase (GSK)-3 is essential for this process. Therefore, inhibiting GSK-3 reversed serum withdrawal-induced cell cycle inhibition and cisplatin-induced apoptosis. Furthermore, inhibiting serine proteases blocked apoptotic stimuli-induced annexin A2 cleavage. Bax activation and Mcl-1 destabilization, which is regulated by PP2A and GSK-3, caused annexin A2 cleavage via an Omi/HtrA2-dependent pathway. Taking these results together, we conclude that GSK-3 and Omi/HtrA2 synergistically cause annexin A2 cleavage and then cell cycle inhibition or apoptosis.
Upcoming challenges for multiple sequence alignment methods in the high-throughput era
Authors: Kemena Carsten , Notredame Cedric
Published: August 2009

This review focuses on recent trends in multiple sequence alignment tools. It describes the latest algorithmic improvements including the extension of consistency-based methods to the problem of template-based multiple sequence alignments. Some results are presented suggesting that template-based methods are significantly more accurate than simpler alternative methods. The validation of existing methods is also discussed at length with the detailed description of recent results and some suggestions for future validation strategies. The last part of the review addresses future challenges for multiple sequence alignment methods in the genomic era, most notably the need to cope with very large sequences, the need to integrate large amounts of experimental data, the need to accurately align non-coding and non-transcribed sequences and finally, the need to integrate many alternative methods and approaches.

Contact:  cedric.notredame@crg.es
CMap 1.01: a comparative mapping application for the Internet
Authors: Youens-Clark Ken , Faga Ben , Yap Immanuel V. , Stein Lincoln , Ware Doreen
Published: August 2009

Summary:CMap is a web-based tool for displaying and comparing maps of any type and from any species. A user can compare an unlimited number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession. CMap is freely available, can run on a variety of database engines and uses only free and open software components.

Availability:  http://www.gmod.org/cmap

Contact:  kclark@cshl.edu
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
Authors: Cloonan Nicole , Xu Qinying , Faulkner Geoffrey J. , Taylor Darrin F. , Tang Dave T. P. , Kolle Gabriel , Grimmond Sean M.
Published: August 2009

Summary: Mapping of next-generation sequencing data derived from RNA samples (RNAseq) presents different genome mapping challenges than data derived from DNA. For example, tags that cross exon-junction boundaries will often not map to a reference genome, and the strand specificity of the data needs to be retained. Here we present RNA-MATE, a computational pipeline based on a recursive mapping strategy for placing strand specific RNAseq data onto a reference genome. Maximizing the mappable tags can provide significant savings in the cost of sequencing experiments. This pipeline provides an automatic and integrated way to align color-space sequencing data, collate this information and generate files for examining gene-expression data in a genomic context.

Availability: Executables, source code, and exon-junction libraries are available from http://grimmond.imb.uq.edu.au/RNA-MATE/

Contact:  n.cloonan@imb.uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics Online.
Gene ranking and biomarker discovery under correlation
Authors: Zuber Verena , Strimmer Korbinian
Published: August 2009

Motivation: Biomarker discovery and gene ranking is a standard task in genomic high-throughput analysis. Typically, the ordering of markers is based on a stabilized variant of the t-score, such as the moderated t or the SAM statistic. However, these procedures ignore gene–gene correlations, which may have a profound impact on the gene orderings and on the power of the subsequent tests.

Results: We propose a simple procedure that adjusts gene-wise t-statistics to take account of correlations among genes. The resulting correlation-adjusted t-scores (‘cat’ scores) are derived from a predictive perspective, i.e. as a score for variable selection to discriminate group membership in two-class linear discriminant analysis. In the absence of correlation the cat score reduces to the standard t-score. Moreover, using the cat score it is straightforward to evaluate groups of features (i.e. gene sets). For computation of the cat score from small sample data, we propose a shrinkage procedure. In a comparative study comprising six different synthetic and empirical correlation structures, we show that the cat score improves estimation of gene orderings and leads to higher power for fixed true discovery rate, and vice versa. Finally, we also illustrate the cat score by analyzing metabolomic data.

Availability: The shrinkage cat score is implemented in the R package ‘st’, which is freely available under the terms of the GNU General Public License (version 3 or later) from CRAN (http://cran.r-project.org/web/packages/st/).

Contact:  strimmer@uni-leipzig.de
Methyl side-chain dynamics prediction based on protein structure
Authors: Carbonell Pablo , Sol Antonio del
Published: August 2009

Motivation: Protein dynamics is believed to influence protein function through a variety of mechanisms, some of which are not fully understood. Thus, prediction of protein flexibility from sequence or structural characteristics would assist in comprehension of the ways dynamics is linked to function, and would be important in protein modeling and design. In particular, quantitative description of side-chain dynamics would allow us to understand the role of side-chain flexibility in different functional processes, such as protein–ligand and protein–protein interactions.

Results: Using a dataset of 18 proteins, we trained a neural network for the prediction of methyl-bearing side-chain dynamics as described by the methyl side-chain generalized order parameters (S2) inferred from NMR data. The network uses 10 input parameters extracted from 3D structures. The average correlation coefficient between the experimental and predicted generalized order parameters is r = 0.71 ± 0.029. Further analysis revealed that the order parameter depends more strongly on the methyl carbon packing density, the methyl carbon distance to the Cα atom, and the knowledge-based pair-wise contact potential between the methyl carbon and neighboring amino acids. In general, we observed an improvement in the prediction of methyl order parameters by our network in comparison with molecular dynamics simulations. The sensitivity of the predictions to minor structural changes was illustrated in two examples (calmodulin and barnase) by comparing the S2 predictions for the unbound and ligand-bound structures. The method was able to correctly predict most of the significant changes in side-chain dynamics upon ligand binding, and identified some residues involved in long-range communications or protein–ligand binding.

Availability:  http://epigenomique.genopole.fr/∼carbonell

Contact:  antdelsol@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Network analyses in systems pharmacology
Authors: Berger Seth I. , Iyengar Ravi
Published: August 2009

Systems pharmacology is an emerging area of pharmacology which utilizes network analysis of drug action as one of its approaches. By considering drug actions and side effects in the context of the regulatory networks within which the drug targets and disease gene products function, network analysis promises to greatly increase our knowledge of the mechanisms underlying the multiple actions of drugs. Systems pharmacology can provide new approaches for drug discovery for complex diseases. The integrated approach used in systems pharmacology can allow for drug action to be considered in the context of the whole genome. Network-based studies are becoming an increasingly important tool in understanding the relationships between drug action and disease susceptibility genes. This review discusses how analysis of biological networks has contributed to the genesis of systems pharmacology and how these studies have improved global understanding of drug targets, suggested new targets and approaches for therapeutics, and provided a deeper understanding of the effects of drugs. Taken together, these types of analyses can lead to new therapeutic options while improving the safety and efficacy of existing medications.

Contact:  ravi.iyengar@mssm.edu
A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge
Authors: Tian Ze , Hwang TaeHyun , Kuang Rui
Published: August 2009

Motivation: Incorporating biological prior knowledge into predictive models is a challenging data integration problem in analyzing high-dimensional genomic data. We introduce a hypergraph-based semi-supervised learning algorithm called HyperPrior to classify gene expression and array-based comparative genomic hybridization (arrayCGH) data using biological knowledge as constraints on graph-based learning. HyperPrior is a robust two-step iterative method that alternatively finds the optimal labeling of the samples and the optimal weighting of the features, guided by constraints encoding prior knowledge. The prior knowledge for analyzing gene expression data is that cancer-related genes tend to interact with each other in a protein–protein interaction network. Similarly, the prior knowledge for analyzing arrayCGH data is that probes that are spatially nearby in their layout along the chromosomes tend to be involved in the same amplification or deletion event. Based on the prior knowledge, HyperPrior imposes a consistent weighting of the correlated genomic features in graph-based learning.

Results: We applied HyperPrior to test two arrayCGH datasets and two gene expression datasets for both cancer classification and biomarker identification. On all the datasets, HyperPrior achieved competitive classification performance, compared with SVMs and the other baselines utilizing the same prior knowledge. HyperPrior also identified several discriminative regions on chromosomes and discriminative subnetworks in the PPI, both of which contain cancer-related genomic elements. Our results suggest that HyperPrior is promising in utilizing biological prior knowledge to achieve better classification performance and more biologically interpretable findings in gene expression and arrayCGH data.

Availability:  http://compbio.cs.umn.edu/HyperPrior

Contact:  kuang@cs.umn.edu

Supplementary information:  Supplementary data are available at bioinformatics online.
metahdep: meta-analysis of hierarchically dependent gene expression studies
Authors: Stevens John R. , Nicholas Gabriel
Published: August 2009

Summary: The metahdep package contains tools for combining the results of multiple gene expression studies. Unlike previous microarray meta-analysis packages, metahdep accounts for both sampling and hierarchical dependence among studies, as well as fundamental covariate differences between studies.

Availability:  http://bioconductor.org/packages/release/Software.html

Contact:  john.r.stevens@usu.edu
Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks
Authors: Tian Feng , Shah Parantu K. , Liu Xiangjun , Negre Nicolas , Chen Jia , Karpenko Oleksiy , White Kevin P. , Grossman Robert L.
Published: August 2009

Motivation: The highly coordinated expression of thousands of genes in an organism is regulated by the concerted action of transcription factors, chromatin proteins and epigenetic mechanisms. High-throughput experimental data for genome wide in vivo protein–DNA interactions and epigenetic marks are becoming available from large projects, such as the model organism ENCyclopedia Of DNA Elements (modENCODE) and from individual labs. Dissemination and visualization of these datasets in an explorable form is an important challenge.

Results: To support research on Drosophila melanogaster transcription regulation and make the genome wide in vivo protein–DNA interactions data available to the scientific community as a whole, we have developed a system called Flynet. Currently, Flynet contains 101 datasets for 38 transcription factors and chromatin regulator proteins in different experimental conditions. These factors exhibit different types of binding profiles ranging from sharp localized peaks to broad binding regions. The protein–DNA interaction data in Flynet was obtained from the analysis of chromatin immunoprecipitation experiments on one color and two color genomic tiling arrays as well as chromatin immunoprecipitation followed by massively parallel sequencing. A web-based interface, integrated with an AJAX based genome browser, has been built for queries and presenting analysis results. Flynet also makes available the cis-regulatory modules reported in literature, known and de novo identified sequence motifs across the genome, and other resources to study gene regulation.

Contact:  grossman@uic.edu

Availability: Flynet is available at https://www.cistrack.org/flynet/.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Galectin‐3: a novel mediator of heart failure development and progression
Authors: de Boer Rudolf A. , Voors Adriaan A. , Muntendam Pieter , van Gilst Wiek H. , van Veldhuisen Dirk J.
Published: August 2009

Galectins are a family of soluble β‐galactoside‐binding lectins that play many important regulatory roles in inflammation, immunity, and cancer. Recently, a role for galectin‐3 in the pathophysiology of heart failure (HF) has been suggested. Numerous studies have demonstrated the up‐regulation of galectin‐3 in hypertrophied hearts, its stimulatory effect on macrophage migration, fibroblast proliferation, and the development of fibrosis. The latter observation is particularly relevant as cardiac remodelling is an important determinant of the clinical outcome of HF and is linked to disease progression and poor prognosis. Because galectin‐3 expression is maximal at peak fibrosis and virtually absent after recovery, routine measurement in patients with HF may prove valuable to identify those patients at highest risk for readmission or death, thus enabling physicians to tailor the level of care to individual patient needs. This review summarizes the most recent advances in galectin‐3 research, with an emphasis on the role galectin‐3 plays in the development and progression of HF.
Efficacy and safety of nebivolol in elderly heart failure patients with impaired renal function: insights from the SENIORS trial
Authors: Cohen‐Solal Alain , Kotecha Dipak , van Veldhuisen Dirk J , Babalis Daphne , Böhm Michael , Coats Andrew J. , Roughton Michael , Poole‐Wilson Philip , Tavazzi Luigi , Flather Marcus ,   on behalf of the SENIORS Investigators
Published: August 2009

Aim

To determine the safety and efficacy of nebivolol in elderly heart failure (HF) patients with renal dysfunction.

Methods and results

SENIORS recruited patients aged 70 years or older with symptomatic HF, irrespective of ejection fraction, and randomized them to nebivolol or placebo. Patients (n = 2112) were divided by tertile of estimated glomerular filtration rate (eGFR). Mean age of patients was 76.1 years, 35% of patients had an ejection fraction of >35%, and 37% were women resulting in a unique cohort, far more representative of clinical practice than previous trials. eGFR was strongly associated with outcomes and nebivolol was similarly efficacious across eGFR tertiles. The primary outcome rate (all‐cause mortality or cardiovascular hospital admission) and adjusted hazard ratio for nebivolol use in those with low eGFR was 40% and 0.84 (95% CI 0.67–1.07), 31% and 0.79 (0.60–1.04) in the middle tertile, and 29% and 0.86 (0.65–1.14) in the highest eGFR tertile. There was no interaction noted between renal function and the treatment effect (P = 0.442). Nebivolol use in patients with moderate renal impairment (eGFR <60) was not associated with major safety concerns, apart from higher rates of drug‐discontinuation due to bradycardia.

Conclusion

Nebivolol is safe and has a similar effect in elderly HF patients with mild or moderate renal impairment.
Latent Infection of Potato Seed Tubers by Phytophthora infestans During Long-Term Cold Storage
Authors: Johnson Dennis A. , Cummings Thomas F.
Published: August 2009

Latent infection of potato seed tubers by Phytophthora infestans was determined following inoculation of tubers and typical seed tuber storage conditions in the Pacific Northwest. Severity of late blight increased over 182 to 209 days during two storage seasons at mean temperatures of 4.1 and 4.2°C. From 0 to 44% of inoculated tubers sampled at given intervals were asymptomatic. However, P. infestans sporangia were observed on slices from these tubers when incubated in a humidity chamber at 15°C or late blight symptoms developed in asymptomatic tubers obtained following storage when incubated at 22 to 23°C for 3 weeks. Development of P. infestans sporangia and symptoms of late blight in asymptomatic seed tubers indicated latent infection of tubers by P. infestans during long-term cold storage. Sporulation was observed after 21 to 24 h on symptomatic tubers and 6 to 20 days on asymptomatic tubers that were removed from storage and incubated in a humidity chamber at 15°C. Latent infection of seed tubers and production of viable sporangia of P. infestans were demonstrated after long-term cold storage of infected potato tubers.
Pathogenic Fitness of Oosporic Progeny Isolates of Phytophthora infestans on Late-Blight-Resistant Tomato Lines
Authors: Klarfeld Shiri , Rubin Avia (Evgenia) , Cohen Yigal
Published: August 2009

Four A1 field isolates and one A2 field isolate of Phytophthora infestans were crossed to produce oospores in tomato leaves. The oospores were extracted and mixed with perlite and water, and healthy tomato leaves were used as bait for oospore-progeny infection. Twenty-nine lesions were obtained from the four crosses and 283 single-sporangium isolates were recovered and tested on four tomato differential lines carrying different major genes (Ph-0, Ph-1, Ph-2, and 3707) for late blight resistance. The pathogenic fitness (number of sporangia per unit leaf area) of parental and progeny isolates was strongly dependent on the host genotype; it decreased in the order Ph-0 > Ph-1 > Ph-2 > 3707. The A2 parent had a higher pathogenic fitness than the A1 parents on Ph-0 and Ph-1 but similar, lower fitness on Ph-2. Different levels of pathogenic fitness were observed across all isolates on Ph-0, although Ph-0 lacks resistance genes. Pathogenic fitness on one tomato genotype was not related to the pathogenic fitness on the other tomato genotypes. Some isolates exhibited reduced pathogenic fitness relative to the respective A1 parent, whereas others demonstrated a higher pathogenic fitness compared with the A2 parent. The tomato genotype Solanum pimpinellifolium L3707/5 was resistant to all five parental isolates of P. infestans. However, 37 of the 283 progeny isolates from 11 different lesions had compatible reactions with this line, producing up to 31 × 103 sporangia/cm2. Overall, reduced fitness was more frequent among the progeny isolates than increased fitness.
Outbreak of Powdery Mildew Caused by Erysiphe cruciferarum on Spider Flower (Cleome hassleriana) in Italy
Authors: Garibaldi A. , Bertetti D. , Gullino M. L.
Published: August 2009

Spider flower (Cleome hassleriana L. [synonym = C. spinosa]) is used as a tall border in parks and gardens worldwide. During July 2008, severe outbreaks of a powdery mildew were observed in a public park in Torino (northern Italy). Leaves were covered with dense, white hyphae and conidia, especially on the adaxial surface. Hyphae were also present on petioles and fruits, but not on petals and stems. As the disease progressed, infected leaves turned chlorotic, curled, and wilted. Conidia were hyaline, cylindrical, single, and measured 31.1 to 48.2 × 12.9 to 17.6 μm (average 37.1 × 15.6 μm). Germ tubes terminating in a moderately lobed appressorium were produced terminally. The cylindrical foot cells of the erect condiophores were 19.2 to 27.8 × 6.5 to 8.6 μm (average 23.3 × 7.7 μm). Fibrosin bodies were absent. Chasmothecia were observed mostly on the lower surfaces of leaves. At maturity, they were dark amber and spherical with a diameter of 92.9 to 151.0 μm (average 121.4 μm). Each chasmothecium contained six stalked asci (average size 63.7 × 35.9 μm). Each ascus contained four ellipsoid ascospores that measured 17.3 to 26.4 × 10.9 to 15.6 μm (average 23.3 × 12.8 μm). The internal transcribed spacer (ITS) region of rDNA was amplified using primers ITS4/ITS6 and sequenced (1). The 602-bp sequence was deposited in GenBank under the Accession No. GQ149478 and was 99% similar to that of Erysiphe cruciferarum (Accession No. EU140958). As proof of pathogenicity, diseased leaves of C. hassleriana were pressed against leaves of three healthy 4-month-old potted plants of the same species for 10 min. Three noninoculated plants served as controls. Inoculated and noninoculated plants were maintained in a greenhouse at 22 to 25°C in isolation. After 11 days, typical powdery mildew colonies developed on inoculated plants. Noninoculated plants did not develop symptoms. The pathogenicity test was repeated once. Powdery mildew on C. hassleriana caused by E. cruciferarum was reported in Italy (2) but the pathogen was not characterized. Herbarium specimens are deposited at AGROINNOVA Collection, University of Torino, Italy.

References: (1) S. F. Altschul et al. Nucleic Acids Res. 25:3389, 1997. (2) U. Braun. The Powdery Mildews (Erysiphales) of Europe. Gustav Fischer Verlag, Jena, Germany, 1995.
First Report of Downy Mildew on Field-Grown Sweet Basil Caused by a Peronospora sp. in San Diego County, California
Authors: Blomquist C. L. , Rooney-Latham S. , Nolan P. A.
Published: August 2009

Sweet basil (Ocimum basilicum) is a culinary herb grown in fields and greenhouses in California. In August of 2008, samples were submitted to the San Diego County Plant Diagnostic Laboratory with a grayish brown, downy growth that covered areas of the abaxial side of the leaf. Early symptoms included leaf chlorosis followed by the appearance of scattered grayish brown conidia and conidiophores in the chlorotic areas. Conidiophore emergence progressed to a grayish brown, velvety growth with some of the chlorotic areas becoming necrotic. Similarly affected plants were submitted to the laboratory from another field 32 km (20 miles) away in the same county. Both fields were drip irrigated and located in inland valleys. Approximately 50 to 60% of the plants were symptomatic. Conidiophores, on the abaxial side of the leaves that were characteristic of Peronospora, branched dichotomously three to five times and measured 390 to 1,100 × 2.5 to 7.0 μm (675.6 × 4.9 μm average). Light brown, globose to ellipsoidal conidia measured 20 to 34 × 18 to 26 μm (26 × 22 μm average). To confirm pathogenicity, three basil plants in 10.2-cm (4-inch) pots were sprayed with a suspension of 4.5 × 105 conidia/ml and incubated in a dew chamber at 20°C for 48 h in the dark. Three noninoculated plants were sprayed with water. Plants were then placed in a growth chamber at 18°C with a 16-h photoperiod. Relative humidity was maintained near 95% by placing the plants over a tray of water and covering each group with a plastic tent. Signs of grayish brown, downy growth were seen approximately 14 days after inoculation. Pathogenicity experiments were repeated once. No symptoms developed on plants sprayed with water. Sequence of the intergenic spacer regions and 5.8S gene was obtained from a sample collected in one field, through amplification with primers DC6 and ITS4 and sequencing with primers ITS6 and ITS4 (2). The sequence (Accession No. FJ436024) from the field sample was identical to GenBank Accession No. AY884605 that represented a Peronospora sp. from basil in Switzerland. On the basis of morphological and sequence information, the Peronospora sp. from San Diego County is most likely the same Peronospora sp. that was identified from sweet basil in Switzerland, Italy (1), and South Africa (4), as well as coleus in New York and Louisiana (3). The basil Peronospora sp. has been shown to be present in seed (1). Since both growers purchased their seed from the same supplier, seeds could have been a possible inoculum source. To our knowledge, this is the first report of a downy mildew on sweet basil in California.

References: (1) L. Belbahri et al. Mycol. Res. 109:1276, 2005. (2) D. E. L. Cooke et al. Fungal Genet. Biol. 30:17, 2000. (3) M. L. Daughtrey et al. Plant Dis. 90:1111, 2006. (4) A. McLeod et al. Plant Dis. 90:1115, 2006.
Sex-specific visual performance: female lizards outperform males in motion detection
Authors: Nava Saúl S. , Conway Mirela , Martins Emília P.
Published: August 2009

In animal communication, complex displays usually have multiple functions and, male and female receivers often differ in their utilization and response to different aspects of these displays. The perceptual variability hypothesis suggests that different aspects of complex signals differ in their ability to be detected and processed by different receivers. Here, we tested whether receiver male and female
Sceloporus graciosus
lizards differ in visual motion detection by measuring the latency to the visual grasp response to a motion stimulus. We demonstrate that in lizards that largely exhibit complex motions as courtship signals, female lizards are faster than males at visually detecting motion. These results highlight that differential signal utilization by the sexes may be driven by variability in the capacity to detect different display properties.