bluuebunny/crossref_metadata_2025_split huggingface dataset:
REFLEXIVE SELF-TALK AND SITUATED FREEDOM IN THE CONTEXT OF SOCIABILITY
Authors: Törrönen Jukka , Maunu Antti 
Published: June 2009

ABSTRACT
This paper analyses narratives in drinking and pub diaries written by young Finns aged 23–35. Drinking occasions in Finland are highly sociable gatherings in which one is oriented towards intensive interaction with one's friends. Thus, in the diaries the writers also reflect upon their expectations, descriptions and evaluations of these gatherings and the sociability they offer. In the analysis we focus on how during these occasions the writers adapt themselves to the perceived expectations of others, integrate these expectations with their own aspirations, or are sometimes compelled to change their aspirations. On this basis, we also pay attention to how this work of reflexive orientation functions to strengthen the expected course of one's own life, or as implying fateful moments, that is, transitions or turning points in the life course. In the analysis we apply G.H. Mead's concepts of ‘I’ and ‘me’. The paper identifies three different kinds of ‘I–me dialogues’. First, loosening oneself momentarily from reflexivity to the collective body of friends; second, binding oneself reflexively to the common will of the group; and third, loosening oneself from group commitments, that is moving towards individual reflexivity and desires. Of these dialogues, the last mentioned contributes most often to fateful activity in which the writers’ life course is at stake. By contrast, the other two more collectively oriented self-talks rather refer to positive peak experiences that give emotional momentum to continue with one's existing life plans.
THE NEXT EUROPEAN EMPIRE?
Authors: Gravier Magali 
Published: June 2009

ABSTRACT
This paper proposes to use the concept of empire for the analysis the European integration process. From a methodological point of view, this concept is an invitation to reintroduce in EU studies the comparative approach as well as long-term history. This paper also leads to a detailed reflection on the concept of empire itself and proposes a modernized definition of it. The use of this concept enables to shed a new light on the EU and some of its policies. If the EU cannot be considered an empire, it can nonetheless be said that it is undergoing a process of imperialization. This raises the question of the transformation of the European project and to the consequences of this transformation.
CIVIC STRATIFICATION AND THE COSMOPOLITAN IDEAL
Authors: Morris Lydia 
Published: June 2009

ABSTRACT
Beck (2006) has suggested that trans-national migration and the consolidation of human rights are features of an emergent cosmopolitan society in which we see a blurring of distinctions with respect to the rights of citizens and non-citizens. This paper argues that the presence of noncitizens on national territory has rather been accompanied by an expansion of distinctions in a system of civic stratification. It outlines the construction of asylum seekers as a ‘target group’ within this complex, and the withdrawal of welfare support from ‘late claimers’. However, the paper also considers the limits placed on the erosion of rights through the human rights challenge that followed, in which the European Convention on Human Rights played a central role. Finally, the paper elaborates the interplay of formal entitlement and informal status in the process of change, and examines the implications of the whole account for cosmopolitan thinking.
Copy number variation has little impact on bead-array-based measures of DNA methylation
Authors: Houseman E. Andrés , Christensen Brock C. , Karagas Margaret R. , Wrensch Margaret R. , Nelson Heather H. , Wiemels Joseph L. , Zheng Shichun , Wiencke John K. , Kelsey Karl T. , Marsit Carmen J. 
Published: June 2009

Abstract
Motivation: Integration of various genome-scale measures of molecular alterations is of great interest to researchers aiming to better define disease processes or identify novel targets with clinical utility. Particularly important in cancer are measures of gene copy number DNA methylation. However, copy number variation may bias the measurement of DNA methylation. To investigate possible bias, we analyzed integrated data obtained from 19 head and neck squamous cell carcinoma (HNSCC) tumors and 23 mesothelioma tumors.
Results: Statistical analysis of observational data produced results consistent with those anticipated from theoretical mathematical properties. Average beta value reported by Illumina GoldenGate (a bead-array platform) was significantly smaller than a similar measure constructed from the ratio of average dye intensities. Among CpGs that had only small variations in measured methylation across tumors (filtering out clearly biological methylation signatures), there were no systematic copy number effects on methylation for three and more than four copies; however, one copy led to small systematic negative effects, and no copies led to substantial significant negative effects.
Conclusions: Since mathematical considerations suggest little bias in methylation assayed using bead-arrays, the consistency of observational data with anticipated properties suggests little bias. However, further analysis of systematic copy number effects across CpGs suggest that though there may be little bias when there are copy number gains, small biases may result when one allele is lost, and substantial biases when both alleles are lost. These results suggest that further integration of these measures can be useful for characterizing the biological relationships between these somatic events.
Contact: E_Andres_Houseman@brown.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events
Authors: Chu Te-Chin , Liu Tsunglin , Lee D. T. , Lee Greg C. , Shih Arthur Chun-Chieh 
Published: June 2009

Abstract
Motivation: Homologous genomic sequences between species usually contain different rearrangement events. Whether some specific patterns existed in the breakpoint regions that caused such events to occur is still unclear. To resolve this question, it is necessary to determine the location of breakpoints at the nucleotide level. The availability of sequences near breakpoints would further facilitate the related studies. We thus need a tool that can identify breakpoints and align the neighboring sequences. Although local alignment tools can detect rearrangement events, they only report a set of discontinuous alignments, where the detailed alignments in the breakpoint regions are usually missing. Global alignment tools are even less appropriate for these tasks since most of them are designed to align the conserved regions between sequences in a consistent order, i.e. they do not consider rearrangement events.
Results: We propose an effective and efficient pairwise sequence alignment algorithm, called GR-Aligner (Genomic Rearrangement Aligner), which can find breakpoints of rearrangement events by integrating the forward and reverse alignments of the breakpoint regions flanked by homologously rearranged sequences. In addition, GR-Aligner also provides an option to view the alignments of sequences extended to the breakpoints. These outputs provide materials for studying possible evolutionary mechanisms and biological functionalities of the rearrangement.
Availability: http://biocomp.iis.sinica.edu.tw/new/GR_Aligner.htm
Contact: arthur@iis.sinica.edu.tw
VarScan: variant detection in massively parallel sequencing of individual and pooled samples
Authors: Koboldt Daniel C. , Chen Ken , Wylie Todd , Larson David E. , McLellan Michael D. , Mardis Elaine R. , Weinstock George M. , Wilson Richard K. , Ding Li 
Published: June 2009

Abstract
Summary: Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants affecting human disease. The unprecedented throughput and relatively short read lengths of Roche/454, Illumina/Solexa, and other platforms have spurred development of a new generation of sequence alignment algorithms. Yet detection of sequence variants based on short read alignments remains challenging, and most currently available tools are limited to a single platform or aligner type. We present VarScan, an open source tool for variant detection that is compatible with several short read aligners. We demonstrate VarScan's ability to detect SNPs and indels with high sensitivity and specificity, in both Roche/454 sequencing of individuals and deep Illumina/Solexa sequencing of pooled samples.
Availability and Implementation: Source code and documentation freely available at http://genome.wustl.edu/tools/cancer-genomics implemented as a Perl package and supported on Linux/UNIX, MS Windows and Mac OSX.
Contact: dkoboldt@genome.wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Reconstructing signaling pathways from RNAi data using probabilistic Boolean threshold networks
Authors: Kaderali Lars , Dazert Eva , Zeuge Ulf , Frese Michael , Bartenschlager Ralf 
Published: June 2009

Abstract
Motivation: The reconstruction of signaling pathways from gene knockdown data is a novel research field enabled by developments in RNAi screening technology. However, while RNA interference is a powerful technique to identify genes related to a phenotype of interest, their placement in the corresponding pathways remains a challenging problem. Difficulties are aggravated if not all pathway components can be observed after each knockdown, but readouts are only available for a small subset. We are then facing the problem of reconstructing a network from incomplete data.
Results: We infer pathway topologies from gene knockdown data using Bayesian networks with probabilistic Boolean threshold functions. To deal with the problem of underdetermined network parameters, we employ a Bayesian learning approach, in which we can integrate arbitrary prior information on the network under consideration. Missing observations are integrated out. We compute the exact likelihood function for smaller networks, and use an approximation to evaluate the likelihood for larger networks. The posterior distribution is evaluated using mode hopping Markov chain Monte Carlo. Distributions over topologies and parameters can then be used to design additional experiments. We evaluate our approach on a small artificial dataset, and present inference results on RNAi data from the Jak/Stat pathway in a human hepatoma cell line.
Availability: Software is available on request.
Contact: lars.kaderali@bioquant.uni-heidelberg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization
Authors: Yang Xuerui , Zhou Yang , Jin Rong , Chan Christina 
Published: June 2009

AbstractMotivation: Reconstructing gene networks from microarray data has provided mechanistic information on cellular processes. A popular structure learning method, Bayesian network inference, has been used to determine network topology despite its shortcomings, i.e. the high-computational cost when analyzing a large number of genes and the inefficiency in exploiting prior knowledge, such as the co-regulation information of the genes. To address these limitations, we are introducing an alternative method, knowledge-driven matrix factorization (KMF) framework, to reconstruct phenotype-specific modular gene networks.Results: Considering the reconstruction of gene network as a matrix factorization problem, we first use the gene expression data to estimate a correlation matrix, and then factorize the correlation matrix to recover the gene modules and the interactions between them. Prior knowledge from Gene Ontology is integrated into the matrix factorization. We applied this KMF algorithm to hepatocellular carcinoma (HepG2) cells treated with free fatty acids (FFAs). By comparing the module networks for the different conditions, we identified the specific modules that are involved in conferring the cytotoxic phenotype induced by palmitate. Further analysis of the gene modules of the different conditions suggested individual genes that play important roles in palmitate-induced cytotoxicity. In summary, KMF can efficiently integrate gene expression data with prior knowledge, thereby providing a powerful method of reconstructing phenotype-specific gene networks and valuable insights into the mechanisms that govern the phenotype.Contact: krischan@msu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
SHREC: a short-read error correction method
Authors: Schröder Jan , Schröder Heiko , Puglisi Simon J. , Sinha Ranjan , Schmidt Bertil 
Published: June 2009

Abstract
Motivation: Second-generation sequencing technologies produce a massive amount of short reads in a single experiment. However, sequencing errors can cause major problems when using this approach for de novo sequencing applications. Moreover, existing error correction methods have been designed and optimized for shotgun sequencing. Therefore, there is an urgent need for the design of fast and accurate computational methods and tools for error correction of large amounts of short read data.
Results: We present SHREC, a new algorithm for correcting errors in short-read data that uses a generalized suffix trie on the read data as the underlying data structure. Our results show that the method can identify erroneous reads with sensitivity and specificity of over 99% and 96% for simulated data with error rates of up to 3% as well as for real data. Furthermore, it achieves an error correction accuracy of over 80% for simulated data and over 88% for real data. These results are clearly superior to previously published approaches. SHREC is available as an efficient open-source Java implementation that allows processing of 10 million of short reads on a standard workstation.
Availability: SHREC source code in JAVA is freely available at http://www.informatik.uni-kiel.de/∼jasc/Shrec/
Contact: jasc@informatik.uni-kiel.de
Different responses to area closures and effort controls for sedentary and migratory harvested species in a multispecies coral reef linefishery
Authors: Little L. Richard , Punt André E. , Mapstone Bruce D. , Begg Gavin A. , Goldman Barry , Ellis Nick 
Published: June 2009

Abstract
Little, L. R., Punt, A. E., Mapstone, B. D., Begg, G. A., Goldman, B., and Ellis, N. 2009. Different responses to area closures and effort controls for sedentary and migratory harvested species in a multispecies coral reef linefishery. – ICES Journal of Marine Science, 66: 1931–1941. We used a simulation model to examine the effect of area closures and fishing effort on the two main target species of the Great Barrier Reef Coral Reef Finfish Fishery: common coral trout (Plectropomus leopardus) and red throat emperor (Lethrinus miniatus). Area closures had greater effect on the more sedentary coral trout, in the areas outside the closures and accessible to the fishery, and little effect on red throat emperor, which was assumed to move among reefs. The effects of effort levels were greater than area closures on the harvest of both species and were seen not only in the areas accessible to the fishery, but also in the biomass of red throat emperor in the areas closed to the fishery. The catch and biomass resulting from a given effort level did not appear to have an equivalent effect attributable to any area closure. Although the effects of effort levels and area closures are confounded in reality by the coincidental implementation of area closures and restructuring of the fishery, the simulation model separated these factors to show that the closures under the 2004 rezoning should have had minimal effect on total-stock biomass and that a greater effect would result from changes in fishing effort.
Using stock assessment information to assess fishing capacity of tuna fisheries
Authors: Arrizabalaga Haritz , Restrepo Victor R. , Maunder Mark N. , Majkowski Jacek 
Published: June 2009

Abstract
Arrizabalaga, H., Restrepo, V. R., Maunder, M. N., and Majkowski, J. 2009. Using stock assessment information to assess fishing capacity of tuna fisheries. – ICES Journal of Marine Science, 66: 1959–1966. In tuna and tuna-like fisheries, there is a need for periodic assessments of fishing capacity to aid management. However, the nature and quantity of data needed to apply conventional methodologies for estimating fishing capacity are not usually available for tuna fisheries. We discuss simple alternative approaches to estimate fishing capacity and related quantities (i.e. capacity utilization, excess capacity, and overcapacity) directly from stock assessment inputs and outputs that are usually available for most tuna (and many other) stocks. Sensitivity analyses are performed to assess the effect of different levels of data aggregation and different assumptions made during the stock assessments on estimates of fishing capacity. Main advantages and disadvantages of the proposed methodologies are also illustrated using stock assessment information from different tuna stocks with different historical developments and trends in fishing mortality.
A Dynamic Interface for Capsaicinoid Systems Biology
Authors: Mazourek Michael , Pujar Anuradha , Borovsky Yelena , Paran Ilan , Mueller Lukas , Jahn Molly M. 
Published: June 2009

AbstractCapsaicinoids are the pungent alkaloids that give hot peppers (Capsicum spp.) their spiciness. While capsaicinoids are relatively simple molecules, much is unknown about their biosynthesis, which spans diverse metabolisms of essential amino acids, phenylpropanoids, benzenoids, and fatty acids. Pepper is not a model organism, but it has access to the resources developed in model plants through comparative approaches. To aid research in this system, we have implemented a comprehensive model of capsaicinoid biosynthesis and made it publicly available within the SolCyc database at the SOL Genomics Network (http://www.sgn.cornell.edu). As a preliminary test of this model, and to build its value as a resource, targeted transcripts were cloned as candidates for nearly all of the structural genes for capsaicinoid biosynthesis. In support of the role of these transcripts in capsaicinoid biosynthesis beyond correct spatial and temporal expression, their predicted subcellular localizations were compared against the biosynthetic model and experimentally determined compartmentalization in Arabidopsis (Arabidopsis thaliana). To enable their use in a positional candidate gene approach in the Solanaceae, these genes were genetically mapped in pepper. These data were integrated into the SOL Genomics Network, a clade-oriented database that incorporates community annotation of genes, enzymes, phenotypes, mutants, and genomic loci. Here, we describe the creation and integration of these resources as a holistic and dynamic model of the characteristic specialized metabolism of pepper.
AINTEGUMENTAandAINTEGUMENTA-LIKE6Act Redundantly to Regulate Arabidopsis Floral Growth and Patterning
Authors: Krizek BethA. 
Published: June 2009

AbstractAn Arabidopsis (Arabidopsis thaliana) flower consists of four types of organs arranged in a stereotypical pattern. This complex floral structure is elaborated from a small number of floral meristem cells partitioned from the shoot apical meristem during reproductive development. The positioning of floral primordia within the periphery of the shoot apical meristem depends on transport of the phytohormone auxin with floral anlagen arising at sites of auxin maxima. An early marker of lateral organ fate is the AP2/ERF-type transcription factor AINTEGUMENTA (ANT), which has been proposed to act downstream of auxin in organogenic growth. Here, I show that the related, AINTEGUMENTA-LIKE6 (AIL6)/PLETHORA3 gene acts redundantly with ANT during flower development. ant ail6 double mutants show defects in floral organ positioning, identity, and growth. These floral defects are correlated with changes in the expression levels and patterns of two floral organ identity genes, APETALA3 and AGAMOUS. ant ail6 flowers also display altered expression of an auxin-responsive reporter, suggesting that auxin accumulation and/or responses are not normal. Furthermore, I show that ANT expression in incipient and young floral primordia depends on auxin transport within the inflorescence meristem. These results show that ANT and AIL6 are important regulators of floral growth and patterning and that they may act downstream of auxin in these processes.
A Role for Multiple Circadian Clock Genes in the Response to Signals That Break Seed Dormancy inArabidopsis
Authors: Penfield Steven , Hall Anthony 
Published: June 2009

AbstractPlant seeds can sense diverse environmental signals and integrate the information to regulate developmental responses, such as dormancy and germination. The circadian clock confers a growth advantage on plants and uses environmental information for entrainment. Here, we show that normal circadian clock gene function is essential for the response to dormancy-breaking signals in seeds. We show that mutations in the clock genes LATE ELONGATED HYPOCOTYL, CIRCADIAN CLOCK ASSOCIATED1 (CCA1), and GIGANTEA (GI) cause germination defects in response to low temperature, alternating temperatures, and dry after-ripening. We demonstrate that the transcriptional clock is arrested in an evening-like state in dry seeds but rapidly entrains to light/dark cycles in ambient temperatures upon imbibition. Consistent with a role for clock genes in seed dormancy control, CCA1 expression is transcriptionally induced in response to dry after-ripening and that after-ripening affects the amplitude of subsequent transcriptional clock gene oscillations. Control of abscisic acid- and gibberellin-related gene expression in seeds requires normal circadian function, and GI and TIMING OF CAB EXPRESSION1 regulate the response to ABA and GA in seeds. We conclude that circadian clock genes play a key role in the integration of environmental signaling controlling dormancy release in plants.