bluuebunny/crossref_metadata_2025_split huggingface dataset:
A max-margin model for efficient simultaneous alignment and folding of RNA sequences
Authors: Do Chuong B. , Foo Chuan-Sheng , Batzoglou Serafim 
Published: June 2008

Abstract
Motivation: The need for accurate and efficient tools for computational RNA structure analysis has become increasingly apparent over the last several years: RNA folding algorithms underlie numerous applications in bioinformatics, ranging from microarray probe selection to de novo non-coding RNA gene prediction.
In this work, we present RAF (RNA Alignment and Folding), an efficient algorithm for simultaneous alignment and consensus folding of unaligned RNA sequences. Algorithmically, RAF exploits sparsity in the set of likely pairing and alignment candidates for each nucleotide (as identified by the CONTRAfold or CONTRAlign programs) to achieve an effectively quadratic running time for simultaneous pairwise alignment and folding. RAF's fast sparse dynamic programming, in turn, serves as the inference engine within a discriminative machine learning algorithm for parameter estimation.
Results: In cross-validated benchmark tests, RAF achieves accuracies equaling or surpassing the current best approaches for RNA multiple sequence secondary structure prediction. However, RAF requires nearly an order of magnitude less time than other simultaneous folding and alignment methods, thus making it especially appropriate for high-throughput studies.
Availability: Source code for RAF is available at:http://contra.stanford.edu/contrafold/
Contact: chuongdo@cs.stanford.edu
Detection of IUPAC and IUPAC-like chemical names
Authors: Klinger Roman , Kolářik Corinna , Fluck Juliane , Hofmann-Apitius Martin , Friedrich Christoph M. 
Published: June 2008

Abstract
Motivation: Chemical compounds like small signal molecules or other biological active chemical substances are an important entity class in life science publications and patents. Several representations and nomenclatures for chemicals like SMILES, InChI, IUPAC or trivial names exist. Only SMILES and InChI names allow a direct structure search, but in biomedical texts trivial names and Iupac like names are used more frequent. While trivial names can be found with a dictionary-based approach and in such a way mapped to their corresponding structures, it is not possible to enumerate all IUPAC names. In this work, we present a new machine learning approach based on conditional random fields (CRF) to find mentions of IUPAC and IUPAC-like names in scientific text as well as its evaluation and the conversion rate with available name-to-structure tools.
Results: We present an IUPAC name recognizer with an F1 measure of 85.6% on a MEDLINE corpus. The evaluation of different CRF orders and offset conjunction orders demonstrates the importance of these parameters. An evaluation of hand-selected patent sections containing large enumerations and terms with mixed nomenclature shows a good performance on these cases (F1 measure 81.5%). Remaining recognition problems are to detect correct borders of the typically long terms, especially when occurring in parentheses or enumerations. We demonstrate the scalability of our implementation by providing results from a full MEDLINE run.
Availability: We plan to publish the corpora, annotation guideline as well as the conditional random field model as a UIMA component.
Contact: roman.klinger@scai.fraunhofer.de
Integrating high dimensional bi-directional parsing models for gene mention tagging
Authors: Hsu Chun-Nan , Chang Yu-Ming , Kuo Cheng-Ju , Lin Yu-Shi , Huang Han-Shen , Chung I-Fang 
Published: June 2008

Abstract
Motivation: Tagging gene and gene product mentions in scientific text is an important initial step of literature mining. In this article, we describe in detail our gene mention tagger participated in BioCreative 2 challenge and analyze what contributes to its good performance. Our tagger is based on the conditional random fields model (CRF), the most prevailing method for the gene mention tagging task in BioCreative 2. Our tagger is interesting because it accomplished the highest F-scores among CRF-based methods and second over all. Moreover, we obtained our results by mostly applying open source packages, making it easy to duplicate our results.
Results: We first describe in detail how we developed our CRF-based tagger. We designed a very high dimensional feature set that includes most of information that may be relevant. We trained bi-directional CRF models with the same set of features, one applies forward parsing and the other backward, and integrated two models based on the output scores and dictionary filtering. One of the most prominent factors that contributes to the good performance of our tagger is the integration of an additional backward parsing model. However, from the definition of CRF, it appears that a CRF model is symmetric and bi-directional parsing models will produce the same results. We show that due to different feature settings, a CRF model can be asymmetric and the feature setting for our tagger in BioCreative 2 not only produces different results but also gives backward parsing models slight but constant advantage over forward parsing model. To fully explore the potential of integrating bi-directional parsing models, we applied different asymmetric feature settings to generate many bi-directional parsing models and integrate them based on the output scores. Experimental results show that this integrated model can achieve even higher F-score solely based on the training corpus for gene mention tagging.
Availability: Data sets, programs and an on-line service of our gene mention tagger can be accessed at http://aiia.iis.sinica.edu.tw/biocreative2.htm
Contact: chunnan@iis.sinica.edu.tw
A maximum common substructure-based algorithm for searching and predicting drug-like compounds
Authors: Cao Yiqun , Jiang Tao , Girke Thomas 
Published: June 2008

Abstract
Motivation: The prediction of biologically active compounds is of great importance for high-throughput screening (HTS) approaches in drug discovery and chemical genomics. Many computational methods in this area focus on measuring the structural similarities between chemical structures. However, traditional similarity measures are often too rigid or consider only global similarities between structures. The maximum common substructure (MCS) approach provides a more promising and flexible alternative for predicting bioactive compounds.
Results: In this article, a new backtracking algorithm for MCS is proposed and compared to global similarity measurements. Our algorithm provides high flexibility in the matching process, and it is very efficient in identifying local structural similarities. To predict and cluster biologically active compounds more efficiently, the concept of basis compounds is proposed that enables researchers to easily combine the MCS-based and traditional similarity measures with modern machine learning techniques. Support vector machines (SVMs) are used to test how the MCS-based similarity measure and the basis compound vectorization method perform on two empirically tested datasets. The test results show that MCS complements the well-known atom pair descriptor-based similarity measure. By combining these two measures, our SVM-based model predicts the biological activities of chemical compounds with higher specificity and sensitivity.
Contact: ycao@cs.ucr.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
BLASTing small molecules—statistics and extreme statistics of chemical similarity scores
Authors: Baldi Pierre , Benz Ryan W. 
Published: June 2008

Abstract
Motivation: Small organic molecules, from nucleotides and amino acids to metabolites and drugs, play a fundamental role in chemistry, biology and medicine. As databases of small molecules continue to grow and become more open, it is important to develop the tools to search them efficiently. In order to develop a BLAST-like tool for small molecules, one must first understand the statistical behavior of molecular similarity scores.
Results: We develop a new detailed theory of molecular similarity scores that can be applied to a variety of molecular representations and similarity measures. For concreteness, we focus on the most widely used measure—the Tanimoto measure applied to chem-ical fingerprints. In both the case of empirical fingerprints and fingerprints generated by several stochastic models, we derive accurate approximations for both the distribution and extreme value distribution of similarity scores. These approximation are derived using a ratio of correlated Gaussians approach. The theory enables the calculation of significance scores, such as Z-scores and P-values, and the estimation of the top hits list size. Empirical results obtained using both the random models and real data from the ChemDB database are given to corroborate the theory and show how it can be applied to mine chemical space.
Availability: Data and related resources are available through http://cdb.ics.uci.edu
Contact: pfbaldi@ics.uci.edu
Performing Desire: Stendhal's Theatrical Heroines
Authors: Scott Maria 
Published: June 2008

Abstract
Stendhal's independent heroines, often associated with a taste for the theatrical, do not tend to win the preference of his male heroes. As a result, they are often considered by critics to be less successful than their more traditionally ‘feminine’ counterparts in achieving their goals. However, this paper argues that characters such as Mathilde de La Mole, la Sanseverina, Lamiel, Mina Wanghen and Mina de Vanghel achieve a level of control over their own destinies unknown to Stendhal's more retiring heroines, such Mme de Rênal, Clélia Conti, Mme de Chasteller and Armance. Consequently, the author's less ‘natural’ female characters turn out in fact to be more authentic, in existential terms at least, than their more traditional sisters. The authenticity of these heroines, interpreted here as their success in defining themselves as subjects rather than objects of desire, is shown by this article to be related, somewhat paradoxically, to their interest in theatrical fakery. In making this argument, the paper engages with the ideas of, among others, Simone de Beauvoir and Jacques Lacan.
Towards an Ethics of Witness, or the Story and History of ‘une minuscule détresse’ in Annie Ernaux's
L'Événement
and Nancy Huston's
Instruments des ténèbres
Authors: Sardin Pascale 
Published: June 2008

Abstract

This paper investigates what is at stake, ethically and aesthetically, in writing about the disturbing issues of abortion and neonaticide. It focuses on
L'Événement
by Annie Ernaux and on Nancy Huston's
Instruments des ténèbres
. Though very different in form and content, these two novels, written from a distinctively female viewpoint, are metatextual works which reflect on the act of writing such taboos, and of representing irrational, defective mothers in the context of poststructuralism and postmodernism. In her exploration of the genre of the memoir and that of historiography as defined by Paul Ricoeur, Ernaux seeks a form of writing which discards pathos and the moral involvement of the reader, while Huston attempts something similar through humour and the grotesque. Yet at the same time, these novelists renegotiate the notion of retelling experience as defined by Walter Benjamin in ‘The storyteller’ — the rewriting of the chronology of excruciating events, drawing a parallel between private and public history. In this perspective, their depiction of dark mothers, which goes against the comforting myth of the good mother, reads as a political and humanistic project. Ernaux's and Huston's respective aesthetics define a new kind of ethics involving the reader and centring on the notion of witness, exhorting their readers to undertake a performative reading.
Mimesis and Alterity: Michel Leiris's Ethnography and Poetics of Spirit Possession
Authors: Albers Irene 
Published: June 2008

Abstract

The title of Leiris's diary
L'Afrique fantôme
has mostly been understood as a critique of European Africanist discourse. However, Leiris does a lot more than just denounce (his own) exoticism. This article argues that the title of his diary has to be read with reference to the French Surrealist and ethnographer's experience during his stay in Gondar while studying the
zar
, a popular cult of spirit possession. These ecstatic cults have been described as performing a mimetic relation to alterity (Taussig) or as an ‘interpretation of the Other by mimesis’ (Kramer). Re-enacting the Other leads to a liberation from its power by means of imitation. It is shown that this corresponds to Leiris's own retrospective studies of the
zar
cult as a cathartic externalization of alterity and as a theatre of alterity. In his failed search for a truly sacral, authentically primitive or salutary ritual, Leiris above all discovered one particular ritual: writing, ‘poésie’. This refers to what now appears as a European form of spirit possession developing its own rituals — rituals of conjuring ‘phantoms’ as well as ones of defence and exorcism. In Leiris, the conjuring (as well as the therapy) becomes a literary domain, whereas the banishment of the phantom is the domain of theory or research. Talking as one who is possessed and talking about possession, inseparably linked in the diary, are associated with discourses of autobiographical self-description and ethnographic description of otherness, of ‘expérience poétique’ and ‘étude ethnologique’.
Integrating commercial and research surveys to estimate the harvestable biomass, and establish a quota, for an “unexploited” abalone population
Authors: Mayfield Stephen , McGarvey Richard , Carlson Ian J. , Dixon Cameron 
Published: June 2008

Abstract
Mayfield, S., McGarvey, R., Carlson, I. J., and Dixon, C. 2008. Integrating commercial and research surveys to estimate the harvestable biomass, and establish a quota, for an “unexploited” abalone population. – ICES Journal of Marine Science, 65: 1122–1130. A key challenge facing many fisheries managers is the absence of information on the level of harvestable biomass. We describe an integrated, two-stage survey approach that was used to measure the spatial distribution and harvestable biomass of a largely unexploited metapopulation of greenlip abalone (Haliotis laevigata) over a large area of northwestern Spencer Gulf, South Australia. In stage 1, commercial fishers conducted systematic surveys to identify subareas with abalone at harvestable densities. Cpue measures from these surveys were used to map and stratify a bounded survey subregion, within which leaded-line, research-diver surveys measured absolute density and harvestable biomass (stage 2). Decision tables, showing minimum biomass at various probabilities vs. harvest fraction, were developed to provide a risk-assessment framework for quota setting. Within two years, our approach allowed, first, the mapping of the broad-scale, spatial distribution and abundance of greenlip abalone in an area of 1143 km2, second, the estimation of harvestable biomass in a smaller (16.9 km2) area, and finally, the allocation by State fishery managers of an additional quota inside a newly defined management subzone. The collaborative approach we describe for providing estimates of absolute biomass over large spatial scales affords multiple advantages for the assessment and management of invertebrate dive fisheries.
Effectiveness of a feedback management procedure based on controlling the size of marine protected areas through catch per unit effort
Authors: Kai Mikihiko , Shirakihara Kunio 
Published: June 2008

Abstract
Kai, M., and Shirakihara, K. 2008. Effectiveness of a feedback management procedure based on controlling the size of marine protected areas through catch per unit effort. – ICES Journal of Marine Science, 65: 1216–1226. The effectiveness of a feedback management procedure using marine protected areas (MPAs) was investigated. This procedure does not control fishing effort, but it does increase the size of the MPA when the catch per unit effort (cpue) is below a predetermined target level and reduces the size when the cpue is above this level. Stability analyses of the approach, which consisted of a population dynamics model and a model to control MPA size, suggest that this procedure can lead to recovery of a depleted population and sustain that population at a predetermined target level, even when there is hyperstability (a non-linear relationship between population size and cpue). An alternative procedure using fishing effort instead of MPA size may also function well, although both procedures may need a long time for a depleted population to approach the target level. Performance of both procedures was examined using numerical simulations focused on system dynamics in the short term after management implementation. The procedure using MPA size was more effective at preventing population collapse. Simulations suggest that if this procedure starts from a desirable level of initial MPA size, it has advantages over the alternative procedure through creating speedier population recovery and a higher level of short-term catch.
An Abscisic Acid-Induced Protein, HVA22, Inhibits Gibberellin-Mediated Programmed Cell Death in Cereal Aleurone Cells
Authors: Guo Woei-Jiun , David Ho Tuan-Hua 
Published: June 2008

Abstract
Plant HVA22 is a unique abscisic acid (ABA)/stress-induced protein first isolated from barley (Hordeum vulgare) aleurone cells. Its yeast homolog, Yop1p, functions in vesicular trafficking and in the endoplasmic reticulum (ER) network in vivo. To examine the roles of plant HVA22, barley HVA22 was ectopically expressed in barley aleurone cells. Overexpression of HVA22 proteins inhibited gibberellin (GA)-induced formation of large digestive vacuoles, which is an important aspect of GA-induced programmed cell death in aleurone cells. The effect of HVA22 was specific, because overexpression of green fluorescent protein or another ABA-induced protein, HVA1, did not lead to the same effect. HVA22 acts downstream of the transcription factor GAMyb, which activates programmed cell death and other GA-mediated processes. Moreover, expression of HVA22:green fluorescent protein fusion proteins showed network and punctate fluorescence patterns, which were colocalized with an ER marker, BiP:RFP, and a Golgi marker, ST:mRFP, respectively. In particular, the transmembrane domain 2 was critical for protein localization and stability. Ectopic expression of the most phylogenetically similar Arabidopsis (Arabidopsis thaliana) homolog, AtHVA22D, also resulted in the inhibition of vacuolation to a similar level as HVA22, indicating function conservation between barley HVA22 and some Arabidopsis homologs. Taken together, we show that HVA22 is an ER- and Golgi-localized protein capable of negatively regulating GA-mediated vacuolation/programmed cell death in barley aleurone cells. We propose that ABA induces the accumulation of HVA22 proteins to inhibit vesicular trafficking involved in nutrient mobilization to delay coalescence of protein storage vacuoles as part of its role in regulating seed germination and seedling growth.
Apoplastic Polyamine Oxidation Plays Different Roles in Local Responses of Tobacco to Infection by the Necrotrophic FungusSclerotinia sclerotiorumand the Biotrophic BacteriumPseudomonas viridiflava
Authors: Marina María , Maiale Santiago Javier , Rossi Franco Rubén , Romero Matías Fernando , Rivas Elisa Isabel , Gárriz Andrés , Ruiz Oscar Adolfo , Pieckenstain Fernando Luis 
Published: June 2008

AbstractThe role of polyamine (PA) metabolism in tobacco (Nicotiana tabacum) defense against pathogens with contrasting pathogenic strategies was evaluated. Infection by the necrotrophic fungus Sclerotinia sclerotiorum resulted in increased arginine decarboxylase expression and activity in host tissues, as well as putrescine and spermine accumulation in leaf apoplast. Enhancement of leaf PA levels, either by using transgenic plants or infiltration with exogenous PAs, led to increased necrosis due to infection by S. sclerotiorum. Specific inhibition of diamine and PA oxidases attenuated the PA-induced enhancement of leaf necrosis during fungal infection. When tobacco responses to infection by the biotrophic bacterium Pseudomonas viridiflava were investigated, an increase of apoplastic spermine levels was detected. Enhancement of host PA levels by the above-described experimental approaches strongly decreased in planta bacterial growth, an effect that was blocked by a PA oxidase inhibitor. It can be concluded that accumulation and further oxidation of free PAs in the leaf apoplast of tobacco plants occurs in a similar, although not identical way during tobacco defense against infection by microorganisms with contrasting pathogenesis strategies. This response affects the pathogen's ability to colonize host tissues and results are detrimental for plant defense against necrotrophic pathogens that feed on necrotic tissue; on the contrary, this response plays a beneficial role in defense against biotrophic pathogens that depend on living tissue for successful host colonization. Thus, apoplastic PAs play important roles in plant-pathogen interactions, and modulation of host PA levels, particularly in the leaf apoplast, may lead to significant changes in host susceptibility to different kinds of pathogens.
Silencing Onion Lachrymatory Factor Synthase Causes a Significant Change in the Sulfur Secondary Metabolite Profile
Authors: Eady Colin C. , Kamoi Takahiro , Kato Masahiro , Porter Noel G. , Davis Sheree , Shaw Martin , Kamoi Akiko , Imai Shinsuke 
Published: June 2008

Abstract
Through a single genetic transformation in onion (Allium cepa), a crop recalcitrant to genetic transformation, we suppressed the lachrymatory factor synthase gene using RNA interference silencing in six plants. This reduced lachrymatory synthase activity by up to 1,544-fold, so that when wounded the onions produced significantly reduced levels of tear-inducing lachrymatory factor. We then confirmed, through a novel colorimetric assay, that this silencing had shifted the trans-S-1-propenyl-l-cysteine sulfoxide breakdown pathway so that more 1-propenyl sulfenic acid was converted into di-1-propenyl thiosulfinate. A consequence of this raised thiosulfinate level was a marked increase in the downstream production of a nonenzymatically produced zwiebelane isomer and other volatile sulfur compounds, di-1-propenyl disulfide and 2-mercapto-3,4-dimethyl-2,3-dihydrothiophene, which had previously been reported in trace amounts or had not been detected in onion. The consequences of this dramatic simultaneous down- and up-regulation of secondary sulfur products on the health and flavor attributes of the onion are discussed.