bluuebunny/crossref_metadata_2025_split huggingface dataset:
An architecture for biological information extraction and representation
Authors: Vailaya Aditya , Bluvas Peter , Kincaid Robert , Kuchinsky Allan , Creech Michael , Adler Annette 
Published: December 2004

AbstractMotivations: Technological advances in biomedical research are generating a plethora of heterogeneous data at a high rate. There is a critical need for extraction, integration and management tools for information discovery and synthesis from these heterogeneous data.Results: In this paper, we present a general architecture, called ALFA, for information extraction and representation from diverse biological data. The ALFA architecture consists of: (i) a networked, hierarchical, hyper-graph object model for representing information from heterogeneous data sources in a standardized, structured format; and (ii) a suite of integrated, interactive software tools for information extraction and representation from diverse biological data sources. As part of our research efforts to explore this space, we have currently prototyped the ALFA object model and a set of interactive software tools for searching, filtering, and extracting information from scientific text. In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation, and representation of information from scientific text. We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation.Contact: aditya_vailaya@agilent.com
Multidimensional support vector machines for visualization of gene expression data
Authors: Komura D. , Nakamura H. , Tsutsumi S. , Aburatani H. , Ihara S. 
Published: December 2004

Abstract
Motivation: Since DNA microarray experiments provide us with huge amount of gene expression data, they should be analyzed with statistical methods to extract the meanings of experimental results. Some dimensionality reduction methods such as Principal Component Analysis (PCA) are used to roughly visualize the distribution of high dimensional gene expression data. However, in the case of binary classification of gene expression data, PCA does not utilize class information when choosing axes. Thus clearly separable data in the original space may not be so in the reduced space used in PCA.
Results: For visualization and class prediction of gene expression data, we have developed a new SVM-based method called multidimensional SVMs, that generate multiple orthogonal axes. This method projects high dimensional data into lower dimensional space to exhibit properties of the data clearly and to visualize a distribution of the data roughly. Furthermore, the multiple axes can be used for class prediction. The basic properties of conventional SVMs are retained in our method: solutions of mathematical programming are sparse, and nonlinear classification is implemented implicitly through the use of kernel functions. The application of our method to the experimentally obtained gene expression datasets for patients' samples indicates that our algorithm is efficient and useful for visualization and class prediction.
Contact: komura@hal.rcast.u-tokyo.ac.jp
Finding differentially expressed genes for pattern generation
Authors: Abul Osman , Alhajj Reda , Polat Faruk , Barker Ken 
Published: December 2004

Abstract
Motivation: It is important to consider finding differentially expressed genes in a dataset of microarray experiments for pattern generation.
Results: We developed two methods which are mainly based on the q-values approach; the first is a direct extension of the q-values approach, while the second uses two approaches: q-values and maximum-likelihood. We present two algorithms for the second method, one for error minimization and the other for confidence bounding. Also, we show how the method called Patterns from Gene Expression (PaGE) (Grant et al., 2000) can benefit from q-values. Finally, we conducted some experiments to demonstrate the effectiveness of the proposed methods; experimental results on a selected dataset (BRCA1 vs BRCA2 tumor types) are provided.
Contact: alhajj@cpsc.ucalgary.ca
An integrated tool for microarray data clustering and cluster validity assessment
Authors: Bolshakova Nadia , Azuaje Francisco , Cunningham Pádraig 
Published: December 2004

AbstractSummary: In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality of the data analysis results, and may support the prediction of the number of relevant clusters in the microarray datasets. This systematic evaluation approach may significantly aid genome expression analyses for knowledge discovery applications. The developed software system may be effectively used for clustering and validating not only DNA microarray expression analysis applications but also other biomedical and physical data with no limitations.Availability: The program is freely available for non-profit use on request at http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.htmlContact: Nadia.Bolshakova@cs.tcd.ie
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
Authors: Stamatakis A. , Ludwig T. , Meier H. 
Published: December 2004

Abstract
Motivation: The computation of large phylogenetic trees with statistical models such as maximum likelihood or bayesian inference is computationally extremely intensive. It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to the true tree more frequently than less elaborate methods such as parsimony or neighbor joining. Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist's PC workstation within reasonable time is limited to trees containing approximately 100 taxa.
Results: In this paper we present the latest release of our program RAxML-III for rapid maximum likelihood-based inference of large evolutionary trees which allows for computation of 1.000-taxon trees in less than 24 hours on a single PC processor. We compare RAxML-III to the currently fastest implementations for maximum likelihood and bayesian inference: PHYML and MrBayes. Whereas RAxML-III performs worse than PHYML and MrBayes on synthetic data it clearly outperforms both programs on all real data alignments used in terms of speed and final likelihood values.
Availability Supplementary information: RAxML-III including all alignments and final trees mentioned in this paper is freely available as open source code at http://wwwbode.cs.tum/~stamatak
Contact: stamatak@cs.tum.edu
Reverse Genetic Characterization of Cytosolic Acetyl-CoA Generation by ATP-Citrate Lyase in Arabidopsis
Authors: Fatland Beth L. , Nikolau Basil J. , Wurtele Eve Syrkin 
Published: December 2004

Abstract
Acetyl-CoA provides organisms with the chemical flexibility to biosynthesize a plethora of natural products that constitute much of the structural and functional diversity in nature. Recent studies have characterized a novel ATP-citrate lyase (ACL) in the cytosol of Arabidopsis thaliana. In this study, we report the use of antisense RNA technology to generate a series of Arabidopsis lines with a range of ACL activity. Plants with even moderately reduced ACL activity have a complex, bonsai phenotype, with miniaturized organs, smaller cells, aberrant plastid morphology, reduced cuticular wax deposition, and hyperaccumulation of starch, anthocyanin, and stress-related mRNAs in vegetative tissue. The degree of this phenotype correlates with the level of reduction in ACL activity. These data indicate that ACL is required for normal growth and development and that no other source of acetyl-CoA can compensate for ACL-derived acetyl-CoA. Exogenous malonate, which feeds into the carboxylation pathway of acetyl-CoA metabolism, chemically complements the morphological and chemical alterations associated with reduced ACL expression, indicating that the observed metabolic alterations are related to the carboxylation pathway of cytosolic acetyl-CoA metabolism. The observations that limiting the expression of the cytosolic enzyme ACL reduces the accumulation of cytosolic acetyl-CoA–derived metabolites and that these deficiencies can be alleviated by exogenous malonate indicate that ACL is a nonredundant source of cytosolic acetyl-CoA.
Cytosolic Ascorbate Peroxidase 1 Is a Central Component of the Reactive Oxygen Gene Network of Arabidopsis
Authors: Davletova Sholpan , Rizhsky Ludmila , Liang Hongjian , Shengqiang Zhong , Oliver David J. , Coutu Jesse , Shulaev Vladimir , Schlauch Karen , Mittler Ron 
Published: December 2004

AbstractReactive oxygen species (ROS), such as O2 − and H2O2, play a key role in plant metabolism, cellular signaling, and defense. In leaf cells, the chloroplast is considered to be a focal point of ROS metabolism. It is a major producer of O2 − and H2O2 during photosynthesis, and it contains a large array of ROS-scavenging mechanisms that have been extensively studied. By contrast, the function of the cytosolic ROS-scavenging mechanisms of leaf cells is largely unknown. In this study, we demonstrate that in the absence of the cytosolic H2O2-scavenging enzyme ascorbate peroxidase 1 (APX1), the entire chloroplastic H2O2-scavenging system of Arabidopsis thaliana collapses, H2O2 levels increase, and protein oxidation occurs. We further identify specific proteins oxidized in APX1-deficient plants and characterize the signaling events that ensue in knockout-Apx1 plants in response to a moderate level of light stress. Using a dominant-negative approach, we demonstrate that heat shock transcription factors play a central role in the early sensing of H2O2 stress in plants. Using knockout plants for the NADPH oxidase D protein (knockout-RbohD), we demonstrate that RbohD might be required for ROS signal amplification during light stress. Our study points to a key role for the cytosol in protecting the chloroplast during light stress and provides evidence for cross-compartment protection of thylakoid and stromal/mitochondrial APXs by cytosolic APX1.
The Inheritance of Apomixis inPoa pratensisConfirms a Five Locus Model with Differences in Gene Expressivity and Penetrance
Authors: Matzk Fritz , Prodanovic Sanja , Bäumlein Helmut , Schubert Ingo 
Published: December 2004

AbstractThe genetic control of apomixis was studied in numerous segregating progenies originated from intercrossing and selfing of obligate sexual and facultative apomictic parents in Poa pratensis by means of the flow cytometric seed screen. The data support a novel model with five major genes required to control asexual seed formation: the Apospory initiator (Ait) gene, the Apospory preventer (Apv) gene, a Megaspore development (Mdv) gene, the Parthenogenesis initiator (Pit) gene, and the Parthenogenesis preventer (Ppv) gene. Differences in expressivity and interactions of these genes are responsible for the wide variation of the mode of reproduction. Apospory and parthenogenesis as well as the initiator and preventer genes of these components segregate independently. The genotypes with the highest expressivity of apospory and parthenogenesis were assigned as Ait-/apvapv/Pit-/ppvppv, those with intermediate expressivity as Ait-/Apv-/Pit-/Ppv-, and those with low expressivity as aitait/apvapv/pitpit/ppvppv. Among the self progenies of obligate sexual individuals, plants with a low capacity for apospory and/or parthenogenesis occurred, indicating that the sexual parents were heterozygous for the preventer genes and homozygous for the recessive initiator alleles (aitait/Apv-/pitpit/Ppv-). The dominant allele Ait exhibits incomplete penetrance. The degree of expressivity of apospory and parthenogenesis was constant among several harvest years of F1 plants.
Two Plant–Viral Movement Proteins Traffic in the Endocytic Recycling Pathway
Authors: Haupt Sophie , Cowan Graham H. , Ziegler Angelika , Roberts Alison G. , Oparka Karl J. , Torrance Lesley 
Published: December 2004

AbstractMany plant viruses exploit a conserved group of proteins known as the triple gene block (TGB) for cell-to-cell movement. Here, we investigated the interaction of two TGB proteins (TGB2 and TGB3) of Potato mop-top virus (PMTV), with components of the secretory and endocytic pathways when expressed as N-terminal fusions to green fluorescent protein or monomeric red fluorescent protein (mRFP). Our studies revealed that fluorophore-labeled TGB2 and TGB3 showed an early association with the endoplasmic reticulum (ER) and colocalized in motile granules that used the ER-actin network for intracellular movement. Both proteins increased the size exclusion limit of plasmodesmata, and TGB3 accumulated at plasmodesmata in the absence of TGB2. TGB3 contains a putative Tyr-based sorting motif, mutations in which abolished ER localization and plasmodesmatal targeting. Later in the expression cycle, both fusion proteins were incorporated into vesicular structures. TGB2 associated with these structures on its own, but TGB3 could not be incorporated into the vesicles in the absence of TGB2. Moreover, in addition to localization to the ER and motile granules, mRFP-TGB3 was incorporated into vesicles when expressed in PMTV-infected epidermal cells, indicating recruitment by virus-expressed TGB2. The TGB fusion protein-containing vesicles were labeled with FM4-64, a marker for plasma membrane internalization and components of the endocytic pathway. TGB2 also colocalized in vesicles with Ara7, a Rab5 ortholog that marks the early endosome. Protein interaction analysis revealed that recombinant TGB2 interacted with a tobacco protein belonging to the highly conserved RME-8 family of J-domain chaperones, shown to be essential for endocytic trafficking in Caenorhabditis elegans and Drosophila melanogaster. Collectively, the data indicate the involvement of the endocytic pathway in viral intracellular movement, the implications of which are discussed.
New Subunits NDH-M, -N, and -O, Encoded by Nuclear Genes, Are Essential for Plastid Ndh Complex Functioning in Higher Plants
Authors: Rumeau Dominique , Bécuwe-Linka Noëlle , Beyly Audrey , Louwagie Mathilde , Garin Jérôme , Peltier Gilles 
Published: December 2004

Abstract
In higher plants, the Ndh complex reduces plastoquinones and is involved in cyclic electron flow around photosystem I, supplying extra-ATP for photosynthesis, particularly under environmental stress conditions. Based on plastid genome sequences, the Ndh complex would contain 11 subunits (NDH-A to -K), but homologies with bacterial complex indicate the probable existence of additional subunits. To identify missing subunits, tobacco (Nicotiana tabacum) NDH-H was His tagged at its N terminus using plastid transformation. A functional Ndh subcomplex was purified by Ni2+ affinity chromatography and its subunit composition analyzed by mass spectrometry. Five plastid encoded subunits (NDH-A, -H, -I, -J, and -K) were identified as well as three new subunits (NDH-M, -N, and -O) homologous to cyanobacterial and higher plant proteins. Arabidopsis thaliana mutants missing one of these new subunits lack a functional Ndh complex, and NDH-M and NDH-N are not detected in a tobacco transformant lacking the Ndh complex. We discuss the involvement of these three nuclear-encoded subunits in the functional integrity of the plastidial complex.
Arabidopsis Membrane Steroid Binding Protein 1 Is Involved in Inhibition of Cell Elongation
Authors: Yang Xiao-Hua , Xu Zhi-Hong , Xue Hong-Wei 
Published: December 2004

Abstract
A putative Membrane Steroid Binding Protein (designated MSBP1) was identified and functionally characterized as a negative regulator of cell elongation in Arabidopsis thaliana. The MSBP1 gene encodes a 220–amino acid protein that can bind to progesterone, 5-dihydrotestosterone, 24-epi-brassinolide (24-eBL), and stigmasterol with different affinities in vitro. Transgenic plants overexpressing MSBP1 showed short hypocotyl phenotype and increased steroid binding capacity in membrane fractions, whereas antisense MSBP1 transgenic plants showed long hypocotyl phenotypes and reduced steroid binding capacity, indicating that MSBP1 negatively regulates hypocotyl elongation. The reduced cell elongation of MSBP1-overexpressing plants was correlated with altered expression of genes involved in cell elongation, such as expansins and extensins, indicating that enhanced MSBP1 affected a regulatory pathway for cell elongation. Suppression or overexpression of MSBP1 resulted in enhanced or reduced sensitivities, respectively, to exogenous progesterone and 24-eBL, suggesting a negative role of MSBP1 in steroid signaling. Expression of MSBP1 in hypocotyls is suppressed by darkness and activated by light, suggesting that MSBP1, as a negative regulator of cell elongation, plays a role in plant photomorphogenesis. This study demonstrates the functional roles of a steroid binding protein in growth regulation in higher plants.
Development of the Interactive Broiler Income Spreadsheet
Authors: Shofner Tara 
Published: December 2004

AbstractThe poultry industry has experienced unprecedented efficiencies since 1960 in large part due to vertical integration facilitated by production contracts between growers and integrators. As growers seek information about contract production they need to be well informed about all aspects of the process, especially potential income. Recent poultry grower complaints have surfaced as a result of incorrect expense and revenue expectations. The Interactive Broiler Income Spreadsheet (IBIS) is developed to enable current and prospective poultry producers to better estimate income. IBIS, an unbiased Excel spreadsheet tool to assist in decision‐making regarding broiler production profitability, uses actual grower expense and revenue information or, alternatively, grower‐panel default data to assess income under various grower‐specified production, expense, and price scenarios.Poultry integrator grower service personnel, lenders, and Cooperative Extension professionals will utilize IBIS to assist growers in operational planning and risk tolerance identification in varying economic situations. Growers may also gauge effects of capital improvements, equipment upgrades, chick placements, and time between flocks on income.
The exploitation argument against commercial surrogacy
Authors: Wilkinson Stephen 
Published: December 2004

This paper discusses the exploitation argument against commercial surrogacy: the claim that commercial surrogacy is morally objectionable because it is exploitative. The following questions are addressed. First, what exactly does the exploitation argument amount to? Second, is commercial surrogacy in fact exploitative? Third, if it were exploitative, would this provide a sufficient reason to prohibit (or otherwise legislatively discourage) it? The focus throughout is on the exploitation of paid surrogates, although it is noted that other parties (e.g. ‘commissioning parents’) may also be the victims of exploitation.It is argued that there are good reasons for believing that commercial surrogacy is often exploitative. However, even if we accept this, the exploitation argument for prohibiting (or otherwise legislatively discouraging) commercial surrogacy remains quite weak. One reason for this is that prohibition may well ‘backfire’ and lead to potential surrogates having to do other things that are more exploitative and/or more harmful than paid surrogacy. It is concluded therefore that those who oppose exploitation should (rather than attempting to stop particular practices like commercial surrogacy) concentrate on: (a) improving the conditions under which paid surrogates ‘work’; and (b) changing the background conditions (in particular, the unequal distribution of power and wealth) which generate exploitative relationships.
Development and validation of a brief, descriptive Danish pain questionnaire (BDDPQ)
Authors: Perkins F. M. , Werner M. U. , Persson F. , Holte K. , Jensen T. S. , Kehlet H. 
Published: December 2004

Background:  A new pain questionnaire should be simple, be documented to have discriminative function, and be related to previously used questionnaires.Methods:  Word meaning was validated by using bilingual Danish medical students and asking them to translate words taken from the Danish version of the McGill pain questionnaire into English. Evaluative word value was estimated using a visual analog scale (VAS). Discriminative function was assessed by having patients with one of six painful conditions (postherpetic neuralgia, phantom limb pain, rheumatoid arthritis, ankle fracture, appendicitis, or labor pain) complete the questionnaire.Results:  We were not able to find Danish words that were reliably back‐translated to the English words ‘splitting’ or ‘gnawing’. A simple three‐word set of evaluative terms had good separation when rated on a VAS scale (‘let’ 17.5±6.5 mm; ‘moderat’ 42.7±8.6 mm; and ‘stærk’ 74.9±9.7 mm). The questionnaire was able to discriminate among the six painful conditions with 77% accuracy by just using the descriptive words. The accuracy of the questionnaire increased to 96% with the addition of evaluative terms (for pain at rest and with activity), chronicity (acute vs. chronic), and location of the pain.Conclusions:  A Danish pain questionnaire that subjects and patients can self‐administer has been developed and validated relative to the words used in the English McGill Pain questionnaire. The discriminative ability of the questionnaire among some common painful conditions has been tested and documented. The questionnaire may be of use in patient care and research.
Comparison of 27‐gauge (0.41‐mm) Whitacre and Quincke spinal needles with respect to post‐dural puncture headache and non‐dural puncture headache
Authors: Santanen U. , Rautoma P. , Luurila H. , Erkola O. , Pere P. 
Published: December 2004

Background:  The incidence of headache after spinal anaesthesia has varied greatly between studies. We compared the incidence of postoperative headache in general and postdural puncture headache (PDPH) when using 27‐gauge (G) (outer diameter 0.41 mm) Quincke and Whitacre spinal needles in ambulatory surgery performed under spinal anaesthesia.Methods:  In a prospective, randomized study, 676 ASA physical status I–II day‐case outpatients were given a spinal anaesthetic through either a 27‐G (0.41 mm) Quincke or a 27‐G (0.41 mm) Whitacre spinal needle. The incidence of any type of postoperative headache was assessed and the type of headache defined using a standardized questionnaire including PDPH criteria. The severity of the headache was defined using a 100‐mm visual analogue scale.Results:  For the final analysis, 529 patients were available (259 patients in the Quincke group and 270 patients in the Whitacre group). The overall incidence of postoperative headache was 20.0%, but the incidence of true PDPH was very low (1.51%). The incidence of PDPH in the Quincke group was 2.70%, while in the Whitacre group it was only 0.37% (P < 0.05). The overall incidence of non‐dural puncture headache was 18.5% and did not differ between the study groups.Conclusions:  True PDPH seldom occurs when a 27‐G (0.41 mm) spinal needle is used, although postoperatively a non‐specific headache is common. Using the 27‐G (0.41 mm) Whitacre spinal needle further reduced the incidence of PDPH. Thus, we recommend routine use of the 27‐G (0.41 mm) Whitacre spinal needle when performing spinal anaesthesia.