bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of alarm pheromones to enhance bait harvest by grass-cutting ants
Authors: Hughes W.O.H. , Goulson D. 
Published: July 2002

AbstractThe enhancement of bait for the control of grass-cutting ants was investigated using two species of grass-cutting ant, Atta bisphaerica (Forel) and Atta capiguara (Gonçalves) (Hymenoptera: Formicidae). Bait was applied in loose piles to obtain a direct relationship between ant attraction and bait harvest. Enhancement with alarm pheromone compounds significantly increased the attractiveness and harvest of bait under certain conditions. A large proportion of the ants attracted to the enhanced bait were minor workers. These ants rarely transport bait because of their small size, and so it may be possible to increase the effect of bait enhancement by using smaller bait granules. Foragers of A. capiguara were less inclined to transport citrus-pulp bait than were those of Atta laevigata (Fr. Smith), a species that also harvests dicotyledonous plants. This emphasizes the importance of developing a bait matrix that is more acceptable to grass-cutting species. Nevertheless, the results suggest that alarm pheromone compounds have significant potential to improve the efficacy of baits for the control of grass-cutting ants.
Operating the production calculus: ordering a production system in the print industry
Authors: Button Graham , Sharrock Wes 
Published: July 2002

ABSTRACTThe topic of shop‐floor work has been extensively examined within sociology. However, the organizational structures within which this work takes place have, in the most part, been taken as unexamined givens. Yet, their operation is also the shop‐floor work of some people. This paper examines the way in which the stable organizational structures within which shop‐floor work takes place are achieved. It is based upon a fieldwork investigation of a large commercial printer and focuses upon the collaborative work of those who are involved in scheduling the production of a job and their use of ‘the production calculus’ in planning the work of the site. The print industry is undergoing considerable technological change and scheduling technologies have been developed to automate this work. However, there has been little take up of these technologies and the paper also considers how the characteristics of operating the production calculus in practice may account for this.
Demography or respect?: work group demography versus organizational dynamics as determinants of meaning and satisfaction at work*
Authors: Hodson Randy 
Published: July 2002

ABSTRACTThis article tests two competing models of meaning and satisfaction at work. First, meaning and satisfaction at work can be influenced by the demographic composition of work groups, especially their racial and gender compositions. Second, meaning and satisfaction can be influenced by management behaviour, especially by leadership in maintaining a productive environment and by respect for workers’ rights. We evaluate these determinants, along with more traditional determinants that focus on socio‐technical characteristics, using a unique data set derived from content analysing the reports provided by book‐length organizational ethnographies (N = 108). Work group composition is found to have only a minor and selective influence on meaning at work. In contrast, management leadership and respect for workers’ rights are found to have much stronger and more widespread effects. The well established role of socio‐technical factors such as job autonomy as foundations for meaning and satisfaction in work is also replicated in the analysis. When contrasted with both work group demography and traditional job and organizational characteristics, a well run organization is found to be the single most important underpinning for a meaningful and satisfying work life. In the concluding section we develop the implication of these findings for organizational analysis.
Confidence measures for protein fold recognition
Authors: Sommer Ingolf , Zien Alexander , von Öhsen Niklas , Zimmer Ralf , Lengauer Thomas 
Published: July 2002

Abstract
Motivation: We present an extensive evaluation of different methods and criteria to detect remote homologs of a given protein sequence. We investigate two associated problems: first, to develop a sensitive searching method to identify possible candidates and, second, to assign a confidence to the putative candidates in order to select the best one.
For searching methods where the score distributions are known, p-values are used as confidence measure with great success. For the cases where such theoretical backing is absent, we propose empirical approximations to p-values for searching procedures.
Results: As a baseline, we review the performances of different methods for detecting remote protein folds (sequence alignment and threading, with and without sequence profiles, global and local). The analysis is performed on a large representative set of protein structures.
For fold recognition, we find that methods using sequence profiles generally perform better than methods using plain sequences, and that threading methods perform better than sequence alignment methods.
In order to assess the quality of the predictions made, we establish and compare several confidence measures, including raw scores, z-scores, raw score gaps, z-score gaps, and different methods of p-value estimation. We work our way from the theoretically well backed local scores towards more explorative global and threading scores.
The methods for assessing the statistical significance of predictions are compared using specificity--sensitivity plots. For local alignment techniques we find that p-value methods work best, albeit computationally cheaper methods such as those based on score gaps achieve similar performance. For global methods where no theory is available methods based on score gaps work best.
By using the score gap functions as the measure of confidence we improve the more powerful fold recognition methods for which p-values are unavailable.
Availability: The benchmark set is available upon request.
Contact: ingolf.sommer@gmd.de
* To whom correspondence should be addressed.
NETASA: neural network based prediction of solvent accessibility
Authors: Ahmad Shandar , Gromiha M. Michael 
Published: July 2002

Abstract
Motivation: Prediction of the tertiary structure of a protein from its amino acid sequence is one of the most important problems in molecular biology. The successful prediction of solvent accessibility will be very helpful to achieve this goal. In the present work, we have implemented a server, NETASA for predicting solvent accessibility of amino acids using our newly optimized neural network algorithm. Several new features in the neural network architecture and training method have been introduced, and the network learns faster to provide accuracy values, which are comparable or better than other methods of ASA prediction.
Results: Prediction in two and three state classification systems with several thresholds are provided. Our prediction method achieved the accuracy level upto 90% for training and 88% for test data sets. Three state prediction results provide a maximum 65% accuracy for training and 63% for the test data. Applicability of neural networks for ASA prediction has been confirmed with a larger data set and wider range of state thresholds. Salient differences between a linear and exponential network for ASA prediction have been analysed.
Availability: Online predictions are freely available at: http://www.netasa.org. Linux ix86 binaries of the program written for this work may be obtained by email from the corresponding author.
Contact: shandar@jamia.net
* To whom correspondence should be addressed at: RIKEN Tsukuba Institute, 3-1-1, Koyadai, Tsukuba 305 0074, Ibaraki, Japan.
† Present address: Computational Biology Research Center (CBRC), AIST 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.
A novel approach to local reliability of sequence alignments
Authors: Schlosshauer Maximilian , Ohlsson Mattias 
Published: July 2002

Abstract
Motivation: The pairwise alignment of biological sequences obtained from an algorithm will in general contain both correct and incorrect parts. Hence, to allow for a valid interpretation of the alignment, the local trustworthiness of the alignment has to be quantified.
Results: We present a novel approach that attributes a reliability index to every pair of residues, including gapped regions, in the optimal alignment of two protein sequences. The method is based on a fuzzy recast of the dynamic programming algorithm for sequence alignment in terms of mean field annealing. An extensive evaluation with structural reference alignments not only shows that the probability for a pair of residues to be correctly aligned grows consistently with increasing reliability index, but moreover demonstrates that the value of the reliability index can directly be translated into an estimate of the probability for a correct alignment.
Contact: mattias@thep.lu.se
BAOBAB: a Java editor for large phylogenetic trees
Authors: Dutheil J. , Galtier N. 
Published: July 2002

Abstract
Summary: BAOBAB is a Java user interface dedicated to viewing and editing large phylogenetic trees. Original features include: (i) a colour-mediated overview of magnified subtrees; (ii) copy/cut/paste of (sub)trees within or between windows; (iii) compressing/ uncompressing subtrees; and (iv) managing sequence files together with tree files.
Availability: http://www.univ-montp2.fr/~genetix/
Contact: julien.dutheil@ens-lyon.frgaltier@univ-montp2.fr
* To whom correspondence should be addressed.
Clustering of proximal sequence space for the identification of protein families
Authors: Abascal Federico , Valencia Alfonso 
Published: July 2002

Abstract
Motivation: The study of sequence space, and the deciphering of the structure of protein families and subfamilies, has up to now been required for work in comparative genomics and for the prediction of protein function. With the emergence of structural proteomics projects, it is becoming increasingly important to be able to select protein targets for structural studies that will appropriately cover the space of protein sequences, functions and genomic distribution.
These problems are the motivation for the development of methods for clustering protein sequences and building families of potentially orthologous sequences, such as those proposed here.
Results: First we developed a clustering strategy (Ncut algorithm) capable of forming groups of related sequences by assessing their pairwise relationships. The results presented for the ras super-family of proteins are similar to those produced by other clustering methods, but without the need for clustering the full sequence space. The Ncut clusters are then used as the input to a process of reconstruction of groups with equilibrated genomic composition formed by closely-related sequences. The results of applying this technique to the data set used in the construction of the COG database are very similar to those derived by the human experts responsible for this database.
Availability: The analysis of different systems, including the COG equivalent 21 genomes are available at http://www.pdg.cnb.uam.es/GenoClustering.html
Contact: valencia@cnb.uam.es
* To whom correspondence should be addressed.
Target space for structural genomics revisited
Authors: Liu Jinfeng , Rost Burkhard 
Published: July 2002

Abstract
Motivation: Structural genomics eventually aims at determining structures for all proteins. However, in the beginning experimentalists are likely to focus on globular proteins to achieve a rapid basic coverage of protein sequence space. How many proteins will structural genomics have to target? How many proteins will be excluded since we already have structural information for these or since they are not globular? We have to answer these questions in the context of our target selection for the North-East Structural Genomics Consortium (NESG).
Results: We estimated that structural information is available for about 6–38% of all proteins; 6% if we require high accuracy in comparative modelling, 38% if we are satisfied with having a rough idea about the fold. Excluding all regions that are not globular, we found that structural genomics may have to target about 48% of all proteins. This corresponded to a similar percentage of residues of the entire proteomes (52%). We explored a number of different strategies to cluster protein space in order to find the number of families representing these 48% of structurally unknown proteins. For the subset of all entirely sequenced eukaryotes, we found over 18 000 fragment clusters each of which may be a suitable target for structural genomics.
Availability: All data are available from the authors, most results are summarized at: http://cubic.bioc.columbia.edu/genomes/RES/2002_bioinformatics/
Contact: rost@columbia.edu
* To whom correspondence should be addressed.
The Reverend and the Ravens: Comment on Seawright
Authors: Clarke Kevin A. 
Published: July 2002

The purpose of this Comment is to put the current debate regarding testing necessary conditions into perspective and to point out a particularly troubling aspect of the “all cases” research design (Seawright 2002).Prior to the recent spate of books and articles in the social sciences (Ragin 1987; Dion 1988; Braumoeller and Goertz 2000), the debate over the testing or the confirmation of necessary conditions took place in the philosophical literature, mainly in terms of Hempel's (1945) paradox of the ravens. In what follows, I briefly review Hempel's paradox and the Bayesian solution to it. I argue that Seawright's account, while Bayesian in nature, relies on an assumption that no Bayesian would be willing to make.
The mechanics of cell fate determination in petals
Authors: Martin Cathie , Bhatt Kiran , Baumann Kim , Jin Hailing , Zachgo Sabine , Roberts Keith , Schwarz-Sommer Zsuzsanna , Glover Beverley , Perez-Rodrigues Maria 
Published: July 2002

The epidermal cells of petals of many species are specialized, having a pronounced conical shape. A transcription factor, MIXTA, is required for the formation of conical cells inAntirrhinum majus; in shoot epidermal cells of several species, expression of this gene is necessary and sufficient to promote conical cell formation. Ectopic expression has also shownMIXTAto be able to promote the formation of multicellular trichomes, indicating that conical cells and multicellular trichomes share elements of a common developmental pathway. Formation of conical cells or trichomes is also mutually exclusive with stomatal formation. InAntirrhinum,MIXTAnormally only promotes conical cell formation on the inner epidermal layer of the petals. Its restricted action in cell fate determination results from its specific expression pattern. Expression ofMIXTA, in turn, requires the activity of B–function genes, and biochemical evidence suggests that the products ofDEFICIENS,GLOBOSAandSEPALLATA–related genes directly activate MIXTA expression late in petal development, after the completion of cell division in the petal epidermis.AMIXTA–like gene,AmMYBML1, is also expressed in petals.AmMYBML1expression is high early in petal development. This gene may direct the formation of trichomes in petals.In specifying the fates of different cell types in petals, regulatory genes likeMIXTAmay have been duplicated. Changes in the timing and spatial localization of expression then provides similar regulatory genes which specify different cell fates.
Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks
Authors: Grosu Paul , Townsend Jeffrey P. , Hartl Daniel L. , Cavalieri Duccio 
Published: July 2002

We have developed a new tool to visualize expression data on metabolic pathways and to evaluate which metabolic pathways are most affected by transcriptional changes in whole-genome expression experiments. Using the Fisher Exact Test, the method scores biochemical pathways according to the probability that as many or more genes in a pathway would be significantly altered in a given experiment by chance alone. This method has been validated on diauxic shift experiments and reproduces well known effects of carbon source on yeast metabolism. The analysis is implemented with Pathway Analyzer, one of the tools of Pathway Processor, a new statistical package for the analysis of whole-genome expression data. Results from multiple experiments can be compared, reducing the analysis from the full set of individual genes to a limited number of pathways of interest. The pathways are visualized with OpenDX, an open-source visualization software package, and the relationship between genes in the pathways can be examined in detail using Expression Mapper, the second program of the package. This program features a graphical output displaying differences in expression on metabolic charts of the biochemical pathways to which the open reading frames are assigned.[Supplementary materials are available athttp://www.cgr.harvard.edu/cavalieri/pp.html andhttp://www.genome.org.]
Dhurrin Synthesis in Sorghum Is Regulated at the Transcriptional Level and Induced by Nitrogen Fertilization in Older Plants
Authors: Busk Peter Kamp , Møller Birger Lindberg 
Published: July 2002

Abstract
The content of the cyanogenic glucoside dhurrin in sorghum (Sorghum bicolor L. Moench) varies depending on plant age and growth conditions. The cyanide potential is highest shortly after onset of germination. At this stage, nitrogen application has no effect on dhurrin content, whereas in older plants, nitrogen application induces an increase. At all stages, the content of dhurrin correlates well with the activity of the two biosynthetic enzymes, CYP79A1 and CYP71E1, and with the protein and mRNA level for the two enzymes. During development, the activity of CYP79A1 is lower than the activity of CYP71E1, suggesting that CYP79A1 catalyzes the rate-limiting step in dhurrin synthesis as has previously been shown using etiolated seedlings. The site of dhurrin synthesis shifts from leaves to stem during plant development. In combination, the results demonstrate that dhurrin content in sorghum is largely determined by transcriptional regulation of the biosynthetic enzymes CYP79A1 and CYP71E1.
Metabolic and Environmental Regulation of 3-Methylcrotonyl-Coenzyme A Carboxylase Expression in Arabidopsis
Authors: Che Ping , Wurtele Eve Syrkin , Nikolau Basil J. 
Published: July 2002

Abstract
3-Methylcrotonyl-coenzyme A carboxylase (MCCase) is a nuclear-encoded, mitochondrial biotin-containing enzyme composed of two types of subunits: the biotinylated MCC-A subunit (encoded by the gene At1g03090) and the non-biotinylated MCC-B subunit (encoded by the gene At4g34030). The major metabolic role of MCCase is in the mitochondrial catabolism of leucine, and it also might function in the catabolism of isoprenoids and the mevalonate shunt. In the work presented herein, the single-copy gene encoding the Arabidopsis MCC-A subunit was isolated and characterized. It contains 15 exons separated by 14 introns. We examined the expression of the single-copy MCC-Aand MCC-B genes in Arabidopsis by monitoring the accumulation of the two protein and mRNA products. In addition, the expression of these two genes was studied in transgenic plants containing the 1.1- and 1.0-kb 5′ upstream sequences of the two MCCase subunit genes, respectively, fused to the β-glucuronidase gene. Light deprivation induces MCCase expression, which is suppressed by exogenous carbohydrates, especially sucrose. Several lines of evidence indicate that the suppressor of MCCase expression is synthesized in illuminated photosynthetic organs, and can be translocated to other organs to regulate MCCase expression. These results are consistent with the hypothesis that the suppressor of MCCase expression is a carbohydrate, perhaps sucrose or a carbohydrate metabolite. We conclude that MCCase expression is primarily controlled at the level of gene transcription and regulated by a complex interplay between environmental and metabolic signals. The observed expression patterns may indicate that one of the physiological roles of MCCase is to maintain the carbon status of the organism, possibly via the catabolism of leucine.
Photochemical Properties of the Flavin Mononucleotide-Binding Domains of the Phototropins from Arabidopsis, Rice, andChlamydomonas reinhardtii
Authors: Kasahara Masahiro , Swartz Trevor E. , Olney Margaret A. , Onodera Akihiko , Mochizuki Nobuyoshi , Fukuzawa Hideya , Asamizu Erika , Tabata Satoshi , Kanegae Hiromi , Takano Makoto , Christie John M. , Nagatani Akira , Briggs Winslow R. 
Published: July 2002

Abstract
Phototropins (phot1 and phot2, formerly designated nph1 and npl1) are blue-light receptors that mediate phototropism, blue light-induced chloroplast relocation, and blue light-induced stomatal opening in Arabidopsis. Phototropins contain two light, oxygen, or voltage (LOV) domains at their N termini (LOV1 and LOV2), each a binding site for the chromophore flavin mononucleotide (FMN). Their C termini contain a serine/threonine protein kinase domain. Here, we examine the kinetic properties of the LOV domains of Arabidopsis phot1 and phot2, rice (Oryza sativa) phot1 and phot2, andChlamydomonas reinhardtii phot. When expressed inEscherichia coli, purified LOV domains from all phototropins examined bind FMN tightly and undergo a self-contained photocycle, characterized by fluorescence and absorption changes induced by blue light (T. Sakai, T. Kagawa, M. Kasahara, T.E. Swartz, J.M. Christie, W.R. Briggs, M. Wada, K. Okada [2001] Proc Natl Acad Sci USA 98: 6969–6974; M. Salomon, J.M. Christie, E. Knieb, U. Lempert, W.R. Briggs [2000] Biochemistry 39: 9401–9410). The photocycle involves the light-induced formation of a cysteinyl adduct to the C(4a) carbon of the FMN chromophore, which subsequently breaks down in darkness. In each case, the relative quantum efficiencies for the photoreaction and the rate constants for dark recovery of LOV1, LOV2, and peptides containing both LOV domains are presented. Moreover, the data obtained from full-length Arabidopsis phot1 and phot2 expressed in insect cells closely resemble those obtained for the tandem LOV-domain fusion proteins expressed in E. coli. For both Arabidopsis and rice phototropins, the LOV domains of phot1 differ from those of phot2 in their reaction kinetic properties and relative quantum efficiencies. Thus, in addition to differing in amino acid sequence, the phototropins can be distinguished on the basis of the photochemical cycles of their LOV domains. The LOV domains ofC. reinhardtii phot also undergo light-activated spectral changes consistent with cysteinyl adduct formation. Thus, the phototropin family extends over a wide evolutionary range from unicellular algae to higher plants.