bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uniformity and representation of taxonomic and other characters and semi-automatic extraction using computer tools
Authors: Fortuner Renaud 
Published: January 2003

AbstractA uniform decomposition of morphological-anatomical characters is proposed, based on results from the GENISYS project. Each character is decomposed into a 'structure' (organs and organ parts), a basic property of this structure, and possible states or values of the character. This decomposition can be applied to any character without enforcing any limitations to data entry by biologists. It is shown that a tool ('Terminator') based on this decomposition can be used for semi-automatic extraction of characters from published descriptions or from new data entry. If built, such a tool can be used to populate a database with the decomposed characters. This database could be used with existing computer identification or systematics tools. The same approach can be applied to the decomposition of other kinds of data, including molecular and physiological data. This would create sets of interrelated databases housing various types of knowledge on biodiversity.
Species delimitation and nematode biodiversity: phylogenies rule
Authors: Nadler Steven 
Published: January 2003

AbstractPractitioners of nematode taxonomy have rarely been explicit about what species represent or how data are being used to delimit species prior to their description. This lack of explicitness reflects the broader species problem common to all biology: there is no universally accepted idea of what species are and, as a consequence, scientists disagree on how to go about finding species in nature. However, like other biologists, nematologists seem to agree that species are real and discrete units in nature, and that they result from descent with modification. This evolutionary perspective provides a conceptual framework for nematologists to view species as independent evolutionary lineages, and provides approaches for their delimitation. Specifically, species may be delimited scientifically by methods that can test the hypothesis of lineage independence. For sequence data, such hypothesis testing should be based on sampling many individual organisms for multiple loci to avoid mistaking tokogeny and gene trees as evidence of species. Evolutionary approaches to analysing data and delimiting species avoid the inherent pitfalls in approaches that use all observed sequence differences to define species through calculation of a genetic distance. To illustrate evolutionary species delimitation, molecular data are used to test the hypothesis that hookworms parasitic in northern fur seals and in California sea lions represent separate species. The advantages and potential caveats of employing nucleotide sequence data for species delimitation are discussed, and the merits of evolutionary approaches are contrasted to inherent problems in similarity-based methods.
Inhibitory motor neurones supply body wall muscles in the locust abdomen
Authors: Schmäh Michael , Wolf Harald 
Published: January 2003

SUMMARYInhibitory motor neurones in the abdominal ganglia of the locust Locusta migratoria were identified by combining extra- and intracellular electrophysiology, labelling of motor neurones by peripheral nerve backfills, and immunocytochemistry directed against the inhibitory transmitter γ-aminobutyric acid. The fifth and sixth abdominal ganglia were studied in particular detail, although general findings were verified in all other abdominal segments.In each abdominal ganglion half, there are two inhibitory motor neurones,CIa and CIb, which supply dorsal (CIa) and ventral (CIb) longitudinal muscles. Their cell bodies are located in the next anterior ganglion to where the axons leave the ventral nerve cord via nerve 1. Both inhibitors have contralateral somata in the posterior ventral soma cortex, looping primary neurites and bilateral dorsal arborisations. There are homonomous (segmentally homologous) motor neurones in the fused abdominal neuromeres, the thoracic ganglia, and at least the third subesophageal neuromere.These body wall inhibitors are distinctly different from the limb muscle inhibitors, CI1-3, described previously. This is signified, for example, by the fact that both types of inhibitory motor neurones coexist in the prothoracic segment and innervate leg and body wall muscles,respectively.
Localization of the vacuolar-type ATPase in swimbladder gas gland cells of the European eel (Anguilla anguilla)
Authors: Boesch S. T. , Niederstätter H. , Pelster B. 
Published: January 2003

SUMMARY
The vacuolar ATPase is a multifunctional enzyme that consists of several subunits. Subunit B is part of the catalytic domain of the enzyme and is present in two isoforms in fish as well as in mammals. Possibly, these two isoforms — vatB1 (kidney isoform) and vatB2 (brain isoform) —serve different functions. A localization of the two isoforms was attempted in swimbladder gas gland cells of the European eel Anguilla anguilla by immunohistochemistry. Two antibodies were produced by immunization of rabbits with synthetic peptides. Specificity of the antibodies, on the one hand, an isoform-specific antibody for vatB1 and, on the other hand, an antibody that recognizes both isoforms (vatB1 and vatB2), was confirmed by western blot analysis using recombinant proteins produced in a bacterial expression system. The immunohistochemical localization with the antibody directed against both isoforms of the B subunit revealed a positive staining in apical membranes of swimbladder gas gland cells as well as in the basolateral membranes. Significant staining was observed in vesicles located near the apical membrane. Staining with the vatB1-specific antibody resulted in a similar picture in the apical region of the cells. In contrast to the staining with the first antibody, only a poor signal was observed in the basal region. The nature of the vesicles in the apical region of the gas gland cells was determined by using an antibody directed against surfactant protein D.
PPNDS is an agonist, not an antagonist, for the ATP receptor of Paramecium
Authors: Wood Christopher R. , Hennessey Todd M. 
Published: January 2003

SUMMARY
Paramecium represents a simple, eukaryotic model system to study the cellular effects of some neuroactive drugs. They respond to the agonistβ,γ-methylene ATP with a transient depolarizing receptor potential,Ca2+-based action potentials and repetitive bouts of forward and backward swimming called `avoiding reactions' (AR). In vivo[32P]ATP binding assays showed saturable [32P]ATP binding with an apparent Kd of approximately 23 nmol l-1. Prolonged (15 min) exposure to 25 μmol l-1β,γ-methylene ATP caused behavioral adaptation and losses of AR,ATP receptor potentials and [32P]ATP binding. While screening various ATP receptor inhibitors, we found that the P2X1 `antagonist'pyridoxal-phosphate naphthylazo-nitro-disulfate (PPNDS) is actually an agonist, producing the same responses as β,γ-methylene ATP.[32P]ATP binding assays suggest that both agonists may bind to the same site as [32P]ATP. Cross-adaptation is also seen between PPNDS and β,γ-methylene ATP in terms of losses in AR, depolarizing receptor potentials and [32P]ATP binding. We conclude that the inhibition caused by PPNDS in Paramecium is due to agonist-induced desensitization. Either this represents a unique new class of ATP receptors,in which PPNDS is an agonist instead of an antagonist, or PPNDS (and other drugs like it) may actually be an agonist in many other cell types in which prolonged exposure is necessary for inhibition.
Transcriptional initiation under conditions of anoxia-induced quiescence in mitochondria fromArtemia franciscanaembryos
Authors: Eads Brian D. , Hand Steven C. 
Published: January 2003

SUMMARYIn response to anoxia, embryos of the brine shrimp Artemia franciscana are able coordinately to downregulate metabolism to levels low enough to permit survival for several years at room temperature. In addition to dramatic decreases in free ATP levels and heat production,intracellular pH drops from 7.8 to 6.3 overnight. Use of isolated mitochondria to study transcriptional responses to anoxia offers several advantages: (1)the localized nature of transcript initiation, processing and degradation, all of which may be followed in organello; (2) the relatively simple cis-and trans-machinery involved and (3) the ability to provide relevant physiological treatments in vitro. In response to anoxic incubation of embryos in vivo for 4 h followed by anoxic mitochondrial isolation and anoxic transcription assay at pH 6.4, a significant decrease in overall UTP incorporation (77%) was seen after 30 min relative to normoxic, pH 7.9 controls. A less severe inhibition of transcription under anoxia (52%) was observed compared with controls when pH was raised to 7.9. Similarly, under normoxia, the incubation at low pH (6.4) reduced transcription by 59%. Ribonuclease protection assays showed that the contribution of in vitro initiation during the assay fell from 78% at pH 7.9 to approximately 32% at pH 6.4 under either normoxic or anoxic conditions. DNA footprinting of putative transcriptional promoters revealed proteins at regular intervals upstream of the 12S rRNA in the control region, which previously had been indirectly inferred to contain promoters for H-strand transcription. The area between 12 030 and 12 065 contains a sequence in the tRNAleu gene believed to bind the transcription termination factor mTERF or TERM, and we provide the first evidence that this sequence is protein-bound in A. franciscana. However, our hypothesis that initiation is reduced at low pH because of a change in DNA binding by mitochondrial transcription factors was not confirmed. We propose that regulation of initiation may be mediated by covalent modification or by protein—protein interactions not detected by footprinting.
The influence of beacon-aiming on the routes of wood ants
Authors: Graham Paul , Fauria Karine , Collett Thomas S. 
Published: January 2003

SUMMARY
Many insects have an innate propensity to approach conspicuous objects. We explore how such beacon aiming determines the shape of a wood ant's habitual route. We find that a single large black cylinder within an arena biases the route taken by ants as they run from a start position at one end of the arena to reach a feeder at the other. Ants learn a stable route with the first segment of their trajectory aimed at the cylinder, which becomes an intermediate goal on the way to the feeder. When in occasional tests the cylinder is removed or displaced, ants head for the usual site of the cylinder. They also aim for the same site when the cylinder is removed and the ant's normal start position is changed. This behaviour suggests that visual features of the arena are learnt from the vantage point of the cylinder and that this stored snapshot guides the ant to that site. Ants thus reinforce their ability to reach the cylinder by learning other visual features in their surroundings that can also steer them to its location. The use of beacon aiming in fixing routes has several benefits. Because the same path will be traversed on every trial, beacon aiming facilitates the acquisition of routes. Beacon aiming also increases the robustness of learnt routes: ants straying from the route will be attracted to the closest beacon and so regain their habitual paths.
Formation of Novel Phosphide Dichloride Zr Complex from Trichloride Zr Complex with a Secondary Phosphine-pendant Cyclopentadienyl Ligand: Structure of [{η5-C5H4(CH2)2PMes-κP}ZrCl2(N-methylimidazole)2] (Mes = 2,4,6-Trimethylphenyl)
Authors: Ishiyama Takeshi , Mizuta Tsutomu , Miyoshi Katsuhiko , Nakazawa Hiroshi 
Published: January 2003

Abstract
The reaction of [{η5-C5H4(CH2)2P(H)Mes-κP}ZrCl3(tht)] (1; Mes = 2,4,6-trimethylphenyl; tht = tetrahydrothiophene) with 1 equiv of NaCPh3, followed by treatment with N-methylimidazole gave a novel phosphide-pendant dichloride complex [{η5-C5H4(CH2)2PMes-κP}ZrCl2(N-methylimidazole)2] (4) with liberation of HCPh3. The product (4) is the first dichloride terminal phosphide Zr complex characterized by X-ray crystallographic analysis.
Scala vestibuli cochlear implantation in patients with partially ossified cochleas
Authors: Berrettini Stefano , Forli Francesca , Neri Emanuele , Segnini Giovanni , Franceschini Stefano Sellari 
Published: January 2003

Partial cochlear obstruction is a relatively common finding in candidates for cochlear implants and frequently involves the inferior segment of the scala tympani in the basal turn of the cochlea. In such patients, the scala vestibuli is often patent and offers an alternative site for implantation. The current report describes two patients with such partial obstruction of the inferior segment of the basal cochlear turn, caused in one case by systemic vasculitis (Takayasu’s disease) and in the other by obliterative otosclerosis. A scala vestibuli implantation allowed for complete insertion of the electrode array. No problems were encountered during the surgical procedures and the good post-operative hearing and communicative outcomes achieved were similar to those reported in patients without cochlear ossification.The importance of accurate pre-operative radiological study of the inner ear is underscored, to disclose the presence and define the features of the cochlear ossification and ultimately to properly plan the surgical approach.
Investigating how individuals conceptually and physically structure file folders for electronic bookmarks: The example of the financial services industry
Authors: Gottlieb Lisa , Dilevko Juris 
Published: January 2003

AbstractPersonal preferences in the development of categorical folders for bookmarks are examined in terms of both the choice and definition of folder domain and the overall structure of the folder system. Study participants from the financial industry were asked to organize the same set of finance‐related bookmarks from a given list, as opposed to describing their organizational approaches using their own personal bookmarks, so that the organizational systems could be compared across the sample. The selection of folder domain is influenced by contextual factors such as intended use and relevancy to current projects. Similarly, the structure of the overall folder system was determined in part by participants' navigational preferences. While the majority of participants created folders that cover the topics of finance, government, accounting, news, law, and tax, the actual definition of these folders and the criteria for inclusion vary across the sample. Furthermore, these criteria cannot be readily discerned from the folder system itself. Variation in folder domain and definition could adversely affect the utility of bookmark management systems for multiple users that involve some degree of standardization. The same variation in interpretation of seemingly identical folders suggests that systems with automatic categorization would not provide users with enough flexibility in how they could organize and access their bookmarks.
GeoSearcher: Location‐based ranking of search engine results
Authors: Watters Carolyn , Amoudi Ghada 
Published: January 2003

AbstractMany web queries have geospatial dimensions. While online shopping is built on the premise that distance and location are irrelevant (with the possible exception of shipping charges), tourism and onsite inspection of goods have a geospatial dimension and distance and location are relevant factors. Current search engines build indices based on keyword occurrence and frequency for query negotiation using these indices. This approach is fast, robust, and generic but when queries are related to physical locations and distances rather than cyberdistances this approach leaves the user to sort through pages of results. In this paper, we describe an algorithm that assigns location coordinates dynamically to web sites based on the URL. A prototype search system was built using this algorithm that uses this information to re‐rank the results of search engines for queries with a geospatial dimension. We found that over 80% of the URLs tested could be assigned correct location coordinates. This work makes a contribution to retrieval on the web by providing an alternative ranking order for search engine results so that users with queries with a geospatial dimension can more readily use the results of general search engines rather than special purpose applications.
Cell‐Type‐Specific adhesion onto polymer surfaces from mixed cell populations
Authors: Quirk Robin A. , Kellam Barrie , Bhandari Rena N. , Davies Martyn C. , Tendler Saul J. B. , Shakesheff Kevin M. 
Published: January 2003

AbstractThe targeted adhesion of a specific cell type from a mixed cell suspension via the surface presentation of a cell‐specific ligand is demonstrated. This generic strategy is illustrated by the covalent attachment of a galactose derivative to a polylysine backbone via the amine functionality. Following adsorption of the resultant material to a polymer surface, hepatocyte adhesion is increased via the interaction between galactose and asialoglycoprotein receptors in a concentration‐dependent manner. The selective nature of the material is demonstrated by the approximate doubling in the adhesion of hepatocytes relative to a nontargeted cell type (hepatic stellate cells), and an inability of the modified polymer surface to attract additional numbers of the nontargeted cells. This strategy provides a mechanism for controlling the ratios of cell types adhering to scaffold supports, thus enabling the rapid creation of defined coculture systems from heterogeneous cell suspensions. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 81: 625–628, 2003.
Pattern identification and classification in gene expression data using an autoassociative neural network model
Authors: Bicciato Silvio , Pandin Mario , Didonè Giuseppe , Di Bello Carlo 
Published: January 2003

AbstractThe application of DNA microarray technology for analysis of gene expression creates enormous opportunities to accelerate the pace in understanding living systems and identification of target genes and pathways for drug development and therapeutic intervention. Parallel monitoring of the expression profiles of thousands of genes seems particularly promising for a deeper understanding of cancer biology and the identification of molecular signatures supporting the histological classification schemes of neoplastic specimens. However, the increasing volume of data generated by microarray experiments poses the challenge of developing equally efficient methods and analysis procedures to extract, interpret, and upgrade the information content of these databases. Herein, a computational procedure for pattern identification, feature extraction, and classification of gene expression data through the analysis of an autoassociative neural network model is described. The identified patterns and features contain critical information about gene–phenotype relationships observed during changes in cell physiology. They represent a rational and dimensionally reduced base for understanding the basic biology of the onset of diseases, defining targets of therapeutic intervention, and developing diagnostic tools for the identification and classification of pathological states. The proposed method has been tested on two different microarray datasets—Golub's analysis of acute human leukemia [Golub et al. (1999) Science 286:531–537], and the human colon adenocarcinoma study presented by Alon et al. [1999; Proc Natl Acad Sci USA 97:10101–10106]. The analysis of the neural network internal structure allows the identification of specific phenotype markers and the extraction of peculiar associations among genes and physiological states. At the same time, the neural network outputs provide assignment to multiple classes, such as different pathological conditions or tissue samples, for previously unseen instances. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 81: 594–606, 2003.
Weak polymer–electrolyte interaction revealed by Fermi resonance perturbed Raman bands
Authors: Ostrovskii Denis , Edvardsson Magnus , Jacobsson Per 
Published: January 2003

AbstractA detailed analysis of isotropic and anisotropic Raman spectra of carbonyl stretching vibrations of ethylene carbonate in different systems was conducted. The variation of Fermi resonance perturbed spectral profiles was used to investigate changes in local molecular surroundings in polymer gel–electrolyte systems as a function of their composition. In poly(methyl methacrylate)‐based gels it is found that the matrix interacts very weakly with the solvent molecules, ethylene and propylene carbonates, mostly playing a role of a hydrogen bond‐breaking agent. In gel systems containing lithium salt, however, a new type of coordination appears. Along with the solvent–solvent and solvent–cation couplings characteristic of liquid electrolytes, the spectra of gels demonstrate the presence of mixed states in which cations, solvent molecules and polymer segments take part. The importance of the mixed states for ionic conduction is discussed. Copyright © 2002 John Wiley & Sons, Ltd.
Transmethylation of 2‐(methylthio)benzothiazole on silver sols: a SERS investigation
Authors: Pergolese Barbara , Bigotto Adriano 
Published: January 2003

AbstractDiscrepancies between the SERS and the normal Raman spectra of 2‐(methylthio)benzothiazole (MTBT) led to an extension of the SERS study to include an investigation of the reactivity of this molecule on a silver surface. Experimental evidence indicates a surface reaction of MTBT on silver sol. In particular, it undergoes an intramolecular transmethylation, rearranging to 3‐methylbenzothiazoline‐2‐thione. Experimental data suggest that this transmethylation takes place only because of the presence of the silver surface, which acts as a catalyst. In contrast, the hypothesis of a reaction photo‐induced by the silver surface seems very unlikely. 3‐Methylbenzothiazoline‐2‐thione adsorbs on the silver surface via the lone pairs of the exocyclic sulphur atom and, to some extent, also via the π‐system of the benzene ring. The molecular orientation is inclined with respect to the metal surface. Copyright © 2002 John Wiley & Sons, Ltd.
Raman spectroscopy of synthetic erythrite, partially dehydrated erythrite and hydrothermally synthesized dehydrated erythrite
Authors: Martens Wayde , Frost Ray L. , Kloprogge J. Theo 
Published: January 2003

AbstractThe Raman spectra of the mono, di and octa (commonly known as the mineral erythrite) hydrates of cobalt(II) arsenate synthesized using hydrothermal techniques were obtained. The hydrates can be distinguished by their water hydroxyl stretching bands. Splitting of the AsO stretching vibrations is observed in the 77 K spectrum. The band at 852 cm−1 is assigned to the ν1 symmetric stretching vibration and the band at 790 cm−1 to the ν3 antisymmetric stretching vibration. The low‐wavenumber region was used to identify bands attributable to the ν4 and ν2 modes. Copyright © 2002 John Wiley & Sons, Ltd.