bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular evaluation using in silico protein
interaction profiles
Authors: Hayashi Yoshiharu , Sakaguchi Katsuyoshi , Kobayashi Mime , Kobayashi Masaki , Kikuchi Yo , Ichiishi Eiichiro
Published: August 2003

Motivation: To find a correlation between the activities and structures of molecules is one of the most important subjects for molecular evaluation study. Traditional quantitative structure-activity relationship (QSAR) methodologies represent those attempts using physicochemical descriptors. Creating a new molecular description factor based on the results of a computational docking study will add new dimensions to molecular evaluation.

Results: We propose a new molecular description factor analysis system called the Comparative Molecular Interaction Profile Analysis (CoMIPA) system in which the AutoDock program is used for docking evaluation of small molecule compound–protein complexes. Interaction energies are calculated, and the data sets obtained are called interaction profiles (IPFs). Using the IPF as a scoring indicator, the system could be a powerful tool to cluster the interacting properties between small molecules and bio macromolecules such as ligand–receptor bindings. Further development of the system will enable us to predict the adverse effects of a drug candidate.

Contact: yhayashi@enkaku.co.jp

* To whom correspondence should be addressed.

† Presend address: New Industry Creation Hatchery Center, Tohoku University, 10 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan.
ClustalW-MPI: ClustalW analysis using distributed and parallel computing
Authors: Li Kuo-Bin
Published: August 2003

Summary: ClustalW is a tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is a distributed and parallel implementation of ClustalW. All three steps have been parallelized to reduce the execution time. The software uses a message-passing library called MPI (Message Passing Interface) and runs on distributed workstation clusters as well as on traditional parallel computers.

Availability:The source codes are written in ISO C and are available at http://www.bii.a-star.edu.sg/software/clustalw-mpi/. An open source implementations of MPI http://www-unix.mcs.anl.gov/mpi/.

Contact: kuobin@bii.a-star.edu.sg
Evaluation of ontology development tools for bioinformatics
Authors: Lambrix Patrick , Habbouche Manal , Pérez Marta
Published: August 2003

Ontologies are being used nowadays in many areas, including bioinformatics. To assist users in developing and maintaining ontologies a number of tools have been developed. In this paper we compare four such tools, Protégé-2000, Chimaera, DAG-Edit and OilEd. As test ontologies we have used ontologies from the Gene Ontology Consortium. No system is preferred in all situations, but each system has its own strengths and weaknesses.

Contact: patla@ida.liu.se

* To whom correspondence should be addressed.
Digital extractor: analysis of digital differential display output
Authors: Madden Stephen F. , O’Donovan Barry , Furney Simon J. , Brady Hugh R. , Silvestre Guenole , Doran Peter P.
Published: August 2003

Summary: Digital Extractor is a program for the high-throughput processing of data sets derived from digital differential display-based comparisons of EST libraries. These comparisons can be utilized to identify discrete subsets of genes whose expression is restricted to distinct tissue types. The program facilitates these investigations by permitting parallel annotation of genes identified as being differentially expressed.

Availability: The executable program, suitable for use on all UNIX-based platforms is freely available to non-profit users.

Contact: pdoran.genome@mater.ie

* To whom correspondence should be addressed.
Comprehensive aligned sequence construction
for automated design of effective probes (CASCADE-P) using 16S rDNA
Authors: DeSantis T. Z. , Dubosarskiy I. , Murray S. R. , Andersen G. L.
Published: August 2003

Motivation: Prokaryotic organisms have been identified utilizing the sequence variation of the 16S rRNA gene. Variations steer the design of DNA probes for the detection of taxonomic groups or specific organisms. The long-term goal of our project is to create probe arrays capable of identifying 16S rDNA sequences in unknown samples. This necessitated the authentication, categorization and alignment of the >75 000 publicly available‘ 16S’ sequences. Preferably, the entire process should be computationally administrated so the aligned collection could periodically absorb 16S rDNA sequences from the public records. A complete multiple sequence alignment would provide a foundation for computational probe selection and facilitates microbial taxonomy and phylogeny.

Results: Here we report the alignment and similarity clustering of 62 662 16S rDNA sequences and an approach for designing effective probes for each cluster. A novel alignment compression algorithm, NAST (Nearest Alignment Space Termination), was designed to produce the uniform multiple sequence alignment referred to as the prokMSA. From the prokMSA, 9020 Operational Taxonomic Units (OTUs) were found based on transitive sequence similarities. An automated approach to probe design was straightforward using the prokMSA clustered into OTUs. As a test case, multiple probes were computationally picked for each of the 27 OTUs that were identified within the Staphylococcus Group. The probes were incorporated into a customized microarray and were able to correctly categorize Staphylococcus aureus and Bacillus anthracis into their correct OTUs. Although a successful probe picking strategy is outlined, the main focus of creating the prokMSA was to provide a comprehensive, categorized, updateable 16S rDNA collection useful as a foundation for any probe selection algorithm.

Availability: http://greengenes.llnl.gov/16S/

Contact: GLAndersen@lbl.gov

Supplementary Information: Complete prokMSA in aligned fasta format: http://greengenes.llnl.gov/16S_cgi/download/update_28Dec02/prokMSA_aligned.fasta.Z Sequences within each Operational Taxonomic Unit: http://greengenes.llnl.gov/16S_cgi/download/update_15Mar02/SeqDescByOTU.txt DNA probe sequences: http://greengenes.llnl.gov/16S_cgi/download/update_15Mar02/15Mar02_StaphGrpPrbs.xls

* To whom correspondence should be addressed.
Rapid classification of a protein fold family using a
statistical analysis of dipolar couplings
Authors: Valafar Homayoun , Prestegard James H.
Published: August 2003

Motivation: One of the primary aims of the structural genomics initiative is the determination of representative structures from each protein fold family. Given this objective, it is important to rapidly identify proteins that belong to a family that is already well populated (so they can be eliminated from further studies), or more importantly identify proteins that represent new families of fold.

Results: A method for rapid classification to a fold family by the statistical analyses of unassigned the 15N–1H residual dipolar couplings is presented. The required NMR data can be quickly acquired and analyzed. Using this method, structure determination efforts can be focused on more unique and interesting structures, and the overall efficiency in the construction of an information-rich library can be increased.

Contact: jpresteg@ccrc.uga.edu

* To whom correspondence should be addressed.
UniFrag and GenomePrimer:
selection of primers for genome-wide production of unique amplicons
Authors: van Hijum Sacha A. F. T. , de Jong Anne , Buist Girbe , Kok Jan , Kuipers Oscar P.
Published: August 2003

Summary: the complementary programs UniFrag and GenomePrimer were developed to provide a reliable high-throughput method to select the most unique regions within genomic DNA sequence(s) and design primers therein, involving minimal user intervention and maximum flexibility.

Availability: Freely available for educational and research purposes by non-profit institutions at http://molgen.biol.rug.nl/molgen/research/molgensoftware.php

Contact: jonga@biol.rug.nl

Supplementary information: http://molgen.biol.rug.nl/publication/primer_data/

* To whom correspondence should be addressed.
PISCES: a protein sequence culling server
Authors: Wang Guoli , Dunbrack Roland L.
Published: August 2003

Summary: PISCES is a public server for culling sets of protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria. PISCES can provide lists culled from the entire PDB or from lists of PDB entries or chains provided by the user. The sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists than servers that use BLAST, which is unable to identify many relationships below 40% sequence identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output.

Availability: The server is located at http://www.fccc.edu/research/labs/dunbrack/pisces

Contact: rl_dunbrack@fccc.edu

* To whom correspondence should be addressed.
Three Distinct Rice Cellulose Synthase Catalytic Subunit Genes Required for Cellulose Synthesis in the Secondary Wall
Authors: Tanaka Katsuyuki , Murata Kazumasa , Yamazaki Muneo , Onosato Katsura , Miyao Akio , Hirochika Hirohiko
Published: September 2003

Several brittle culm mutations of rice (Oryza sativa) causing fragility of plant tissues have been identified genetically but not characterized at a molecular level. We show here that the genes responsible for three distinct brittle mutations of rice, induced by the insertion of the endogenous retrotransposon Tos17, correspond to CesA (cellulose synthase catalytic subunit) genes, OsCesA4, OsCesA7 and OsCesA9. Three CesA genes were expressed in seedlings, culms, premature panicles, and roots but not in mature leaves, and the expression profiles were almost identical among the three genes. Cellulose contents were dramatically decreased (8.9%-25.5% of the wild-type level) in the culms of null mutants of the three genes, indicating that these genes are not functionally redundant. Consistent with these results, cell walls in the cortical fiber cells were shown to be thinner in all the mutants than in wild-type plants. Based on these observations, the structure of a cellulose-synthesizing complex involved in the synthesis of the secondary cell wall is discussed.
Golden Indica and Japonica Rice Lines Amenable to Deregulation
Authors: Hoa Tran Thi Cuc , Al-Babili Salim , Schaub Patrick , Potrykus Ingo , Beyer Peter
Published: September 2003

As an important step toward free access and, thus, impact of GoldenRice, a freedom-to-operate situation has been achieved for developing countries for the technology involved. Specifically, to carry the invention beyond its initial “proof-of-concept” status in a Japonica rice (Oryza sativa) cultivar, we report here on two transformed elite Indica varieties (IR64 and MTL250) plus one Japonica variety Taipei 309. Indica varieties are predominantly consumed in the areas with vitamin A deficiency. To conform with regulatory constraints, we changed the vector backbone, investigated the absence of beyond-border transfer, and relied on Agrobacterium tumefaciens-mediated transformation to obtain defined integration patterns. To avoid an antibiotic selection system, we now rely exclusively on phosphomannose isomerase as the selectable marker. Single integrations were given a preference to minimize potential epigenetic effects in subsequent generations. These novel lines, now in the T3 generation, are highly valuable because they are expected to more readily receive approval for follow-up studies such as nutritional and risk assessments and for breeding approaches leading to locally adapted variety development.
Reduction of Stability of Arabidopsis Genomic and Transgenic DNA-Repeat Sequences (Microsatellites) by Inactivation of AtMSH2 Mismatch-Repair Function
Authors: Leonard Jeffrey M. , Bollmann Stephanie R. , Hays John B.
Published: September 2003

Highly conserved mismatch repair (MMR) systems promote genomic stability by correcting DNA replication errors, antagonizing homeologous recombination, and responding to various DNA lesions. Arabidopsis and other plants encode a suite of MMR protein orthologs, including MSH2, the constant component of various specialized eukaryotic mismatch recognition heterodimers. To study MMR roles in plant genomic stability, we used Arabidopsis AtMSH2::TDNA mutant SALK_002708 and AtMSH2 RNA-interference (RNAi) lines. AtMSH2::TDNA and RNAi lines show normal growth, development, and fertility. To analyze AtMSH2 effects on germ line DNA fidelity, we measured insertion-deletion mutation of dinucleotide-repeat sequences (microsatellite instability) at nine loci in 16 or more progeny of two to four different wild-type or AtMSH2-deficient plants. Scoring 992 total alleles revealed 23 (2.3%) unique and 51 (5.1%) total repeat length shifts ([+2], [-2], [+4], or [-4] bp). For the six longest repeat loci, the corresponding frequencies were 22/608 and 50/608. Two of four AtMSH2-RNAi plants showed similar microsatellite instability. In wild-type progeny, only one unique repeat length allele was found in 576 alleles tested. This endogenous microsatellite instability, shown for the first time in MMR-defective plants, is similar to that seen in MMR-defective yeast and mice, indicating that plants also use MMR to promote germ line fidelity. We used a frameshifted reporter transgene, (G)7  GUS, to measure insertion-deletion reversion as blue-staining β-glucuronidase-positive leaf spots. Reversion rates increased only 5-fold in AtMSH2::TDNA plants, considerably less than increases in MSH2-deficient yeast or mammalian cells for similar mononucleotide repeats. Thus, MMR-dependent error correction may be less stringent in differentiated leaf cells than in plant equivalents of germ line tissue.
New Insights into the Respiratory Chain of Plant Mitochondria. Supercomplexes and a Unique Composition of Complex II
Authors: Eubel Holger , Jänsch Lothar , Braun Hans-Peter
Published: September 2003

A project to systematically investigate respiratory supercomplexes in plant mitochondria was initiated. Mitochondrial fractions from Arabidopsis, potato (Solanum tuberosum), bean (Phaseolus vulgaris), and barley (Hordeum vulgare) were carefully treated with various concentrations of the nonionic detergents dodecylmaltoside, Triton X-100, or digitonin, and proteins were subsequently separated by (a) Blue-native polyacrylamide gel electrophoresis (PAGE), (b) two-dimensional Blue-native/sodium dodecyl sulfate-PAGE, and (c) two-dimensional Blue-native/Blue-native PAGE. Three high molecular mass complexes of 1,100, 1,500, and 3,000 kD are visible on one-dimensional Blue native gels, which were identified by separations on second gel dimensions and protein analyses by mass spectrometry. The 1,100-kD complex represents dimeric ATP synthase and is only stable under very low concentrations of detergents. In contrast, the 1,500-kD complex is stable at medium and even high concentrations of detergents and includes the complexes I and III2. Depending on the investigated organism, 50% to 90% of complex I forms part of this supercomplex if solubilized with digitonin. The 3,000-kD complex, which also includes the complexes I and III, is of low abundance and most likely has a III4I2 structure. The complexes IV, II, and the alternative oxidase were not part of supercomplexes under all conditions applied. Digitonin proved to be the ideal detergent for supercomplex stabilization and also allows optimal visualization of the complexes II and IV on Blue-native gels. Complex II unexpectedly was found to be composed of seven subunits, and complex IV is present in two different forms on the Blue-native gels, the larger of which comprises additional subunits including a 32-kD protein resembling COX VIb from other organisms. We speculate that supercomplex formation between the complexes I and III limits access of alternative oxidase to its substrate ubiquinol and possibly regulates alternative respiration. The data of this investigation are available at http://www.gartenbau.uni-hannover.de/genetik/braun/AMPP.
Functional Characterization and Expression Analyses of the Glucose-Specific AtSTP9 Monosaccharide Transporter in Pollen of Arabidopsis
Authors: Schneidereit Alexander , Scholz-Starke Joachim , Büttner Michael
Published: September 2003

A genomic clone and the corresponding cDNA of a new Arabidopsis monosaccharide transporter AtSTP9 were isolated. Transport analysis of the expressed protein in yeast showed that AtSTP9 is an energy-dependent, uncoupler-sensitive, high-affinity monosaccharide transporter with a K  m for glucose in the micromolar range. In contrast to all previously characterized monosaccharide transporters, AtSTP9 shows an unusual specificity for glucose. Reverse transcriptase-polymerase chain reaction analyses revealed that AtSTP9 is exclusively expressed in flowers, and a more detailed approach using AtSTP9 promoter/reporter plants clearly showed that AtSTP9 expression is restricted to the male gametophyte. AtSTP9 expression is not found in other floral organs or vegetative tissues. Further localization on the cellular level using a specific antibody revealed that in contrast to the early accumulation of AtSTP9 transcripts in young pollen, the AtSTP9 protein is only found weakly in mature pollen but is most prominent in germinating pollen tubes. This preloading of pollen with mRNAs has been described for genes that are essential for pollen germination and/or pollen tube growth. The pollen-specific expression found for AtSTP9 is also observed for other sugar transporters and indicates that pollen development and germination require a highly regulated supply of sugars.
An exploration of the inside‐out model: e‐commerce integration in UK SMEs
Authors: Daniel Elizabeth
Published: September 2003

Organisational integration is being heralded as a critical “dynamic capability” and is seen as an important strategic issue for firms in the future. This study seeks to explore this issue in the specific context of e‐commerce and information system integration, by considering the model proposed by Poon and Swatman, in the case of small‐ and medium‐sized enterprises (SMEs) in the UK. Poon and Swatman propose that the model of business transformation enabled by traditional IT turns “inside out” when applied to the e‐commerce domain. Their model suggests a hierarchy of levels of e‐commerce integration. At the lowest level firms develop inter‐organisational systems. At the next level they undertake limited integration with existing internal systems, and only at the highest level do they achieve full internal integration. The study, which was carried out by a mailed questionnaire, found that the proposed model is indeed valid. Three distinct groups of firms are identified that correspond to the hierarchical levels proposed in the model. The benefits realised by the firms were found to increase with increasing integration, but the level of process change required was found to be independent of the level of integration. Contextual variables, such as industry sector and organisational size, are explored for firms at the three different levels of integration. Developments of the Poon and Swatman model are suggested.
Business strategies for small firms in the new economy
Authors: Tse Terence , Soufani Khaled
Published: September 2003

The development of the new economy through the advent of the Internet and the World Wide Web has created many threats and opportunities for firms in general and small businesses in particular. There appears to be an inextricable linkage among the new economy, new enterprise, and the new technology, which may have a potential effect on the way small businesses formulate their business strategies. This paper provides a theoretical approach that looks at the advantages of the digitisation of the economy and strategy formulation of small businesses taking three specific themes into account – virtualisation, molecularisation, and disintermediation. The strengths and weaknesses of various e‐commerce strategies in the context of these dimensions are discussed. Some strategies that are suitable for small companies are recommended and four principles are stated in order to assist these firms to formulate strategy in the new economy.
Sibling Differentiation: Sibling and Parent Relationship Trajectories in Adolescence
Authors: Feinberg Mark E. , McHale Susan M. , Crouter Ann C. , Cumsille Patricio
Published: September 2003

Studied here were the links between sibling differences in trajectories of change in the qualities of parent–child relationships and the qualities of sibling relationships across a 2‐year period in adolescence. Participants were first‐ and second‐born siblings (M age=14.94 years for firstborns and M age=12.46 years for secondborns) from 185 predominantly White, working and middle‐class families. In home interviews, siblings reported on their dyadic family relationships. For reports of parent–child warmth but not parent–child conflict, results were consistent with sibling differentiation theory: Increasing differences between siblings over time in parent–child warmth were linked to trajectories of increasing warmth and decreasing conflict in the sibling relationship as reported by firstborns, and increasing warmth in the sibling relationship as reported by secondborns. The findings support the view that sibling differentiation may be a strategy for managing sibling conflict and rivalry.
Perceptions and Functions of Play and Real Fighting in Early Adolescence
Authors: Pellegrini Anthony D.
Published: September 2003

The hypothesis is tested that adolescent boys' (mean age of 12.8 years) intrasexual rough‐and‐tumble play (R&T) is used for dominance and intersexual R&T is used to establish heterosexual relationships. In Study 1, boys' observed R&T was related to both dominance and aggression. In the first half of the school year, R&T occurred primarily between males, possibly to establish dominance. In the second half of the year, both boys and girls engaged in R&T, possibly to establish heterosexual relationships. Counter to the hypothesis, observed aggression increased across the year. In Study 2, youngsters viewed taped R&T bouts in which they were participants or nonparticipants. Participant, more than nonparticipant, males saw R&T as related to dominance whereas participant, more than nonparticipant, females saw it as playful.
An Ethnographic Consideration of Rule‐Following
Authors: Sidnell Jack
Published: August 2003

Rules are an essential feature of social life and anthropologists have long debated the role they play in human forms of organization and activity. But what does it mean to follow a rule? The article addresses this issue by examining particular, ethnographically specified, cases drawn from fieldwork in an Indo‐Guyanese village. In doing so, it argues that an anthropological account of rule‐following might profitably draw on the writings of Garfinkel and the later Wittgenstein.
Art and Agency: A Reassessment
Authors: Layton Robert
Published: August 2003

In his book,Art and agency, Alfred Gell presents a theory of art based neither on aesthetics nor on visual communication. Art is defined by the distinctive function it performs in advancing social relationships through ‘the abduction of agency’. Art objects are indexes of the artist's or model's agency. This article examines Gell's use of agency, particularly in relation to the ritual art that is central to his argument. Focusing on Gell's employment of Peirce's term ‘index’ (out of his triad of index, icon, and symbol), I note that Peirce's approach deflects attention from signification towards the link between art works and the things to which they refer. I consider what Peirce meant by abduction, and conclude that while Gell makes a good case for the agency of art objects he does not explain the distinctive ways in which art objects extend their maker's or user's agency. Gell lacked the time to make detailed revisions before publication and I acknowledge that, given more time, he might have revised some parts of the book.
Palaeolithic Grandmothers? Life History Theory and EarlyHomo
Authors: Kennedy G.E.
Published: August 2003

The acknowledged success of earlyHomohas generally been thought to reflect male‐dominated provisioning and associated patterns of co‐operative social organization; recently, however, such conclusions have been challenged with the argument that post‐menopausal females, instead, played a significant role in early human subsistence activities; males, it has been proposed, had a very minor role in food acquisition in earlyHomo. The fossil record, however, indicates minimal old‐age survivorship of either sex and heavy young adult mortality, a pattern which is also seen in larger prehistoric and ethnographic samples. Heavy young adult mortality, when combined with characteristically slow maturation, represents a paradox which humans have solved through new reproductive strategies (early weaning and alloparenting) and new life history stages (childhood and adolescence). Stone tools, when used to acquire marrow and brain tissue to feed needful youngsters, may also have been among the strategies developed in response to frequent early parental death.
A MULTIDISCIPLINARY APPROACH TO THE CHARACTERIZATION OF ROMAN GRAVESTONES FROM AQUILEIA (UDINE, ITALY)*
Authors: Maritan L. , Mazzoli C. , Melis E.
Published: August 2003

The results of an archaeometric study on gravestone production in Aquileia (northeastern Italy) during Roman Republican times are reported here. The artefacts are made of limestone, quarried from the sedimentary sequence of the Trieste Karst (Carnican Alps, northeastern Italy), as testified by historical sources which refer to the ‘Roman Quarry’ at Aurisina. The rock types used for the gravestones are petrographically, geochemically and geochronologically homogeneous, and display similar faunal assemblages. In addition, their age is restricted to the Santonian – Lower Campanian. Comparisons between archaeological finds and rock specimens from various active and inactive quarries in this area suggest that quarrying during Roman Republican times was limited to a specific stratigraphic horizon of the sedimentary sequence, corresponding to the higher part of the ‘Roman Quarry’.
THE PETROGRAPHY AND CHEMISTRY OF THIN‐WALLED WARE FROM AN HELLENISTIC– ROMAN SITE AT SEGESTA (SICILY)*
Authors: Montana G. , Mommsen H. , Iliopoulos I. , Schwedt A. , Denaro M.
Published: August 2003

Samples of Roman thin‐walled ware from Segesta (northwestern Sicily), dating back to the early Imperial period, were studied by optical microscopy (OM) and Neutron Activation Analysis (NAA). Up to now, this class of Roman fine tableware has only occasionally been evaluated archaeometrically. Nevertheless, numerous production centres are believed to have been simultaneously active in the western Mediterranean area. Petrographic and chemical data seem to be in agreement with the archaeological hypothesis of local manufacture in Segesta for most of the analysed samples, through a comparison with kiln wasters and local raw materials. The effectiveness of thin‐section petrography for determining the provenance of such a tiny tempered class of pottery and the integrated use of two different grouping procedures (petrography and chemistry) were also tested.
ELEMENTAL ANALYSES OF A GROUP OF GLAZED TERRACOTTA ANGELS FROM THE ITALIAN RENAISSANCE, AS A TOOL FOR THE RECONSTRUCTION OF A COMPLEX CONSERVATION HISTORY*
Authors: Zucchiatti A. , Bouquillon A. , Castaing J. , Gaborit J. R.
Published: August 2003

A group of Italian glazed terracotta sculptures, attributed to the della Robbia workshop of Florence, is partly displayed in the Louvre Museum. Analyses of the apparently homogeneous sculptures by techniques such as PIXE, SEM, ICP/AES and ICP/MS have identified differences in the materials used. The data provide a subdivision of the sculptures, which is compatible with what is known from historical documents and artistic considerations, and suggest a date for this ensemble at the end of the 15th century, when the della Robbia family was involved in the decoration of the San Frediano church in Florence.
LEAD ISOTOPE ANALYSES OF ISLAMIC POTTERY GLAZES FROM FUSTAT, EGYPT*
Authors: Wolf S. , Stos S. , Mason R. , Tite M. S.
Published: August 2003

Lead isotope analyses have been undertaken on a group of Islamic lead‐glazed pottery artefacts from Fustat, Egypt, spanning the period from the eighth to the 14th century ad, that had previously been the subject of a comprehensive typological, chronological, petrographic and technological study. Comparison of the lead isotope ratios for the glazes with those for lead ores from Egypt, Iran, Tunisia, Anatolia, Greece, Sardinia and Spain provided information on the possible sources of the lead used in the production of the glazes. The results show that the lead used in glaze production by the Islamic potters at Fustat was most probably obtained from distant ore sources in Iran or Tunisia, Sardinia, Spain and the Taurus Mountains. Different ore sources were favoured in different periods and, to a limited extent, for different types of pottery, but at no time did the Fustat potters use the potentially more accessible Egyptian ore sources.
EVALUATION OF THE ANALYTICAL POTENTIAL OF LASER‐INDUCED BREAKDOWN SPECTROMETRY (LIBS) FOR THE ANALYSIS OF HISTORICAL GLASSES*
Authors: Müller K. , Stege H.
Published: August 2003

The novel and—for archaeometrical applications—still rarely used Laser‐Induced Breakdown Spectrometry (LIBS) was tested on various standard glasses for its spectrometric performance. LIBS is an almost non‐destructive method based on the time‐resolved detection of optical emission following direct laser ablation. A frequency‐quadrupoled Nd:YAG laser at 266 nm was found to cause a hardly visible crater of c. 200 µm in diameter. The application of an innovative high‐resolution Echelle spectrograph allows the fast and simultaneous determination of up to 90 elements in the spectral range from 200 to 780 nm, with a resolution of 10–30 pm under ambient conditions. In principle, LIBS has a high analytical potential for archaeometry; in particular, for the determination of light elements (Li, Be, B and others). Because the measurement parameters (laser energy, delay time and number of pulses) do not independently influence the emission signal, their optimization proved to be complex and is rather a compromise for the range of elements. The effects of sample distance, surface roughness and the accumulation of depth profiles were studied. Problems arose for the determination of sodium and potassium in higher contents due to self‐absorption effects. Quantification tests using a silicon line as internal standard yielded a precision range between 3% and 20% relative, but in general no satisfying accuracy for a number of elements. However, these problems might be overcome in the near future by improved spectrometer set‐ups and matrix correction approaches.
ROMAN GLASS‐MAKING AT COPPERGATE, YORK? ANALYTICAL EVIDENCE FOR THE NATURE OF PRODUCTION*
Authors: Jackson C. M. , Joyner L. , Booth C. A. , Day P. M. , Wager E. C. W. , Kilikoglou V.
Published: August 2003

Ceramic vessels and associated vitreous debris, excavated at Coppergate, York, UK, have been interpreted as the remains of Roman glass‐making from the raw materials. This paper reports the results of analysis of this assemblage by XRF, ICPS, XRD, SEM–
EDAX and thin‐section petrography. These findings suggest that some ceramic vessels, used as crucibles, have been subjected to temperatures up to 1200°C, well above the firing temperatures of the local domestic assemblage from which they were selected. Analysis of quartz‐rich debris, intimately mixed with glass in some samples and in others interleaved with glassy phases, indicates partially reacted glass‐making raw materials, with α‐quartz, tridymite and cristoballite phases represented. This could represent evidence either of a failed attempt to frit the raw materials, or a batch that had not fully fused. Variability in the composition of glass at the site is viewed in the light of glass‐making technology, and possible interpretations concerning this episode are discussed in the light of the archaeological evidence.
HUMAN MOBILITY AT THE EARLY NEOLITHIC SETTLEMENT OF VAIHINGEN, GERMANY: EVIDENCE FROM STRONTIUM ISOTOPE ANALYSIS*
Authors: Bentley R. A. , Krause R. , Price T. D. , Kaufmann B.
Published: August 2003

As evidence concerning human mobility during the transition to agriculture in central Europe, we present the results of strontium isotope analysis of human skeletons from the Neolithic village of Vaihingen, Germany. We find significantly more ‘non‐local’87Sr/86Sr values from humans buried in a Neolithic ditch surrounding Vaihingen than from those buried within the settlement. These results fit with previous studies showing a correlation between burial circumstances and strontium isotope signatures from LBK cemeteries of southwestern Germany (Price et al. 2001; Bentley et al. 2002). A pilot study of Neolithic animal teeth from Vaihingen suggests that either ‘local’87Sr/86Sr signatures were more variable than the analysed human bones suggest, or that these domestic animals themselves were mobile, perhaps ranged by mobile pastoralists.
DATING ARCHAEOMETALLURGICAL SLAGS USING THERMOLUMINESCENCE*
Authors: Haustein M. , Roewer G. , Krbetschek M. R. , Pernicka E.
Published: August 2003

Thermoluminescence has a great potential for dating archaeometallurgical slags, because the smelting process leads to a well‐defined resetting of the ‘luminescence clock’. However, the complex compositions of slags have unpleasant consequences for TL measurements if the bulk slag substance is used. To overcome this problem, quartz has been separated out of slag matrices by chemical and physical procedures. The TL measurements were carried out on this defined mineral phase. This method was tested with seven slag samples from different locations and ages. In most cases, the TL ages determined show good agreement with reference data.
How Reassuring are Risk Comparisons to Pollution Standards and Emission Limits?
Authors: Johnson Branden B. , Chess Caron
Published: September 2003

Pollutant emissions or ambient levels are often justified by reference to a higher benchmark, such as a public health standard or permit limit. However, does this risk comparison persuade the public audiences to whom it is frequently directed that such pollution levels are “acceptable”? A substantial proportion of people living within one mile of New Jersey's industrial facilities, perhaps as much as half, is indeed reassured by a comparison to such benchmarks. Positive attitudes toward discharge limits were linked to speaking English at home; positive attitudes toward drinking water standards were associated with seeing local benefits of industry as outweighing its risks, not speaking English, and relative youth (49 years old or less). Three scenarios involving drinking water contamination varied pre‐ and post‐treatment levels of the pollutant, though all post‐treatment levels were below the standard. In all cases great concern was expressed, with no significant differences across scenarios; net benefits, being white, and non‐English speaking were linked to lower concern. Relative trust seems a better explanation of different attitudes toward benchmark comparisons than varying levels of knowledge, but both hypotheses have drawbacks that merit further testing. These results imply that people with negative views of industry or government, the ones officials might most wish to reassure, will tend to doubt that regulatory benchmarks offer a valid risk comparison.
Determination of an Occupational Exposure Guideline for Manganese Using the Benchmark Method
Authors: Clewell Harvey J. , Lawrence Gregory A. , Calne Donald B. , Crump Kenny S.
Published: September 2003

An occupational risk assessment for manganese (Mn) was performed based on benchmark dose analysis of data from two epidemiological studies providing dose‐response information regarding the potential neurological effects of exposure to airborne Mn below the current Occupational Safety and Health Administration (OSHA) Permissible Exposure Level (PEL) of 5 mg Mn/m3. Based on a review of the scientific evidence regarding the toxicity of Mn, it was determined that the most appropriate measure of exposure to airborne Mn for the subclinical effects measured in these studies is recent (rather than historical or cumulative) concentration of Mn in respirable (rather than total) particulate. For each of the studies analyzed, the individual exposure and response data from the original study had been made available by the investigators. From these two studies benchmark concentrations calculated for eight endpoints ranged from 0.09 to 0.27 mg Mn/m3. From our evaluation of these results, and considering the fact that the subtle, subclinical effects represented by the neurological endpoints tested in these studies do not represent material impairment, we believe an appropriate occupational exposure guideline for manganese would be in the range of 0.1 to 0.3 mg Mn/m3, based on the respirable particulate fraction only, and expressed as an 8‐hour time‐weighted average.
Deference and Defiance: The Shifting Rhythms of Executive‐Legislative Relations in Foreign Policy
Authors: Lindsay James M.
Published: September 2003

The return of the deferential Congress after September 11 was another chapter in the fluctuating balance of power in executive‐legislative relations on foreign policy. The reason for this ebb and flow lies not in the Constitution but in politics. How aggressively Congress exercises its formal foreign policy powers turns foremost on whether the country sees itself as threatened or secure and to a lesser extent on how well the president handles foreign policy. Congress's action on the 2001 Use of Force Resolution, the 2002 Iraq Resolution, the U.S.A. Patriot Act, and other issues illustrates the nature of, and limits to, congressional deference.
Optimization of secondary ion mass spectrometry detection limit for N in SiC
Authors: Pivovarov A. L. , Stevie F. A. , Griffis D. P. , Guryanov G. M.
Published: September 2003

Controlled changes in the Cs+ primary ion beam density and analytical expressions describing the sources (bulk concentration, memory effect, and adsorption of N from the residual vacuum) of secondary ion mass spectrometry analyte secondary ion intensities were used to determine the contributions to the N secondary ion intensity obtained during the analysis of trace levels of N in bulk SiC. This methodology allows the determination of N concentrations that can be substantially less than the apparent N secondary ion background intensity. It was shown that for the Cameca IMS-6F instrumental conditions used, memory effect is the main contributor to the N background signal. Taking into consideration the Cs+ beam diameter, the raster size, the diameter of the ion-extracted area, and the impurity secondary ion intensity, an optimized combination of primary ion beam current and raster size was determined that resulted in the best detection limit for N in bulk SiC. This detection limit for N in bulk SiC (∼6×1014 atoms/cm3) was obtained for a primary ion current of 100 nA, a raster size of 45 μm×45 μm, and a secondary ion extraction area diameter of 30 μm.
Measurements of neutral plasma species in an argon/isopropyl alcohol plasma for the deposition of organic films
Authors: Guerin Daniel C. , Fernsler Richard F. , Shamamian Vasgen A.
Published: September 2003

The neutral gas-phase chemistry of an isopropyl alcohol/argon pulsed plasma was investigated. Appearance potential mass spectrometry was used to identify the neutral species present in the plasma. This article complements the previously published study of the positive ion flux to the deposition surface. Of particular interest was the identification of the reactive species in the plasma that exist as neutrals as well as ions. We determined that neutral radicals were produced by hydrogen-exchange mechanisms as well as electron-impact dissociation reactions. The electron-impact dissociation ionization of the precursor in the plasma resulted in reactive ions that did not occur as neutral species. A byproduct of this reaction was a large concentration of the neutral methyl radical. At low pressures, the methyl radicals diffuse to the surface and are incorporated into the deposited films. At elevated pressures, the neutral methyl radicals abstract hydrogen from gas-phase isopropyl alcohol molecules to form methane. Furthermore, as the pressure increases, the plasma becomes more remote from the deposition surface. Molecular ions created in the remote discharge preserve their chemical identity while diffusing to the surface, since the energies of charge-exchange limit the extent of reaction with the precursor.
Impact of plasma processing on integrated circuit technology migration: From 1 μm to 100 nm and beyond
Authors: Tachi Shinichi
Published: September 2003

Plasma processing has been a key technology for large-volume integrated circuit manufacturing for more than 30 years. In particular, various configurations of plasma reactors, along with a range of plasma chemistries, have enabled high-throughput anisotropic and selective etching of materials with attendant precision transfer of resist patterns for feature sizes from 1 μm down to 100 nm and below. This article surveys the historical developments in oxide, metal, gate, and crystalline silicon etching, along with future challenges.
Geodesics and geodesic deviation in a two-dimensional black hole
Authors: Koley Ratna , Pal Supratik , Kar Sayan
Published: September 2003

We introduce an exactly solvable example of timelike geodesic motion and geodesic deviation in the background geometry of a well-known two-dimensional black hole spacetime. The effective potential for geodesic motion turns out to be either a harmonic oscillator or an inverted harmonic oscillator or a linear function of the spatial variable corresponding to the three different domains of a constant of the motion. The geodesic deviation equation also is exactly solvable. The corresponding deviation vector is obtained and the nature of the deviation is briefly discussed by highlighting a specific case.
Structural Basis of a Phototropin Light Switch
Authors: Harper Shannon M. , Neil Lori C. , Gardner Kevin H.
Published: September 2003

Phototropins are light-activated kinases important for plant responses to blue light. Light initiates signaling in these proteins by generating a covalent protein–flavin mononucleotide (FMN) adduct within sensory Per-ARNT-Sim (PAS) domains. We characterized the light-dependent changes of a phototropin PAS domain by solution nuclear magnetic resonance spectroscopy and found that an α helix located outside the canonical domain plays a key role in this activation process. Although this helix associates with the PAS core in the dark, photoinduced changes in the domain structure disrupt this interaction. We propose that this mechanism couples light-dependent bond formation to kinase activation and identifies a signaling pathway conserved among PAS domains.
Cyclic voltammetric studies of tris(alkylisocyanide)bis (triarylphosphine)cobalt(II) and tris(alkylisocyanide) bis(triarylphosphine)cobalt(I) complexes exhibiting synthetic interconvertability
Authors: Ahmad Jamil , Bothata-Nareetsile Florence , Becker Clifford AL
Published: September 2003

Nine pairs of corresponding [CoI(CNR)3(PR'3)2]X, [CoII(CNR)3(PR'3)2]X2complexes  where X = ClO4, BF4; CNR = CNCMe3, CNCHMe2, CNC6H11, CNCH2Ph; PR'3= PPh3, P(C6H4Me-p)3, P(C6H4OMe-p)3 have been studied using cyclic voltammetry in CH3CN solutions. All cycles are reversible, and E1/2for the Co(I) complexes, initially oxidized, are within experimental error identical to E1/2values for the corresponding Co(II) complexes, initially reduced. E1/2values are strongly dependent on the triarylphosphine ligand, decreasing in the order PPh3> > P(C6H4Me-p)3> P(C6H4OMe-p)3, and weakly dependent on the alkylisocyanide ligand, decreasing in the order CNCH2Ph > CNCMe3> CNC6H11[Formula: see text] CNCHMe2. Solution ν(-N[Formula: see text]C) IR patterns reveal that the [CoI(CNR)3(PR'3)2]X complexes do not have regular trigonal bipyramidal coordination, their structure being determined by the particular CNR ligand, while the [CoII(CNR)3(PR'3)2]X2complexes, specifically in CF3CH2OH, appear to have regular trigonal bipyramidal coordination.Key words: cyclic voltammetry, cobalt(I) complexes, cobalt(II) complexes, alkylisocyanide ligands, triarylphosphine ligands.
Synthesis and molecular recognition of the uridine-containing derivative ofp-tert-butylcalix[4]arene
Authors: Liang Jian , Fu Haiying , Liu Yu , Wang Li , Ye Zhifeng , Shi Xianfa
Published: September 2003

The new uridine-containing derivative of p-tert-butylcalix[4]arene  5,11,17,23-tetra-tert-butyl-25,26,27-trihydroxyl-28-oxyuridinecalix[4]arene (CU)  was synthesized and characterized by1H NMR,13C NMR, IR, EI-MS, and ESI-MS spectra. By the aid of UVvis spectra, the molecular recognition of CU was studied. The hypochromic effect in UVvis spectra showed the obvious molecular recognition of CU to ATP. This recognition is actually the hydrogen bond interaction between the uracil group of CU and the base radical of ATP. The association constant between CU and adenine was determined by UV titration at low concentrations.Key words: calixarene, uridine, molecular recognition, UVvis spectra.
Broadband Geoacoustic Deduction
Authors: Hamson R. M. , Ainslie M. A.
Published: August 2003

A two-stage approach to the geoacoustic inversion problems of selected Workshop '97 test cases is described. Initial parameters are deduced by inspection of transmission losses versus range, depth and frequency, and comparison with the calibration case. These provide a starting point for a conventional matched-field inversion applied to individual frequency data sets for a vertical array at 5-km range using the normal mode model SUPERSNAP and the standard Bartlett processor. Grid searches are carried out over pairs of parameters using: 500-Hz data to establish the sediment density and top sediment sound speed, 100-Hz data to estimate the sound speed gradient in the sediment layer and 25-Hz data for the remaining parameters. Results and error bounds are presented for two realizations of the SD workshop case. Partial results are presented for the SO case. Issues regarding SUPERSNAP/SAFARI mismatches are also discussed.
Neural Direct Approaches for Geoacoustic Inversion
Authors: Stephan Yann , Demoulin Xavier , Sarzeaud Olivier
Published: August 2003

This paper presents different neural network approaches for geoacoustic inversion. The basic idea of neural inversion is to approximate the inverse function from a set of behaviors, i.e. relations between acoustic fields and geoacoustic parameters. In this work, such methods have been applied in two different forms: a global approach which aims to estimate all parameters from all data, and a hierarchical approach in which the most sensitive parameters are estimated before the least sensitive. The methods are tested using synthetic data. Statistical results, as well as benchmark results show that such approaches are efficient and have similar performances.
Simultaneous Reconstruction of Compressional Wave Speed and Density Profiles from Modal Eigenvalues
Authors: Rajan Subramaniam D.
Published: August 2003

In this paper we present a simple approach for estimating the compressional wave speed and density profiles of sediments in a shallow water environments from modal eigenvalues. Methods published earlier in the literature called for data at two frequencies and had to make the assumption that the density profile is a continuous function. Further, the processing scheme was difficult to implement. The method presented here requires data from only one frequency and allows for discontinuities in the density profile. The performance of the proposed method is studied using synthetic data.