bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure, dynamics and reactions of protein hydration water
Authors: Smith Jeremy C. , Merzel Franci , Bondar Ana-Nicoleta , Tournier Alexander , Fischer Stefan
Published: July 2004

The apparent simplicity of the water molecule belies the wide range of fascinating protein phenomena in which it participates. We review recent computer simulation work on buried, internal water molecules, discussing the thermodynamics of water molecule binding and the participation of water in proton transfer reactions. Surface water molecules are also considered, with emphasis on the modification of average solvent structure on a protein surface, the role of water in the protein dynamical ‘glass’ transition and a simplified description of the protein motions thereby activated.
So, why is water biologically important?
Authors: Lilley Terence H.
Published: July 2004

Some brief impressionistic and necessarily subjectively based comments on the content of the Discussion Meeting are made. It is pointed out that the principal thrust of most of the presentations was directed towards structural aspects of proteins in various media. Comments are also made on the necessary interplay between the medium in which biomolecules occur and the interatomic forces between the atoms comprising the biomolecules. Some speculation is made on the possibility of life–forms existing in extreme environments.
Regulation of multimers via truncated isoforms: a novel mechanism to control nitric-oxide signaling
Authors: Stasiv Yuri , Kuzin Boris , Regulski Michael , Tully Tim , Enikolopov Grigori
Published: July 2004

Nitric oxide (NO) is an essential regulator of Drosophila development and physiology. We describe a novel mode of regulation of NO synthase (NOS) function that uses endogenously produced truncated protein isoforms of Drosophila NOS (DNOS). These isoforms inhibit NOS enzymatic activity in vitro and in vivo, reflecting their ability to form complexes with the full-length DNOS protein (DNOS1). Truncated isoforms suppress the antiproliferative action of DNOS1 in the eye imaginal disc by impacting the retinoblastoma-dependent pathway, yielding hyperproliferative phenotypes in pupae and adult flies. Our results indicate that endogenous products of the dNOS locus act as dominant negative regulators of NOS activity during Drosophila development.
Clustering of DNA Sequences in Human Promoters
Authors: FitzGerald Peter C. , Shlyakhtenko Andrey , Mir Alain A. , Vinson Charles
Published: July 2004

We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression.
Haplotype and Missing Data Inference in Nuclear Families
Authors: Lin Shin , Chakravarti Aravinda , Cutler David J.
Published: July 2004

Determining linkage phase from population samples with statistical methods is accurate only within regions of high linkage disequilibrium (LD). Yet, affected individuals in a genetic mapping study, including those involving cases and controls, may share sequences identical-by-descent stretching on the order of 10s to 100s of kilobases, quite possibly over regions of low LD in the population. At the same time, inferring phase from nuclear families may be hampered by missing family members, missing genotypes, and the noninformativity of certain genotype patterns. In this study, we reformulate our previous haplotype reconstruction algorithm, and its associated computer program, to phase parents with information derived from population samples as well as from their offspring. In applications of our algorithm to 100-kb stretches, simulated in accordance to a Wright-Fisher model with typical levels of LD in humans, we find that phase reconstruction for 160 trios with 10% missing data is highly accurate (>90%) over the entire length. Furthermore, our algorithm can estimate allelic status for missing data at high accuracy (>95%). Finally, the input capacity of the program is vast, easily handling thousands of segregating sites in ≥1000 chromosomes.
Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum
Authors: Coulson Richard M.R. , Hall Neil , Ouzounis Christos A.
Published: July 2004

The life cycle of the parasite Plasmodium falciparum, responsible for the most deadly form of human malaria, requires specialized protein expression for survival in the mammalian host and insect vector. To identify components of processes controlling gene expression during its life cycle, the malarial genome—along with seven crown eukaryote group genomes—was queried with a reference set of transcription-associated proteins (TAPs). Following clustering on the basis of sequence similarity of the TAPs with their homologs, and together with hidden Markov model profile searches, 156 P. falciparum TAPs were identified. This represents about a third of the number of TAPs usually found in the genome of a free-living eukaryote. Furthermore, the P. falciparum genome appears to contain a low number of sequences, which are highly conserved and abundant within the kingdoms of free-living eukaryotes, that contribute to gene-specific transcriptional regulation. However, in comparison with these other eukaryotic genomes, the CCCH-type zinc finger (common in proteins modulating mRNA decay and translation rates) was found to be the most abundant in the P. falciparum genome. This observation, together with the paucity of malarial transcriptional regulators identified, suggests Plasmodium protein levels are primarily determined by posttranscriptional mechanisms.
Segmental Duplications Flank the Multiple Sclerosis Locus on Chromosome 17q
Authors: Chen Daniel C. , Saarela Janna , Clark Royden A. , Miettinen Timo , Chi Anthony , Eichler Evan E. , Peltonen Leena , Palotie Aarno
Published: July 2004

Large chromosomal rearrangements, duplications, and inversions are relatively common in mammalian genomes. Here we report interesting features of DNA strands flanking a Multiple Sclerosis (MS) susceptibility locus on Chromosome 17q24. During the positional cloning process of this 3-Mb locus, several markers showed a radiation hybrid clone retention rate above the average (1.8-fold), suggestive for the existence of duplicated sequences in this region. FISH studies demonstrated multiple signals with three of the tested regional BACs, and 24 BACs out of 187 showed evidence for duplication in shotgun sequence comparisons of the 17q22–q24 region. Specifically, the MS haplotype region proved to be flanked by palindromic sequence stretches and by long segmental intrachromosomal duplications in which highly homologous DNA sequences (>96% identity) are present at both ends of the haplotype. Moreover, the 3-Mb DNA segment, flanked by the duplications, is inverted in the mouse genome when compared with the orientation in human and chimp. The segmental duplication architecture surrounding the MS locus raises the possibility that a nonallelic homologous recombination between duplications could affect the biological activity of the regional genes, perhaps even contributing to the genetic background of MS.
The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide
Authors: Mukhopadhyay Rituparna , Yu WenQiang , Whitehead Joanne , Xu JunWang , Lezcano Magda , Pack Svetlana , Kanduri Chandrasekhar , Kanduri Meena , Ginjala Vasudeva , Vostrov Alexander , Quitschke Wolfgang , Chernukhin Igor , Klenova Elena , Lobanenkov Victor , Ohlsson Rolf
Published: July 2004

All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations document that the properties of CTCF include reading and propagating the epigenetic state of the differentially methylated H19 imprinting control region. To assess whether these findings may reflect a universal role for CTCF targets, we identified more than 200 new CTCF target sites by generating DNA microarrays of clones derived from chromatin-immunopurified (ChIP) DNA followed by ChIP-on-chip hybridization analysis. Target sites include not only known loci involved in multiple cellular functions, such as metabolism, neurogenesis, growth, apoptosis, and signalling, but potentially also heterochromatic sequences. Using a novel insulator trapping assay, we also show that the majority of these targets manifest insulator functions with a continuous distribution of stringency. As these targets are generally DNA methylation-free as determined by antibodies against 5-methylcytidine and a methyl-binding protein (MBD2), a CTCF-based network correlates with genome-wide epigenetic states.
Comparative Evolutionary Genomics of Androgen-Binding Protein Genes
Authors: Emes Richard D. , Riley Matthew C. , Laukaitis Christina M. , Goodstadt Leo , Karn Robert C. , Ponting Chris P.
Published: July 2004

Allelic variation within the mouse androgen-binding protein (ABP) α subunit gene (Abpa) has been suggested to promote assortative mating and thus prezygotic isolation. This is consistent with the elevated evolutionary rates observed for theAbpagene, and theAbpbandAbpggenes whose products (ABPβ and ABPγ) form heterodimers with ABPα. We have investigated the mouse sequence that contains the threeAbpa/b/ggenes, and orthologous regions in rat, human, and chimpanzee genomes. Our studies reveal extensive “remodeling” of this region: Duplication rates ofAbpa-like andAbpbg-like genes in mouse are >2 orders of magnitude higher than the average rate for all mouse genes; synonymous nucleotide substitution rates are twofold higher; and theAbpabggenomic region has expanded nearly threefold since divergence of the rodents. During this time, one in six amino acid sites in ABPβγ-like proteins appear to have been subject to positive selection; these may constitute a site of interaction with receptors or ligands. Greater adaptive variation amongAbpbg-like sequences than amongAbpa-like sequences suggests that assortative mating preferences are more influenced by variation inAbpbg-like genes. We propose a role for ABPα/β/γ proteins as pheromones, or in modulating odorant detection. This would account for the extraordinary adaptive evolution of these genes, and surrounding genomic regions, in murid rodents.
cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes
Authors: Castillo-Davis Cristian I. , Hartl Daniel L. , Achaz Guillaume
Published: July 2004

The relationship between protein and regulatory sequence evolution is a central question in molecular evolution. It is currently not known to what extent changes in gene expression are coupled with the evolution of protein coding sequences, or whether these changes differ among orthologs (species homologs) and paralogs (duplicate genes). Here, we develop a method to measure the extent of functionally relevant cis-regulatory sequence change in homologous genes, and validate it using microarray data and experimentally verified regulatory elements in different eukaryotic species. By comparing the genomes of Caenorhabditis elegans and C. briggsae, we found that protein and regulatory evolution is weakly coupled in orthologs but not paralogs, suggesting that selective pressure on gene expression and protein evolution is quite similar and persists for a significant amount of time following speciation but not gene duplication. Additionally, duplicates of both species exhibit a dramatic acceleration of both regulatory and protein evolution compared to orthologs, suggesting increased directional selection and/or relaxed selection on both gene expression patterns and protein function in duplicate genes.
Incongruent Patterns of Local and Global Genome Size Evolution in Cotton
Authors: Grover Corrinne E. , Kim HyeRan , Wing Rod A. , Paterson Andrew H. , Wendel Jonathan F.
Published: July 2004

Genome sizes in plants vary over several orders of magnitude, reflecting a combination of differentially acting local and global forces such as biases in indel accumulation and transposable element proliferation or removal. To gain insight into the relative role of these and other forces, ∼105 kb of contiguous sequence surrounding the cellulose synthase geneCesA1was compared for the two coresident genomes (ATand DT) of the allopolyploid cotton species,Gossypium hirsutum. These two genomes differ approximately twofold in size, having diverged from a common ancestor ∼5–10 million years ago (Mya) and been reunited in the same nucleus at the time of polyploid formation, ∼1–2 Mya. Gene content, order, and spacing are largely conserved between the two genomes, although a few transposable elements and a single cpDNA fragment distinguish the two homoeologs. Sequence conservation is high in both intergenic and genic regions, with 14 conserved genes detected in both genomes yielding a density of 1 gene every 7.5 kb. In contrast to the twofold overall difference in DNA content, no disparity in size was observed for this 105-kb region, and 555 indels were detected that distinguish the two homoeologous BACs, approximately equally distributed between ATand DTin number and aggregate size. The data demonstrate that genome size evolution at this phylogenetic scale is not primarily caused by mechanisms that operate uniformly across different genomic regions and components; instead, the twofold overall difference in DNA content must reflect locally operating forces between gene islands or in largely gene-free regions.
Creating metadata practices for MIT’s OpenCourseWare Project
Authors: Lubas Rebecca L. , Wolfe Robert H.W. , Fleischman Maximilian
Published: July 2004

The MIT libraries were called upon to recommend a metadata scheme for the resources contained in MIT’s OpenCourseWare (OCW) project. The resources in OCW needed descriptive, structural, and technical metadata. The SCORM standard, which uses IEEE Learning Object Metadata for its descriptive standard, was selected for its focus on educational objects. However, it was clear that the Libraries would need to recommend how the standard would be applied and adapted to accommodate needs that were not addressed in the standard’s specifications. The newly formed MIT Libraries Metadata Unit adapted established practices from AACR2 and MARC traditions when facing situations in which there were no precedents to follow.
Future considerations: the functional library systems record
Authors: Coyle Karen
Published: July 2004

The paper performs a thought experiment on the concept of a record based on the Functional Requirements for Bibliographic Records and library system functions, and concludes that if we want to develop a functional bibliographic record we need to do it within the context of a flexible, functional library systems record structure. The article suggests a new way to look at the library systems record that would allow libraries to move forward in terms of technology but also in terms of serving library users.
A bibliographic metadata infrastructure for the twenty‐first century
Authors: Tennant Roy
Published: July 2004

The current library bibliographic infrastructure was constructed in the early days of computers – before the Web, XML, and a variety of other technological advances that now offer new opportunities. General requirements of a modern metadata infrastructure for libraries are identified, including such qualities as versatility, extensibility, granularity, and openness. A new kind of metadata infrastructure is then proposed that exhibits at least some of those qualities. Some key challenges that must be overcome to implement a change of this magnitude are identified.
A comparative review of common user interface products
Authors: Dorner Daniel G. , Curtis AnneMarie
Published: July 2004

A common user interface replaces the multiple interfaces found among individual electronic library resources, reducing the time and effort spent by the user in both searching and learning to use a range of databases. Although the primary function of a common user interface is to simplify the search process, such products can be holistic solutions designed to address requirements other than searching, such as user authentication and site branding. This review provides a detailed summary of software currently on the market. The products reviewed were EnCompass, MetaLib, Find‐It‐All OneSearch, ZPORTAL, CPORTAL, InfoTrac Total Access, MetaFind, MuseSearch, SiteSearch, Single Search, Chameleon Gateway, and WebFeat.
Visual image repositories at the Washington State University Libraries
Authors: Bond Trevor J.
Published: July 2004

The World Civilizations Image Repository (WCIR) and Photos Online are two collaborative image database projects under way at the Washington State University (WSU) Libraries. These projects demonstrate how the WSU Libraries have employed OCLC/DiMeMa's (Digital Media Management) CONTENTdm in partnership with other University departments to develop visual collections free from copyright restrictions, as well as to manage “born digital” images on a collaborative basis.
ProPrint world‐wide print‐on‐demand services for study and research
Authors: Mittler Elmar , Schulz Matthias
Published: July 2004

The libraries of more and more universities and research institutions have local digital repositories, and the amount of material is increasing every day. Users need an integrated retrieval interface that allows aggregated searching across multiple document servers without having to resort to manual processes. ProPrint offers an on‐demand print service within Germany for over 2,000 monographs and 1,000 journals. Partners worldwide are now invited to join.
The use of a decomposed theory of planned behavior to study Internet banking in Taiwan
Authors: Shih Ya‐Yueh , Fang Kwoting
Published: July 2004

With the liberalization and internalization of financial markets, in terms of the entrance of the World Trade Organization, banks in Taiwan face pressures in service quality and administrative efficiency. Predicting customers’ intention to adopt Internet banking is an important issue. Attempts to understand how an individual's belief, embracing attitude, subjective norm and perceived behavioral control, can influence intention. Two versions of the model of the theory of planned behavior (TPB) – pure and decomposed – are examined and compared to the theory of reasoned action (TRA). Data are collected from approximately 425 respondents and structural equation modeling is used to analyze the responses. Results generally support TRA and TPB and provide a good fit to the data.
Consumer acceptance of online banking: an extension of the technology acceptance model
Authors: Pikkarainen Tero , Pikkarainen Kari , Karjaluoto Heikki , Pahnila Seppo
Published: July 2004

Advances in electronic banking technology have created novel ways of handling daily banking affairs, especially via the online banking channel. The acceptance of online banking services has been rapid in many parts of the world, and in the leading e‐banking countries the number of e‐banking contracts has exceeded 50 percent. Investigates online banking acceptance in the light of the traditional technology acceptance model (TAM), which is leveraged into the online environment. On the basis of a focus group interview with banking professionals, TAM literature and e‐banking studies, we develop a model indicating online‐banking acceptance among private banking customers in Finland. The model was tested with a survey sample (n=268). The findings of the study indicate that perceived usefulness and information on online banking on the Web site were the main factors influencing online‐banking acceptance.
At the crossroads of marketing communications and the Internet: experiences of UK advertisers
Authors: Lace Jonathan M.
Published: July 2004

The crossroads between new media (predominantly the Internet) and marketing communications is a topic of growing interest and importance. Several themes are addressed in this paper including the involvement of the advertising agency, the role and features of Web sites, the measurement of effectiveness, Internet advertising and e‐commerce and the management of new media marketing communications. The author presents empirical evidence from a comprehensive study amongst UK marketers on contemporary practice, and proffers advice on best practice.
Determinants of online information search: a critical review and assessment
Authors: Kulviwat Songpol , Guo Chiquan , Engchanil Napatsawan
Published: July 2004

Developments in electronic technology are changing the way business is normally done. This paper investigates how Internet technology reshapes consumer behavior, specifically in online information search. While information search has been a major research stream in the consumer behavior literature, online search for product/service information is a relatively new area. This paper proposes a conceptual framework for studying the determinants of online information search. Since information search online is a precursor to online purchase, an in‐depth understanding of how consumers gather information online is critical to Internet business success.
Knowledge management strategies: a multi‐case study
Authors: Smith Alan D.
Published: July 2004

The goal of every organization is to manage their knowledge successfully. A firm’s knowledge management strategy should reflect its internal competitive strategy. The strategy chosen should create value for the firm’s customers, turn a profit for the firm and focus on how the firm’s employees deliver on the value, differentiation, and speed. The primary thrust of this paper is to inspect the knowledge management (KM) practices of three organizations and discuss the commonalties based on a grounded theory approach. The results of this research effort are intended to show some of the tools and methods that successful organizations have used to manage their knowledge.
Characterizing knowledge management in the small business environment
Authors: Yew Wong Kuan , Aspinwall Elaine
Published: July 2004

Most of the literature on knowledge management (KM) and its application has, until recently, been centered on large organizations. Pertinent issues in small businesses have to a large extent been neglected. However, small businesses do not necessarily share the same characteristics and ideals as large ones. There are certain unique features of small businesses that need to be understood before KM is implemented in their environment. This paper aims to redress some of this imbalance in the literature by putting KM into the context of small businesses. It looks at their characteristics, their advantages and disadvantages, their strengths and weaknesses, and their key problems and issues, all associated with KM. Recognition of all these elements is crucial in order to provide a well‐suited KM approach for small businesses. The paper culminates with recommendations that will provide important insights to help them accomplish this.
Informal network players, knowledge integration, and competitive advantage
Authors: Awazu Yukika
Published: July 2004

In today’s hyper‐competitive environments, generation and dissipation of knowledge can no longer be understood from within the boundaries of formal organizational mechanisms. Previously, researchers have studied knowledge management based on formal mechanisms; however, few have examined the role played by informal mechanisms. In this paper, we examine the roles of informal network players in knowledge integration and discuss their effects on competitive advantage. For researchers, our paper provides testable propositions and a future research agenda. For practitioners, our paper shows how informal network players influence an organization and offers human resource management implications.
Multi‐level complexity in the management of knowledge networks
Authors: Beesley Lisa
Published: July 2004

While it is widely acknowledged that economic growth is now dependent on the realization of a knowledge based economy, there remains much confusion as to how this is actualized. Effective management of knowledge is endorsed as an essential element for organizational survival and competitive advantage, yet again, the ways in which knowledge moves through knowledge networks remains poorly understood. This paper is the result of a three‐year qualitative investigation of the dynamic relationships among knowledge creation, diffusion, and utilization occurringin situin a collaborative knowledge network. In an attempt to better understand how knowledge unfolds in such a system, this paper explores emergent patterns, not only within individual, group, organizational and inter‐organizational levels of learning, but also among them. Two theoretical models acknowledging the multi‐level complexity of knowledge management in organizations while simultaneously identifying the common influences among them, are presented. In combination, it is then possible develop a theoretical framework through which to better understand the relationships among knowledge creation, diffusion, and utilization in collaborative knowledge networks, and thereby, optimize the utility of knowledge designed for organizational application.
Social context and social capital as enablers of knowledge integration
Authors: Chinying Lang Josephine
Published: July 2004

This paper argues that social contexts and social capital enable knowledge integration; that different social contexts combined with different types of social capital enable different types of knowledge integration. Four types of social contexts are distinguished based on the extent of social embeddedness and closeness of interorganizational coupling; four types of social capital are also described. Based on the diversity of knowledge streams, the extent of tacitness of knowledge to be exchanged, and value created through such exchanges, four modes of knowledge integration are identified, namely frontier, incremental, combinative, and instrumental. This paper provides new insights about the processes of interorganizational transfer of knowledge: the unique combination of a specific social context with a specific type of social capital means firms can achieve equally effective yet highly differentiated approaches to different modes of knowledge integration.
Applying knowledge management principles to enhance cross‐functional team performance
Authors: Mohamed Mirghani , Stankosky Michael , Murray Arthur
Published: July 2004

Traditional organizations with heavy internal competition, rigid functional silos and undue compartmentalization exhibit sub‐optimal performance by inhibiting critical knowledge flows. Cross‐functional teaming attempts to solve this problem by building organizational connections across functional silos. However, merely bringing members of formerly isolated departments together produces only marginal increases in performance. Any synergistic collaboration is likely to arise serendipitously and unpredictably. We propose a systematic approach for combining the principles of knowledge management and cross‐functional teaming in ways that purposefully enhance knowledge flows and result in significant improvements in organizational performance as measured by cost, time and quality.
Identifying the dimensions to retail centre image
Authors: Kupke Valerie
Published: July 2004

First feelings and first impressions largely govern and delimit the kinds of experiences one expects and seeks. This paper reviews the application of multidimensional scaling (MDS) to retail market research and discusses how MDS is able to map these impressions and hence explain the retail centre image held by consumers. It proposes that retail centre image is not just relevant to marketers and retailers, but is also of importance to property managers who need an informed and holistic consumer orientation in order to create and sustain property value. By means of illustration MDS is applied to data based on shopper evaluations of seven retail centre items and an interpretation the results is offered.
Is the case for structural separation of the local loop persuasive?
Authors: Xavier Patrick , Ypsilanti Dimitri
Published: July 2004

This paper responds to continuing arguments about the necessity for structural separation of the telecommunications local loop. It attempts to strike a balance by stressing that in fact a wide range of questions are yet to be answered. And the onus is fairly placed on the proponents of structural separation to provide persuasive answers proving that the drastic action they call for is necessary. In addition, many of the benefits of structural separation are unquantifiable and, indeed, conjectural, while the costs of this severe measure are more certain and substantial. Moreover, while seemingly simple in concept, there is a formidable range of difficulties relating to the implementation of structural separation.
Generic reference model for the analysis of relevant communications markets: fundamental competition concepts
Authors: Briglauer Wolfgang
Published: July 2004

Under the new European regulatory communications framework coming into effect in summer 2003, market analyses will be subject to a different and much wider analytical scope. Whereas traditional market analysis has been primarily based on critical market share values, the relevant articles of the framework directive explicitly call for a more holistic and economically based perspective in carrying out competition analyses in predefined communications markets. This article discusses institutional aspects and provides an organizational framework for conducting market analyses that is applicable to all relevant communication markets. The resulting reference model is shown to be embedded in traditional competition concepts.
Impact of location‐aware services on the privacy/security balance
Authors: Rodríguez Casal Carlos
Published: July 2004

This article is based on a report to the Committee on Citizens' Freedoms and Rights, Justice and Home Affairs of the European Parliament by IPTS, addressing increasing concerns about the impact of emerging information and communication technologies and services on security and personal privacy. This paper presents the findings on location‐based services from the above report. It explores in more depth the effect that the processing of location data (for use in services supported by mobility and integrated within the ambient intelligence context), will have on the future balance between security and privacy.
Interactions between FGF and Wnt signals and Tbx3 gene expression in mammary gland initiation in mouse embryos
Authors: Eblaghie Maxwell C. , Song Soo‐Jin , Kim Jae‐Young , Akita Keiichi , Tickle Cheryll , Jung Han‐Sung
Published: July 2004

Interactions between Wnts, Fgfs and Tbx genes are involved in limb initiation and the same gene families have been implicated in mammary gland development. Here we explore how these genes act together in mammary gland initiation. We compared expression of Tbx3, the gene associated with the human condition ulnar–mammary syndrome, expression of the gene encoding the dual‐specificity MAPK phosphatase Pyst1/MKP3, which is an early response to FGFR1 signalling (as judged by sensitivity to the SU5402 inhibitor), and expression of Lef1, encoding a transcription factor mediating Wnt signalling and the earliest gene so far known to be expressed in mammary gland development. We found that Tbx3 is expressed earlier than Lef1 and that Pyst1 is also expressed early but only transiently. Patterns of expression of Tbx3, Pyst1 and Lef1 in different glands suggest that the order of mammary gland initiation is 3, 4, 1, 2 and 5. Consistent with expression of Pyst1 in the mammary gland, we detected expression of Fgfr1b, Fgf8 and Fgf9 in both surface ectoderm and mammary bud epithelium, and Fgf4 and Fgf17 in mammary bud epithelium. Beads soaked in FGF‐8 applied to the flank of mouse embryos, at a stage just prior to mammary bud initiation, induce expression of Pyst1 and Lef1 and maintain Tbx3 expression in flank tissue surrounding the bead. Grafting beads soaked in the FGFR1 inhibitor, SU5402, abolishes Tbx3, Pyst1 and Lef1 expression, supporting the idea that FGFR1 signalling is required for early mammary gland initiation. We also showed that blocking Wnt signalling abolishes Tbx3 expression but not Pyst1 expression. These data, taken together with previous findings, suggest a model in which Tbx3 expression is induced and maintained in early gland initiation by both Wnt and Fgf signalling through FGFR1.
The appearance and distribution of mature T and B cells in the developing immune tissues of the stripe‐faced dunnart (Sminthopsis macroura)
Authors: Old J. M. , Selwood L. , Deane E. M.
Published: July 2004

This paper describes the initial appearance and distribution of mature T and B cells in the developing immune tissues of the stripe‐faced dunnart (Sminthopsis macroura) based on the use of species cross‐reactive antibodies to the lymphocyte cell surface markers CD3, CD5 and CD79b. At birth no mature T or B cells were detected in the liver or bone marrow using anti‐CD3, anti‐CD5 or anti‐CD79b antibodies. T cells were detected in the thymus with anti‐CD3 by day 12 and anti‐CD5 by day 50 postpartum, and T cells in the spleen were detected by day 43 and day 80 postpartum using anti‐CD3 and anti‐CD5, respectively. B cells were observed in the dunnart spleen by 43 days after birth. CD3‐ and CD79b‐positive cells were detected in the lymph nodes by 50 days and CD5 by day 15 after birth, and in the gut‐associated lymphoid tissues by day 50 and anti‐CD5 by day 57 postpartum. The development and distribution of T and B cells in the immune tissues of dunnart pouch young is similar to that described in other marsupial species. Low numbers or absence of mature lymphocytes in immune tissues of early pouch young dunnarts further support the proposition that young marsupials are reliant on non‐specific defence strategies and/or maternal strategies for a significant period of their time of development in the pouch.
Morphological study of the perireticular nucleus in human fetal brains
Authors: Tulay Cumhur Murat , Elevli Levent , Duman Uğur , Sarımehmetoğlu Ayşe , Çavdar Safiye
Published: July 2004

The perireticular nucleus consists of scattered neurons that are located in the internal capsule. The presence of perireticular neurons in the rat, ferret, cat and human has been described previously. Evidence suggests that the perireticular neurons in various species decrease in number with increasing gestation, but in humans this finding has not been supported by quantitative data. This study aimed to investigate (1) the morphology of the human fetal perireticular neurons, (2) the average number of perireticular neurons within the anterior and posterior crus of the internal capsule per unit area, and (3) the magnitude and the stage of neuronal loss in the human perireticular nucleus subsequent to maturation. Nissl‐stained sections of the internal capsule of human fetal brains of 24, 26.5, 32, 35, 37 and 39 weeks of gestation showed a number of clearly distinguishable large perireticular and small microglia cells. A regular increase of both perireticular and microglial cells was observed up to 32 weeks of gestation, after which a dramatic reduction in the number of both perireticular and microglia cells was observed. The average number of perireticular and the microglia cells per unit area, located within the posterior crus, was more than in the anterior crus of the internal capsule. In the adult, no perireticular neurons were detected within the internal capsule. The results show that perireticular neurons are not restricted to the region lateral to the thalamus and medial to the globus pallidus (posterior crus) but are also present at the region lateral to the caudate nucleus and medial to the globus pallidus (anterior crus).
Connections between the facial, vestibular and cochlear nerve bundles within the internal auditory canal
Authors: Özdoğmuş Ömer , Sezen Ozan , Kubilay Utku , Saka Erdinç , Duman Uğur , Şan Tangül , Çavdar Safiye
Published: July 2004

The vestibular, cochlear and facial nerves have a common course in the internal auditory canal (IAC). In this study we investigated the average number of nerve fibres, the average cross‐sectional areas of the nerves and nerve fibres, and the apparent connections between the facial, cochlear and vestibular nerve bundles within the IAC, using light and scanning electron microscopy. The anatomical localization of the nerves within the IAC was not straightforward. The general course showed that the nerves rotated anticlockwise in the right ear from the inner ear end towards the brainstem end and vice versa for the left ear. The average number of fibres forming vestibular, cochlear, and facial nerves was not constant during their courses within the IAC. The superior and the inferior vestibular nerves showed an increase in the number of nerve fibres from the inner ear end towards the brainstem end of the IAC, whereas the facial and the cochlear nerves showed a reduction in the number of fibres. This suggests that some of the superior and inferior vestibular nerve bundles may receive fibres from the facial and/or cochlear nerves. Scanning electron microscopic evaluations showed superior vestibular–facial and inferior vestibular–cochlear connections within the IAC, but no facial–cochlear connections were observed. Connections between the nerves of the IAC can explain the unexpected vestibular disturbances in facial paralysis or persistence of tinnitus after cochlear neurectomy in intractable tinnitus cases. The present study offers morphometric and scanning electron microscopic data on the fibre connections of the nerves of the IAC.
Distribution patterns of immunocompetent cells in the pregnant mouse uteri carrying allogeneic mouse and xenogeneic vole embryos
Authors: Widayati Diah Tri , Ohmori Yasushige , Fukuta Katsuhiro
Published: July 2004

Mouse and vole embryos were allogeneically and xenogeneically transferred into pseudopregnant CD‐1 and immunodeficient (scid) female mice, and we investigated the distribution of immunocompetent cells, uterine natural killer (uNK) cells, mast cells and macrophages, in the implantation sites on days 6, 7 and 8 of gestation. The survival rate of the vole embryos decreased gradually with increased gestation, but the rate was higher in thesciduteri than in the CD‐1 mice. The number of uNK cells increased markedly at the mesometrial triangle and the outer decidual area in the CD‐1 uteri containing vole embryos; by contrast,sciduteri having vole embryos showed almost the same number as those having mouse embryos. Mast cells were present in large numbers at the myometrium, but rarely in the decidua in all types of pregnant uteri. Cells at the myometrium were more numerous in xenogeneic than in allogeneic transfer. Many mast cells appeared in the inner decidua where xenogeneically transferred vole embryos were dead and aborted. Macrophages were present in the outer decidua and myometria in all types of pregnant uteri, and their distribution pattern did not change even in aborted uterine sites. These results suggest: (1) the response of macrophages to dead embryos is completely inhibited, (2) uNK cells and mast cells increase near dead and aborted embryos, and (3) the increment in uNK cells responding to xenogeneic embryos is suppressed inscidmice, and the suppression may contribute partly to survival of the embryos.
The development and distribution of the interstitial cells of Cajal in the intestine of the equine fetus and neonate
Authors: Fintl C. , Pearson G. T. , Ricketts S. W. , Mayhew I. G. , Hudson N. P. H.
Published: July 2004

This study set out to determine the pattern of development and distribution of the interstitial cells of Cajal (ICC) in the intestinal tract of the equine fetus and neonate. Intestinal tissue samples from 12 naturally aborted equine fetuses and three euthanized neonates were collected and fixed in formalin prior to applying standard immunohistochemical labelling techniques targeting the c‐Kit protein of the ICC. At 6 months of gestation, a network of ICC was present in the myenteric plexus region of both the small and the large intestine. ICC were also present within the circular muscle layer. In the large intestine, a proximal to distal gradient of distribution was evident, with few ICC observed in the more distal parts of the large intestine in the younger fetuses compared with the near‐term animals. A transmural gradient of distribution was also evident within the large intestine, with the most luminal part of the muscularis externa being the last area to be colonized by ICC. This region did not appear fully developed until the early neonatal period. An increased density of ICC was noted throughout the large intestine in the regions of the taenial bands in all animals. This study is the first to describe ICC development and distribution in the equine fetus and neonate.
Development of a new analytical electron microscopy technique to quantify the chemistry of planar defects and to measure accurately solute segregation to grain boundaries
Authors: WALTHER T.
Published: July 2004

A new technique of analytical transmission electron microscopy called ConceptEM has been developed for determining highly accurately small amounts of solute or dopant atoms incorporated into well‐defined planar defects such as stacking faults, grain boundaries or interfaces. The method is based on recording series of analytical spectra taken with different electron beam diameters on the same position centred above a defect that is orientated either edge‐on or slightly inclined with respect to the electron beam. It can be applied to energy‐dispersive X‐ray spectroscopy or electron energy‐loss spectroscopy and necessitates only a nano‐probe modus but no scanning unit. Reliability and accuracy have been tested numerically under various conditions using simulations for a specific geometry, as a function of specimen thickness, material, acceleration voltage, collection angle, random beam displacements and solid solubility. The accuracy has been found to be substantially better (by factors of 5–10) than that of any other current standard technique based on single measurements. Our calculations suggest an accuracy in the determination of the Gibbsian solute excess at a special grain boundary down to ±1% of a monolayer, i.e. around ±0.1 atoms nm−2 under typical experimental conditions, with a maximum error about twice as large. The parameter limiting a straightforward analysis is found to be the solid solubility, which itself, however, can be measured accurately by the technique so that it can be taken into account quantitatively and the above‐stated precision is retained.
Non‐optical bimorph‐based tapping‐mode force sensing method for scanning near‐field optical microscopy
Authors: SHANG G. Y. , LEI F. H. , TROYON M. , QIAO W. H. , TRUSSARDI‐REGNIER A. , MANFAIT M.
Published: July 2004

A non‐optical bimorph‐based tapping‐mode force sensing method for tip–sample distance control in scanning near‐field optical microscopy is developed. Tapping‐mode force sensing is accomplished by use of a suitable piezoelectric bimorph cantilever, attaching an optical fibre tip to the extremity of the cantilever free end and fixing the guiding portion of the fibre to a stationary part near the tip to decouple it from the cantilever. This method is mainly characterized by the use of a bimorph, which carries out simultaneous excitation and detection of mechanical vibration at its resonance frequency owing to piezoelectric and anti‐piezoelectric effects, resulting in simplicity, compactness, ease of implementation and lack of parasitic optical background. In conjugation with a commercially available SPM controller, tapping‐mode images of various samples, such as gratings, human breast adenocarcinoma cells, red blood cells and a close‐packed layer of 220‐nm polystyrene spheres, have been obtained. Furthermore, topographic and near‐field optical images of a layer of polystyrene spheres have also been taken simultaneously. The results suggest that the tapping‐mode set‐up described here is reliable and sensitive, and shows promise for biological applications.
X‐ray high‐resolution vascular network imaging
Authors: PLOURABOUÉ F. , CLOETENS P. , FONTA C. , STEYER A. , LAUWERS F. , MARC‐VERGNES J.‐P.
Published: July 2004

This paper presents the first application of high‐resolution X‐ray synchrotron tomography to the imaging of large microvascular networks in biological tissue samples. This technique offers the opportunity of analysing the full three‐dimensional vascular network from the micrometre to the millimetre scale. This paper presents the specific sample preparation method and the X‐ray imaging procedure. Either barium or iron was injected as contrast agent in the vascular network. The impact of the composition and concentration of the injected solution on the X‐ray synchrotron tomography images has been studied. Two imaging modes, attenuation and phase contrast, are compared. Synchrotron high‐resolution computed tomography offers new prospects in the three‐dimensional imaging of in situ biological vascular networks.
Shape modelling of spatial particles from planar central sections – a case study
Authors: HANNILA M.‐L. , JENSEN E. B. VEDEL , HOBOLTH A. , NYENGAARD J. R.
Published: July 2004

In this paper we develop statistical tools for shape modelling of spatial particles from central sections through the particles. The particles are assumed to be star‐shaped with respect to a reference point inside the particles and are modelled as stochastic deformations of spheres centred at the reference points. The resulting particles are rotation invariant with respect to the reference point. As an illustration, the model is applied to study shape differences between neurons in the Granular and CA1 layer in the human hippocampus.