Hypertext in the Semantic Web

The Semantic Web extends the current state of the Web with well-defined meaning. We advocate the use of ontological hypertext as an application of the Semantic Web to provide a principled and structured approach to navigating the resources on the Web. This paper demonstrates how we have applied this concept to two real-world scenarios

Hypertext in the Semantic Web

The Semantic Web extends the current state of the Web with well-defined meaning. We advocate the use of ontological hypertext as an application of the Semantic Web to provide a principled and structured approach to navigating the resources on the Web. This paper demonstrates how we have applied this concept to two real-world scenarios

Linking with Meaning: Ontological Hypertext for Scholars

The links in ontological hypermedia are defined according to the relationships between real-world objects. An ontology that models the significant objects in a scholar’s world can be used toward producing a consistently interlinked research literature. Currently the papers that are available online are mainly divided between subject- and publisher-specific archives, with little or no interoperability. This paper addresses the issue of ontological interlinking, presenting two experimental systems whose hypertext links embody ontologies based on the activities of researchers and scholars

Digitometric Services for Open Archives Environments

We describe “digitometric” services and tools that add value to open-access eprint archives using the Open Archives Initiative (OAI) Protocol for Metadata Harvesting. Celestial is an OAI cache and gateway tool. Citebase Search enhances OAI-harvested metadata with linked references harvested from the full-text to provide a web service for citation navigation and research impact analysis. Digitometrics builds on data harvested using OAI to provide advanced visualisation and hypertext navigation for the research community. Together these services provide a modular, distributed architecture for building a “semantic web” for the research literature

The Semantics of Semantic Annotation

Semantic metadata will play a significant role in the provision of the Semantic Web. Agents will need metadata that describes the content of resources in order to perform operations, such as retrieval, over those resources. In addition, if rich semantic metadata is supplied, those agents can then employ reasoning over the metadata, enhancing their processing power. Key to this approach is the provision of annotations, both through automatic and human means. The semantics of these annotations, however, in terms of the mechanisms through which they are interpreted and presented to the user, are sometimes unclear. In this paper, we identify a number of candidate interpretations of annotation, and discuss the impact these interpretations may have on Semantic Web applications

Differentiation, Quantification and Identification of Abrin and Abrus precatorius Agglutinin

Abrin, the toxic lectin from the rosary pea plant Abrus precatorius, has gained considerable interest in the recent past due to its potential malevolent use. However, reliable and easy-to-use assays for the detection and discrimination of abrin from related plant proteins such as Abrus precatorius agglutinin or the homologous toxin ricin from Ricinus communis are sparse. To address this gap, a panel of highly specific monoclonal antibodies was generated against abrin and the related Abrus precatorius agglutinin. These antibodies were used to establish two sandwich ELISAs to preferentially detect abrin or A. precatorius agglutinin (limit of detection 22 pg/mL for abrin; 35 pg/mL for A. precatorius agglutinin). Furthermore, an abrin-specific lateral flow assay was developed for rapid on-site detection (limit of detection ~1 ng/mL abrin). Assays were validated for complex food, environmental and clinical matrices illustrating broad applicability in different threat scenarios. Additionally, the antibodies turned out to be suitable for immuno-enrichment strategies in combination with mass spectrometry-based approaches for unambiguous identification. Finally, we were able to demonstrate for the first time how the developed assays can be applied to detect, identify and quantify abrin from a clinical sample derived from an attempted suicide case involving A. precatorius.Peer Reviewe

Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays

Statistical analysis on tiling array data is extremely challenging due to the astronomically large number of sequence probes, high noise levels of individual probes and limited number of replicates in these data. To overcome these difficulties, we first developed statistical error estimation and weighted ANOVA modeling approaches to high-density tiling array data, especially the former based on an advanced error-pooling method to accurately obtain heterogeneous technical error of small-sample tiling array data. Based on these approaches, we analyzed the high-density tiling array data of the temporal replication patterns during cell-cycle S phase of synchronized HeLa cells on human chromosomes 21 and 22. We found many novel temporal replication patterns, identifying about 26% of over 1 million tiling array sequence probes with significant differential replication during the four 2-h time periods of S phase. Among these differentially replicated probes, 126 941 sequence probes were matched to 417 known genes. The majority of these genes were found to be replicated within one or two consecutive time periods, while the others were replicated at two non-consecutive time periods. Also, coding regions found to be more differentially replicated in particular time periods than noncoding regions in the gene-poor chromosome 21 (25% differentially replicated among genic probes versus 18.6% among intergenic probes), while such a phenomenon was less prominent in gene-rich chromosome 22. A rigorous statistical testing for local proximity of differentially replicated genic and intergenic probes was performed to identify significant stretches of differentially replicated sequence regions. From this analysis, we found that adjacent genes were frequently replicated at different time periods, potentially implying the existence of quite dense replication origins. Evaluating the conditional probability significance of identified gene ontology terms on chromosomes 21 and 22, we detected some over-represented molecular functions and biological processes among these differentially replicated genes, such as the ones relevant to hydrolase, transferase and receptor-binding activities. Some of these results were confirmed showing >70% consistency with cDNA microarray data that were independently generated in parallel with the tiling arrays. Thus, our improved analysis approaches specifically designed for high-density tiling array data enabled us to reliably and sensitively identify many novel temporal replication patterns on human chromosomes

Pyramidal cell types drive functionally distinct cortical activity patterns during decision-making

Understanding how cortical circuits generate complex behavior requires investigating the cell types that comprise them. Functional differences across pyramidal neuron (PyN) types have been observed within cortical areas, but it is not known whether these local differences extend throughout the cortex, nor whether additional differences emerge when larger-scale dynamics are considered. We used genetic and retrograde labeling to target pyramidal tract, intratelencephalic and corticostriatal projection neurons and measured their cortex-wide activity. Each PyN type drove unique neural dynamics, both at the local and cortex-wide scales. Cortical activity and optogenetic inactivation during an auditory decision task revealed distinct functional roles. All PyNs in parietal cortex were recruited during perception of the auditory stimulus, but, surprisingly, pyramidal tract neurons had the largest causal role. In frontal cortex, all PyNs were required for accurate choices but showed distinct choice tuning. Our results reveal that rich, cell-type-specific cortical dynamics shape perceptual decisions

Aspects of bovine herpesvirus-1 infection in dairy and beef herds in the Republic of Ireland

<p>Abstract</p> <p>Background</p> <p>Infection with bovine herpesvirus-1 (BHV-1) causes a wide range of disease manifestations, including respiratory disease and abortion, with world-wide distribution. The primary objective of the present study was to describe aspects of BHV-1 infection and control on Irish farms, including herd-level seroprevalence (based on pooled sera) and vaccine usage.</p> <p>Methods</p> <p>The characteristics of a diagnostic indirect BHV-1 antibody ELISA test when used on serum pools were evaluated using laboratory replicates for use in the seroprevalence study. The output from this indirect ELISA was expressed as a percentage positivity (PP) value. A proposed cut off (PCO) PP was applied in a cross-sectional study of a stratified random sample of 1,175 Irish dairy and beef cattle herds in 2009, using serum pools, to estimate herd seroprevalence. The study was observational, based primarily on the analysis of existing samples, and only aggregated results were reported. For these reasons, ethical approval was not required. Bulk milk samples from a subset of 111 dairy herds were analysed using the same ELISA. Information regarding vaccine usage was determined in a telephone survey.</p> <p>Results</p> <p>A PCO PP of 7.88% was determined to give 97.1% sensitivity and 100% specificity relative to the use of the ELISA on individual sera giving maximization of the prevalence independent Youden's index, on receiver operating characteristics analysis of replicate results. The herd-level BHV-1 seroprevalence was 74.9% (95% CI - 69.9%-79.8%), with no significant difference between dairy and beef herds. 95.5% agreement in herd classification was found between bulk milk and serum pools. Only 1.8 percent of farmers used BHV-1 marker vaccine, 80% of which was live while 75% of vaccinated herds were dairy.</p> <p>A significant association was found between herd size (quartiles) and seroprevalence (quartiles).</p> <p>Conclusions</p> <p>The results from this study indicate BHV-1 infection is endemic, although BHV-1 vaccines are rarely used, in the cattle population in Ireland.</p