A semantic-based system for querying personal digital libraries

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-540-28640-0_4. Copyright @ Springer 2004.The decreasing cost and the increasing availability of new technologies is enabling people to create their own digital libraries. One of the main topic in personal digital libraries is allowing people to select interesting information among all the different digital formats available today (pdf, html, tiff, etc.). Moreover the increasing availability of these on-line libraries, as well as the advent of the so called Semantic Web [1], is raising the demand for converting paper documents into digital, possibly semantically annotated, documents. These motivations drove us to design a new system which could enable the user to interact and query documents independently from the digital formats in which they are represented. In order to achieve this independence from the format we consider all the digital documents contained in a digital library as images. Our system tries to automatically detect the layout of the digital documents and recognize the geometric regions of interest. All the extracted information is then encoded with respect to a reference ontology, so that the user can query his digital library by typing free text or browsing the ontology

Nutrigenomics: a controversy

Nutrigenomics is an emerging science which investigates a certain area of nutrition that uses molecular tools to search access and understand the several responses obtained through a certain diet applied between individual and population groups. The increased need for the use of personalised nutrition in patients is increasing and research is being made on its possible effects. However, research on nutrigenomics and in particular, obesity is still ongoing. Following a current metanalysis on thirty-eight nutrigenomics genes, it seems that a definite association between the genes usually examined in nutrigenomics testing and several diet-related diseases is lacking, even though there is a limited number of studies associating them. In 2014, literature search results in a great number of studies on several polymorphisms. This heterogeneity could only show the way towards new research aims. Nutrigenomics was born due to the need to move from Epidemiology and Physiology to Molecular Biology and Genetics. Currently, there are steps that need to be considered in order for nutrigenomics to be applied: the genes, the gene/protein network, and the strategy towards the determination of the nutrients' influence on gene/protein expression. It is certainly an interesting evolving science with many areas to be investigated further and from different perspectives, as it involves ethics, medicine, genetics and nutritio

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a thorough phylogenomic analysis using five recently available Sparidae gene-sets and 26 high-quality, genome-predicted teleost proteomes. Our analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used. By analytically comparing this result to our own previous contradicting finding, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general

Sympathetic Activation in Deadlines of Deskbound Research - A Study in the Wild

Paper and proposal deadlines are important milestones, conjuring up emotional memories to researchers. The question is if in the daily challenging world of scholarly research, deadlines truly incur higher sympathetic loading than the alternative. Here we report results from a longitudinal, in the wild study of n = 10 researchers working in the presence and absence of impeding deadlines. Unlike the retrospective, questionnaire-based studies of research deadlines in the past, our study is real-time and multimodal, including physiological, observational, and psychometric measurements. The results suggest that deadlines do not significantly add to the sympathetic loading of researchers. Irrespective of deadlines, the researchers' sympathetic activation is strongly associated with the amount of reading and writing they do, the extent of smartphone use, and the frequency of physical breaks they take. The latter likely indicates a natural mechanism for regulating sympathetic overactivity in deskbound research, which can inform the design of future break interfaces

Relating Statistical Image Differences and Degradation Features

Document images are degraded through bilevel processes such as scanning, printing, and photocopying. The resulting image degradations can be categorized based either on observable degradation features or on degradation model parameters. The degradation features can be related mathematically to model parameters. In this paper we statistically compare pairs of populations of degraded character images created with different model parameters. The changes in the probability that the characters are from different populations when the model parameters vary correlate with the relationship between observable degradation features and the model parameters. The paper also shows which features have the largest impact on the image

Hierarchically coupled ultradian oscillators generating robust circadian rhythms

Ensembles of mutually coupled ultradian cellular oscillators have been proposed by a number of authors to explain the generation of circadian rhythms in mammals. Most mathematical models using many coupled oscillators predict that the output period should vary as the square root of the number of participating units, thus being inconsistent with the well-established experimental result that ablation of substantial parts of the suprachiasmatic nuclei (SCN), the main circadian pacemaker in mammals, does not eliminate the overt circadian functions, which show no changes in the phases or periods of the rhythms. From these observations, we have developed a theoretical model that exhibits the robustness of the circadian clock to changes in the number of cells in the SCN, and that is readily adaptable to include the successful features of other known models of circadian regulation, such as the phase response curves and light resetting of the phase

Multi-membership gene regulation in pathway based microarray analysis

This article is available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. Results: We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. Conclusions: We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.The work was sponsored by the studentship scheme of the School of Information Systems, Computing and Mathematics, Brunel Universit

On the equivalence between hierarchical segmentations and ultrametric watersheds

We study hierarchical segmentation in the framework of edge-weighted graphs. We define ultrametric watersheds as topological watersheds null on the minima. We prove that there exists a bijection between the set of ultrametric watersheds and the set of hierarchical segmentations. We end this paper by showing how to use the proposed framework in practice in the example of constrained connectivity; in particular it allows to compute such a hierarchy following a classical watershed-based morphological scheme, which provides an efficient algorithm to compute the whole hierarchy.Comment: 19 pages, double-colum

A comparison of the socio-psycho-educational and personality characteristics of learning disabled and dyslexic children with normal controls

Introduction: LD-dyslexic children experience more social isolation, social exclusion, loneliness less access to social goods -i. e. in education, employment, welfare, etc. (Bryan & Bryan, 1990). Students with learning disorders view themselves as more lonely and report lower levels of the sense of coherence than the average achieving pupils. (Wiener, 1998). Their reading and other learning problems are likely to continue into adulthood, with destructive effects on their feelings of self worth, personal relationships and job opportunities. Last but not least, learning disabilities have been associated with juvenile delinquency. A variety of theories concerning this purported causal relationship have been proposed. Although the assumption that learning disability plays a primary role in a delinquent outcome, remains open to question. Aim: This study examined whether: 1) There is a significant correlation between the socio-psycho-educational- environmental problems and learning disabilities. 2) They can be differentiated from their normal controls on the basis of their psycho-socio-educational profile. Material: The parents of normal controls participating in the study were individually given a questionnaire to complete about their children's reactions and social behaviour. The dyslexic children's parents had already filled in an extended questionnaire that was especially developed by Professor G. Pavlidis for students with Learning Difficulties and Dyslexia. Subiects: Two hundred and twenty seven (227 - 122 boys and 104 girls) children and their parents, took part in this research. The children attended grades 3 through 6. The sample consisted of a hundred and thirty six (136) normal controls -57 boys and 78 girls, and ninety one (91) dyslexics and learning disabled children -65 boys and 26 girls-drawn from the Dyslexia and I. Q. Center, where they were diagnosed by Prof. Pavlidis. The controls were indentified according to their parents answers who had filled in the Pavlidis Questionnaire that was mentioned above. (LD children had similar characteristics as the dyslexics, however they did not fulfil all the criteria to be classified as dyslexics. For instance, for a child to be diagnosed as dyslexic it is necessary to fall significantly behind in reading. Our LD child had similar problems with dyslexic and ADHD in their written expression etc but their reading was not as bad). The subjects' selection as well as their testing took place according to standard ethics and after the necessary permissions were received and the appropriate informed consents were filled out. Results: The LD-dyslexic children's psycho-socio-educational characteristics were found to be significantly different worse than those of the normal controls of the same age. In fact, the two groups different so much that on the basis of their psycho-socio-educational profile the Discriminant Analysis (DA) successfully classified the two groups with accuracy of 94,6%. The LD-dyslexic group was correctly identified with 97,6% while the normal controls were classified with 93,7% accuracy. Conclusions: The very high discrimination accuracy between the two groups raises the possibility to use the Pavlidis Questionnaire as a quick, easy to administer, inexpensive and highly accurate screening tool for children with suspected LD-dyslexia. This potential will be of particular importance to countries like Greece, where only few and very limited possibilities exist within the educational system for the diagnosis of the LD-dyslexic children. However, one has to be cautions to the strong possibility not to be able to discriminate between specific LD-dyslexics and children with general learning retardation, whichQ may have very different etiology, e.g. due to low IQ.EThOS - Electronic Theses Online ServiceGBUnited Kingdo