Structuring and extracting knowledge for the support of hypothesis generation in molecular biology

Background: Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. The requirement of automated support is exemplified by the difficulty of considering all relevant facts that are contained in the millions of documents available from PubMed. Semantic Web provides tools for sharing prior knowledge, while information retrieval and information extraction techniques enable its extraction from literature. Their combination makes prior knowledge available for computational analysis and inference. While some tools provide complete solutions that limit the control over the modeling and extraction processes, we seek a methodology that supports control by the experimenter over these critical processes. Results: We describe progress towards automated support for the generation of biomolecular hypotheses. Semantic Web technologies are used to structure and store knowledge, while a workflow extracts knowledge from text. We designed minimal proto-ontologies in OWL for capturing different aspects of a text mining experiment: the biological hypothesis, text and documents, text mining, and workflow provenance. The models fit a methodology that allows focus on the requirements of a single experiment while supporting reuse and posterior analysis of extracted knowledge from multiple experiments. Our workflow is composed of services from the 'Adaptive Information Disclosure Application' (AIDA) toolkit as well as a few others. The output is a semantic model with putative biological relations, with each relation linked to the corresponding evidence. Conclusion: We demonstrated a 'do-it-yourself' approach for structuring and extracting knowledge in the context of experimental research on biomolecular mechanisms. The methodology can be used to bootstrap the construction of semantically rich biological models using the results of knowledge extraction processes. Models specific to particular experiments can be constructed that, in turn, link with other semantic models, creating a web of knowledge that spans experiments. Mapping mechanisms can link to other knowledge resources such as OBO ontologies or SKOS vocabularies. AIDA Web Services can be used to design personalized knowledge extraction procedures. In our example experiment, we found three proteins (NF-Kappa B, p21, and Bax) potentially playing a role in the interplay between nutrients and epigenetic gene regulation

Mapping and optimization of the AVS video decoder on a high performance chip multiprocessor

Modern multimedia workloads provide increased levels of quality and compression efficiency at the expense of substantially increased computational complexity. It is important to leverage the off-the-shelf emerging multi-core processor architectures and exploit all levels of parallelism of such workloads in order to achieve real time functionality at a reasonable cost. This paper presents the implementation, optimization and characterization of the AVS video decoder on Intel Core i7, a quad-core, hyper-threaded, chip multiprocessor (CMP). AVS (Audio Video Standard), a new compression standard from China, is competing with H.264 to potentially replace MPEG-2, mainly in the Chinese market. We show that it is necessary to perform a. © 2010 IEEE

Handedness, asthma and allergic disorders: Is there an association?

Left-handedness has often been associated with asthma and allergic disorders. In view of previous findings, we investigated the distribution of laterality scores, using the Edinburgh Handedness Inventory, among 172 children. These children were asthmatic and allergic children of pre-school age and adolescence, who visited the Lung Function Laboratory of the Physiology Department of the University of Thessaly, and their controls. We failed to find an association of left-handedness and asthma at pre-school age. We found an association of left-handedness and other allergies at pre-school age and an association of left-handedness and asthma in adolescence, due to hereditary reasons. Our data suggest that both asthma or other allergies and handedness are inherited, especially through the maternal line

Left-handedness and parental psychopathology in the course of bronchial asthma in childhood

Psychopathology in the family seems to have a role in the course of a child's asthma. The purpose of this study was to examine the possible impact of parental anxiety and depression on the course of asthma, as well as to examine the relationship between left-handedness and asthma in children. The International Study of Asthma and Allergy in Childhood (ISAAC), the Foulds and Bedford Inventory for Anxiety and Depression (DSSI/sAD), and the Edinburgh Left-handedness Inventory were administered to 70 families with asthmatic children 4-8 years old. One year later, the children's asthma was reevaluated using a brief questionnaire based on ISAAC. A sample of 70 families with nonasthmatic healthy children were used as controls. The majority of children in the study group had mild asthma. Allergic rhinitis was found in 31.4% and allergic dermatitis in 20% of the sample. The parents of the asthmatic children scored significantly higher in DSSI/sAD compared to parents of the controls. Maternal anxiety reached the level of clinical disease. Maternal anxiety and left-handedness of the child were associated with asthmatic attacks 1 year later. These results suggest an important psychological role in the evolution of asthma. A possible genetic link between asthma and psychiatric diseases may exist

Smoking in health science students with asthma

It is expected that asthmatic students in a health science department would avoid the hazards of cigarette smoking due to the knowledge they gain through their studies. Surprisingly, health science students with asthma had a higher prevalence of smoking than their healthy colleagues. © 2004 Pulsus Group Inc. All rights reserved

Therapeutic value of antidepressants in asthma

Laboratory and clinical data provide evidence that a biological linkage exists between asthma and depression. Cytokines are key molecules in both diseases. They promote allergic reaction as well as depressive symptomatology. Antidepressants may have a therapeutic role in asthma by suppressing production of proinflammatory cytokines, inducing production of anti-inflammatory ones and preventing their brain effects. Most antidepressants also induce adaptive changes in central monoaminergic neurotransmission, which itself might modulate immune reactivity and central actions of cytokines. Antidepressants may also have direct effects on the immune cells. Their impact on hypothalamus-pituitary-adrenal axis is discussed. Antidepressants are expected to terminate the cascade of inflammatory events in other inflammatory diseases as well. The use of antidepressants in experimental clinical trials in patients with asthma is suggested. (c) 2004 Elsevier Ltd. All rights reserved

Fetal sensitivity to testosterone, left-handedness and development of bronchial asthma: a new approach

In contrast to Geschwind, Behan and Galaburda (GBG) theory, there is strong evidence that inheritance through maternal line is responsible for the coexistence of asthma and left-handedness early in childhood. A new model that incorporates GBG's theory and maternal inheritance is proposed. This hypothesis suggests that maternal atopy is the most important factor in the evolution of asthma and that GBG's theory applies mainly in childhood. An inherited enhanced sensitivity of fetus to testosterone may be the underlying mechanism that leads to the development of bronchial asthma. (C) 2003 Elsevier Ltd. All rights reserved

Implementation and Performance Comparison of the Motion Compensation Kernel of the AVS Video Decoder on FPGA, GPU and Multicore Processors

Next generation video standards have strict and increasing performance demands due to real-time requirements and the trend towards higher frame resolutions and bitrates. Leveraging the advantages of reconfigurable logic and emerging multi-core processor architectures to exploit all levels of parallelism of such workloads is necessary to achieve real time functionality at a reasonable cost

Implementation and performance comparison of the motion compensation kernel of the AVS video decoder on FPGA, GPU and multicore processors

Next generation video standards have strict and increasing performance demands due to real-time requirements and the trend towards higher frame resolutions and bit rates. Leveraging the advantages of reconfigurable logic and emerging multi-core processor architectures to exploit all levels of parallelism of such workloads is necessary to achieve real time functionality at a reasonable cost. © 2011 IEEE