Representation of probabilistic scientific knowledge

This article is available through the Brunel Open Access Publishing Fund. Copyright © 2013 Soldatova et al; licensee BioMed Central Ltd.The theory of probability is widely used in biomedical research for data analysis and modelling. In previous work the probabilities of the research hypotheses have been recorded as experimental metadata. The ontology HELO is designed to support probabilistic reasoning, and provides semantic descriptors for reporting on research that involves operations with probabilities. HELO explicitly links research statements such as hypotheses, models, laws, conclusions, etc. to the associated probabilities of these statements being true. HELO enables the explicit semantic representation and accurate recording of probabilities in hypotheses, as well as the inference methods used to generate and update those hypotheses. We demonstrate the utility of HELO on three worked examples: changes in the probability of the hypothesis that sirtuins regulate human life span; changes in the probability of hypotheses about gene functions in the S. cerevisiae aromatic amino acid pathway; and the use of active learning in drug design (quantitative structure activity relation learning), where a strategy for the selection of compounds with the highest probability of improving on the best known compound was used. HELO is open source and available at https://github.com/larisa-soldatova/HELO.This work was partially supported by grant BB/F008228/1 from the UK Biotechnology & Biological Sciences Research Council, from the European Commission under the FP7 Collaborative Programme, UNICELLSYS, KU Leuven GOA/08/008 and ERC Starting Grant 240186

Matrix representation of the Kaliningrad regional accounts system: experimental development and modelling prospects

This article addresses the task of creating a regional Social Accounting Matrix (SAM) in the Kaliningrad region. Analyzing the behavior of economic systems of national and sub-national levels in the changing environment is one of the main objectives of macroeconomic research. Matrices are used in examining the flow of financial resources, which makes it possible to conduct a comprehensive analysis of commodity and cash flows at the regional level. The study identifies key data sources for matrix development and presents its main results: the data sources for the accounts development and filling the social accounting matrix are identified, regional accounts consolidated, the structure of regional matrix devised, and the multiplier of the regional social accounting matrix calculated. An important aspect of this approach is the set target, which determines the composition of matrix accounts representing different aspects of regional performance. The calculated multiplier suggests the possibility of modelling of a socioeconomic system for the region using a social accounting matrix. The regional modelling approach ensures the matrix compliance with the methodological requirements of the national syste

Accurate solution of the boundary integral equation in 2d lagrangian vortex method for flow simulation around curvilinear airfoils

The problem of numerical solution of the boundary integral equation is considered for 2D case. Viscous vortex domains (VVD) method is used for flow simulation, so vorticity is generated on the whole surface line of the airfoil, and there are a lot of vortex elements close to the airfoil. The aim of the research is to provide high accuracy of numer- ical solution of the integral equation; at the same time the computational complexity of the numerical algorithm should be at rather low level. The third-order accuracy numerical scheme, based on piecewise-quadratic solution representation on the curvilinear panels is presented, approximate analytic expressions are obtained for the matrix coefficients. These schemes work perfect in the case of potential flow simulation, when vorticity is absent and also when vortex elements are placed rather far from the airfoil surface line. A trivial way to the accuracy improvement for the closely located vortices, which consists in extremely fine surface line discretization, leads to unacceptably high numerical complexity of the algorithm. This problem is solved by developing semi-analytical correcti- on procedure which makes it possible to achieve high accuracy at extremely coarse surface line discretization. For example, in the model problem of flow simulation around elliptical airfoil with 2:1 semiaxes ratio only 20 panels are required to achieve the error level less than 1 % for arbitrary position of the vortex element in the flow

EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

Automation Of Making Innovative Decisions In Development Of City Infrastructure

An automated method for evaluating expert questionnaires proposed, in which the questionnaire considered as a linguo-numerical model of the city infrastructure object under study, which makes it possible to present it in a form convenient for automated processing in decision support systems (DSS) based on the proposed procedures

Applicability of the Online Short Spatial Ability Battery to university students testing

Introduction. Multiple studies advocate an importance of spatial abilities (SA) for educational and occupational success, especially in STEM. Recently an Online Short Spatial Ability Battery (OSSAB) was developed and normed for SA testing in adolescents. The battery includes mechanical reasoning, paper folding, pattern assembly, and shape rotation tests. The battery has shown good psychometric characteristics (high reliability and validity, low redundancy, discriminative power), and is available in open access and free to use. Aim. The present research aims: 1) to examine the applicability of the OSSAB for university student testing; 2) to describe its psychometric properties and structure; and 3) to investigate links between SA and educational performance. Methods. A total of 772 university students (aged from 18 to 26, mean age (SD) = 19.55 (1.51), 63.1% females) participated in the study. Participants provided information about their age, gender, university major, and academic achievement, and completed a battery of tests that included the OSSAB tests. Results. The study reports psychometric norms for using the OSSAB in university students. Students’ performance in the OSSAB was similar to that shown in previous research in adolescents in terms of means and variance. The OSSAB showed adequate psychometric properties in this sample: no floor or ceiling effects; low redundancy; moderate to high internal consistency; high discriminative power across university majors; and high external validity. The results indicated that around 6% of the students showed very high levels of SA (higher than 1.5 SD above the mean), and around 8% of students showed very low levels of SA (lower than 1.5 SD below mean). In addition, the OSSAB scores were linked to educational profile choice and exam scores, with small-to-medium effect sizes. Scientific novelty. The study provides psychometric norms for a short online open measure of spatial ability in university students. Practical significance. The OSSAB can be used to provide individual recommendations to students (e.g. SA training), to identify spatially gifted students, and for research purposes in university contexts

Ontology of core data mining entities

In this article, we present OntoDM-core, an ontology of core data mining entities. OntoDM-core defines themost essential datamining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. The ontology has been thoroughly assessed following the practices in ontology engineering, is fully interoperable with many domain resources and is easy to extend

Association between HSPA8 Gene Variants and Ischemic Stroke: A Pilot Study Providing Additional Evidence for the Role of Heat Shock Proteins in Disease Pathogenesis

HSPA8 is involved in many stroke-associated cellular processes, playing a pivotal role in the protein quality control system. Here we report the results of the pilot study aimed at determining whether HSPA8 SNPs are linked to the risk of ischemic strok

Chronotropic action of immobilized subtilisins during the perfusion of an isolated rat heart

The pharmacological experiments on isolated organs (ex vivo) are the preferred method for assessing the primary pharmacodynamics of the studied drugs, since this method is completely excluded the systemic influence of neurohumoral regulation. In the last decade, a new group of thrombolytic drugs based on immobilized subtilisins has been formed. At the stage of registrational preclinical and clinical studies, their pleiotropic pharmacological effects have not been studied. Meanwhile, there is a reason to consider that their pharmacological activity in the bloodstream is not limited to thrombolytic action, but may be extended to a systemic effect on the cardiovascular system. The aim of the study was to investigate the chronotropic effects of an isolated heart during its perfusion with solutions of immobilized subtilisins at different concentrations. Material and methods. The isolated rat heart model according to Langendorff was used in the study. The experiment included 50 Wistar rats, which were divided into 5 groups: isolated hearts perfused only with Krebs – Henseleit solution (control) or with immobilized subtilisins in 4 concentrations (170, 340, 510 и 1020 U/l). Results and discussion. The immobilized subtilisins have a negative chronotropic effect. The onset of the effect depends on the drug concentration in the solution: the higher concentration, the earlier effect. From 5 to 10 minutes of perfusion, a negative chronotropic effect is observed using of immobilized subtilisins at any dose. The duration of its increase is manifested up to 10–20 minutes, depending on the drug concentration in solution. After 20 minutes of perfusion, the achieved negative chronotropic effect remains at a plateau level up to 40 minutes. Conclusion. The immobilized subtilisins have an independent pharmacological effect on heart rate

Modelling of regulatory factor and managerial impact assessment in the regional economy sectors: a case-study of the Kaliningrad region (Russia)

This article discusses the methodology of developing tools for assessing regulatory factors and managerial impacts on the regional economy and individual sectors and businesses. The potential of projection models is investigated, including balance models, convergence of regional and sectoral projection and compiling reliable and representative data sets capable of describing the current economic situation. An attempt was made to develop a series of models for several regional economies; to that end, the modelling of managerial and regulatory impact assessment was used in combination with the well-known value chain approach. In the interests of effective public administration, one of the requirements is to create sectoral model formats compatible with the regional projection models. Results of pilot modelling managerial and regulatory impacts on Kaliningrad region’s economies are presented through examples of agribusiness, transport, industry, tourism and recreation. Implementation of regulatory impact modelling in the framework of the suggested approach is proved for other regions. The main advantage of the developed models for the regional management is their ability to reduce uncertainty in decision-making due to obtaining estimates of the impact of the decisions on the changing situation and the conditions for the development of sectors and industries