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

Принципы градостроительного зонирования в судебной практике

The present article deals with the study of the principles of legal zoning through their disclosure in judicial practice. The topic is underdeveloped. The purpose of the study is to identify the role of judicial practice in the legal regulation of urban zoning, as well as the impact on law enforcement and lawmaking activities in this area. The authors propose to use a classification of principles of legal zoning by level of their action (general legal principles, principles of sectoral legislation and special principles) and revealing their content through the analysis of judicial practice materials. In addition to general scientific methods, the comparative legal, formal legal and interpretation methods made it possible to achieve better results. The analysis was conducted with respect to judicial acts adopted by the Supreme Court of the Russian Federation, as well as judicial acts of courts of general jurisdiction and arbitration courts of cassation and appeal instances. More than 150 judicial acts in several catego-ries were examined in total:– Challenging general plan and land use rules as a legal act;– Challenging the refusal to grant permission for permitted use or challenging the granted permission for permitted use;– Challenging the refusal to grant permission to deviate from the maximum parameters of permitted construction, reconstruction of the object of construction or challenging the permission to deviate from the maximum parameters of permitted construction.According to the results of the study it is possible to identify several ways of working with the principles of legal zoning:– direct quotation and application, if it is a principle of sectoral legislation, which is enshrined, for example, in the Urban Planning Code of the Russian Federation;– disclosure of content without precise formulation, for example, the principle of protection of previously arisen rights of right holders of land plots when changing legal zoning, which is not directly mentioned in judicial acts, but is disclosed through references to current legislation;– the formation of new principles not enshrined in the current legal acts, such as the principle of primacy of the master plan or the principle of belonging of a land plot only to one territorial zone. Approaches and legal provisions, broadcasted by judicial practice, are reflected in the law enforcement and law-making activities of local self-government bodies. The authors draw attention to the fact that local self-governing bodies assess and take into account the emerging judicial practice in different ways. This fact is confirmed by the current editions of the rules of land use and development in different Russian cities.Раскрываются принципы градостроительного зонирования через анализ материалов судебной практики. По мнению авторов, именно судебная практика выступает сегодня значимой методологической базой в указанной сфере. Классификация принципов дана по основанию уровня их действия (общеправовые принципы, принципы отраслевого законодательства, специальные принципы), а их содержание раскрыто по результатам исследования судебных актов различных инстанций. Подтверждена гипотеза о значительном влиянии судебной практики на правоприменительную и правотворческую деятельность органов местного самоуправления, что подтверждается теми политиками и решениями, которые транслируются в настоящее время в правилах землепользования и застройки разных городов Российской Федерации

TECHNOLOGICAL PROPERTIES OF FLOUR AND THEIR EFFECT ON QUALITY INDICATORS OF SUGAR COOKIES

The main recipe component of most types of flour confectionery is wheat flour, the technological properties of which largely effect not only the quality indicators of the finished product, but also the stability of the technological flow of its production. However, today, in Russia there are no specialized requirements for the quality of wheat flour for confectionery, in contrast to the requirements for the baking wheat flour. The article lists the main problems and features of the quality of Russian wheat flour consisting in the absence of target classifications of grain and a decrease in its qualitative potential, in particular, a decrease in the amount of gluten and improvement of its quality. As part of the work, the influence of the technological properties of wheat flour on the rheological parameters of the dough and the quality of sugar cookies, which are traditionally in high demand of population groups of every age, was studied, while the share of domestic products is more than 85%. The work was performed in the laboratory of flour confectionery products of All-Russian Scientific Research Institute of Confectionery Industry. The determination of organoleptic, physical and chemical, structural and mechanical indicators of raw materials, semi-finished products and finished products was carried out by standard methods.The main recipe component of most types of flour confectionery is wheat flour, the technological properties of which largely effect not only the quality indicators of the finished product, but also the stability of the technological flow of its production. However, today, in Russia there are no specialized requirements for the quality of wheat flour for confectionery, in contrast to the requirements for the baking wheat flour. The article lists the main problems and features of the quality of Russian wheat flour consisting in the absence of target classifications of grain and a decrease in its qualitative potential, in particular, a decrease in the amount of gluten and improvement of its quality. As part of the work, the influence of the technological properties of wheat flour on the rheological parameters of the dough and the quality of sugar cookies, which are traditionally in high demand of population groups of every age, was studied, while the share of domestic products is more than 85%. The work was performed in the laboratory of flour confectionery products of All-Russian Scientific Research Institute of Confectionery Industry. The determination of organoleptic, physical and chemical, structural and mechanical indicators of raw materials, semi-finished products and finished products was carried out by standard methods

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

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

HNO Binding in a Heme Protein: Structures, Spectroscopic Properties, and Stabilities

HNO can interact with numerous heme proteins, but atomic level structures are largely unknown. In this work, various structural models for the first stable HNO heme protein complex, MbHNO (Mb, myoglobin), were examined by quantum chemical calculations. This investigation led to the discovery of two novel structural models that can excellently reproduce numerous experimental spectroscopic properties. They are also the first atomic level structures that can account for the experimentally observed high stabilities. These two models involve two distal His conformations as reported previously for MbCNR and MbNO. However, a unique dual hydrogen bonding feature of the HNO binding was not reported before in heme protein complexes with other small molecules such as CO, NO, and O2. These results shall facilitate investigations of HNO bindings in other heme proteins

Impact of renal impairment on atrial fibrillation: ESC-EHRA EORP-AF Long-Term General Registry

Background: Atrial fibrillation (AF) and renal impairment share a bidirectional relationship with important pathophysiological interactions. We evaluated the impact of renal impairment in a contemporary cohort of patients with AF. Methods: We utilised the ESC-EHRA EORP-AF Long-Term General Registry. Outcomes were analysed according to renal function by CKD-EPI equation. The primary endpoint was a composite of thromboembolism, major bleeding, acute coronary syndrome and all-cause death. Secondary endpoints were each of these separately including ischaemic stroke, haemorrhagic event, intracranial haemorrhage, cardiovascular death and hospital admission. Results: A total of 9306 patients were included. The distribution of patients with no, mild, moderate and severe renal impairment at baseline were 16.9%, 49.3%, 30% and 3.8%, respectively. AF patients with impaired renal function were older, more likely to be females, had worse cardiac imaging parameters and multiple comorbidities. Among patients with an indication for anticoagulation, prescription of these agents was reduced in those with severe renal impairment, p <.001. Over 24 months, impaired renal function was associated with significantly greater incidence of the primary composite outcome and all secondary outcomes. Multivariable Cox regression analysis demonstrated an inverse relationship between eGFR and the primary outcome (HR 1.07 [95% CI, 1.01–1.14] per 10 ml/min/1.73 m2 decrease), that was most notable in patients with eGFR <30 ml/min/1.73 m2 (HR 2.21 [95% CI, 1.23–3.99] compared to eGFR ≥90 ml/min/1.73 m2). Conclusion: A significant proportion of patients with AF suffer from concomitant renal impairment which impacts their overall management. Furthermore, renal impairment is an independent predictor of major adverse events including thromboembolism, major bleeding, acute coronary syndrome and all-cause death in patients with AF

Clinical complexity and impact of the ABC (Atrial fibrillation Better Care) pathway in patients with atrial fibrillation: a report from the ESC-EHRA EURObservational Research Programme in AF General Long-Term Registry

Background: Clinical complexity is increasingly prevalent among patients with atrial fibrillation (AF). The ‘Atrial fibrillation Better Care’ (ABC) pathway approach has been proposed to streamline a more holistic and integrated approach to AF care; however, there are limited data on its usefulness among clinically complex patients. We aim to determine the impact of ABC pathway in a contemporary cohort of clinically complex AF patients. Methods: From the ESC-EHRA EORP-AF General Long-Term Registry, we analysed clinically complex AF patients, defined as the presence of frailty, multimorbidity and/or polypharmacy. A K-medoids cluster analysis was performed to identify different groups of clinical complexity. The impact of an ABC-adherent approach on major outcomes was analysed through Cox-regression analyses and delay of event (DoE) analyses. Results: Among 9966 AF patients included, 8289 (83.1%) were clinically complex. Adherence to the ABC pathway in the clinically complex group reduced the risk of all-cause death (adjusted HR [aHR]: 0.72, 95%CI 0.58–0.91), major adverse cardiovascular events (MACEs; aHR: 0.68, 95%CI 0.52–0.87) and composite outcome (aHR: 0.70, 95%CI: 0.58–0.85). Adherence to the ABC pathway was associated with a significant reduction in the risk of death (aHR: 0.74, 95%CI 0.56–0.98) and composite outcome (aHR: 0.76, 95%CI 0.60–0.96) also in the high-complexity cluster; similar trends were observed for MACEs. In DoE analyses, an ABC-adherent approach resulted in significant gains in event-free survival for all the outcomes investigated in clinically complex patients. Based on absolute risk reduction at 1 year of follow-up, the number needed to treat for ABC pathway adherence was 24 for all-cause death, 31 for MACEs and 20 for the composite outcome. Conclusions: An ABC-adherent approach reduces the risk of major outcomes in clinically complex AF patients. Ensuring adherence to the ABC pathway is essential to improve clinical outcomes among clinically complex AF patients