From genetics to genomics in plants and animals

The classical concepts in plant and livestock selection for economically important quantitative traits traditionally are based on phenotypic records, aiming at improvement of the traits by obtaining better genetic gain. The increase in genetic variation together with shortening of the generation interval is the major target of long term improvement of methods and tools for selection activities. The discoveries and implementations of biotechnology and molecular biology for selection purposes provide a stable background for generating of new knowledge and practical use in agricultural research and practice as well as to meet the growing demand for more and with better quality food and feed. The innovations in molecular knowledge related to practical selection aside with the quick quantification in breeding schemes allowed to reconsider the opportunities for sustainable development of selection methods for improvement of the traits of interest in agriculture, the quick invention and practical application of new high-throughput technologies for studying of the genomic variation, evolution, translation of proteins and metabolite determination altogether put in an open and communicative environment of information technologies provide a new holistic platform for better research and more knowledge for practical application of selection decisions

An Algorithmic Approach to Inferring Cross-Ontology Links while Mapping Anatomical Ontologies

ACM Computing Classification System (1998): J.3.Automated and semi-automated mapping and the subsequently merging of two (or more) anatomical ontologies can be achieved by (at least) two direct procedures. The first concerns syntactic matching between the terms of the two ontologies; in this paper, we call this direct matching (DM). It relies on identities between the terms of the two input ontologies in order to establish cross-ontology links between them. The second involves consulting one or more external knowledge sources and utilizing the information available in them, thus providing additional information as to how terms (concepts) from the two input ontologies are related/linked to each other. Each of the two ontologies is aligned to an external knowledge source and links representing synonymy, is-a parent-child, and part-of parent-child relations, are drawn between the ontology and the knowledge source. These links are then run through a set of simple logical rules in order to come up with cross-ontology links between the two input ontologies. This method is known as semantic matching. It proves usefu

Experts react: 2014 Bulgarian parliamentary elections

Bulgaria held parliamentary elections on 5 October following the resignation of the country’s government in July. We asked six experts in Bulgarian politics for their reactions to the result, which saw former Prime Minister Boyko Borisov’s Citizens for European Development of Bulgaria (GERB) emerge with the largest share of seats in parliament. Dimitar Bechev: “Who’s the winner then? Arguably, the smaller parties“ Aneta Spendzharova: “The new government will need a thick skin to solve the country’s latest predicaments – and, perhaps, a hint of magic” Boyko Vassilev: “Bulgarian media have a problem – public awareness on this issue is crucial” James Dawson: “GERB finds itself in a very strong position internationally” Cristina Chiva: “Given the options, the real question is whether GERB can afford to keep the Movement for Rights and Freedoms out of government“ Dragomir Stoyanov: “The elections show the increasing alienation of citizens from the democratic political process

Implementation of an Ontology-Based Decision Support System for Dietary Recommendations for Diabetes Mellitus

Along with the massive influence of computing technologies in medical research and practice, the wide generation of patient, clinical and lab test data makes the assistance of intelligent information systems a very important factor for correct therapy, surveillance and advising of the patients. In this context decision support systems play an increasingly important role in medical practice. The implementation of a decision support system (DSS) in diabetes treatment and in particular in organizing an improved regime of food balance and patient diets is the target area of the presented study. Based on the recently created Diabetes Mellitus Treatment Ontology (DMTO), our DSS for dietary recommendations generates broader and more precise advices to patients with a known clinical history and lab test profiles. These recommendations are rule-based decisions derived using the DMTO subontologies for patient’s lifestyle improvement and the data from the patient records.National Scientific Program “eHealth” in Bulgaria. Methodological support was received from Project BG05M2P001-1.001-0004 “Universities for Science, Informatics and Technologies in the e-Society (UNITe)” funded by Operational Program “Science and Education for Smart Growth” co-funded by European Regional Development Fund

Predicting and Scoring Links in Anatomical Ontology Mapping

The paper presents a work performed in the area of automatic and semi-automatic ontology mapping. A method for inferring additional cross-ontology links while mapping anatomical ontologies is described and the results of some experiments performed with various external knowledge sources and scoring schemes are discussed as well

A Swedish heterodyne facility instrument for the APEX telescope

In March 2008, the APEX facility instrument was installed on the telescope at the site of Lliano Chajnantor in northern Chile. The main objective of the paper is to introduce the new instrument to the radio astronomical community. It describes the hardware configuration and presents some initial results from the on-sky commissioning. The heterodyne instrument covers frequencies between 211 GHz and 1390 GHz divided into four bands. The first three bands are sideband-separating mixers operating in a single sideband mode and based on superconductor-insulator-superconductor (SIS) tunnel junctions. The fourth band is a hot-electron bolometer, waveguide balanced mixer. All bands are integrated in a closedcycle temperature-stabilized cryostat and are cooled to 4 K. We present results from noise temperature, sideband separation ratios, beam, and stability measurements performed on the telescope as a part of the receiver technical commissioning. Examples of broad extragalactic lines are also included

Experiences with workflows for automating data-intensive bioinformatics

High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out data management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However, workflow systems can incur significant development and administration overhead so bioinformatics pipelines are often still built without them. We present the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead. The organizations are working on similar problems, but we have addressed them with different strategies and solutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution.Pubblicat

Long-term aerosol and cloud database from correlative EARLINET-CALIPSO observations

The European Aerosol Research Lidar Network, EARLINET, performs correlative observations during CALIPSO overpasses based on a sophisticated measurement strategy since June 2006. Within a dedicated activity supported by the European Space Agency (ESA), sixteen EARLINET stations contributed about 1500 measurements during an intensive observational period from May 2008 to October 2009. From these measurements, we establish a long-term aerosol and cloud database of correlative EARLINET-CALIPSO observations. This database shall provide a basis for homogenizing long-term space-borne observations conducted with different lidar instruments operating at different wavelengths on various platforms over the next decade(s). The database is also used to study the quality and representativeness of satellite lidar cross sections along an orbit against long-term lidar network observations on a continental scale.Postprint (published version

EARLINET instrument intercomparison campaigns: overview on strategy and results

This paper introduces the recent European Aerosol Research Lidar Network (EARLINET) quality-assurance efforts at instrument level. Within two dedicated campaigns and five single-site intercomparison activities, 21 EARLINET systems from 18 EARLINET stations were intercompared between 2009 and 2013. A comprehensive strategy for campaign setup and data evaluation has been established. Eleven systems from nine EARLINET stations participated in the EARLINET Lidar Intercomparison 2009 (EARLI09). In this campaign, three reference systems were qualified which served as traveling standards thereafter. EARLINET systems from nine other stations have been compared against these reference systems since 2009. We present and discuss comparisons at signal and at product level from all campaigns for more than 100 individual measurement channels at the wavelengths of 355, 387, 532, and 607¿nm. It is shown that in most cases, a very good agreement of the compared systems with the respective reference is obtained. Mean signal deviations in predefined height ranges are typically below ±2¿%. Particle backscatter and extinction coefficients agree within ±2¿¿×¿¿10-4¿km-1¿sr-1 and ±¿0.01¿km-1, respectively, in most cases. For systems or channels that showed larger discrepancies, an in-depth analysis of deficiencies was performed and technical solutions and upgrades were proposed and realized. The intercomparisons have reinforced confidence in the EARLINET data quality and allowed us to draw conclusions on necessary system improvements for some instruments and to identify major challenges that need to be tackled in the future.Peer ReviewedPostprint (published version

Object-oriented Analysis for Design of Protein Fingerprints

A new approach, based on object-oriented programming, for search and classification of protein patterns in a protein database is developed. Aiming at an improvement of the analysis of protein sequences and structures, certain basic patterns – such as motifs and fingerprints – are used. An unknown protein sequence can be classified by searching for those fingerprints from the database, assessing matches by estimating the statistical significance. The current implementation of the model algorithm for searching is a powerful tool that uses the PRINTS database as an example, however it does not support the option of adding of new features due to the conservative design of the program and the lack of publicly available code. A new version of the PRINTS database has recently been developed and this will require adding new features in the future. A novel object-oriented model for the implementation of the algorithm is proposed. This model is used to build a web application prototype, written in Python—the most widely used programming language in bioinformatics at present. The result of this study is a maintainable software with open source code that can easily be extended with new functionalities