Proteomic applications of automated GPCR classification

The G-protein coupled receptor (GPCR) superfamily fulfils various metabolic functions and interacts with a diverse range of ligands. There is a lack of sequence similarity between the six classes that comprise the GPCR superfamily. Moreover, most novel GPCRs found have low sequence similarity to other family members which makes it difficult to infer properties from related receptors. Many different approaches have been taken towards developing efficient and accurate methods for GPCR classification, ranging from motif-based systems to machine learning as well as a variety of alignment-free techniques based on the physiochemical properties of their amino acid sequences. This review describes the inherent difficulties in developing a GPCR classification algorithm and includes techniques previously employed in this area.

Novel 5-HT7 ligands as antidepressants:automated synthesis of N-substituted-N-[1-methyl-3-(4-methylpiperidin-1-yl)propyl]-arylsulfon amides

The 5-HT7 receptor is linked with various CNS disorders. Using an automated solution phase synthesis a combinatorial library of 384 N-substituted N-[1-methyl-3-(4-methylpiperidin-1-yl)propyl]-arylsulfonamides was prepared with 24 chemically diverse amines 1-24 and 16 sulfonyl chlorides A-P. The chemical library of alkylated sulfonamides was evaluated in a receptor binding assay with [3]H-5-CT as ligand. The key synthetic step was the alkylation of a sulfonamide with iodide E, which was prepared from butanediol in 4 synthetic steps. The target compounds 1A, 1B .....24A ... 24P were purified by solvent extraction on a Teacan liquid handling system. Sulfonamide J20, B23, D23, G23, G23, J23 , I24 and O24 displayed a binding affinity IC50 between 100 nM and 10 nM. The crystalline J20 (IC50=39 nM) and O24 (IC50=83 nM) were evaluated further in the despair swimming test and the tail suspension assay. A significant antidepressant activity was found in mice of a greater magnitude than imipramine and fluoxetine at low doses. © 2006 Bentham Science Publishers Ltd.

Automated Response to Query System

SMS (Short Message Service) is now a hugely popular and a very powerful business communication technology for mobile phones. In order to respond correctly to a free form factual question given a large collection of texts, one needs to understand the question at a level that allows determining some of constraints the question imposes on a possible answer. These constraints may include a semantic classification of the sought after answer and may even suggest using different strategies when looking for and verifying a candidate answer. In this paper we focus on various attempts to overcome the major contradiction: the technical limitations of the SMS standard, and the huge number of found information for a possible answer.

An Approach to Designing the Interface of the Automated Documentary System

n the paper the procedure for calculation, designing and estimation of the ergonomics of the interface of systems of document circulation is considered. The original computation procedure and the data received during the designing of the interface of documentary system are given.

Automated System for Effective Internet Marketing Campaign (ASEIMC)

The purpose of the paper is to present an automated system for realization of effective internet marketing campaign (ASEIMC). The constantly growing number of websites available online brings more problems for the contemporary enterprises to reach their potential customers. Therefore the companies have to discover novel approaches to increase their online sales. The presented ASEIMC system gives such an approach and helps small and medium enterprises to compete for customers with big corporations in the Internet space.

Fuzzy Model of the Automated System of Module Knowledge Control

The author analyzes some peculiarities of information perception and the problems of tests evaluation. A fuzzy model of tests evaluation as means of increasing the effectiveness of knowledge control is suggested.

A framework for automated construction of resource space based on background knowledge

Resource Space Model is a kind of data model which can effectively and flexibly manage the digital resources in cyber-physical system from multidimensional and hierarchical perspectives. This paper focuses on constructing resource space automatically. We propose a framework that organizes a set of digital resources according to different semantic dimensions combining human background knowledge in WordNet and Wikipedia. The construction process includes four steps: extracting candidate keywords, building semantic graphs, detecting semantic communities and generating resource space. An unsupervised statistical language topic model (i.e., Latent Dirichlet Allocation) is applied to extract candidate keywords of the facets. To better interpret meanings of the facets found by LDA, we map the keywords to Wikipedia concepts, calculate word relatedness using WordNet's noun synsets and construct corresponding semantic graphs. Moreover, semantic communities are identified by GN algorithm. After extracting candidate axes based on Wikipedia concept hierarchy, the final axes of resource space are sorted and picked out through three different ranking strategies. The experimental results demonstrate that the proposed framework can organize resources automatically and effectively.©2013 Published by Elsevier Ltd. All rights reserved.

An automated tool for semantic accessing to formal software models

Many software engineers have found that it is difficult to understand, incorporate and use different formal models consistently in the process of software developments, especially for large and complex software systems. This is mainly due to the complex mathematical nature of the formal methods and the lack of tool support. It is highly desirable to have software models and their related software artefacts systematically connected and used collaboratively, rather than in isolation. The success of the Semantic Web, as the next generation of Web technology, can have profound impact on the environment for formal software development. It allows both the software engineers and machines to understand the content of formal models and supports more effective software design in terms of understanding, sharing and reusing in a distributed manner. To realise the full potential of the Semantic Web in formal software development, effectively creating proper semantic metadata for formal software models and their related software artefacts is crucial. This paper proposed a framework that allows users to interconnect the knowledge about formal software models and other related documents using the semantic technology. We first propose a methodology with tool support is proposed to automatically derive ontological metadata from formal software models and semantically describe them. We then develop a Semantic Web environment for representing and sharing formal Z/OZ models. A method with prototype tool is presented to enhance semantic query to software models and other artefacts. © 2014.

Automated Problem Domain Cognition Process in Information Systems Design

An automated cognitive approach for the design of Information Systems is presented. It is supposed to be used at the very beginning of the design process, between the stages of requirements determination and analysis, including the stage of analysis. In the context of the approach used either UML or ERD notations may be used for model representation. The approach provides the opportunity of using natural language text documents as a source of knowledge for automated problem domain model generation. It also simplifies the process of modelling by assisting the human user during the whole period of working upon the model (using UML or ERD notations).

Algorithm BIDIMS for Automated Systematization of Data Array. Case Study: Rediscovering Mendeleev’s Periodic Table of Chemical Elements

The method (algorithm BIDIMS) of multivariate objects display to bidimensional structure in which the sum of differences of objects properties and their nearest neighbors is minimal is being described. The basic regularities on the set of objects at this ordering become evident. Besides, such structures (tables) have high inductive opportunities: many latent properties of objects may be predicted on their coordinates in this table. Opportunities of a method are illustrated on an example of bidimentional ordering of chemical elements. The table received in result practically coincides with the periodic Mendeleev table.

Managing Interval Resources in Automated Planning

In this paper RDPPLan, a model for planning with quantitative resources specified as numerical intervals, is presented. Nearly all existing models of planning with resources require to specify exact values for updating resources modified by actions execution. In other words these models cannot deal with more realistic situations in which the resources quantities are not completely known but are bounded by intervals. The RDPPlan model allow to manage domains more tailored to real world, where preconditions and effects over quantitative resources can be specified by intervals of values, in addition mixed logical/quantitative and pure numerical goals can be posed. RDPPlan is based on non directional search over a planning graph, like DPPlan, from which it derives, it uses propagation rules which have been appropriately extended to the management of resource intervals. The propagation rules extended with resources must verify invariant properties over the planning graph which have been proven by the authors and guarantee the correctness of the approach. An implementation of the RDPPlan model is described with search strategies specifically developed for interval resources.

Codon-precise, synthetic, antibody fragment libraries built using automated hexamer codon additions and validated through next generation sequencing

We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR) in antibody fragment libraries and next generation sequencing (NGS) analysis of their quality and diversity.

EPCIS Event-Based traceability in pharmaceutical supply chains via automated generation of linked pedigrees

In this paper we show how event processing over semantically annotated streams of events can be exploited, for implementing tracing and tracking of products in supply chains through the automated generation of linked pedigrees. In our abstraction, events are encoded as spatially and temporally oriented named graphs, while linked pedigrees as RDF datasets are their specific compositions. We propose an algorithm that operates over streams of RDF annotated EPCIS events to generate linked pedigrees. We exemplify our approach using the pharmaceuticals supply chain and show how counterfeit detection is an implicit part of our pedigree generation. Our evaluation results show that for fast moving supply chains, smaller window sizes on event streams provide significantly higher efficiency in the generation of pedigrees as well as enable early counterfeit detection.

Access to Digital Cultural Heritage: Innovative Applications of Automated Metadata Generation

Access to Digital Cultural Heritage: Innovative Applications of Automated Metadata Generation Edited by: Krassimira Ivanova, Milena Dobreva, Peter Stanchev, George Totkov Authors (in order of appearance): Krassimira Ivanova, Peter Stanchev, George Totkov, Kalina Sotirova, Juliana Peneva, Stanislav Ivanov, Rositza Doneva, Emil Hadjikolev, George Vragov, Elena Somova, Evgenia Velikova, Iliya Mitov, Koen Vanhoof, Benoit Depaire, Dimitar Blagoev Reviewer: Prof., Dr. Avram Eskenazi Published by: Plovdiv University Publishing House "Paisii Hilendarski" ISBN: 978-954-423-722-6 2012, Plovdiv, Bulgaria First Edition

Automated Software Reengineering Model and Framework

Тодор П. Чолаков, Димитър Й. Биров - Тази статия представя цялостен модел за автоматизиран реинженеринг на наследени системи. Тя описва в детайли процесите на превод на софтуера и на рефакторинг и степента, до която могат да се автоматизират тези процеси. По отношение на превода на код се представя модел за автоматизирано превеждане на код, съдържащ указатели и работа с адресна аритметика. Също така се дефинира рамка за процеса на реинженеринг и се набелязват възможности за по-нататъшно развитие на концепции, инструменти и алгоритми.