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D. V. Shpilchin, M. K. Baimuldin, I. S. Azizov, Ye. А. Zakharova
AUTOMATIZATION OF MATHEMATICAL ALGORITHMS OF BACTERIA TYPING
Karaganda State Technical University, Karaganda State Medical University
The precise microbiological diagnosis is a crucial factor in the treatment of many infectious diseases. According to the diagnostic criteria, reflected in the current classification of some infectious diseases such as chronic prostatitis, infections, sexually transmitted diseases, etc., diagnostics and establishment of forms of the disease can only be based on the results of microbiological studies. It is important for the microbiologist can correct determinate susceptibility accurate identification of the microorganism to antimicrobial drugs (AMD). This is due to the fact that many microorganisms have a natural resistance to certain AMD and accurate knowledge of the taxonomy of the pathogen in each case allows the doctor to avoid a priori wrong choice of antimicrobial drugs.
In present, an identification of microorganisms is possible if using several methods. However, the dominant part of the microbiology laboratories in the routine practice of conducting the identification of microorganisms based on the study of biochemical activity (determination of the ability to ferment carbohydrates and to decarboxylate or to deaminate amino acids). The identification based on biochemical activity determination has several advantages compared with other more modern methods. First, this method is simple and compared with others, for example, compared with chromatog-raphy, conducting the polymerase chain reaction, immunological methods or mass spectrometry. Secondly, the identification of microorganisms based on the study of biochemical activity of microorganisms does not require the special equipment, unlike other methods. At the final stage of the identification based on the study of biochemical activity, it is necessary to compare these results with the properties of microorganisms as described in the tables - conduct a search form with a similar reaction. To do this, there are a number of programs offered by manufacturers of different test systems, for example, the program «Identity», «MICROBE-AUTO-MATON», etc. However, these programs often focus on the use of any particular instrument, for example, the program «MICROBE-AUTOMATON» oriented for work with the unit «Multiscan Ascent », which is inconvenient because requires that specified device. In addition, the above-mentioned programs perform only the function of identification of microorganisms, and only when using the specified number of tests, which does not provide the user a choice of tests, which does not allow the researcher to choose among the available laboratory resources and makes the researcher more time consuming. Also in
available commercial software it does not provide the feature descriptions of different genera of microorganisms that have medical value, which reduces the value of these software products.
Based on the foregoing, the aim of our work was to create a software product that allows the identification of microorganisms on the basis of available in each laboratory set of features, as well as containing a description of microorganisms that have medical value.
The Information systems department of Karaganda State Technical University in cooperation with the microbiology laboratory of the Research Center of Karaganda State Medical University developed a software package «SIM» greatly simplifies the genera and species of microorganisms identification, as well as providing quick access to reference the information concerning as specific groups of microorganisms, so as the methodic and reference materials prescription.
The system of microorganisms' identification «SIM» built on the «client-server». An example of this architecture is depicted in Figure 1.
Server
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Figure 1. The architecture «Client-Server» scheme
The «Client-Server» architecture implies the presence of server and client side. The server side is the total for the entire system, and its task is to service the customer and to ensure a uniform and relevant data set for all users [1]. The client can be anywhere in the local area network and allows the user to obtain relevant data.
In other words, the server is a common data store, and the client is a means to obtain the relevant data necessary to the user. The advantage of this architecture is the ability for many users to work with one set of data, even if they are in different places geographically. At the same time, guided by considerations of maintainability and scalability of the system, the logic of the system is distributed between the client and the server. The client part of the system developed in the programming environment Delphi. As a SQL-server it is used a database management system InterBase. Those InterBase qualities such as high performance and reliability of the server with minimal requirements to hardware, ease of installation and server support, user-friendly and not require special training mechanism for database administration make the InterBase an excellent choice for implementing enterprise systems for small and medium-scale .
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The server side of «SIM» is called «the data server». Its basic task is keeping the table identification and processing of requests for them, collecting data on research results and save them into a single database, placement and storage of reference articles and hypertext links., There are the business rules implemented on the server, that are intended to maintain the database in a consistent state. The data server is installed on a central workstation, and on the same computer the database is located, which contains configuration and log system events.
The client part of «SIM» called «The user workplace». The client part can be located on any computer network, so as on the server. The full access to the functions of the identification system, including its background implemented with use of client side.
The system interface is intuitive and fully compliant with the standards of Windows. System «SIM» realized in the form of window protection [2].
The main heading lists: «Hierarchical directories», «Module-qualifiers», «Description» are disposed in the basic window «Catalogue of documents». The category «Hierarchical directories» includes an expert system - the identifier with an extensive (tree) structure.
The microorganisms' identification is carried out step by step, by choosing from a menu of relevant answers to unambiguous questions (presence / absence of symptoms). After that the program offers a transition to the determinant module for the final species identification. At any stage of the expert system operator has the ability to obtain additional background information on the method determines the trait.
The section «Module determinants» is designed for experienced physicians, microbiologists, capable of independently without the help of an identifier to hold a generic identification. This module includes module-determinants for the main groups of microorganisms, separated in accordance with the groups set forth in international reference «Bergey's Manual of determinative bacteriology», of the 9th edition [3].
The module-determinant is the main type of document in the «SIM» program. It is through the modules the user holds the identification of microorganisms and analyzing the results of identification. The module is the determinant of the following representations, among which it may navigate using the tabs at the top of the window: a description of family and genus of microorganisms, a table indicating the species of features, which conducted the identification of the determinant.
The each module includes a detailed description of microorganisms' kinds with modern taxonomy bringing, including a detailed bibliography (International Journal of Systematic of Bacteriology) on changes in the systematic nomenclature of microorganisms after the 9th edition of the determinant of the bacteria Burgee. The module also provides details about the types of species traits and microbi-
al identification system.
The developed identification system can work with any set of identification tests, and test set is formed at the discretion of the user and can be changed flexibly to the needs of a specific laboratory.
The work with the identifier is streamlined and built in steps. In the first stage the user is prompted to select species for differentiation, this step has been taken to provide opportunities for selective identification within the genus (e.g., when it is necessary to differentiate the species between themselves).
In the second stage the user is prompted to create a list of identifying features. The choice of signs made with the help of Mouse, which eliminates the problem of knowledge of computer keyboard and eliminates the problems associated with the psychological barrier of using the computer keyboard. In addition, the program allows automatic registration results based on the customized matrix of available biochemical test systems.
In the third stage the user is offered to fill a form of obtained evidence. And the form completing is realized by selecting from recording feature from the drop down menu.
The output form of ID obtained at the last stage, the list provided for the formation of microorganisms with the highest probability characteristics. With probability characteristics, not exceeding the thresholds (also can be configured by the user), the system offers a number of recommendations designed to correct formation of the list of tests used and the choice of an identification module.
Given the thrust of modern laboratory technology to the standards of GLP in the program is provided the protocol preservation with the formation of the identification journal.
In the «Help» section, user can seek information on the use of the program as a menu system, and using keywords or complex Boolean expressions.
Thus, the «SIM» system is a workstation of physician-microbiologist. The idea of a system based on the fundamental purpose of the application of innovative technologies in medicine, which is the formation of a superstructure over the existing methodological solutions, which allows preservation of generally accepted, approved and proven methods of treatment and diagnosis significantly improve their efficiency and reduce the time and economic costs of their use. The system allows to flexible change the list of using tests and not focusing on rigid certain schemes, while introducing the user to obtain the probabilistic characteristics match the identified microorganism types of symptoms.
«SIM» system designed for specific identification of microorganisms on the basis of standard morphological, tinctorial, cultural and biochemical characteristics. The system uses original algorithms to genera and species identification of microorganisms.
The development of a program conducted with use of the programming language Delphi. As a methodological basis for «SIM» program used a
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Экология и гигиена
«Bergey's Manual of determinative bacteriology», of 9th edition and the methodological and normative literature is used in routine microbiological practice. Client-server architecture is implemented using SQLserver InterBase.
The program performs several functions that allow conducting the primary identification of microorganisms to genus, and conclusive identification to species. The peculiarities of organization of the program's interface and implementation of algorithms for identification, greatly simplify the process of genera and species identification of microorganisms.
The program focuses on practical microbiologists, medical microbiologists, epidemiologists, teachers and students of medical microbiology and biological universities.
LITERATURE
1. Скляр А.Я. Введение в InterBase. М.: Горячая линия - Телеком; 2002: 5.
2. Бильфельд Н.В., Затонский А.В. Основы разработки интерфейсов. Реализация в системе Borland Delphi [Учеб. пособие] Пермь; 2010: 96.
3. Определитель бактерий Берджи [Под ред. Д. Хоулта, Н. Крига, П. Снита]. М: Мир; 1997; 2: 541-554
4. Вейант Р.. Моос У., Уивер Р., Холлис Д., Джрдан Дж., Кук Э., Деншвар М. Определитель нетривиальных патогенных грамотрицательных бактерий. М: Мир; 1999.
5. Руководство по медицинской микробиологи. Общая и санитарная микробиология [Под. ред. А.С. Лабинской, Е.Г. Волиной]. М.: БИНОМ; 2008; Книга I: 1080.
6. EuzebyJ.P.: List of bacterial names with standing in nomenclature http://www.bacterio.cict.fr/
7. Truper (H.G.): How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryote nomenclature. FEMS Microbiol. Rev., 1999; 23: 231-249.
8. International Journal of Systematic Bacteriology (ссылки на статьи представлены в идентификационных модулях).
Поступила 20.11.2011 г.
Д. В. Шпильчин, М. К. Баймолдин, И. С. Азизов, Е. А. Захарова
БАКТЕРИЯЛАРДЫ ТИПТЕНД1РУДЩ МАТЕМАТИКАЛЬЩ АЛРЫШАРТЫН АВТОМАТТАНДЫРУ
Акпараттык технологияларды классикалык бактериологиялык зерттеулер Yдерiсiне енпзу иннова-цияларды казiргi заманры микробиологиялык зертханалар жардайында колданудыч сэтл мысалы болып табылады. Макалада «SIM» автоматты акпарат жYЙесiнде жузеге асырылран идентификациялау YДерiсi сипатталран, оныч интерфейсы мен микроорганизмдердi идентификациялаудыч алрышарты суреттелген. Медицинаныч осы саласында бткт кездердщ жYргiзген зерттеулершщ нэтижесiнде жэне вздерi жасаран жумыс корытындысы бойынша алынран мэлiметтерге талдау жасалып, соныч негiзiнде компьютерлiк логика туррысынан тужырымдалран турде алрышарт усынылран. Микроорганизмдердi идентификация-лаудыч алрышартын автоматтандыратын усынылран компьютерлк бардарламаны колдану микроорганизм-дердi идентификациялаудыч жылдамдыры мен дэлдiгiн едэуiр арттырура мYмкiндiк бередi.
Д. В. Шпильчин, М. К. Баймулдин, И. С. Азизов, Е. А. Захарова АВТОМАТИЗАЦИЯ МАТЕМАТИЧЕСКОГО АЛГОРИТМА ТИПИРОВАНИЯ БАКТЕРИЙ
Внедрение информационных технологий в процесс классических бактериологических исследований является удачным примером применения инноваций в условиях современной микробиологической лаборатории. В статье описан процесс идентификации, реализованный в автоматизированной информационной системе «SIM», с описанием ее интерфейса и алгоритма идентификации микроорганизмов. Проведен анализ данных, полученных в результате научного исследования компетентных в рассматриваемой области медицинских источников, а также анализ собственных данных, на основании которого представлен алгоритм в унифицированном виде с точки зрения компьютерной логики. Использование предлагаемой компьютерной программы, автоматизирующей алгоритм идентификации микроорганизмов, позволит существенно увеличить скорость и повысить точность идентификации микроорганизмов.
Г. Г. Еремичева
ДИАГНОСТИКА ДВИГАТЕЛЬНЫХ НАРУШЕНИЙ ЖЕЛУДКА И ДВЕНАДЦАТИПЕРСТНОЙ КИШКИ У ДЕТЕЙ
Карагандинский государственный медицинский университет
В педиатрической практике нередко приходится сталкиваться с поздней диагностикой заболеваний пищеварительного тракта, сопровождающихся нарушением моторно-эвакуаторной функции верхних отделов ЖКТ у детей [1, 2, 3]. Ряд
авторов связывают эту патологию с частым вовлечением в патологический процесс других органов пищеварительной системы, недостаточным знанием клинической симптоматики и сложностью инструментального обследования, большинство из которых являются инвазивными [4, 5, 9].
Цель работы - оценка метода поэтажной манометрии в диагностике моторно-эвакуаторных нарушений желудка и двенадцатиперстной кишки (ДПК) при хроническом гастрите (ХГ) и хроническом гастродуодените (ХГД) у детей.
МАТЕРИАЛЫ И МЕТОДЫ Под наблюдением находились 100 детей (10-18 лет) с хроническим гастритом (41) и хро-
