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At least 1,729 records · Page 96Linked to original sources
PubMed2005

Characterization of cancer stroma markers: in silico analysis of an mRNA expression database for fibroblast activation protein and endosialin.

Standardized, high-throughput RNA detection with microarray chips allows for the construction of genome-wide databases for tissue specimens suitable for in silico electronic Northern blot (eNorthern) analysis of marker genes. We used the BioExpress database, which contains transcriptional profiles of normal and cancer samples, to examine two putative markers of cancer stroma: fibroblast activation protein-alpha (FAP-alpha) and endosialin. Analyses for FAP-alpha showed that normal tissues generally lack RNA signals, with the exception of endometrium. Typing of tumors revealed prominent FAP-alpha signals in cancer types marked by desmoplasia, and localization of FAP-alpha in reactive cancer stroma was confirmed by immunohistochemistry. A subset of sarcomas displayed prominent FAP-alpha signals localizing to the malignant cells. For endosialin, eNorthern analyses showed low to moderate RNA signals in many normal organs, whereas immunohistochemistry revealed endosialin in only some tissues, such as endometrium. Endosialin was detected at the RNA and protein level in sarcomas, notably malignant fibrous histiocytomas. Low to moderate endosialin RNA signals were found in epithelial cancer types for which immunostaining identifies expression in subsets of tumor capillaries or fibroblasts. These findings extend the FAP-alpha and endosialin profiling in silico to an unbiased tumor database and place both molecules in a novel context of endometrial biology and sarcoma subtyping. Our findings suggest that BioExpress can be searched directly for tumor stroma markers but may need prior enrichment for markers with narrow cellular representation, such as endosialin. Constructing databases from microdissected cancer tissues may be an essential step for tumor stroma-targeted therapies.

Adult↗
PubMed2005

Predicting missing values in a home care database using an adaptive uncertainty rule method.

OBJECTIVES: Contemporary literature illustrates an abundance of adaptive algorithms for mining association rules. However, most literature is unable to deal with the peculiarities, such as missing values and dynamic data creation, that are frequently encountered in fields like medicine. This paper proposes an uncertainty rule method that uses an adaptive threshold for filling missing values in newly added records. A new approach for mining uncertainty rules and filling missing values is proposed, which is in turn particularly suitable for dynamic databases, like the ones used in home care systems. METHODS: In this study, a new data mining method named FiMV (Filling Missing Values) is illustrated based on the mined uncertainty rules. Uncertainty rules have quite a similar structure to association rules and are extracted by an algorithm proposed in previous work, namely AURG (Adaptive Uncertainty Rule Generation). The main target was to implement an appropriate method for recovering missing values in a dynamic database, where new records are continuously added, without needing to specify any kind of thresholds beforehand. RESULTS: The method was applied to a home care monitoring system database. Randomly, multiple missing values for each record's attributes (rate 5-20% by 5% increments) were introduced in the initial dataset. FiMV demonstrated 100% completion rates with over 90% success in each case, while usual approaches, where all records with missing values are ignored or thresholds are required, experienced significantly reduced completion and success rates. CONCLUSIONS: It is concluded that the proposed method is appropriate for the data-cleaning step of the Knowledge Discovery process in databases. The latter, containing much significance for the output efficiency of any data mining technique, can improve the quality of the mined information.

Algorithms↗
PubMed2006

[Presence of the biomedical periodicals of Hungarian editions in international databases].

Presence of the biomedical periodicals of Hungarian editions in international databases. The majority of Hungarian scientific results in medical and related sciences are published in scientific periodicals of foreign edition with high impact factor (IF) values, and they appear in international scientific literature in foreign languages. In this study the authors dealt with the presence and registered citation in international databases of those periodicals only, which had been published in Hungary and/or in cooperation with foreign publishing companies. The examination went back to year 1980 and covered a 25-year long period. 110 periodicals were selected for more detailed examination. The authors analyzed the situation of the current periodicals in the three most often visited databases (MEDLINE, EMBASE, Web of Science), and discovered, that the biomedical scientific periodicals of Hungarian interests were not represented with reasonable emphasis in the relevant international bibliographic databases. Because of the great number of data the scientific literature of medicine and related sciences could not be represented in its entirety, this publication, however, might give useful information for the inquirers, and call the attention of the competent people.

Bibliometrics↗
PubMed2005

[Estimation of China soil organic carbon storage and density based on 1:1,000,000 soil database].

Based on 1:1,000,000 soil database, and employing the methods of spatial expression, this paper estimated the soil organic carbon storage (SOCS) and density (SOCD) of China. The database consists of 1:1,000,000 digital soil map, soil profile attribution database, and soil reference system. The digital soil map contained 926 soil mapping units, 690 soil families, and 94 000 or more polygons, while the soil profile attribution database collected 7292 soil profiles, including 81 attribution fields. The SOCDs of soil profiles were calculated and linked to the soil polygons in the digital soil map by the method of "GIS linkage based on soil type", resulting in a vector map of 1:1,000,000 China SOCD. The SOCS of the country or of a soil could be estimated by summing up the SOCS of all polygons or the polygons of a soil, and their SOCD were the SOCS of them derived by their areas. The estimated SOCS and SOCD of the country was 89. 14 Pg (1 Pg = 10(15) g) and 9.60 kg m(-2), respectively, covered all the soils with a total area of 928.10 x 10(4) km2, which might be considered closest to the real value.

Carbon↗
PubMedDate not supplied

dbNEI: a specific database for neuro-endocrine-immune interactions.

OBJECTIVES: To construct a specific database for the neuro-endocrine-immune (NEI) interactions. METHODS/RESULTS: Version 1.0 database for neuro-endocrine-immune (dbNEI) serves as a web-based knowledge resource specific for the NEI systems. dbNEI collects 1,058 NEI related signal molecules, their 940 interactions and 72 affiliated tissues from the Cell Signaling Networks database, manually selects 982 NEI papers from PubMed, and gives links to 27,848 NEI generally related genes from UniGene database. NEI related information, such as signal transductions, regulations and control subunits, is integrated. Especially, dbNEI represents as graphic visualization, by which control subunits can be automatically obtained according to the inquiring issues, the combinative queries and the NEI related diseases respectively. CONCLUSIONS: dbNEI, which can be accessed at http://bioinfo.au.tsinghua.edu.cn/dbNEIweb/, provides a knowledge environment for understanding the main regulatory systems of NEI in a molecular level.

Animals↗
PubMed2005

[Study on the geographic information system databases regarding the control of schistosomiasis in Zhongxiang, Hubei province, China].

OBJECTIVE: Using geographic information system (GIS) and the remote sensing techniques (RS), we developed a schistosomiasis database and geographic distribution map in Zhongxiang city,Hubei province in order to display and analyze the endemic situation longitudinally after the water conservancy project is completed. METHODS: Epidemiological data of schistosomiasis and the correlated climate and hydrology data for the last 30 years were collected and the relevant GIS databases were established under Artificial Neural Networks(ANN) and network training of Landsat TM images. RESULTS: GIS database of schistosomiasis in Zhongxiang city, Hubei province and its vicinity areas were developed including 1 maps regarding the epidemic situation of schistosomiasis. The areas of snail distributing were 4.4 hm2, 8.2 hm2, 24 hm2, 130.4 hm2, 8.13 hm2 and 7.53 hm2, respectively. CONCLUSION: The maps created by GIS database and RS techniques supported the complicated query on space and property, providing a new way in keeping,updating and analyzing available data. The techniques used should be able to provide evidence for the control of schistosomiasis to this water conservancy project.

Animals↗
PubMed2006

DBCollHIV: a database system for collaborative HIV analysis in Brazil.

We developed a database system for collaborative HIV analysis (DBCollHIV) in Brazil. The main purpose of our DBCollHIV project was to develop an HIV-integrated database system with analytical bioinformatics tools that would support the needs of Brazilian research groups for data storage and sequence analysis. Whenever authorized by the principal investigator, this system also allows the integration of data from different studies and/or the release of the data to the general public. The development of a database that combines sequences associated with clinical/epidemiological data is difficult without the active support of interdisciplinary investigators. A functional database that securely stores data and helps the investigator to manipulate their sequences before publication would be an attractive tool for investigators depositing their data and collaborating with other groups. DBCollHIV allows investigators to manipulate their own datasets, as well as integrating molecular and clinical HIV data, in an innovative fashion.

Brazil↗
PubMed1991

Estimating frequency of disease findings from combined hospital databases: a UMLS project.

Merging data from the Salt Lake VA hospital database and the LDS hospital HELP system into a UMLS sponsored unified patient database has demonstrated that distribution of variables within a disease is hospital independent. Although disease prevalence is clearly not the same among hospitals, analysis of data within a disease group across hospitals can be done using such a merged database. This unified patient database would allow study of unusual diseases not possible using data from a single institution.

Databases, Factual↗
PubMed1991

AuthorBase: a database of authoring systems software.

A working prototype database of authoring system software was developed as part of a study of authoring software conducted by the National Library of Medicine. The database and development issues ranging from the scope of the database to what information to document are described. The protype demonstrates that records of reasonable integrity can be derived from vendor supplied information as long as users understand the database is only an initial starting point in searching for authoring software and a resource for becoming generally familiar with the technology.

Authorship↗
PubMed1990

Key health indicators database.

A new database developed by the Canadian Centre for Health Information (CCHI) contains 40 key health indicators and lets users select a range of disaggregations, categories and variables. The database can be accessed through CANSIM, Statistics Canada's electronic database and retrieval system, or through a package for personal computers. This package includes the database on diskettes, as well as software for retrieving and manipulating data and for producing graphics. A data dictionary, a user's guide and tables and graphs that highlight aspects of each indicator are also included.

Canada↗
PubMed1990

NRL-3D: a sequence-structure database derived from the protein data bank (PDB) and searchable within the PIR environment.

The protein identification resource (PIR) and the Brookhaven National Laboratory protein data bank (PDB) are well-known databases for primary sequences and three-dimensional structures of proteins, respectively. Lesk et al, have compared the primary sequences in these two databases and concluded that the sequences in them are not redundant. Moreover, PIR programs can not be used directly on PDB files to access primary sequences because the FORMATS of these two data bases are different. We have developed a sequence-structure database, called NRL-3D, from the sequences, chain identification and the residue numbers of proteins in the PDB. This new database is designed such that it can be used in conjunction with PIR programs to search and extract sequences of interest and the corresponding three-dimensional coordinates from the structures in PDB.

Amino Acid Sequence↗
PubMedDate not supplied

Development of a Database Management System for an obstetrics unit.

This article discusses the use of computer technology in expediting and simplifying the retrieval of data generated from clinical practice. The article describes the collaboration between academic faculty and nurse clinicians in developing a computerized database to report birth statistics incurred by a busy obstetrical unit. A secondary purpose of the article is to assist the reader in understanding the importance of planning the content to be entered into the database and to become familiar with the basics of developing a database that could be used to sort and retrieve data. Facilitators and barriers to the development of a database management system in clinical practice are also discussed.

Database Management Systems↗
PubMed1988

Design of clinical database management systems and associated software to facilitate medical statistical research.

Clinical databases are growing rapidly. The clinical database is heavily used for medical research in many settings. This paper discusses design features for medical databases that facilitate their use for research. The database management system should allow complex data structures, have a syntax-facilitating collection of longitudinal data, interface with major statistical software packages, allow an extensive data dictionary, conveniently merge files, facilitate archival documentation, have an associated data entry system that allows complex logical checking, and have coordinated mainframe and microcomputer software.

Biometry↗
PubMedDate not supplied

A research database for improved data management and analysis in longitudinal studies.

We developed a research database for a five-year prospective investigation of the medical, social, and developmental correlates of chronic lung disease during the first three years of life. We used the Ingres database management system and the Statit statistical software package. The database includes records containing 1300 variables each, the results of 35 psychological tests, each repeated five times (providing longitudinal data on the child, the parents, and behavioral interactions), both raw and calculated variables, and both missing and deferred values. The four-layer menu-driven user interface incorporates automatic activation of complex functions to handle data verification, missing and deferred values, static and dynamic backup, determination of calculated values, display of database status, reports, bulk data extraction, and statistical analysis.

Bronchopulmonary Dysplasia↗
PubMed1995

The application of an anthropometric database of elderly and disabled people.

We report on the development of an anthropometric database of elderly and disabled people for use by designers. The problems encountered by the designer in developing products for the elderly and disabled are highlighted. Reference is made to previous work carried out using computer modelling to simulate the human product interface, and the problems in specifying the anthropometric data are discussed. From a review of existing anthropometric databases we have noted the lack of data on the elderly and disabled. Not only is there insufficient dynamic anthropometric data available, but there are no standards for the measurement techniques to produce this data. We report briefly on parallel work by the group which is looking at anthropometric measurement techniques, and the computer modelling of the human product interface for elderly and disabled people. The lack of dynamic anthropometric data that is appropriate for use by designers and rehabilitation engineers is the major area to be addressed by the database. We investigate the use of existing medical data available as a possible solution to the problem. The database will also seek to address the problem through its methodology of interpretation and presentation.

Aged↗
PubMed1994

Database and software for the analysis of mutations at the human hprt gene.

A computerized database containing DNA sequence information regarding human HPRT mutants has been created. The database itself is in the dBASE format and contains information on about 1500 mutants. In addition, an IBM PC compatible software package to analyze the information in the database has been developed. Both the database and software are freely available via the Internet.

Animals↗
PubMed1994

Database and software for the analysis of mutations at the human p53 gene.

A computerized database containing DNA sequence information regarding human p53 mutants has been created. The database itself is in the dBASE format and contains information on nearly 3000 mutants. In addition, an IBM PC compatible software package to analyze the information in the database has been developed. Both the database and software are freely available via the Internet.

Base Sequence↗
PubMed1994

PRINTS--a database of protein motif fingerprints.

PRINTS is a compendium of protein motif 'fingerprints'. A fingerprint is defined as a group of motifs excised from conserved regions of a sequence alignment, whose diagnostic power or potency is refined by iterative databasescanning (in this case the OWL composite sequence database). Generally, the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. The use of groups of independent, linearly- or spatially-distinct motifs allows protein folds and functionalities to be characterised more flexibly and powerfully than conventional single-component patterns or regular expressions. The current version of the database contains 200 entries (encoding 950 motifs), covering a wide range of globular and membrane proteins, modular polypeptides, and so on. The growth of the databaseis influenced by a number of factors; e.g. the use of multiple motifs; the maximisation of sequence information through iterative database scanning; and the fact that the database searched is a large composite. The information contained within PRINTS is distinct from, but complementary to the consensus expressions stored in the widely-used PROSITE dictionary of patterns.

Amino Acid Sequence↗