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At least 559 records · Page 31Linked to original sources
PubMed2002

Clinical databases of patients receiving antidepressants. The missing link between research and practice?

BACKGROUND: In the last 10 years the use of antidepressants has increased drastically. Unfortunately, the epidemiology of these compounds has shown significant gaps between recommendations derived from randomised controlled trials and current clinical practice. METHODS: We argue for the need to develop and maintain clinical databases of patients receiving antidepressants as a way of bridging this situation. RESULTS: In addition to experimental data generated in selected patients and settings, observational databases of large cohorts of typical patients, followed in typical settings, should be developed and maintained. Clinical databases could collect information on patient social and demographic characteristics, clinical symptoms, diagnosis and pharmacological and non-pharmacological treatments. In addition, they can provide accurate estimates of probabilities of different outcomes and on factors that affect outcome. CONCLUSION: Clinical databases should not be seen as another expensive administrative task for busy doctors. Clinical databases should be developed, organised and utilised only by clinicians who are interested in monitoring their clinical practice and want to provide patients, relatives and the public with information on prognosis and outcome in their specific context of care. Maintaining clinical databases is a routine process, nested in everyday clinical activity, which aims at constituting a permanent link between research and practice.

Antidepressive Agents↗
PubMed2001

A database generator for human brain imaging.

Sharing scientific data containing complex information requires new concepts and new technology. NEUROGENERATOR is a database generator for the neuroimaging community. A database generator is a database that generates new databases. The scientists submit raw PET and fMRI data to NEUROGENERATOR, which then processes the data in a uniform way to create databases of homogeneous data suitable for data sharing, met-analysis and modelling the human brain at the systems level. These databases are then distributed to the scientists.

Brain↗
PubMed2001

Searching fee and non-fee toxicology information resources: an overview of selected databases.

Toxicology profiles organize information by broad subjects, the first of which affirms identity of the agent studied. Studies here show two non-fee databases (ChemFinder and ChemIDplus) verify the identity of compounds with high efficiency (63% and 73% respectively) with the fee-based Chemical Abstracts Registry file serving well to fill data gaps (100%). Continued searching proceeds using knowledge of structure, scope and content to select databases. Valuable sources for information are factual databases that collect data and facts in special subject areas organized in formats available for analysis or use. Some sources representative of factual files are RTECS, CCRIS, HSDB, GENE-TOX and IRIS. Numerous factual databases offer a wealth of reliable information; however, exhaustive searches probe information published in journal articles and/or technical reports with records residing in bibliographic databases such as BIOSIS, EMBASE, MEDLINE, TOXLINE and Web of Science. Listed with descriptions are numerous factual and bibliographic databases supplied by 11 producers. Given the multitude of options and resources, it is often necessary to seek service desk assistance. Questions were posed by telephone and e-mail to service desks at DIALOG, ISI, MEDLARS, Micromedex and STN International. Results of the survey are reported.

Bibliographies as Topic↗
PubMed2000

The use of databases to manage fertility.

Dairy farming now needs more records to be kept for quality assurance as well as for management. Herd fertility management is best brought about through the use of computerised records for each animal that integrate fertility, health and production. The development of dairy information systems over the last 25 years has allowed the creation of databases that give rise to "standards" of performance and "interference levels". These databases are of limited use for research unless the coding system has a structure and definition that works across herds. There is an increasing need to incorporate carefully coded disease records into these databases as there is increasing concern about welfare, zoonoses, assurance and the environment. Rules can be determined for satisfactory fertility so interference at an early stage is cost-effective. Integrated indices have been developed (using databases) that incorporate the costs of wastage caused by poor fertility, thus highlighting the priorities for management. Databases are best operated near to the farm, either in the veterinarian's office or on-line in the farm office. Databases can be made into expert systems that deliver high standards of fertility management. A checklist is included that can be followed to analyse the causes of poor fertility in a dairy herd.

Animals↗
PubMed2001

Image matching algorithms for breech face marks and firing pins in a database of spent cartridge cases of firearms.

On the market several systems exist for collecting spent ammunition data for forensic investigation. These databases store images of cartridge cases and the marks on them. Image matching is used to create hit lists that show which marks on a cartridge case are most similar to another cartridge case. The research in this paper is focused on the different methods of feature selection and pattern recognition that can be used for optimizing the results of image matching. The images are acquired by side light images for the breech face marks and by ring light for the firing pin impression. For these images a standard way of digitizing the images used. For the side light images and ring light images this means that the user has to position the cartridge case in the same position according to a protocol. The positioning is important for the sidelight, since the image that is obtained of a striation mark depends heavily on the angle of incidence of the light. In practice, it appears that the user positions the cartridge case with +/-10 degrees accuracy. We tested our algorithms using 49 cartridge cases of 19 different firearms, where the examiner determined that they were shot with the same firearm. For testing, these images were mixed with a database consisting of approximately 4900 images that were available from the Drugfire database of different calibers.In cases where the registration and the light conditions among those matching pairs was good, a simple computation of the standard deviation of the subtracted gray levels, delivered the best-matched images. For images that were rotated and shifted, we have implemented a "brute force" way of registration. The images are translated and rotated until the minimum of the standard deviation of the difference is found. This method did not result in all relevant matches in the top position. This is caused by the effect that shadows and highlights are compared in intensity. Since the angle of incidence of the light will give a different intensity profile, this method is not optimal. For this reason a preprocessing of the images was required. It appeared that the third scale of the "à trous" wavelet transform gives the best results in combination with brute force. Matching the contents of the images is less sensitive to the variation of the lighting. The problem with the brute force method is however that the time for calculation for 49 cartridge cases to compare between them, takes over 1 month of computing time on a Pentium II-computer with 333MHz. For this reason a faster approach is implemented: correlation in log polar coordinates. This gave similar results as the brute force calculation, however it was computed in 24h for a complete database with 4900 images.A fast pre-selection method based on signatures is carried out that is based on the Kanade Lucas Tomasi (KLT) equation. The positions of the points computed with this method are compared. In this way, 11 of the 49 images were in the top position in combination with the third scale of the à trous equation. It depends however on the light conditions and the prominence of the marks if correct matches are found in the top ranked position. All images were retrieved in the top 5% of the database. This method takes only a few minutes for the complete database if, and can be optimized for comparison in seconds if the location of points are stored in files. For further improvement, it is useful to have the refinement in which the user selects the areas that are relevant on the cartridge case for their marks. This is necessary if this cartridge case is damaged and other marks that are not from the firearm appear on it.

Algorithms↗
PubMed2001

A brief history of the formation of DNA databases in forensic science within Europe.

The introduction of DNA analysis to forensic science brought with it a number of choices for analysis, not all of which were compatible. As laboratories throughout Europe were eager to use the new technology different systems became routine in different laboratories and consequently, there was no basis for the exchange of results. A period of co-operation then started in which a nucleus of forensic scientists agreed on an uniform system. This collaboration spread to incorporate most of the established forensic science laboratories in Europe and continued through two major changes in the technology. At each step agreement was reached on which systems to use. From the beginning it was realised that DNA databases would provide the criminal justice systems with an efficient way of crime solving and consequently some local databases were created. It was not until the introduction of the amplification technology linked to the analysis of short tandem repeats that a sufficiently sensitive and robust system was available for the formation of efficient and effective DNA databases. Comprehensive legislation enacted in the UK in 1995 enabled forensic scientists to set up the first national DNA database which would hold both personal DNA profiles together with results obtained from crime scenes. Other countries quickly followed but in some the legislation has severely restricted the amount and type of data which can be retained and, therefore, effectiveness of the databases is limited. The widespread use of commercially produced multiplex kits has produced a situation in which nearly all European laboratories are using compatible systems and there is, therefore, the potential for the introduction of a pan-European DNA database. However, the exchange of results between countries is hampered by the various legislations which currently exist.

DNA Fingerprinting↗
PubMed2001

Impact of different definitions on estimates of accuracy of the diagnosis data in a clinical database.

Computerized medical databases are increasingly used for research. The influence of different definitions of the accuracy of matching on the estimated accuracy of diagnosis data was assessed in a database of visits to a public pediatric clinic. Differences between definitions involved 1) unit of analysis, 2) number of diagnoses required to match per visit, and/or 3) whether database contents are required to match the medical record or medical record contents are required to be matched in the database. Overall, 90% of diagnoses in the database (391/435) were accurately coded relative to the medical record. Alternatively, 77% of diagnoses listed in the medical record (391/506) were accurately coded in the database. When individual visits were used as the unit of analysis, estimates of accuracy using six definitions ranged from 65% to 92%. The most appropriate definition to use for estimating accuracy of diagnosis data likely depends on the purpose of the study. Use of two or more such definitions may enhance portrayal of the accuracy of diagnosis data.

Algorithms↗
PubMed1999

A new way of building a database of EEG findings.

Whereas computer-based electroencephalography (EEG) is widely applied, the EEG interpretations are usually not stored in a way that favours exploitation of modern computer technology. This paper reports an EEG description system facilitating categorization of EEG data in a computerized database. The system interactively communicates with the digital EEG system and also with the general patient administrative system. The main new quality of this system is the methods for data input and automatic data retrieval from several systems, rather than the establishment of a database of EEG data itself. The EEGs are visually analysed and categorized. Manually marked EEG events are automatically transferred to the database and such events as well as defined electrode positions within these epochs are directly linked to their corresponding descriptions. The database is updated without demand for filling in the events in the database in a second operation. Thereby, the EEG interpreter builds the database while analysing the EEG. This system provides an improved accessibility of EEG data for clinical, normative, educational and scientific use.

Brain↗
PubMed1995

Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database.

A method to correlate uninterpreted tandem mass spectra of modified peptides, produced under low-energy (10-50 eV) collision conditions, with amino acid sequences in a protein database has been developed. The fragmentation patterns observed in the tandem mass spectra of peptides containing covalent modifications is used to directly search and fit linear amino acid sequences in the database. Specific information relevant to sites of modification is not contained in the character-based sequence information of the databases. The search method considers each putative modification site as both modified and unmodified in one pass through the database and simultaneously considers up to three different sites of modification. The search method will identify the correct sequence if the tandem mass spectrum did not represent a modified peptide. This approach is demonstrated with peptides containing modifications such as S-carboxymethylated cysteine, oxidized methionine, phosphoserine, phosphothreonine, or phosphotyrosine. In addition, a scanning approach is used in which neutral loss scans are used to initiate the acquisition of product ion MS/MS spectra of doubly charged phosphorylated peptides during a single chromatographic run for data analysis with the database-searching algorithm. The approach described in this paper provides a convenient method to match the nascent tandem mass spectra of modified peptides to sequences in a protein database and thereby identify previously unknown sites of modification.

Algorithms↗
PubMed2004

Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring.

Detection and identification of pathogenic bacteria and their protein toxins play a crucial role in a proper response to natural or terrorist-caused outbreaks of infectious diseases. The recent availability of whole genome sequences of priority bacterial pathogens opens new diagnostic possibilities for identification of bacteria by retrieving their genomic or proteomic information. We describe a method for identification of bacteria based on tandem mass spectrometric (MS/MS) analysis of peptides derived from bacterial proteins. This method involves bacterial cell protein extraction, trypsin digestion, liquid chromatography MS/MS analysis of the resulting peptides, and a statistical scoring algorithm to rank MS/MS spectral matching results for bacterial identification. To facilitate spectral data searching, a proteome database was constructed by translating genomes of bacteria of interest with fully or partially determined sequences. In this work, a prototype database was constructed by the automated analysis of 87 publicly available, fully sequenced bacterial genomes with the GLIMMER gene finding software. MS/MS peptide spectral matching for peptide sequence assignment against this proteome database was done by SEQUEST. To gauge the relative significance of the SEQUEST-generated matching parameters for correct peptide assignment, discriminant function (DF) analysis of these parameters was applied and DF scores were used to calculate probabilities of correct MS/MS spectra assignment to peptide sequences in the database. The peptides with DF scores exceeding a threshold value determined by the probability of correct peptide assignment were accepted and matched to the bacterial proteomes represented in the database. Sequence filtering or removal of degenerate peptides matched with multiple bacteria was then performed to further improve identification. It is demonstrated that using a preset criterion with known distributions of discriminant function scores and probabilities of correct peptide sequence assignments, a test bacterium within the 87 database microorganisms can be unambiguously identified.

Algorithms↗
PubMed2004

Bacterial identification by protein mass mapping combined with an experimentally derived protein mass database.

A protein mass mapping approach using mass spectrometry (MS) combined with an experimentally derived protein mass database is presented for rapid and effective identification of bacterial species. A prototype mass database from the protein extracts of nine bacterial species has been created by off-line high-performance liquid chromatography (HPLC) matrix-assisted laser desorption/ionization (MALDI) MS, in which the microbiological parameter of bacterial growth time is considered. A numerical method using a statistical weight factor algorithm is devised for matching the protein masses of an unknown bacterial sample against the database. The sum of these weight factors produces a corresponding summed weight factor score for each bacterial species listed in the database, and the database species producing the highest score represents the identity of the respective unknown bacterium. The applicability and reliability of this protein mass mapping approach has been tested with seven bacterial species in a single-blind study by both direct MALDI MS and HPLC electrospray ionization MS methods, and identification results with 100% accuracy are obtained. Our studies have demonstrated that the protein mass database can be rapidly established and readily adopted with relatively less dependency on experimental factors. Furthermore, it is shown that a number of proteins can be detected using a protein sample amount equivalent to an extract of less than 1000 cells, demonstrating that this protein mass mapping approach can potentially be highly sensitive for rapid bacterial identification.

Bacteria↗
PubMedDate not supplied

A new rapid and effective chemistry space filter in recognizing a druglike database.

To develop a new chemistry space filter with high efficiency and accuracy, an analysis on distributions of as many as 50 structural and physicochemical properties was carried out on both druglike and nondruglike databases, viz. MACCS-II Drug Data Report (MDDR), Comprehensive Medicinal Chemistry (CMC), and Available Chemicals Directory (ACD). Based on the analysis results, a chemistry space filter was developed that can effectively discriminate a druglike database from a nondruglike database. The filter is composed of two descriptors: one is a molecular saturation related descriptor, and the other is associated with the proportion of heteroatoms in a molecule. Both are molecular size independent. Therefore, the profiles of a druglike database could be characterized as proper molecular saturation and proper percentage of heteroatoms, revealing direct indices for designing and optimizing combinatorial libraries. The application of the new filter on the Chinese Natural Product Database (CNPD) suggested that CNPD is, as expected, a potential druglike database, testifying that the new filter is reliable. Therefore, this newly developed chemistry space filter should be a potent tool for identifying druglike molecules, thus, it would have potential applications in the research of combinatorial library design and virtual high throughput screening using computational approaches for drug discovery.

Combinatorial Chemistry Techniques↗
PubMedDate not supplied

Virtual hydrocarbon and combinatorial databases for use with CAVEAT.

Three new virtual databases have been developed for use with the bond-orientation-based database searching program CAVEAT. These consist of a database of trisubstituted monocyclic hydrocarbons having ethyl, vinyl, and phenyl substituents; a database of unsubstituted bicyclic hydrocarbons; and a database of core structures from established combinatorial synthetic methods having hydrogen, ethyl, vinyl, and phenyl substituents at the readily varied positions. Each collection of molecules was subjected to a batch conformational search, minimization, and conversion to a vector database for use with CAVEAT.

Bridged Bicyclo Compounds↗
PubMed2002

Suitability of molecular descriptors for database mining. A comparative analysis.

Database mining methods rely on the molecular descriptors used to characterize a structural database. In the present investigation, five different types of descriptors (log P, UNITY fingerprints, ISIS keys, VolSurf, and GRIND) are applied to characterize various databases (n = 1007, 100, and 229) comprising drugs almost exclusively. The validity of the descriptors is comparatively analyzed via principal component analysis and its hierarchical variant, consensus principal component analysis. Both pharmacodynamic and pharmacokinetic aspects of database mining are treated. For pharmacodynamic aspects, clustering behavior achieved with the different descriptors is tested on the chemically homogeneous beta-blockers, benzodiazepines, and penicillins and on the chemically more diverse class I antiarrhythmics. The following ranking is observed: UNITY fingerprints > ISIS keys and GRIND > VolSurf > log P. Regarding information content, the CPCA superweight plot indicates similarity between fingerprints and ISIS keys as well as between VolSurf and log P, while GRIND differs from all the remaining descriptors. Solubility data and blood/brain barrier penetrating behavior serve as test cases for pharmacokinetic aspects. Comparison of the descriptors applied to these data reveals that VolSurf has the most realistic and consistent behavior, GRIND shows intermediate behavior, while UNITY fingerprints and ISIS keys are not well suited for pharmacokinetic profiling. From this comparative analysis, we conclude that VolSurf descriptors exhibit particular advantages in treating pharmacokinetic aspects; UNITY fingerprints, ISIS keys, and GRIND descriptors are of special value for tackling pharmacodynamic aspects of database mining. The parameter log P is of limited applicability in database mining because of rather poor reliability and lack of completeness of data.

Computing Methodologies↗
PubMed1997

Database diversity assessment: new ideas, concepts, and tools.

We present some new ideas for characterizing and comparing large chemical databases. The comparison of the contents of large databases is not trivial since it implies pairwise comparison of hundreds of thousands of compounds. We have developed methods for categorizing compounds into groups or series based on their ring-system content, using precalculated structure-based hashcodes. Two large databases can then be compared by simply comparing their hashcode tables. Furthermore, the number of distinct ring-system combinations can be used as an indicator of database diversity. We also present an independent technique for diversity assessment called the saturation diversity approach. This method is based on picking as many mutually dissimilar compounds as possible from a database or a subset thereof. We show that both methods yield similar results. Since the two methods measure very different properties, this probably says more about the properties of the databases studied than about the methods.

Benzene Derivatives↗
PubMed2002

Identification of protein functions from a molecular surface database, eF-site.

A bioinformatics method was developed to identify the protein surface around the functional site and to estimate the biochemical function, using a newly constructed molecular surface database named the eF-site (electrostatic surface of Functional site. Molecular surfaces of protein molecules were computed based on the atom coordinates, and the eF-site database was prepared by adding the physical properties on the constructed molecular surfaces. The electrostatic potential on each molecular surface was individually calculated solving the Poisson-Boltzmann equation numerically for the precise continuum model, and the hydrophobicity information of each residue was also included. The eF-site database is accessed by the internet (http://pi.protein.osaka-u.ac.jp/eF-site/). We have prepared four different databases, eF-site/antibody, eF-site/prosite, eF-site/P-site, and eF-site/ActiveSite, corresponding to the antigen binding sites of antibodies with the same orientations, the molecular surfaces for the individual motifs in PROSITE database, the phosphate binding sites, and the active site surfaces for the representatives of the individual protein family, respectively. An algorithm using the clique detection method as an applied graph theory was developed to search of the eF-site database, so as to recognize and discriminate the characteristic molecular surfaces of the proteins. The method identifies the active site having the similar function to those of the known proteins.

Antibodies↗
PubMed2001

Development of a database of functional assessment measures related to work disability.

The development of the Functional Assessment Measures Database is described. The database provides a method to organize and search for measures that are used to assess the functional abilities of people with medical impairments to determine work disability. The project identified 4,200 different measures that are used in the functional assessment of persons with disability across the life span, 812 of which are used to evaluate adults in terms of work disability. The database has 3,033 scales that are found in 633 measures. In the database, each measure is described and is linked to at least one functional assessment construct. The use of the database in the Social Security Administration Redesign Project is described. Other possible uses for the database are presented.

Databases, Factual↗
PubMed2003

Allergen databases.

Allergies represent a significant medical and industrial problem. Molecular and clinical data on allergens are growing exponentially and in this article we have reviewed nine specialized allergen databases and identified data sources related to protein allergens contained in general purpose molecular databases. An analysis of allergens contained in public databases indicates a high level of redundancy of entries and a relatively low coverage of allergens by individual databases. From this analysis we identify current database needs for allergy research and, in particular, highlight the need for a centralized reference allergen database.

Allergens↗