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PubMed2004

Data quality aspects of a database for abdominal septic shock patients.

Since many years, medical researchers have investigated the mechanisms that may cause a septic shock. Despite many approaches that analyzed smaller parts of the relevant data or single variables, respectively, no larger database with all the possible relevant data existed. Our work was to bridge this gap. We built a large database for abdominal septic shock patients. While building it, we were confronted with many problems concerning the database realization and the data quality. Thus, we will demonstrate how we built our database and how we assured data quality. This is of interest for all medical or computer scientists who are concerned with building medical databases with retrospective data, e.g. for data mining purposes.

Abdomen↗

PubMed2005

Content-based image database system for epilepsy.

We have designed and implemented a human brain multi-modality database system with content-based image management, navigation and retrieval support for epilepsy. The system consists of several modules including a database backbone, brain structure identification and localization, segmentation, registration, visual feature extraction, clustering/classification and query modules. Our newly developed anatomical landmark localization and brain structure identification method facilitates navigation through an image data and extracts useful information for segmentation, registration and query modules. The database stores T1-, T2-weighted and FLAIR MRI and ictal/interictal SPECT modalities with associated clinical data. We confine the visual feature extractors within anatomical structures to support semantically rich content-based procedures. The proposed system serves as a research tool to evaluate a vast number of hypotheses regarding the condition such as resection of the hippocampus with a relatively small volume and high average signal intensity on FLAIR. Once the database is populated, using data mining tools, partially invisible correlations between different modalities of data, modeled in database schema, can be discovered. The design and implementation aspects of the proposed system are the main focus of this paper.

Brain↗

PubMed2004

Searching multiple databases for systematic reviews: added value or diminishing returns?

OBJECTIVE: To explore whether searching specialised bibliographic databases identified additional relevant papers to those located by a Medline search for a systematic review of exercise therapy. METHOD: Searches were performed in Medline, two further generalised medical databases (Embase, Cochrane Library) and four specialised databases (CancerLit, Cinahl, PsychInfo, SportDiscus) to identify controlled trials of exercise interventions for cancer patients. RESULTS: A total of 749 different publications were located through the search, of which 18 met inclusion criteria. Fifteen (83%) of these were identified through Medline and three (17%) from three individual specialised databases. A further seven studies meeting inclusion criteria were located through reference lists and contact with experts. CONCLUSION: In this example, searching Medline and additional specialised databases along with checking reference lists and contacting experts was the most effective means of ensuring that all relevant papers were included in the review. Searching Medline alone for systematic reviews of exercise or other unconventional therapies is likely to be inadequate.

Databases, Bibliographic↗

PubMed2004

Lessons learned from the data analysis of the second harvest (1998-2001) of the Society of Thoracic Surgeons (STS) Congenital Heart Surgery Database.

OBJECTIVE: The analysis of the second harvest of the STS Congenital Heart Surgery Database produced meaningful outcome data and several critical lessons relevant to congenital heart surgery outcomes analysis worldwide. METHODS: This data harvest represents the first STS multi-institutional experience with software utilizing the nomenclature and database requirements adopted by the STS and EACTS (April 2000 Annals of Thoracic Surgery). Members of the STS Congenital Heart Committee analyzed the STS data. RESULTS: This STS harvest includes data from 16 centers (12787 cases, 2881 neonates, 4124 infants). In 2002, the EACTS reported similar outcome data utilizing the same database definitions (41 centers, 12736 cases, 2245 neonates, 4195 infants). Lessons from the analysis include: (1) Death must be clearly defined. (2) The Primary Procedure in a given operation must be documented. (3) Inclusionary and exclusionary criteria for all diagnoses and procedures must be agreed upon. (4) Missing data values remain an issue for the database. (5) Generic terms in the nomenclature lists, that is terms ending in Not Otherwise Specified (NOS), are redundant and decrease the clarity of data analysis. (6) Methodology needs to be developed and implemented to assure and verify data completeness and data accuracy. 'Operative Mortality' and 'Mortality Assigned to this Operation' were defined by the STS and EACTS; these definitions were not utilized uniformly. 'Thirty Day Mortality' was problematic because some centers did not track mortality after hospital discharge. Only 'Mortality Prior to Discharge' was consistently reported. Designation of Primary Procedure for a given operation determines its location for analysis. Until Complexity Scores lead to automated methodology for choosing the Primary Procedure, the surgeon must designate the Primary Procedure. Inclusionary and exclusionary criteria for all diagnoses and procedures have been developed in an effort to define acceptable concomitant diagnoses and procedures for each analysis. Improvements in data completeness can be achieved using a variety of techniques including developing more functional techniques of data entry at individual institutions and software improvements. Future versions of the STS Congenital Database will request that the coding of diagnoses and procedures avoid the terms ending in NOS. CONCLUSIONS: Lessons from this data harvest should improve congenital heart surgery outcome analysis.

Databases, Factual↗

PubMed2004

Reference ballistic imaging database performance.

Ballistic imaging databases allow law enforcement to link recovered cartridge cases to other crime scenes and to firearms. The success of these databases has led many to propose that all firearms in circulation be entered into a reference ballistic image database (RBID). To assess the performance of an RBID, we fired 4200 cartridge cases from 600 9mm Para Sig Sauer model P226 series pistols. Each pistol fired two Remington cartridges, one of which was imaged in the RBID, and five additional cartridges, consisting of Federal, Speer, Winchester, Wolf, and CCI brands. Randomly selected samples from the second series of Remington cartridge cases and from the five additional brands were then correlated against the RBID. Of the 32 cartridges of the same make correlated against the RBID, 72% ranked in the top 10 positions. Likewise, of the 160 cartridges of the five different brands correlated against the database, 21% ranked in the top 10 positions. Generally, the ranking position increased as the size of the RBID increased. We obtained similar results when we expanded the RBID to include firearms with the same class characteristics for breech face marks, firing pin impressions, and extractor marks. The results of our six queries against the RBID indicate that a reference ballistics image database of new guns is currently fraught with too many difficulties to be an effective and efficient law enforcement tool.

Databases, Factual↗

PubMed2004

Forensic DNA databases.

Genetic databases have been created in several countries: the United Kingdom was the first European country to have, in 1995, a DNA database. Subsequently, the Netherlands and Austria (1997), Germany (1998), Finland and Norway (1999) and many others have introduced or are preparing databases. Different national legal systems have conditioned the DNA databases and so there is a great heterogeneity between countries. The criteria for an entry of a DNA profile, the criteria for a removal, the criteria for a search, etc., can lead to very distinct databases.

DNA Fingerprinting↗

PubMed2004

Protecting patient privacy by quantifiable control of disclosures in disseminated databases.

One of the fundamental rights of patients is to have their privacy protected by health care organizations, so that information that can be used to identify a particular individual is not used to reveal sensitive patient data such as diagnoses, reasons for ordering tests, test results, etc. A common practice is to remove sensitive data from databases that are disseminated to the public, but this can make the disseminated database useless for important public health purposes. If the degree of anonymity of a disseminated data set could be measured, it would be possible to design algorithms that can assure that the desired level of confidentiality is achieved. Privacy protection in disseminated databases can be facilitated by the use of special ambiguation algorithms. Most of these algorithms are aimed at making one individual indistinguishable from one or more of his peers. However, even in databases considered "anonymous", it may still be possible to obtain sensitive information about some individuals or groups of individuals with the use of pattern recognition algorithms. In this article, we study the problem of determining the degree of ambiguation in disseminated databases and discuss its implications in the development and testing of "anonymization" algorithms.

Algorithms↗

PubMed2006

A randomized database study in general practice yielded quality data but patient recruitment in routine consultation was not practical.

OBJECTIVE: To assess patient recruitment and quality of data in a randomized database study. STUDY DESIGN AND SETTING: A randomized database study was conducted in the Integrated Primary Care Information (IPCI) general practice research database. Software was built to allow for automated patient identification and recruitment, and randomization. As an application, we compared gastrointestinal tolerability in persons treated with diclofenac and celecoxib for osteoarthritis. The outcomes were assessed in the IPCI database. To assess accuracy of exposure and outcome, we also collected information by self-administrated patient questionnaires. For all eligible subjects, we assessed the main reason for noninclusion. Physicians were interviewed to evaluate the study and to identify the major obstacles. RESULTS: Forty-two general practice physicians collaborated with the study and 7,127 potential study subjects were identified. Among these subjects, 170 were eligible for recruitment and 20 (11.8%) were randomized. Of the eligible patients, 96 (56.5%) were not recruited because the physician was too busy or the patient was treated by another healthcare provider and 54 (31.8%) were not recruited because of exclusion criteria. CONCLUSION: Concordance between questionnaires and IPCI data and the outcome was good (kappa=0.7; SD=0.14). The physicians reported that recruitment during routine visits was too time-consuming, in particular because of the need for informed consent. Although a randomized database study is feasible, patient recruitment during routine consultations should be avoided.

Adult↗

PubMedDate not supplied

FEMME database: topologic and geometric information of macromolecules.

FEMME (Feature Extraction in a Multi-resolution Macromolecular Environment: http://www.biocomp.cnb.uam.es/FEMME/) database version 1.0 is a new bioinformatics data resource that collects topologic and geometric information obtained from macromolecular structures solved by three-dimensional electron microscopy (3D-EM). Although the FEMME database is focused on medium resolution data, the methodology employed (based on the so-called alpha-shape theory) is applicable to atomic resolution data as well. The alpha-shape representation allows the automatic extraction of structural features from 3D-EM volumes and their subsequent characterisation. FEMME is being populated with 3D-EM data stored in the electron microscopy database EMD-DB (http://www.ebi.ac.uk/msd/). However, and since the number of entries in EMD-DB is still relatively small, FEMME is also being populated in this initial phase with structural data from PDB and PQS databases (http://www.rcsb.org/pdb/ and pqs.ebi.ac.uk/, respectively) whose resolution has been lowered accordingly. Each FEMME entry contains macromolecular geometry and topology information with a detailed description of its structural features. Moreover, FEMME data have facilitated the study and development of a method to retrieve macromolecular structures by their structural content based on the combined use of spin images and neural networks with encouraging results. Therefore, the FEMME database constitutes a powerful tool that provides a uniform and automatic way of analysing volumes coming from 3D-EM that will hopefully help the scientific community to perform wide structural comparisons.

Computational Biology↗

PubMedDate not supplied

Web portal to an image database for high-resolution three-dimensional reconstruction.

The exponential increase of image data in high-resolution reconstructions by electron cryomicroscopy (cryoEM) has posed a need for efficient data management solutions in addition to powerful data processing procedures. Although relational databases and web portals are commonly used to manage sequences and structures in biological research, their application in cryoEM has been limited due to the complexity in accomplishing the dual tasks of interacting with proprietary software and simultaneously providing data access to users without database knowledge. Here, we report our results in developing web portal to SQL image databases used by the Image Management and Icosahedral Reconstruction System (IMIRS) to manage cryoEM images for subnanometer-resolution reconstructions. Fundamental issues related to the design and deployment of web portals to image databases are described. A web browser-based user interface was designed to accomplish data reporting and other database-related services, including user authentication, data entry, graph-based data mining, and various query and reporting tasks with interactive image manipulation capabilities. With an integrated web portal, IMIRS represents the first cryoEM application that incorporates both web-based data reporting tools and a complete set of data processing modules. Our examples should thus provide general guidelines applicable to other cryoEM technology development efforts.

Cryoelectron Microscopy↗

PubMed2005

Data-partitioning using the Hilbert space filling curves: effect on the speed of convergence of Fuzzy ARTMAP for large database problems.

The Fuzzy ARTMAP algorithm has been proven to be one of the premier neural network architectures for classification problems. One of the properties of Fuzzy ARTMAP, which can be both an asset and a liability, is its capacity to produce new nodes (templates) on demand to represent classification categories. This property allows Fuzzy ARTMAP to automatically adapt to the database without having to a priori specify its network size. On the other hand, it has the undesirable side effect that large databases might produce a large network size (node proliferation) that can dramatically slow down the training speed of the algorithm. To address the slow convergence speed of Fuzzy ARTMAP for large database problems, we propose the use of space-filling curves, specifically the Hilbert space-filling curves (HSFC). Hilbert space-filling curves allow us to divide the problem into smaller sub-problems, each focusing on a smaller than the original dataset. For learning each partition of data, a different Fuzzy ARTMAP network is used. Through this divide-and-conquer approach we are avoiding the node proliferation problem, and consequently we speedup Fuzzy ARTMAP's training. Results have been produced for a two-class, 16-dimensional Gaussian data, and on the Forest database, available at the UCI repository. Our results indicate that the Hilbert space-filling curve approach reduces the time that it takes to train Fuzzy ARTMAP without affecting the generalization performance attained by Fuzzy ARTMAP trained on the original large dataset. Given that the resulting smaller datasets that the HSFC approach produces can independently be learned by different Fuzzy ARTMAP networks, we have also implemented and tested a parallel implementation of this approach on a Beowulf cluster of workstations that further speeds up Fuzzy ARTMAP's convergence to a solution for large database problems.

Algorithms↗

PubMed2005

A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy.

A comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain was developed based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. By using both manual tracing and an atlas-based semi-automatic segmentation approach, T2-weighted magnetic resonance microscopy images of 10 adult male formalin-fixed, excised C57BL/6J mouse brains were segmented into 20 anatomical structures. These structures included the neocortex, hippocampus, amygdala, olfactory bulbs, basal forebrain and septum, caudate-putamen, globus pallidus, thalamus, hypothalamus, central gray, superior colliculi, inferior colliculi, the rest of midbrain, cerebellum, brainstem, corpus callosum/external capsule, internal capsule, anterior commissure, fimbria, and ventricles. The segmentation data were formatted and stored into a database containing three different atlas types: 10 single-specimen brain atlases, an average brain atlas and a probabilistic atlas. Additionally, quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, were computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities.

Anatomy, Artistic↗

PubMed2006

Distinguishing gorilla mitochondrial sequences from nuclear integrations and PCR recombinants: guidelines for their diagnosis in complex sequence databases.

Nuclear integrations of mitochondrial DNA (Numts) are widespread in many taxa and if left undetected can confound phylogeny interpretation and bias estimates of mitochondrial DNA (mtDNA) diversity. This is particularly true in gorillas, where recent studies suggest multiple integrations of the first hypervariable (HV1) domain of the mitochondrial control region. Problems can also arise through the inadvertent incorporation of artifacts produced by in vitro recombination between sequence types during polymerase chain reaction amplification. This issue has attracted little attention yet could potentially exacerbate errors in databases already contaminated by Numts. Using a set of existing diagnostic tools, this study set out to systematically inventory Numts and PCR recombinants in a gorilla HV1 sequence database and address the degree to which existing public databases are contaminated. Phylogenetic analysis revealed three distinct gorilla HV1 Numt groups (I, II, and III) that could be readily differentiated from mtDNA sequences by Numt-specific diagnostic sites and sequence-based motifs. Several instances of genuine recombination were also identified by a suite of detection methods. The location of putative breakpoints was identified by eye and by likelihood analysis. Findings from this study reveal widespread nuclear contamination of gorilla HV1 GenBank databases and underline the importance of recognizing not only Numts but also PCR recombinant artifacts as potential sources of data contamination. Guidelines for the routine identification of Numts and in vitro recombinants are presented and should prove useful in the detection of similar artifacts in other species mtDNA databases.

Animals↗

PubMed2000

Quality assessment and lipid management: considerations for computer databases for tracking patients.

Improving the quality of lipid management requires an objective assessment of current practice and the ability to monitor whether quality is improved by implementing changes in practice. In a competitive healthcare environment, documentation of quality of care and patient outcomes may be important in securing contracts. It would be almost impossible to perform a meaningful clinical-outcome analysis in a timely fashion without the support of a computerized database. However, evaluating, selecting, and implementing computerized databases can be a daunting task. Before the purchase of a database, the following steps should be performed: (1) consider and prioritize the goals for the computerized database; (2) audit charts to determine whether the existing chart format meets the current guidelines for reimbursement and medical-legal standards; (3) revise the paper chart to improve fulfillment of the goals from step 1; (4) consider the specific clinical environment, including the skill level of personnel using the system, how user-friendly the system is, whether the system is multifunctional, and the costs associated with the software and implementation. We have evaluated 3 types of computerized databases and report their strengths and weaknesses; we also briefly discuss the electronic medical record.

Continuity of Patient Care↗

PubMed1997

Establishing and using a local/regional cardiac surgery database.

BACKGROUND: In 1993, the Minnesota Society of Thoracic Surgeons and the Minnesota Cardiac Surgery Database were organized in response to a third-party payer demand for data about practice protocols and patient outcomes. It has matured to an active organization of 46 cardiothoracic surgeons, 14 institutions, and more than 7,000 patients who have undergone coronary artery bypass grafting. METHODS: Data are validated for completeness and accuracy through a statewide auditing process. They are coded by hospital, analyzed using the standard Society of Thoracic Surgeons National Cardiac Surgery Database format and definitions, and reviewed quarterly in a continuous quality improvement process. RESULTS: Through data review and exchange site visits, variations in practice protocols and outcomes have been identified. For example, our statewide data review and continuous quality improvement process identified prolonged ventilation (more than 24 hours) as one variation. Multidisciplinary teams were defined, and statewide exchange site visits led by cardiovascular surgeons were implemented. An example of the improvement in the accuracy and completeness of the data used to study procedure outcomes is represented by the improved reporting of ejection fraction values that has resulted from this process. CONCLUSIONS: Using the standardized Society of Thoracic Surgeons National Cardiac Surgery Database and the Minnesota Society of Thoracic Surgeons organizational structure to establish a high-quality database will allow for statewide peer review, exchange of practice guidelines, and promotion of standardization, which eventually can improve outcomes and reduce costs. This organization or model can be replicated at any local, state, or regional level. Thoracic surgeons faced with similar challenges for public disclosure of surgical results can learn much from the successful development of the Minnesota Cardiac Surgery Database.

Clinical Protocols↗

PubMed1997

Using information from databases to improve clinical practice: lessons learned under fire.

BACKGROUND: Information derived from a clinical database can be used to produce reports with valid, applicable data, to assemble outcomes data for purposes of marketing or practice survival, and to improve and optimize patient care. METHODS: In response to lay-press figures suggesting a high risk-adjusted mortality at St. Peter's Hospital (Albany, NY), a multidisciplinary group at the hospital undertook a collaborative review of information from our clinical database to identify any patterns that could explain this disturbing summary statistic. RESULTS: This review showed that for the vast majority (> 95%) of cases mortality was on a par with or lower than the statewide average. The elevated mortality was confined to a small and specific subset of high-risk patients. Once identified, attention was focused on this group of patients, and both cardiologists and surgeons discussed practice changes based on information from the clinical database. Since program changes were instituted in 1993, mortality has decreased in both high-risk and all other patients. Overall mortality for coronary artery bypass graft patients has decreased from 4.5% to about 1.5%. CONCLUSIONS: Use of a database to extract a single number reflecting patient-care performance, eg, short-term mortality, can conceal more information than it conveys. Only in-depth analysis of the information in the database can identify areas for improvement in clinical practice.

Coronary Artery Bypass↗

PubMed2000

Congenital Heart Surgery Nomenclature and Database Project: overview and minimum dataset.

The International Congenital Heart Surgery Nomenclature and Database Project was organized for the purpose of standardizing nomenclature and reporting strategies that would establish the foundations for an international database. Worldwide representatives met for a series of conferences, at which time, issues of nomenclature were discussed and debated. Authors were chosen to review the various congenital heart diagnoses and reflect the mediated debate that followed. Manuscripts were prepared that reviewed the appropriate extant nomenclature, made recommendations for an inclusive rather than an exclusive method of reporting, and determined a hierarchical database scheme that would allow several levels of reporting based on the data input. This manuscript outlines two datasets for an international congenital heart surgery database, a minimum dataset and a comprehensive dataset. The comprehensive dataset includes all the imagined variables, in a hierarchical scheme, which are detailed enough to generate risk stratification analyses. The minimum dataset will include data points that would create an essential dataset, which would be mandatory for data sharing and would lend itself to basic interpretation of trends. The minimum dataset has four drop-down menus for short lists of: (1) noncardiac abnormalities/general preoperative risk factors, (2) diagnoses, (3) procedures, and (4) complications, from which clinicians can choose for entry into the minimum dataset. There was universal agreement for these datasets and short lists by the assembled members of the Society of Thoracic Surgeons-Congenital Heart Surgery Database Committee and representatives from the European Association for Cardiothoracic Surgery. The datasets and short lists were also unanimously approved by the Congenital Heart Surgery Committee of The European Association for Cardiothoracic Surgery and adopted by the European Congenital Heart Surgeons Foundation.

Databases, Factual↗

PubMed1999

History, implementation, and current status of the National Spinal Cord Injury Database.

OBJECTIVE: To summarize a 25-year history of the Model Spinal Cord Injury Program and the coexistent National Spinal Cord Injury Database and provide the status of the Database with a discussion of the strengths and weaknesses. DESIGN: Inception cohort. SETTING: Model spinal cord injury systems throughout the United States. RESULTS: As of September 1998, the National Spinal Cord Injury Database included abbreviated registry records on 6,085 new patients, more complete initial injury and hospitalization records on 18,969 new patients, and 78,627 annual follow up records on those persons. Although stability and continuity of the Database has been a priority since it was started, some changes were needed to meet the changes in health care, health care policy, and new technology. CONCLUSION: This large database can now provide a wealth of information about short- and long-term outcomes, provide data on which future health care policies can be evaluated, and act as a source for answers to future research questions.

Cohort Studies↗