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PubMed2001

History and trends in clinical information systems in the United States.

PURPOSE: To provide a synopsis of issues about clinical information systems for nurses not schooled in nursing informatics. ORGANIZING CONSTRUCT: The past, present, and future of clinical computing, including major factors resulting in the early hospital information systems (HIS) and decision support systems (DSS) in the United States, current advances and issues in managing clinical information, and future trends and issues. METHODS: Literature review and analysis. FINDINGS AND CONCLUSIONS: The first HIS and DSS were used in the late 1960s and were focused on applications for acute care. The change from fee-for-service to managed care required a change in the design of clinical information systems toward more patient-centered systems that span the care continuum, such as the computer-based patient record (CPR). Current difficulties with CPR systems include lack of systems integration, data standardization, and implementation. Increased advances in information and technology integration and increased use of the Internet for health information will shape the future of clinical information systems.

Decision Making, Computer-Assisted↗

PubMed2003

Autofocus algorithm for dispersion correction in optical coherence tomography.

Practical clinical optical coherence tomography (OCT) systems require automatic tools for identifying and correcting flaws in OCT images. One type of flaw is the loss of image detail owing to the dispersion of the medium, which in most cases is unknown. We present an autofocus algorithm for estimating the delay line and material dispersion from OCT reflectance data, integrating a previously presented dispersion compensation algorithm to correct the data. The algorithm is based on minimizing the Renyi entropy of the corrected axial-scan image, which is a contrast-enhancement criterion. This autofocus algorithm can be used in conjunction with a high-speed, digital-signal-processor-based OCT acquisition system for rapid image correction.

Algorithms↗

PubMed2000

An infrastructure for comparative genomics to functionally characterize genes and proteins.

Current genome projects are resulting in a flood of sequence data. The interpretation of these sequences is lagging, and optimized data analysis strategies need to be developed. Much can be learned from comparing different genomes, as genomes of distant organisms may still encode proteins with high sequence similarity. The order of genes (co linearity) in genomes may also be conserved to some extend. We have employed both these observations to create a multi-functional, computational analysis system (genomeSCOUT) which allows for rapid identification and functional characterization of genes and proteins through genome comparison. With a number of independent algorithms, information about different levels of protein homology (concerning e.g. paralogs, orthologs and clusters of orthologous groups, COGs) and gene order is collected and stored in several value added databases. These databases are then used for interactive comparison of genomes and subsequent analysis. The application is based on the well established data integration system SRS. This ensures (1) fast handling of large genomic data sets, (2) straightforward access to a multitude of biological databases, (3) unique linking functions between these databases, (4) highly efficient collection of information on genes and proteins, and 5. fully integrated and user friendly graphical representations of search results. This application can be used for projects as diverse as the correct annotation of genomes, the optimization of (micro) organisms for industrial production, or the identification of drug targets.

Computational Biology↗

PubMed1995

Integrated genetic map of human chromosome 2.

A framework genetic map of human chromosome 2 is described, integrating data from the Centre d'Etude du Polymorphisme Humain (CEPH) version 6 database, the CEPH chromosome 2 consortium database, the National Institute of Health (NIH)/CEPH Collaborative Mapping group and other laboratories. A comprehensive map is also presented, showing regional locations of a large number of additional loci. The framework map is used to identify an informative set of meiotic breakpoints within the CEPH families, and the utility of this information for mapping new markers is discussed. The degree of typing error within the data set is estimated, as are the sex-specific interference parameters. A location database for these genetic and additional cytogenetic data is constructed using algorithms which map genetic distances on to a physical scale, and the potential for this approach to aid the integration of genetic and physical data is examined.

Chromosome Mapping↗

PubMed1998

The unpackaging of routine in older women.

OBJECTIVE: A qualitative research design using grounded theory procedures and techniques was used to explore how routine changed in later adulthood for seven Caucasian, college-educated, middle-class women who were not employed and who were free of major functional impairments. METHOD: In-depth interviews, observations, an autobiography, and researcher-generated memos provided data. Data analysis involved concept formation, concept development, and conceptual modification and integration. Data collection and analysis were concurrent, iterative, reflective, and reflexive. RESULTS: Although the participants used routines to facilitate their well-being, they reported doing so to a lesser extent than when they had children living at home or when they worked. These participants unpackaged routines and molded them into increasingly flexible time-use strategies in response to age-related changes in their ecocultural niche, philosophy of life, and physical status. CONCLUSION: That the participants sought less obligation and more freedom as they aged may influence the way they respond to a health care practitioner's advocating for an increase in routine. Interventions with older women must be compatible with existing routines and family themes and directly linked to well-being.

Activities of Daily Living↗

PubMed1991

SESAM: a relational database for structure and sequence of macromolecules.

A system is described that provides ways of integrating data on protein structure, sequence, and survey results, with molecular graphics and molecular mechanics software. Its major component is the relational database SESAM, presently implemented under the commercial package SYBASE. By design, the database allows full integration--within the same data organization--of raw data on protein structure, sequence, ligands, and heterogroups, obtained from the Brookhaven Protein Databank, with pure sequence information available from other databanks such as SWISS-PROT. It contains in addition higher level descriptions of structural and topological properties, as well as survey results, obtained by executing specialized computer programs. Aside from the very useful attribute of closely combining structural and nonstructural information, other important features distinguish it from analogous systems developed elsewhere. It includes a molecular dictionary with complete description of geometric properties and energy parameters used in modeling and conformational energy calculations. Using this dictionary, structural data are validated by checking for localized inconsistencies in atomic coordinates, atomic symbols, chirality definitions, and flagging errors and incomplete entries. Because of both the dictionary and the validation procedures, SESAM can be readily interfaced with conventional molecular graphics and mechanics software packages, or with other specialized application programs. With the aid of appropriate interfaces, data access is sufficiently fast for SESAM to be interrogated interactively. Prototypes of user interfaces, as well as an interface with the molecular graphics package BRUGEL, are described and the power of the system is illustrated in applications such as homology-based protein modeling, computer-aided protein design, protein structure predictions, analysis of local structure motifs, and of relationships between protein sequence and structure.

Amino Acid Sequence↗

PubMed1996

Optimal normalization tests for shoulder muscle activation: an electromyographic study.

To accurately compare electromyographic data from different muscles and different subjects, it is necessary to normalize the integrated data obtained from each muscle. The purpose of this study was to identify the manual muscle testing positions that elicit maximal neural activation (integrated electromyography) of three rotator cuff muscles (supraspinatus, infraspinatus, and subscapularis) and five shoulder synergists (pectoralis major, latissimus dorsi, and anterior, middle, and posterior deltoids). The electromyographic activity of these eight muscles was examined in the nondominant shoulders of nine subjects. Indwelling wire electrodes (supraspinatus, infraspinatus, and subscapularis) and surface adhesive electrodes (pectoralis major, latissimus dorsi, and anterior, middle, and posterior deltoids) were placed. Each subject performed a series of 27 isometric contractions, and optimal tests (maximal neural activation) were identified for each muscle. Four tests were identified that resulted in the maximal neural activation of all eight shoulder muscles: 90 degrees of scapular elevation with -45 degrees of humeral rotation for the supraspinatus, anterior deltoid, and middle deltoid: external rotation at 90 degrees of scapular elevation and -45 degrees of humeral rotation for the infraspinatus and posterior deltoid: internal rotation at 90 degrees of scapular elevation and neutral humeral rotation for the subscapularis and latissimus dorsi: and internal rotation at 0 degree of elevation and neutral rotation for the pectoralis major. These results identify four standard testing positions that will provide reference values for normalization of maximal voluntary contraction for the eight muscles of the shoulder examined in this study. Standardization of these test positions offers normalization guidelines that can be used in future dynamic electromyography studies of the shoulder.

Adult↗

PubMed1996

Physician's profile: fact or fiction?

Many physicians are bombarded with endless reams of data regarding their performance. In the current climate, the data frequently have a more implicit financial viewpoint. In an effort to economize healthcare delivery, several factors are under investigation. Manpower, resource use, and product delivery are just a few examples of factors investigated. Managerial trends have led to the development of numerical data on how specific physicians treat particular disease processes on a dollar-and-cents basis. Physicians need a better understanding of these managerial data. Integrated healthcare delivery systems are developing in most regions of the country. External customers are using physician profile data for exclusion or inclusion criteria in contract negotiation. The purpose of this study was to illustrate a situation in which physician profile data are a more appropriate reflection of the integrated healthcare system's profile.

Aged↗

PubMed2002

Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML.

Ontologies are useful for organizing large numbers of concepts having complex relationships, such as the breadth of genetic and clinical knowledge in pharmacogenomics. But because ontologies change and knowledge evolves, it is time consuming to maintain stable mappings to external data sources that are in relational format. We propose a method for interfacing ontology models with data acquisition from external relational data sources. This method uses a declarative interface between the ontology and the data source, and this interface is modeled in the ontology and implemented using XML schema. Data is imported from the relational source into the ontology using XML, and data integrity is checked by validating the XML submission with an XML schema. We have implemented this approach in PharmGKB (http://www.pharmgkb.org/), a pharmacogenetics knowledge base. Our goals were to (1) import genetic sequence data, collected in relational format, into the pharmacogenetics ontology, and (2) automate the process of updating the links between the ontology and data acquisition when the ontology changes. We tested our approach by linking PharmGKB with data acquisition from a relational model of genetic sequence information. The ontology subsequently evolved, and we were able to rapidly update our interface with the external data and continue acquiring the data. Similar approaches may be helpful for integrating other heterogeneous information sources in order make the diversity of pharmacogenetics data amenable to computational analysis.

Databases, Factual↗

PubMed2002

Public health, GIS, and the internet.

Internet access and use of georeferenced public health information for GIS application will be an important and exciting development for the nation's Department of Health and Human Services and other health agencies in this new millennium. Technological progress toward public health geospatial data integration, analysis, and visualization of space-time events using the Web portends eventual robust use of GIS by public health and other sectors of the economy. Increasing Web resources from distributed spatial data portals and global geospatial libraries, and a growing suite of Web integration tools, will provide new opportunities to advance disease surveillance, control, and prevention, and insure public access and community empowerment in public health decision making. Emerging supercomputing, data mining, compression, and transmission technologies will play increasingly critical roles in national emergency, catastrophic planning and response, and risk management. Web-enabled public health GIS will be guided by Federal Geographic Data Committee spatial metadata, OpenGIS Web interoperability, and GML/XML geospatial Web content standards. Public health will become a responsive and integral part of the National Spatial Data Infrastructure.

Geographic Information Systems↗

PubMed2003

Regional myocardial function in healthy adults: assessment through tissue Doppler echocardiography.

OBJECTIVE: To characterize left ventricular regional myocardial function through tissue Doppler echocardiography in healthy adults and to assess the influence of aging in this function. METHODS: In 45 healthy volunteers divided in two groups (< 45 and > 45 years old) we assessed longitudinal and radial regional function (velocities, times intervals and velocity-time integrals). Data were compared in each group and between groups. RESULTS: Systolic function: a). longitudinal: higher velocities and integrals in lateral and inferior walls and in basal segments, with a trend to reduction of these parameters with aging; b). radial: higher basal velocities, no significant change with aging. Diastolic function: a). longitudinal: higher velocities in lateral and inferior walls and in basal segments. With aging e and e/a velocities and integrals decreased, a increased and older individuals showed lower percentage of segments with e/a >1; b). radial: aging was associated with lower e and higher a velocities. CONCLUSION: 1). Tissue Doppler echocardiography detects physiological differences between regional myocardial function of different ventricular segments, in velocities, times intervals and integrals, with physiological heterogeneity and asynchrony; 2). Many of these data are age dependent; 3). Our data contribute to define normal values, and may become useful when compared with data from populations with heart diseases.

Adult↗

PubMed1980

MEDIC: a language to process clinical data for elementary statistical purposes.

A new language has been developed which is helpful for handling data, already collected and stored on disk, with the aim of producing reports of clinical interest. For each clinical data bank a dictionary is generated, which contains all information needed to fully identify each medical item (e.g., name, type, attributes, indexed/single value). Now the user can write programs in a very easy way using the statements of the MEDIC language which give him the possibility of powerfully filtering data, making calculations and producing reports. Data integrity is achieved by the fact that users can only accede to data from the data bank and cannot alter data or modify them on disk. A special emphasis has been given, when designing MEDIC, to the possibility of counting data which satisfy certain sets of conditions, and to special output functions, as histograms. Programs written in MEDIC language are processed by MEDIC generator, are immediately executable, and have the possibility of tracing/debugging (the tracing option is chosen when program is starting execution). At execution time the user chooses in a very easy way the rules of scanning data bank, for example, the whole data bank and single ranges of records.

Computers↗

PubMed2026

Clinical applications of digital twin technology in In Vitro Fertilisation.

BACKGROUND: Digital twin technology, originating from aerospace and manufacturing industries, has emerged as a transformative tool in healthcare. In vitro fertilisation (IVF) faces persistent challenges including suboptimal embryo selection, unpredictable treatment outcomes, and limited personalisation of protocols. Despite advances in assisted reproductive technology, existing literature exhibits fragmentation: artificial intelligence applications in embryo selection, ovarian stimulation, and endometrial assessment have been developed independently without systematic integration into comprehensive treatment frameworks. Digital twin technology offers unprecedented opportunities to create virtual replicas of biological systems, enabling real-time monitoring, predictive modelling, and personalised treatment strategies. AIM: This narrative review aims to critically examine the current applications of digital twin technology in IVF, evaluate its potential benefits and limitations, synthesize existing evidence into an integrative conceptual model, and identify future directions for implementation in reproductive medicine. METHOD: A comprehensive narrative review was conducted using PubMed, Scopus, Web of Science, and IEEE Xplore databases. A narrative review approach was selected over systematic review to accommodate the heterogeneity of evidence types in this emerging field, including theoretical frameworks, simulation studies, and proof-of-concept implementations that would be excluded from systematic reviews. Search terms included "digital twin," "IVF," "in vitro fertilisation," "assisted reproductive technology," "embryo selection," and "predictive modelling." Studies published between 2015 and 2025 were included, focusing on original research articles, systematic reviews, and proof-of-concept studies describing digital twin applications in reproductive medicine. RESULTS: Digital twin technology in IVF demonstrates significant potential across multiple domains including embryo development simulation, ovarian response prediction, endometrial receptivity modelling, and personalised stimulation protocols. Current applications integrate artificial intelligence, machine learning algorithms, time-lapse imaging, and omics data to create comprehensive virtual models. Early evidence suggests improvements in embryo selection accuracy, ovarian response prediction, and treatment protocol optimization, though large-scale randomized controlled trials remain limited. Implementation challenges include data integration complexity, computational requirements, regulatory considerations, and validation requirements. CONCLUSION: Digital twin technology represents a paradigm shift in IVF practice, offering personalised, predictive, and precision medicine approaches. This review synthesizes existing evidence to propose an integrative conceptual model for digital twin implementation across the IVF treatment spectrum, identifies critical knowledge gaps, and establishes research priorities to advance clinical translation. Despite current limitations, continued advancement promises improved success rates and patient outcomes.

Humans↗

PubMed2002

Analyses of single-copy Arabidopsis T-DNA-transformed lines show that the presence of vector backbone sequences, short inverted repeats and DNA methylation is not sufficient or necessary for the induction of transgene silencing.

In genetically transformed plants, transgene silencing has been correlated with multiple and complex insertions of foreign DNA, e.g. T-DNA and vector backbone sequences. Occasionally, single-copy transgenes also suffer transgene silencing. We have compared integration patterns and T-DNA/plant DNA junctions in a collection of 37 single-copy T-DNA-transformed Arabidopsis lines, of which 13 displayed silencing. Vector sequences were found integrated in five lines, but only one of these displayed silencing. Truncated T-DNA copies, positioned in inverse orientation to an intact T-DNA copy, were discovered in three lines. The whole nptII gene with pnos promoter was present in the truncated copy of one such line in which heavy silencing has been observed. In the two other lines no silencing has been observed over five generations. Thus, vector sequences and short additional T-DNA sequences are not sufficient or necessary to induce transgene silencing. DNA methylation of selected restriction endonuclease sites could not be correlated with silencing. Our collection of T-DNA/plant DNA junctions has also been used to evaluate current models of T-DNA integration. Data for some of our lines are compatible with T-DNA integration in double-strand breaks, while for others initial invasion of plant DNA by the left or by the right T-DNA end seem important.

Arabidopsis↗

PubMedDate not supplied

Information architects: data by design.

HMOs and other network-based health plans are harnessing the power of information--building integrated data infrastructures to meet the needs of members, caregivers, and employers.

Community Networks↗

PubMed2003

S-adenosyl-L-methionine is able to reverse micronucleus formation induced by sodium arsenite and other cytoskeleton disrupting agents in cultured human cells.

Deficiencies of folic acid and methionine, two of the major components of the methyl metabolism, correlate with an increment of chromosome breaks and micronuclei. It has been proposed that these effects may arise from a decrease of S-adenosyl-L-methionine (SAM), the universal methyl donor. Some xenobiotics, such as arsenic, originate a reduction of SAM levels, and this is believed to alter some methylation processes (e.g. DNA methylation). The aim of the present work was to analyze the effects of exogenous SAM on the micronucleus (MN) frequency induced by sodium arsenite in human lymphocytes treated in vitro and to investigate whether these effects are related to DNA methylation. Results showed a reduction in the MN frequency in cultures treated with sodium arsenite and SAM compared to those treated with arsenite alone. To understand the mechanism by which SAM reduced the number of micronucleated cells, its effect on MN induced by other xenobiotics was also analyzed. Results showed that SAM did not have any effect on the increase in MN frequency caused by alkylating (mitomycin C or cisplatin) or demethylating agents (5-azacytidine, hydralazine, ethionine and procainamide), but it reduced the number of micronucleated cells in those treated with agents that inhibit microtubule polymerization (albendazole sulphoxide and colcemid). Since albendazole sulphoxide and colcemid inhibit microtubule polymerization, we decided to evaluate the effect of SAM on microtubule integrity. Data obtained from these evaluations showed that sodium arsenite, albendazole sulphoxide, and colcemid affect the integrity and organization of microtubules and that these effects are significantly reduced when cultures were treated at the same time with SAM. The data taken all together point out that the positive effects of SAM could be due to its ability to protect microtubules through an unknown mechanism.

Arsenites↗

PubMed2000

Information Management System for Site Remediation Efforts.

/ Environmental regulatory agencies are responsible for protecting human health and the environment in their constituencies. Their responsibilities include the identification, evaluation, and cleanup of contaminated sites. Leaking underground storage tanks (USTs) constitute a major source of subsurface and groundwater contamination. A significant portion of a regulatory body's efforts may be directed toward the management of UST-contaminated sites. In order to manage remedial sites effectively, vast quantities of information must be maintained, including analytical dataon chemical contaminants, remedial design features, and performance details. Currently, most regulatory agencies maintain such information manually. This makes it difficult to manage the data effectively. Some agencies have introduced automated record-keeping systems. However, the ad hoc approach in these endeavors makes it difficult to efficiently analyze, disseminate, and utilize the data. This paper identifies the information requirements for UST-contaminated site management at the Waste Cleanup Section of the Department of Environmental Resources Management in Dade County, Florida. It presents a viable design for an information management system to meet these requirements. The proposed solution is based on a back-end relational database management system with relevant tools for sophisticated data analysis and data mining. The database is designed with all tables in the third normal form to ensure data integrity, flexible access, and efficient query processing. In addition to all standard reports required by the agency, the system provides answers to ad hoc queries that are typically difficult to answer under the existing system. The database also serves as a repository of information for a decision support system to aid engineering design and risk analysis. The system may be integrated with a geographic information system for effective presentation and dissemination of spatial data.

Journal Article↗

PubMed2003

Genomic clocks and evolutionary timescales.

For decades, molecular clocks have helped to illuminate the evolutionary timescale of life, but now genomic data pose a challenge for time estimation methods. It is unclear how to integrate data from many genes, each potentially evolving under a different model of substitution and at a different rate. Current methods can be grouped by the way the data are handled (genes considered separately or combined into a 'supergene') and the way gene-specific rate models are applied (global versus local clock). There are advantages and disadvantages to each of these approaches, and the optimal method has not yet emerged. Fortunately, time estimates inferred using many genes or proteins have greater precision and appear to be robust to different approaches.

Amino Acid Substitution↗