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PubMed1996

Web-based delivery and open-architecture database support in the ITreS Counselor Information System.

ITreS is a prototype information system for substance abuse counselors and clinicians. ITreS integrates client records, on-line screening and assessment instruments, and knowledge bases into a single integrated system. This paper discusses two aspects of the development of ITres: the use of the World Wide Web as a development and delivery environment and the use of an attributed translation-based data model to integrate data from various sources into a single client record.

Computer Communication Networks↗
PubMed2004

The integration of pharmacokinetics and pathogen susceptibility data in the design of rational dosing regimens.

The integration of pharmacokinetic and pathogen susceptibility data has had an increasing impact on the design of dosage regimens. Pathogen susceptibility is often described by the minimum inhibitory concentration (MIC). While the MIC is an indicator of drug potency, it does not predict pharmacologic response in vivo when drug concentrations are fluctuating. To this end, three pharmacokinetic/pharmacodynamic (PK/PD) parameters that result from indexing pharmacokinetics to MIC have proven quite useful. A number of experimental models of infection have determined the magnitude of each parameter, AUC/MIC, Cmax/MIC and %T>MIC, required for the optimal treatment of specific pathogens. These measurements have proven to be predictive of clinical outcomes as well. As a result, PK/PD breakpoints have been determined based on the likelihood that the pharmacokinetic profile of a given dose will achieve a target PK/PD parameter value. These breakpoints correlate well with treatment success or failure, particularly evident in infections conducive to microbiologic sampling such as otitis media. Therefore, PK/PD assessments have fostered a much more targeted approach to the treatment of patients with infectious diseases, and have proven useful in the selection of antimicrobial therapy and the development of novel dosing strategies.

Anti-Infective Agents↗
PubMedDate not supplied

Integrating query of relational and textual data in clinical databases: a case study.

OBJECTIVES: The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS). DESIGN: Using commodity software, which supports interactive, attribute-centric text and relational searches, the mart houses 2.8 million documents that span a five-year period and supports basic IR features such as Boolean searches, stemming, and proximity and fuzzy searching. MEASUREMENTS: Results are relevance-ranked using either "total documents per patient" or "report type weighting." RESULTS: Non-curated medical text has a significant degree of malformation with respect to spelling and punctuation, which creates difficulties for text indexing and searching. Presently, the IR facilities of RDBMS packages lack the features necessary to handle such malformed text adequately. CONCLUSION: A robust IR+RDBMS system can be developed, but it requires integrating RDBMSs with third-party IR software. RDBMS vendors need to make their IR offerings more accessible to non-programmers.

Abstracting and Indexing↗
PubMed2000

Integration of computer-assembled digital images and text data as evidence for the oncological record.

Digitally created visual images of pertinent patient data have been integrated with text information to formulate a visual evaluation and summary sheet (VESS) using computer processing. The VESS incorporates images of a patient's physical appearance, radiological images, pharmacokinetic graphs, and text information into a 1-page document of the patient's condition. Thus, computer processing of digital images and other information helps to refine patient data presentation, analysis, interpretation, and communication. This form of data management is especially valuable in oncological research, where clinical trials demand rapid, ongoing assessment of results and analysis of large amounts of data. The VESS is an effective mechanism for monitoring both the progress of individual patients and the endpoints of the overall clinical trial.

Diagnostic Imaging↗
PubMed1997

Demystifying mental health information needs through integrated definition (IDEF) activity and data modeling.

Today, the process of mental health assessments and treatment are difficult to describe and assimilate into other medical areas. Integrated patient summaries and treatment descriptions are poorly standardized. Any aggregate data analysis must rely on the very few standardized patient data points that may include some demographic information, diagnosis and codable procedures. This paper describes one of the first published attempts to use business process reengineering (BPR) Integrated Computer Assisted Manufacturing Definition (IDEF) activity and data modeling within a focused clinical setting. The clinician's desire to focus on patient care has been used to create both a current and an idealized activity and data model. Clinical patient information was used to build an analyzable database. This provides the potential to track a patient in data throughout a continuum of care. Conceptually, outcomes management is able to use clinical, rather than administrative or claims, data. These models were used to create a prototype for a computer-based patient record which would allow outcomes management. It was tested successfully as a proof of concept.

Ambulatory Care Information Systems↗
PubMedDate not supplied

Data quality assurance for thermophysical property databases--applications to the TRC SOURCE data system.

To a significant degree processes of database development are based upon human activities, which are susceptible to various errors. Propagation of errors in the processing leads to a decrease in the value of original data as well as that of any database products. Data quality is a critical issue that every database producer must handle as an inseparable part of the database management. Within the Thermodynamics Research Center (TRC), a systematic approach to implement database integrity rules was established through the use of modern database technology, statistical methods, and thermodynamic principles. The four major functions of the system--error prevention, database integrity enforcement, scientific data integrity protection, and database traceability--are detailed in this paper.

Journal Article↗
PubMed2025

The Effect of Alcohol Intake on Brain White Matter Microstructural Integrity: A New Causal Inference Framework for Incomplete Phenomic Data.

Although substance use, such as alcohol intake, is known to be associated with cognitive decline during aging, its direct influence on the central nervous system remains incompletely understood. In this study, we investigate the influence of alcohol intake frequency on reduction of brain white matter microstructural integrity in the fornix, a brain region considered a promising marker of age-related microstructural degeneration, using a large UK Biobank (UKB) cohort with extensive phenomic data reflecting a comprehensive lifestyle profile. Two major challenges arise: (a) potentially nonlinear confounding effects from phenomic variables and (b) a limited proportion of participants with complete phenomic data. To address these challenges, we develop a novel ensemble learning framework tailored for robust causal inference and introduce a data integration step to incorporate information from UKB participants with incomplete phenomic data, improving estimation efficiency. Our analysis reveals that daily alcohol intake may significantly reduce fractional anisotropy, a neuroimaging-derived measure of white matter structural integrity, in the fornix and increase systolic and diastolic blood pressure levels. Moreover, extensive numerical studies demonstrate the superiority of our method over competing approaches in terms of estimation bias, while outcome regression-based estimators may be preferred when minimizing mean squared error is prioritized. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.

Brain aging↗
PubMed1997

Community and self: concepts for rural physician integration and retention.

Low physician availability in rural areas of the United States is a long-standing issue. While most research has focused upon the locational decisions of physicians to understand the causes of the problem, a relatively new and neglected research focus is the retention of rural physicians. This paper takes the perspective that integration of physicians within rural communities is the basis for retention. It introduces concepts of self and community as a basis for understanding "domains" of rural physician integration. From data collected during in-depth qualitative research in rural Kentucky, a framework of integration domains is developed. The three domains of physician self, medical community, and community-at-large are elaborated with examples from the data. To further explain the relationships among the integration domains and their value, the findings are combined with three concepts from social theory. Social capital, core participation, and community reconstruction add dynamic and meaningful aspects to the context in which integration and retention occur, and they provide a conceptual basis to use when investigating or devising actions to facilitate integration.

Attitude to Health↗
PubMed1980

Data processing in microbiology: an integrated, simplified system.

A MUMPS based computer system is described for the processing of data in a microbiology laboratory. The system uses visual display units and mnemonic codes for data input. All functions are carried out within the department by the medical, technical, and clerical staff. While the system described is integrated with other user-systems in the hospital, it is readily adaptable, and portable to a stand-alone system.

Laboratories↗
PubMed1999

Agriculture sector resource and environmental policy analysis: an economic and biophysical approach.

Agricultural pollution of the environment is jointly determined by economic decisions driving land use, production practices, and stochastic biophysical processes associated with agricultural production, land and climate characteristics. It follows that environmental and economic statistics, traditionally collected independently of each other, offer little insight into non-point pollutant loadings. We argue that effective policy development would be facilitated by integrating environmental and economic data gathering, combined with simulation modelling linking economic and biophysical components. Integrated data collection links economics, land use, production methods and environmental loadings. An integrated economic/biophysical modelling framework facilitates policy analysis because monetary incentives to reduce pollution can be evaluated in the context of market costs and returns that influence land use and production activity. This allows prediction of environmental and economic outcomes from alternative policies to solve environmental problems. We highlight steps taken to merge economic and biophysical modelling for policy analysis within the Economic Research Service of the United States Department of Agriculture. An example analysis of a policy to reduce agricultural nitrogen pollution is presented, with the economic and environmental results illustrating the value of linked economic and biophysical analysis.

Agriculture↗
PubMed2005

Integration of a handheld based anaesthesia rounding system into an anaesthesia information management system.

BACKGROUND: At the University Hospital Giessen, an anesthesia information management system (AIMS) is used for online record keeping of perioperative patient care, but preoperative anaesthesia assessments were still being recorded on paper and subsequently entered into the AIMS. Personal digital assistants (PDAs) seem to be useful instruments to establish a seamless digital anesthesiological documentation. OBJECTIVES: We decided to implement a solution for direct integration of data gathered during the preoperative assessment into the existing data management infrastructure. Parallel to the development of the system, we surveyed the future users to match their wishes and needs as far as possible. SYSTEM DESCRIPTION: A C program embedding the preoperative AIMS' data fields was developed. Data alignment with the Hospital information system (HIS) is controlled by a Java desktop software. The anaesthesiologist completes the available fields at the patient's bedside following the same algorithm and integrity check as the PC version. STATUS REPORT: Overall, 68% of the surveyed physicians supported the implementation of the system. The PDA solution has been available since May 2002. Data replication into the handheld and integration of mobile collected data into the AIMS generally work without problems. The HIS interconnection software converts the PDA file into the AIMS format for further processing. DISCUSSION: The preoperative anaesthetic assessment is a standardised task well suitable for conversion to an electronic data storage medium. Changing from redundant data entry in the OR to direct electronic recording at the patient's bedside seems simply logical. Handheld computers are inexpensive, flexible gadgets to realize this.

Anesthesia↗
PubMed1998

Detection of multiple stimulus features forces a trade-off in the pyramidal cell network of a gymnotiform electric fish's electrosensory lateral line lobe.

Modification of an existing neural structure to support a second function will produce a trade-off between the two functions if they are in some way incompatible. The trade-off between two such sensory functions is modeled here in pyramidal neurons of the gymnotiform electric fish's medullar electrosensory lateral line lobe (ELL). These neurons detect two electric stimulus features produced when a nearby object interferes with the fish's autogenous electric field: (1) amplitude modulation across a cell's entire receptive field and (2) amplitude variation within a cell's receptive field produced by an object's edge. A model of sensory integration shows that detection of amplitude modulation and enhancement of spatial contrast involve an inherent mechanistic trade-off and that the severity of the trade-off depends on the particular algorithm of sensory integration. Electrophysiology data indicate that of the two algorithms for sensory integration modeled here for the gymnotiform fish Brachyhypopomus pinnicaudatus, the algorithm with the better trade-off function is used. Further, the intrinsic trade-off within single cells has been surmounted by the replication of ELL into multiple electrosensory map segments, each specialized to emphasize different sensory features.

Animals↗
PubMed1986

The effect of phenothiazines upon maintenance of membrane integrity in the cultured myocardial cell.

The cultured myocardial cell provides a defined model for examining factors which are responsible for maintaining cellular viability and sarcolemmal integrity. Our data indicates that the spontaneous loss of myocyte membrane integrity is a calcium-dependent process and thus provides a method for examining the mechanism through which calcium exerts this effect. Antimyosin antibody staining and propidium iodide uptake were used to quantitate membrane integrity. The integrity of the cell membrane was inversely related to the calcium concentration in the culture medium. This loss of membrane integrity was calmodulin-dependent as demonstrated by the following: phenothiazines (trifluoperazine greater than chlorpromazine greater than promethazine) and structurally dissimilar calmodulin-inhibitors prevented the formation of sarcolemmal defects at concentrations similar to those known to inhibit calmodulin; phenothiazines and calcium demonstrated a competitive interaction with respect to this effect on membrane integrity. Electron microscopy confirmed the integrity of the sarcolemma of the cells exposed to high phenothiazine concentrations although metabolic alterations occurred in these cells as evidenced by an increased membrane permeability to the low molecular weight probe propidium iodide, degenerative changes in the fine structure of the mitochondria, the accumulation of autophagic vacuoles in the cytoplasm and the loss of contractile ability. These findings indicate that calmodulin inhibitory compounds are capable of preserving the membrane integrity of cardiac myocytes, interfering with a calcium-dependent process that is associated with the spontaneous attrition of these cells in culture. Significant intracellular alterations appear at high doses of these agents even while the sarcolemma is free of gross defects.

Animals↗
PubMed2006

Quantification of protein half-lives in the budding yeast proteome.

A complete description of protein metabolism requires knowledge of the rates of protein production and destruction within cells. Using an epitope-tagged strain collection, we measured the half-life of >3,750 proteins in the yeast proteome after inhibition of translation. By integrating our data with previous measurements of protein and mRNA abundance and translation rate, we provide evidence that many proteins partition into one of two regimes for protein metabolism: one optimized for efficient production or a second optimized for regulatory efficiency. Incorporation of protein half-life information into a simple quantitative model for protein production improves our ability to predict steady-state protein abundance values. Analysis of a simple dynamic protein production model reveals a remarkable correlation between transcriptional regulation and protein half-life within some groups of coregulated genes, suggesting that cells coordinate these two processes to achieve uniform effects on protein abundances. Our experimental data and theoretical analysis underscore the importance of an integrative approach to the complex interplay between protein degradation, transcriptional regulation, and other determinants of protein metabolism.

Fungal Proteins↗
PubMed2004

A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles.

Flowers are icons in developmental studies of complex structures. The vast majority of 250,000 angiosperm plant species have flowers with a conserved organ plan bearing sepals, petals, stamens, and carpels in the center. The combinatorial model for the activity of the so-called ABC homeotic floral genes has guided extensive experimental studies in Arabidopsis thaliana and many other plant species. However, a mechanistic and dynamical explanation for the ABC model and prevalence among flowering plants is lacking. Here, we put forward a simple discrete model that postulates logical rules that formally summarize published ABC and non-ABC gene interaction data for Arabidopsis floral organ cell fate determination and integrates this data into a dynamic network model. This model shows that all possible initial conditions converge to few steady gene activity states that match gene expression profiles observed experimentally in primordial floral organ cells of wild-type and mutant plants. Therefore, the network proposed here provides a dynamical explanation for the ABC model and shows that precise signaling pathways are not required to restrain cell types to those found in Arabidopsis, but these are rather determined by the overall gene network dynamics. Furthermore, we performed robustness analyses that clearly show that the cell types recovered depend on the network architecture rather than on specific values of the model's gene interaction parameters. These results support the hypothesis that such a network constitutes a developmental module, and hence provide a possible explanation for the overall conservation of the ABC model and overall floral plan among angiosperms. In addition, we have been able to predict the effects of differences in network architecture between Arabidopsis and Petunia hybrida.

Arabidopsis↗
PubMed1984

A tutor programme in obstetrics and gynaecology.

A Tutor Programme was created in a third-year clerkship in obstetrics and gynaecology to remedy a student complaint of insufficient contact with teaching staff. Data obtained through the use of observational methodologies were integrated with data from questionnaires and student/teacher interviews to assess programme content, its contribution to student education, and the characteristics of student-teacher interactions. Teachers and students both expressed satisfaction at this opportunity to 'get to know each other'. A unique contribution of the programme was the discussion of a set of topics categorized as 'Medicine as a Career and Lifestyle', e.g. how to make career decisions, residency selection, etc.). These topics were not addressed elsewhere in the curriculum yet were of great importance to the students. The value of observational methods in comprehensive programme evaluation was reaffirmed.

Chicago↗
PubMedDate not supplied

Qualitative models and fuzzy systems: an integrated approach for learning from data.

This paper presents a method for the identification of the dynamics of non-linear systems by learning from data. The key idea which underlies our approach consists of the integration of qualitative modeling techniques with fuzzy logic systems. The resulting hybrid method exploits the a priori structural knowledge on the system to initialize a fuzzy inference procedure which determines, from the available experimental data, a functional approximation of the system dynamics that can be used as a reasonable predictor of the patient's future state. The major advantage which results from such an integrated framework lies in a significant improvement of both efficiency and robustness of identification methods based on fuzzy models which learn an input output relation from data. As a benchmark of our method, we have considered the problem of identifying the response to the insulin therapy from insulin-dependent diabetic patients: the results obtained are presented and discussed in the paper.

Algorithms↗
PubMed1995

Cryopreserved cord blood myeloid progenitor cells can serve as targets for retroviral-mediated gene transduction and gene-transduced progenitors can be cryopreserved and recovered.

To determine future possibilities for gene transfer, we evaluated whether myeloid progenitor cells from human umbilical cord blood (CB) could be frozen, thawed in viable form and transduced with a Neomycin resistance (NeoR) gene using retroviral vectors, and if fresh progenitor cells transduced with a Neo gene could be cryopreserved and recovered. Fresh and thawed cryopreserved nonadherent low-density T-lymphocyte depleted (NALT-) CB cells were assayed before and after gene transduction for colony formation in the presence of multiple growth factors in the absence and presence of G418. The results demonstrate that the NeoR gene could be introduced into thawed cryopreserved myeloid progenitor cells at an efficiency similar to that of fresh cells and that fresh cells transduced with the NeoR gene could be frozen in a cryopreserved state and recovered after thawing. Proviral integration, as assessed by PCR/Southern Analysis, confirmed the G418R colony data. Proviral integration was detected not only in primary G418R-colonies, but also in replated colonies in secondary dishes derived from G418R-multipotential progenitor cells (CFU-GEMM) suggesting stable integration of the transduced gene into early subsets of replatable progenitors. This information may be of use clinically.

3T3 Cells↗