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PubMed2006

Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.

Identification of transcriptional regulatory sites plays an important role in the investigation of gene regulation. For this propose, we designed and implemented a data warehouse to integrate multiple heterogeneous biological data sources with data types such as text-file, XML, image, MySQL database model, and Oracle database model. The utility of the biological data warehouse in predicting transcriptional regulatory sites of coregulated genes was explored using a synexpression group derived from a microarray study. Both of the binding sites of known transcription factors and predicted over-represented (OR) oligonucleotides were demonstrated for the gene group. The potential biological roles of both known nucleotides and one OR nucleotide were demonstrated using bioassays. Therefore, the results from the wet-lab experiments reinforce the power and utility of the data warehouse as an approach to the genome-wide search for important transcription regulatory elements that are the key to many complex biological systems.

Algorithms↗
PubMed1988

The global impact of the Chernobyl reactor accident.

Radioactive material was deposited throughout the Northern Hemisphere as a result of the accident at the Chernobyl Nuclear Power Station on 26 April 1986. On the basis of a large amount of environmental data and new integrated dose assessment and risk models, the collective dose commitment to the approximately 3 billion inhabitants is calculated to be 930,000 person-gray, with 97% in the western Soviet Union and Europe. The best estimates for the lifetime expectation of fatal radiogenic cancer would increase the risk from 0 to 0.02% in Europe and 0 to 0.003% in the Northern Hemisphere. By means of an integration of the environmental data, it is estimated that approximately 100 petabecquerels of cesium-137 (1 PBq = 10(15) Bq) were released during and subsequent to the accident.

Accidents↗
PubMed1996

Analysis of necropsy request behaviour of clinicians.

AIM: To develop a necropsy related audit system to record accurate information in relation to necropsy requests, necropsy rates and coronial referrals. METHODS: A simple audit form was used to record detailed necropsy related data via an integrated questionnaire design and data entry system based on available optical image scanning technology. The system recorded the numbers and locations of deaths, referrals to the coroner, clinical necropsy requests, hospital and medicolegal necropsies, the grade of clinician involved in these processes, and the identity of the consultant in charge of the case. The overall, hospital and medicolegal necropsy rates were calculated by individual consultant, specialty and for the whole hospital. Necropsy request rates and coronial referral rates were also calculated and these data were related to the grade of clinician. All data were available on a monthly or an accumulative basis. RESULTS: Of 1398 deaths, 534 (38%) were discussed with the local coroner's office and 167 of these were accepted for further investigation. House officers and senior house officers referred over 80% of all cases, whereas consultants referred only 2%. There were no significant differences in case acceptance rates by grade of clinician. Clinicians made 307 hospital necropsy requests (overall hospital necropsy request rate 22%). House officers made 65% of all necropsy requests. Consultant necropsy requests represented 13% of all requests. There were no significant differences in necropsy request success rates by grade of clinician. CONCLUSIONS: The referral of cases to coroners and clinical necropsy requests are still being inappropriately delegated to the most junior clinicians. This study illustrates the type of useful information which can be produced for individual clinicians, specialty audit groups and pathology departments using a simple necropsy related audit system.

Autopsy↗
PubMed1998

The experience of registered nurses nursing in the general adult intensive care unit. A phenomenological qualitative research study.

In this article a phenomenological qualitative research study is discussed. More attention will be given to the methodology of the research. The objectives of the study are two-fold: firstly to explore and describe the experience of registered nurses nursing in the adult intensive care unit (this is the first phase of the research) and to describe guidelines based on the information obtained in the first phase to support the nurses in the form of a support programme in the second phase. The units of research are the registered nurses in the intensive care unit. The characteristics of the unit of research led to the emergence of a qualitative phenomenological research design of an explorative, descriptive and contextual nature. In the discussion of research methodology attention will be given to phase one: data gathering (ethical considerations and informed consent; purposive selection, phenomenological interviews and field notes); data analysis (Tesch's method of data analysis, methods to ensure trustworthiness, organisation of raw data and integration of findings supported by literature. Five themes were identified through the data analysis: impaired communication with management; discrimination: white on black racism; lack of fair, competitive remuneration and disregard for professional worth; non-conducive physical environment, and stressful working environment. Phase two: Guidelines were described to support the registered nurses in the intensive care unit based on the information obtained in phase one of the research.

Adult↗
PubMed1994

Pulmonary function testing in the critically ill neonate, Part III: Case studies.

Accurate monitoring of respiratory status is of vital importance for the bedside nurse caring for the critically ill neonate. Pulmonary function testing can be utilized to effectively diagnose and quantitate lung disease in infants. Data obtained can be integrated into the nursing assessment and facilitate appropriate nursing interventions. The case studies provided in Part III of this series illustrate the utility of such testing in neonates with a range of illnesses and different diagnostic and therapeutic dilemmas. Case study one is an infant with chronic lung disease complicated by bronchospasm, case study two is an infant with bronchomalacia, and case study three demonstrates fine tuning of the ventilator in an infant with respiratory distress syndrome. Every study describes the usefulness of pulmonary function testing on a specific patient, each with different pulmonary pathology. These case studies, and the discussion in parts I and II of this series, illustrate the value of integrating pulmonary function data with ongoing clinical assessment to optimize the care of the sick or convalescing neonate. Tests ordered on a routine and/or as-needed basis will provide detailed information on the infant's pulmonary status that may be readily available at the infant's bedside. The neonatal nurse's involvement in requesting, performing, and interpreting these tests may enhance the treatment of the infant in intensive care.

Bronchial Spasm↗
PubMed2026

Integrating multi-omics technologies to decipher microbiome functions.

Multi-omics approaches have revolutionized our understanding of microbial communities by enabling simultaneous interrogation of genomic, transcriptomic, proteomic, and metabolomic data. The systematic integration and analysis of these deep datasets help decipher the functional roles of microbiomes, providing critical insights into microbial activities, interactions, and dynamics across diverse environments. Biological complexity makes multi-omics analysis of a single, isolated organism demanding but highly informative, yet this complexity increases further when samples comprise hundreds to thousands of individual species. As microbiome research continues to expand into clinical, environmental, and engineered systems, standardized workflows, benchmarked datasets, and community-driven initiatives are essential to ensure reproducibility, standardization and interpretability. Establishing and disseminating best practices for experimental design, data processing, and integrative analyses will be critical for maximizing comparability and scientific rigor across studies. This perspective highlights recent advances in multi-omics microbiome research, outlines key obstacles in data integration and metadata harmonization, and proposes a collaborative roadmap for scalable, FAIR-compliant multi-omics investigations and potentially disruptive Artificial Intelligence (AI) advances comparable to those of AlphaFold in the field of microbiome science.

Multiomics↗
PubMed2005

Proton magnetic resonance spectroscopic imaging integrated into image-guided surgery: correlation to standard magnetic resonance imaging and tumor cell density.

OBJECTIVE: In this study, we attempted to improve the delineation of the infiltration zone in gliomas using proton magnetic resonance spectroscopic imaging (1H MRSI). In conventional magnetic resonance imaging (MRI), the boundaries of gliomas sometimes are underestimated. 1H MRSI is a noninvasive tool that can be used to investigate the spatial distribution of metabolic changes in brain lesions. The purpose was to correlate tumor cell density from histopathological specimens with metabolic levels and the coregistered metabolic maps. METHODS: We developed a method to integrate spectroscopic data depicted as metabolic maps of biochemically pathological tissue into frameless stereotaxy. In seven patients harboring gliomas, we performed 1H MRSI with high spatial resolution and evaluated the spectral data. An algorithm was developed for user-independent calculation of pathological voxels and for visualization as metabolic maps. These maps were integrated into a three-dimensional MRI data set used for frameless stereotaxy. Stereotactic biopsies were taken from three different areas in and around the tumor involving the maximum pathological change, the border zone, and an area from outside the spectroscopically suspicious area. These specimens were correlated to the exact voxel positions in the stereotactic image space and evaluated histopathologically. RESULTS: In all cases, the implementation of the metabolic maps into frameless stereotaxy was successful, and stereotactic biopsies were acquired by use of the spectral data. A relation could be demonstrated between the metabolic changes and tumor cell density ranging from 60 to 100% in the maximum pathological area to 5 to 15% in the border zone. Interestingly, the tumor areas defined by the metabolic maps and histopathologically confirmed by biopsy exceeded the T2-weighted signal change in all cases, ranging from 6 to 32% in the examined volume. CONCLUSION: Our preliminary data suggest that 1H MRSI may be useful in combination with frameless stereotaxy to define more exactly the tumor infiltration zone in glioma surgery compared with conventional anatomic MRI alone.

Algorithms↗
PubMed1996

BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web.

The BCM Search Launcher is an integrated set of World Wide Web (WWW) pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to (1) nucleic acid sequence searches, (2) multiple and pair-wise sequence alignments, (3) gene feature searches, (4) protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http:@gc.bcm.tmc.edu:8088/search-launcher.html.

Animals↗
PubMed1998

[Online infection recording within the scope of total quality management].

The continuous and exact recording of infections is a condition sine qua non for total quality management. Therefore, at the Diakoniekrankenhaus Rotenburg (Wümme) a program which offers the possibility of online recording of data was integrated into the hospital intranet. The recording is done with network clients. The recording of data is supported by a series of plausibility controls. The advantage consists in immediate evaluation of up to date and extensive statistics of infections. By integration into the existing system, relevant influences and consequences such as the prolongation of hospitalisation, use of material, and frequency of reoperation can by recognized and immediately considered with high validity.

Cross Infection↗
PubMed2006

Significantly improved prediction of subcellular localization by integrating text and protein sequence data.

Computational prediction of protein subcellular localization is a challenging problem. Several approaches have been presented during the past few years; some attempt to cover a wide variety of localizations, while others focus on a small number of localizations and on specific organisms. We present a comprehensive system, integrating protein sequence-derived data and text-based information. Itis tested on three large data sets, previously used by leading prediction methods. The results demonstrate that our system performs significantly better than previously reported results, for a wide range of eukaryotic subcellular localizations.

Artificial Intelligence↗
PubMed2001

A JAVA-based DICOM server with integration of clinical findings and DICOM-conform data encryption.

The transfer of large amounts of medical data within heterogeneous hard and software infrastructures and the exploitation of distributed resources require a fast, secure, and platform-independent data exchange. To avoid costly vendor-specific solutions, a DICOM server was implemented in JAVA. Data access was enabled via internet browser technology. Relevant patient and image acquisition information was extracted from the DICOM images and stored into a relational database. Patient information such as radiological findings were transferred from the Radiological Information System into the database. Image data were accessed either by a fast preview tool or using a JAVA-based DICOM viewer. Since data security mechanisms are not yet part of the DICOM standard, a DICOM-conform encryption of sensitive patient data was implemented. The method allowed a dynamic selection of the data to be encrypted. Integrating this module into the image server enabled the fast and secure transfer of image data across insecure networks as well as long-term storage on CD-Recordables.

CD-ROM↗
PubMed2000

Challenges in electronic importing of health data.

The objective of this article is to increase awareness among public health personnel of the complexities involved in integrating existing data systems. This article describes the electronic importing feature of the Centers for Disease Control and Prevention (CDC) software package called staffTRAK-TB, and users' experience with it.

Attitude of Health Personnel↗
PubMed2005

Application of satellite remote-sensing data for source analysis of fine particulate matter transport events.

Satellite sensors have provided new datasets for monitoring regional and urban air quality. Satellite sensors provide comprehensive geospatial information on air quality with both qualitative imagery and quantitative data, such as aerosol optical depth. Yet there has been limited application of these new datasets in the study of air pollutant sources relevant to public policy. One promising approach to more directly link satellite sensor data to air quality policy is to integrate satellite sensor data with air quality parameters and models. This paper presents a visualization technique to integrate satellite sensor data, ground-based data, and back trajectory analysis relevant to a new rule concerning the transport of particulate matter across state boundaries. Overlaying satellite aerosol optical depth data and back trajectories in the days leading up to a known fine particulate matter with an aerodynamic diameter of <2.5 microm (PM2.5) event may indicate whether transport or local sources appear to be most responsible for high PM2.5 levels in a certain location at a certain time. Events in five cities in the United States are presented as case studies. This type of analysis can be used to help understand the source locations of pollutants during specific events and to support regulatory compliance decisions in cases of long distance transport.

Aerosols↗
PubMed2006

[Surveillance of antimicrobial resistance and antimicrobial use in a university-affiliated hospital: implementation of a computerized system].

UNLABELLED: After half a century of antibiotic use, the increasing problem of the emergence and spread of antimicrobial-resistant pathogens has created a problem of public health. The causes of this problem are multifactorial, but the excessive and inappropriate use of antimicrobials is the principal cause. The current guidelines for the control of antimicrobial resistance in hospitals recommend the implementation of a surveillance system of antimicrobial use and antimicrobial resistance data. AIM OF THE STUDY: The objective of our project was to develop a computerised tool to survey the antibiotic consumption data and the antimicrobial resistance. MATERIALS AND METHODS: We have collected antimicrobial resistance data from the software of the bacteriology laboratory, antibiotic use data from the pharmacy and demographical data from the hospital's admission department. These data were integrated in a database server and available with a web application. Antimicrobial resistance data of 15 major microorganisms were extracted and expressed as a frequency with elimination of repeats by using time criteria (7, 14 or 28 days). Antibiotic use data were converted into defined daily doses (DDD) and expressed per 1000 patient-days. RESULTS: Data are available for consultation in the form of tables or graphs per unit, type of units (medicine, surgery, pediatrics, intensive care units) or in the whole hospital. The system allows the confrontation on the same graph of antimicrobial resistance and antibiotic use data. CONCLUSION: Our surveillance system constitutes a needed prerequisite to the implementation of a global strategy of antibiotic use improvement in our hospital.

Anti-Infective Agents↗
PubMedDate not supplied

Implementation of a surveillance system for stroke based on administrative and clinical data in the Lazio region (Italy): methodological aspects.

Stroke is the third leading cause of death and the most important cause of long-term disability in Italy and other developed countries, heavily influencing quality of life and costs of health care. In spite of the widespread occurrence of the disease and its relevant impact in Italy, there is neither a national nor a regional surveillance system of cerebrovascular diseases. A regional surveillance system for stroke has two important aims: to help to interpret the geographical and temporal trends of the disease for health care planning and resource allocation and to allow close monitoring of the quality of stroke services. Age-standardized mortality rates for cerebrovascular diseases in the Lazio region (5,242,709 inhabitants) in the period 1998-99 were 69.4 for males and 59.4 for females per 100,000 inhabitants. In the year 2000, about 3% of all hospital discharges were for cerebrovascular diseases with a hospitalisation rate of 4.36 per 1000 inhabitants. The mean length of stay is 12 days (median of 9 days) and in-hospital death is 15.4%. The admission rate for cerebrovascular diseases to emergency departments is 3.40 per 1000 inhabitants. The goal of the Lazio Regional Health Authority is to implement a surveillance system for stroke based both on current data (mortality and discharge data) and on information collected in a registry for quality assessment of stroke care. The first step of the study is to develop a regional register of acute stroke using an 'ad hoc' data sheet integrated in the computer-based patient record system of clinical and administrative data (GIPSE) operating in all emergency departments in the region.

Aged↗
PubMed1988

Management of clinical data in urology. Experience with integrated personal computers and a relational database.

The use of microcomputers in medicine is rapidly increasing. To handle clinical data and to facilitate clinical research, a system based on several personal computers that can be linked together was developed. Commercially available software was used, consisting of a powerful relational database complemented by programs for statistics, graphics and desk top publishing. The low cost, modular and flexible system was handled by untrained personnel; computer specialists were not needed. Data on more than 1100 patients have been entered so far and data retrieval can be done by the physician "on the spot" using standard prefabricated reports. Data can then be analysed statistically and processed to graphics and publications.

Computers↗
PubMed1995

Issues in incorporation semantic integrity in molecular biological object-oriented databases.

Issues critical to ensuring semantic integrity in molecular biological data collections have been identified and include complexity, exceptions, missing data, changing models, holism and integration, delocalized data, interoperability and nomenclature. This combination is peculiar to biology and presents some interesting problems as a result. Little is known about semantic checking in object-oriented databases in general, but because such technology appears highly suitable for modeling biological data, it is appropriate to examine the ways in which object-oriented technology can support this functionality. It is concluded that object-oriented technology will support semantic checking even in a complex domain like biology. We propose 10 guidelines for future work including ways of treating exceptional cases and 'positioning' of constraints in a schema.

Biotechnology↗
PubMed1996

Integrated multimedia timeline of medical images and data for thoracic oncology patients.

A prototype multimedia medical database has been developed to provide image and textual data for thoracic oncology patients undergoing treatment of advanced malignancies. The database integrates image data from the hospital picture archiving and communication system with textual reports from the radiology information system, alphanumeric data contained in the hospital information system, and other electronic medical data. The database presents information in a timeline format and also contains visualization programs that permit the user to view and annotate radiographic measurements in tabular or graphic form. The database provides an efficient and intuitive display of the changing status of oncology patients. The ability to integrate, manage, and access relevant multimedia information may substantially enhance communication among distributed multidisciplinary health care providers and may ensure greater consistency and completeness of patient-related data.

Databases, Factual↗