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PubMed2006

Bridging clinical information systems and grid middleware: a Medical Data Manager.

This paper describes the effort to deploy a Medical Data Management service on top of the EGEE grid infrastructure. The most widely accepted medical image standard, DICOM, was developed for fulfilling clinical practice. It is implemented in most medical image acquisition and analysis devices. The EGEE middleware is using the SRM standard for handling grid files. Our prototype is exposing an SRM compliant interface to the grid middleware, transforming on the fly SRM requests into DICOM transactions. The prototype ensures user identification, strict file access control and data protection through the use of relevant grid services. This Medical Data Manager is easing the access to medical databases needed for many medical data analysis applications deployed today. It offers a high level data management service, compatible with clinical practices, which encourages the migration of medical applications towards grid infrastructures. A limited scale testbed has been deployed as a proof of concept of this new service. The service is expected to be put into production with the next EGEE middleware generation.

Databases as Topic↗
PubMed1994

Role of the histone amino termini in facilitated binding of a transcription factor, GAL4-AH, to nucleosome cores.

Facilitated, "cooperative" binding of GAL4-AH to nucleosomal DNA occurred in response to inhibition from the core histone amino termini. The binding of GAL4-AH (which contains the DNA-binding and dimerization domains of GAL4) to nucleosome cores containing multiple binding sites initiated at the end of a nucleosome core and proceeded in a cooperative manner until all sites were occupied. However, following tryptic removal of the core histone amino termini, GAL4-AH binding appeared to be noncooperative, similar to binding naked DNA. Binding of GAL4-AH to nucleosomes bearing a single GAL4 site at different positions indicated that inhibition of GAL4 binding was largely mediated by the histone amino termini and primarily occurred at sites well within the core and not near the end. When the histone amino termini were intact, binding of GAL4-AH to sites near the center of a nucleosome core was greatly enhanced by the presence of additional GAL4 dimers bound to more-accessible positions. These data illustrate that the binding of a factor to more-accessible sites, near the end of a nucleosome, allows facilitated binding of additional factors to the center of the nucleosome, thereby overcoming repression from the core histone amino termini. This mechanism may contribute to the binding of multiple factors to complex promoter and enhancer elements in cellular chromatin.

Base Sequence↗
PubMed2006

From psychiatric ward to the streets and shelters.

The issue of discharge from hospital ward to the streets is seldom explored in the literature, but all too commonly experienced by individuals experiencing psychiatric disorders. The Community University Research Alliance on Housing and Mental Health sought to determine how frequently people were discharged from psychiatric wards to shelters or the street in London, Ontario, Canada. A number of data sources were accessed to determine instances of discharges to shelters or the street. Data were analysed to determine the number of moves occurring between hospital and shelter or no fixed address. All datasets revealed the problem of discharge to shelters or the street occurred regularly. All data sources used have the difficulty of likely underestimating the extent of the problem. This type of discharge occurred at least 194 times in 2002 in London, Ontario, Canada. Policies that contribute to this problem include income-support policies, the reduction in psychiatric hospital beds and the lack of community supports. Without recognition, this problem is at risk of remaining invisible with no further improvements to the situation.

Adult↗
PubMed2006

Properties of a federated epidemiology query system.

PURPOSE: The purpose of the study was to establish knowledge about how online access to epidemiological data from general practitioners (GPs) electronic health record (EHR) system should be provided. Before such systems are developed and deployed a decision about the appropriate system architecture must be made. Such a decision should ideally be based on knowledge about the properties of different system architectures. This choice is important because the system architecture may affect the willingness of GPs to participate in providing epidemiological data from their EHR system. METHOD: Verifying the performance and properties of an architectural approach by implementing and deploying a system on a trans-institutional level and performing evaluations studies is a very resource demanding method to establish a foundation for the decision of appropriate system architecture. Instead, we have tried to create this foundation by constructing a prototype system, establish knowledge about the properties of the system using experiments, and finally compare the properties of the federated approach to the properties of the centralised approach. By using this methodological approach we provide the best available knowledge, on this stage, for the appropriate system architecture to use for providing access to epidemiological data from the local population. RESULTS: Our experimental results show that it is possible to improve the timeliness and the temporal and spatial resolution of epidemiological data, compared to traditional centralised disease surveillance systems. Up-to-date epidemiological data from the local population may be provided directly from the source EHR system within 4s. The responsiveness of the system is minimally affected (0.1s) as the number of participating data providers grows from 1 to 49 data providers. The comparison of the federated approach to the centralised approach indicates that federated approaches avoid the privacy issues involved, as intended; it offers better scalability when computing speed is compared, and it provides better specificity because more data about the patient may be used. CONCLUSION: The conclusion from our study is that the federated approach to providing epidemiological data about the local population has many benefits over the traditional centralised approach. A federated approach to an epidemiology system may raise the GPs awareness of local disease outbreak because it is possible to share information about incidence rates of communicable diseases and use of laboratory requests in a geographical area that predates laboratory-based disease surveillance. The effects of the federated approach could be improved data quality in the EHR systems and improved representativeness of the epidemiological data for the areas covered by such systems.

Database Management Systems↗
PubMed2001

The MetaFam Server: a comprehensive protein family resource.

MetaFam is a comprehensive relational database of protein family information. This web-accessible resource integrates data from several primary sequence and secondary protein family databases. By pooling together the information from these disparate sources, MetaFam is able to provide the most complete protein family sets available. Users are able to explore the interrelationships among these primary and secondary databases using a powerful graphical visualization tool, MetaFamView. Additionally, users can identify corresponding sequence entries among the sequence databases, obtain a quick summary of corresponding families (and their sequence members) among the family databases, and even attempt to classify their own unassigned sequences. Hypertext links to the appropriate source databases are provided at every level of navigation. Global family database statistics and information are also provided. Public access to the data is available at http://metafam.ahc.umn.edu/.

Computational Biology↗
PubMed2002

[PACS: from project to reality. Report of experiences on full digitalisation of the radiology department of a major hospital].

OBJECTIVE: To assess the time needed and the resulting effects of a complete digitalisation of a radiological department of a major hospital (856 beds, 28,000 in-patients, 35,000 out-patients/year) a pilot study was performed. This had to be done without interrupting routine services. RESULTS: After intensive preparations were performed and the hospital-network was completed, within a two year period all radiological functions (mammography excluded), reporting stations and archives were changed to a complete digital workflow. All modalities (provided by 3 different companies) are now connected by DICOM-work lists. The picture-files (4 GB/day) are automatically routed to the work-stations (n = 10), where the reporting and file shows are performed, to the digital archive and to the peripheral viewing-stations (n = 44). The distribution of the digital pictures takes place all over the hospital including the ORs and special units. We accomplished, to connect electronically the report and the image data. The clinical file shows are also performed completely digitally. The access to the data of the deep archive is possible by the dept. of radiology without any manual interaction. The film consumption was reduced to an amount of less than 10%, as compared to the prior PACS situation. Since PACS has been introduced the radiological productivity increased by more than 15% and throughput-time was clearly reduced. CONCLUSIONS: The complete digitalisation increases productivity and attractiveness of a hospital-radiology and helps to shorten diagnostic and therapeutic decision-making. The transfer from a conventional to a digital workflow is possible without interrupting the clinical services. Extensive preparations and ongoing assistance of such projects though are clearly needed.

Computer Systems↗
PubMed1993

Fertility and infertility assessment by review of records.

The assessment of fertility and infertility in dairy herds requires accurate and complete data that are collected in a timely manner. The data must be entered in a record system that provides easy accessibility. An understanding of terminology and statistical calculations, along with knowledge of industry standards, reproductive physiology, and pathology is essential if problem solving is to occur. Problem solving begins by developing an understanding of the events influencing past reproductive performance. Progress is made by establishing a detailed reproductive management plan to monitor the current breeding herd and to identify potential problems before they occur. The introduction of microcomputers and on-farm record systems has greatly enhanced the veterinarian's ability to access and process data. For the first time in history, cowside health data collection systems integrated with production records are being used. This provides the opportunity to collect and summarize and analyze reproductive and production data as the events occur. Successful reproductive performance depends on effective and efficient management. For veterinarians to effectively and positively influence the reproductive performance of the herd, they must influence management. This requires working with dairy management to make changes in job assignments and description. Taking time to assess records with managers is an invaluable tool to convince dairy management of the necessity for change.

Animals↗
PubMed2025

Evaluation of sequencing reads at scale using rdeval.

MOTIVATION: Large sequencing datasets are being produced and deposited into public archives at unprecedented rates. The availability of tools that can reliably and efficiently generate and store sequencing read summary statistics has become critical. RESULTS: As part of the effort by the Vertebrate Genomes Project (VGP) to generate high-quality reference genomes at scale, we sought to address the community's need for efficient sequence data evaluation by developing rdeval, a standalone tool to quickly compute and interactively display sequencing read metrics. Rdeval can either run on the fly or store key sequence data metrics in tiny read 'snapshot' files. Statistics can then be efficiently recalled from snapshots for additional processing. Rdeval can convert fa*[.gz] files to and from other popular formats including BAM and CRAM for better compression. Overall, while CRAM achieves the best compression, the gain compared to BAM is marginal, and BAM achieves the best compromise between data compression and access speed. Rdeval also generates a detailed visual report with multiple data analytics that can be exported in various formats. We showcase rdeval's functionalities using long-read data from different sequencing platforms and species, including human. For PacBio long-read sequencing, our analysis shows dramatic improvements in both read length and quality over time, as well as the benefit of increased coverage for genome assembly, though the magnitude varies by taxa. AVAILABILITY AND IMPLEMENTATION: Rdeval is implemented in C++ for data processing and in R for data visualization. Precompiled releases (Linux, MacOS, Windows) and commented source code for rdeval are available under MIT license at https://github.com/vgl-hub/rdeval. Documentation is available on ReadTheDocs (https://rdeval-documentation.readthedocs.io). Rdeval is also available in Bioconda and in Galaxy (https://usegalaxy.org). An automated test workflow ensures the consistency of software updates.

Software↗
PubMed2005

Importance of communication between producers and consumers of publicly available experimental data.

The application of mass spectrometry to discover new cancer biomarkers is in its infancy. Many of these new markers are low-abundance proteins that exist as fragments associated with carrier proteins. Although reproducibility is key to the use of mass spectrometry for ion fingerprint analysis, the scientific community has yet to establish a common platform or standardized operating procedures that are necessary for intra- and inter-laboratory comparison. In an effort to assist others who are perfecting mass spectrometry platforms for profiling, ongoing experimental data were posted for public consumption. An unintended consequence of unrestricted access to experimental data is the risk of inappropriate conclusions drawn and publicly disseminated that could have been avoided by communication between the producers and consumers of the data. Such disputes, however, should not divert us from the validation of this promising new approach.

Biomarkers, Tumor↗
PubMed1995

Modern image capture and data collection technology.

Computer data collection technology is intended to facilitate patient management and clinic administration. The systems should be devised for ease of usage and careful consideration should be given to the core set of data required and the task to be performed by the system. Security of data is important, and it must cover not only the inadvertent access to confidential data, but also must stop corrupt data from entering the system. Audit is becoming increasingly important, and the ability to achieve this should be inbuilt into any data collection system. A staged introduction of these systems is suggested without trying to achieve too much at the initial attempt. Adaptability is important so that as new technologies are introduced, the old systems should not be made redundant. Eventually it should be possible to achieve the goals set, and include fields for image capture of the colposcopic findings, which although not an essential requirement for such systems, is certainly a desirable one.

Colposcopes↗
PubMed2005

Using blood glucose data as an indicator for epidemic disease outbreaks.

In the future, transfer of vital sensor data from patients to the public health care system is likely to become commonplace. Systems for automatic transfer of sensor data are now at the prototype stage. As electronic health record (EHR) systems adapt such functionality, widespread use may become an actuality in the foreseeable future.To prevent spreading of diseases, an early detection of infection is important. At the time an outbreak is diagnosed, many people may already be infected due to the incubation period. This study suggests an approach for detecting an epidemic outbreak at an early stage by monitoring blood glucose data collected from people with diabetes. Continuous analysis of blood glucose data may have the potential to prevent large outbreaks of infectious diseases, such as different strains of Influenza, Cholera, Plague, Ebola, Anthrax and SARS.When a person gets infected, the blood glucose value increases. If the blood glucose data from a large number of patients with diabetes are collected in a central database, it may be possible to detect an epidemic disease outbreak at an early stage. Advanced data analysis on the data may detect predominant numbers of incidences, indicating a possible outbreak. This gives the health authorities the possibilities to take actions to limit the outbreak and its consequences for all the inhabitants in an affected area.At the Norwegian Centre for Telemedicine, a mobile system for automatic transfer of blood glucose values has been constructed. By using wireless communication standards such as Bluetooth and GSM, the system transfers blood glucose data to an electronic health record system. Combined with a system accessing and querying data from EHR systems for patient surveillance we are extending our work into an Epidemic Disease Detection using blood Glucose (EDDG) system.

Blood Glucose↗
PubMed2006

Sharable EHR systems in Finland.

In Finland, the shared record is a virtual electronic health record (EHR). It consists of health data generated, maintained and preserved by different health care service providers. Two different kinds of technologies for integrating regional EHR-systems are applied, but mainly by using a common middleware. Services provided by this middleware are EHR location services using a link repository and combining EHR-viewing services with security management services including consent management and identification services for health professionals. The Regional Health Information Organization (UUMA) approach is based on a stepwise implementation of integrated regional healthcare services to create a virtually borderless healthcare organization--a patient centered virtual workspace. In the virtual workspace multi-professional teams and patients collaborate and share information regardless of time and place. Presently the regional health information network (RHIN) is comprised of three integrated services between primary, secondary and tertiary care within the county of Uusimaa. The regional healthcare modules consist of an (1) eReferral network, (2) integrated EHR service between health care professionals and (3) PACS system. The eReferral between primary and secondary care not only speeds up the transfer, but also offers an option for communication in the form of eConsultation between general practitioners and hospital specialists. By sharing information and knowledge remote eConsultations create a new working environment for integrated delivery of eServices between the health care providers. Over 100,000 eReferral messages (40 %) were transferred between health care providers. Interactive eConsultations enable supervised care leading to the reduction of outpatient visits and more timely appointments. One third (10/31) of the municipal health centers are connected to the clinics in the Helsinki University Central Hospital by the eReferral system. The link directory service extends the dimensions of networking between organizations by combining legacy systems within regional primary and secondary care. The link directory is an interface to diverse patient information systems, like HUSpacs, containing links pointing to the actual patient data located in remote information systems. The original data including images can be viewed with a web browser, but data can be accessed only with the patient's informed consent. Currently the reference data base includes 9.5 million links from 1.4 million patients with over 2.000 daily users. We aim to create a new working environment for professionals by incorporation of innovative information and communication technology, new organization of work and re-engineering of workflows. In the near-future, the citizen will have an active role participating in decisions on his care, carrying out guided self-care and taking steps of pro-active prevention.

Computer Communication Networks↗
PubMed1996

A Web-based repository manager for brain mapping data.

The Web provides a rapid prototyping environment for building platform-independent graphical user interfaces. A Web-based console can be implemented as a suite of CGI scripts that generate HTML code, manipulate files, execute system commands, and invoke external tools. Often these tools share data by reading and writing flat files, which must be explicitly maintained by the CGI programmer. In a repository system, meta-data about each file object are maintained in a database, and access to all data is regulated by a layer of control services. This paper describes the design and implementation of a Web-based Repository Manager (WRM), which provides an application programmer's interface for controlling applications, generating HTML documents, handling Web forms, and managing multi-media data. The WRM is being used to develop a console for the Brain Mapping Framework, a system for visualizing cortical stimulation data obtained during neurosurgery.

Brain Mapping↗
PubMed2000

Managing the primary care practice on the Web

Physicians and administrators have little hope of responding appropriately to the challenges of the health care market without data to support decision making. Desired Mayo Clinic s Primary Care Practice was to have the ability to access and integrate data from many platforms in many formats from the Enterprise and bring this information to the desktop in a robust interactive display. The solution was delivery of the data to the Web through an interface using Java with access to Online Analytical Processing (OLAP) tools for summarization, graphical display and reporting. Communicating major trends, assisting in planning and management, visually displaying alerts in summary data and individual patients that are all possible through an easy-to-use Web application. To really understand what the summarized data represents, the physicians must be able to drill down, download and explore their own detail data. A pilot project was developed to test the capabilities of the development environment, the acceptance Web tools, the ability to deliver timely information and the methodology of using a multi-dimensional database to define the data. The Family Medicine practice at four separate locations was chosen for the demonstration project. Two practices in Rochester, MN and practices in two smaller towns, totaling 50 physicians and administrative personnel, were the first clients using the system. A cross-functional team examined a variety of development issues such as data sources, data definitions, levels of security, data analysis types, and style of display. Demonstrations of the prototype met with an overwhelming positive response from administrators and department leaders. The Physician Patient Management solution collects, analyzes, and communicates the information needed to meet today s health care challenges.

Journal Article↗
PubMedDate not supplied

[Computers and medico-surgical ethics].

The confidence of physicians and surgeons in computerized medical systems is highly related to data reliability, while the confidence of the public depends on the protection of medical information in automated systems. In order to assure to patients medical data privacy, the MIM is of opinion that deontological and legal rules concerning access to identifiable medical data in automated information systems shall be the same as those that are applicable to conventional medical records. The access to medical data banks should be exclusively reserved to physicians responsible for patient care and to the personnel mandated by them.

Belgium↗
PubMed2006

A HIPAA-compliant architecture for securing clinical images.

The Health Insurance Portability and Accountability Act (HIPAA, instituted April 2003) Security Standards mandate health institutions to protect health information against unauthorized use or disclosure. One approach to addressing this mandate is by utilizing user access control and generating audit trails of the various authorized as well as unauthorized user access of health data. Although most current clinical image systems [e.g., picture archiving and communication system (PACS)] have components that generate log files for application debugging purposes, there is a lack of methodology to obtain and synthesize the pertinent data from the large volumes of log data generated by these multiple components within a PACS. We have designed a HIPAA-compliant architecture specifically for tracking and auditing the image workflow of clinical imaging systems such as PACS. As an initial first step, we developed HIPAA-compliant auditing system (H-CAS) based on parts of this HIPAA-compliant architecture. H-CAS was implemented within a test-bed PACS simulator located in the Image Processing and Informatics lab at the University of Southern California. Evaluation scenarios were developed where different user types performed legal and illegal access of PACS image data within each of the different components in the PACS simulator. Results were based on whether the scenarios of unauthorized access were correctly identified and documented as well as on normal operational activity. Integration and implementation pitfalls were also noted and included.

California↗
PubMed2001

Aldrin and dieldrin: a review of research on their production, environmental deposition and fate, bioaccumulation, toxicology, and epidemiology in the United States.

In the last decade four international agreements have focused on a group of chemical substances known as persistent organic pollutants (POPs). Global agreement on the reduction and eventual elimination of these substances by banning their production and trade is a long-term goal. Negotiations for these agreements have focused on the need to correlate data from scientists working on soil and water sampling and air pollution monitoring. Toxicologists and epidemiologists have focused on wildlife and human health effects and understanding patterns of disease requires better access to these data. In the last 20 years, substantial databases have been created and now are becoming available on the Internet. This review is a detailed examination of 2 of the 12 POPs, aldrin and dieldrin, and how scientific groups identify and measure their effects. It draws on research findings from a variety of environmental monitoring networks in the United States. An overview of the ecologic and health effects of aldrin and dieldrin provides examples of how to streamline some of the programs and improve access to mutually useful scientific data. The research groups are located in many government departments, universities, and private organizations. Identifying databases can provide an "information accelerator" useful to a larger audience and can help build better plant and animal research models across scientific fields.

Aldrin↗
PubMed2006

Data withholding and the next generation of scientists: results of a national survey.

PURPOSE: To provide the first national data on the nature, extent, and consequences of withholding among life science trainees. METHOD: In 2003, the authors surveyed 1,077 second-year doctoral students and postdoctoral fellows in life sciences at 50 U.S. universities, with a comparison group of trainees in computer science and chemical engineering. The study variables examined trainees' exposure to and the consequences of data withholding. RESULTS: Two hundred forty-six trainees (23.0%) reported that they had asked for and been denied access to information, data, materials, or programming associated with published research and 221 (20.6%) to unpublished research. Eighty-five trainees (7.9%) reported that they had denied another academic scientist's request(s) related to their own published research. Five hundred thirty-three trainees (50.8%) reported that withholding had had a negative effect on the progress of their research, 508 (48.5%) on the rate of discovery in their lab/research group, 472 (45.0%) on the quality of their relationships with academic scientists, 346 (33.0%) on the quality of their education, and 299 (28.5%) on the level of communication in their lab/research group. Trainees denied access to research were significantly more likely to report that data withholding had had a negative effect on several aspects of the educational experience. CONCLUSIONS: Data withholding had demonstrated negative effects on trainees. The life sciences, more so than chemical engineering or computer science, will have to address this issue among its trainees. Failure to do so could result in delayed research, inefficient training, and a culture of withholding among future life scientists.

Access to Information↗