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PubMed2000

PhysioBank, PhysioToolkit, and PhysioNet: components of a new research resource for complex physiologic signals.

The newly inaugurated Research Resource for Complex Physiologic Signals, which was created under the auspices of the National Center for Research Resources of the National Institutes of Health, is intended to stimulate current research and new investigations in the study of cardiovascular and other complex biomedical signals. The resource has 3 interdependent components. PhysioBank is a large and growing archive of well-characterized digital recordings of physiological signals and related data for use by the biomedical research community. It currently includes databases of multiparameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and from patients with a variety of conditions with major public health implications, including life-threatening arrhythmias, congestive heart failure, sleep apnea, neurological disorders, and aging. PhysioToolkit is a library of open-source software for physiological signal processing and analysis, the detection of physiologically significant events using both classic techniques and novel methods based on statistical physics and nonlinear dynamics, the interactive display and characterization of signals, the creation of new databases, the simulation of physiological and other signals, the quantitative evaluation and comparison of analysis methods, and the analysis of nonstationary processes. PhysioNet is an on-line forum for the dissemination and exchange of recorded biomedical signals and open-source software for analyzing them. It provides facilities for the cooperative analysis of data and the evaluation of proposed new algorithms. In addition to providing free electronic access to PhysioBank data and PhysioToolkit software via the World Wide Web (http://www.physionet. org), PhysioNet offers services and training via on-line tutorials to assist users with varying levels of expertise.

Databases as Topic↗
PubMed2006

Gene expression profiling of chicken primordial germ cell ESTs.

BACKGROUND: Germ cells are the only cell type that can penetrate from one generation to next generation. At the early embryonic developmental stages, germ cells originally stem from primordial germ cells, and finally differentiate into functional gametes, sperm in male or oocyte in female, after sexual maturity. This study was conducted to investigate a large-scale expressed sequence tag (EST) analysis in chicken PGCs and compare the expression of the PGC ESTs with that of embryonic gonad. RESULTS: We constructed 10,851 ESTs from a chicken cDNA library of a collection of highly separated embryonic PGCs. After chimeric and problematic sequences were filtered out using the chicken genomic sequences, there were 5,093 resulting unique sequences consisting of 156 contigs and 4,937 singlets. Pearson chi-square tests of gene ontology terms in the 2nd level between PGC and embryonic gonad set showed no significance. However, digital gene expression profiling using the Audic's test showed that there were 2 genes expressed significantly with higher number of transcripts in PGCs compared with the embryonic gonads set. On the other hand, 17 genes in embryonic gonads were up-regulated higher than those in the PGC set. CONCLUSION: Our results in this study contribute to knowledge of mining novel transcripts and genes involved in germline cell proliferation and differentiation at the early embryonic stages.

Animals↗
PubMedDate not supplied

Three-dimensional modeling by combining artificial with real data.

Issues arising in the graphics simulation of bone grafting and in the use of commercial libraries to create custom-designed models revolve on the ability to combine data defined in Volume Representation--as that generated by Computed Tomography scans--and user-defined data introduced in Boundary Representation--as vertices of polygons, for instance. To address these issues the authors propose a hybrid filling technique, which also processes conflicting adjacency information created by subsampling or digitization errors. A graphics experiment has been designed to illustrate the problems arising in the presence of objects defined partially in Volume and partially in Boundary Representation, and a method to handle them.

Algorithms↗
PubMed2002

Spreadsheets for automated data collection, analysis, and report generation for diagnostic medical physics: publicly available on the world wide web.

A library of spreadsheets has been developed to facilitate the practice of diagnostic physics quality assurance. Each spreadsheet follows a standard template and uses the highest ranking controlling authority (within the United States) for pass/fail criteria and testing procedures. Sheets are now available for CT (computed tomography), MR (magnetic resonance), US (ultrasound), screen-film mammography, stereotactic breast, radiographic, fluoroscopic, computed radiography, film digitizer, and display quality control. Use is made of spreadsheet "workbooks" so that each testing event is a single sheet in the workbook. Thus, results over the lifetime of the device are gathered in a single file, and historical control charts are gathered on the first sheet. The spreadsheets are available at http://radweb.mcis.washington.edu/~sglanger, and are released under the Gnu (a recursive acronym. Gnu's Not Unix) public license. It is expected that others will add improvements, and they are expected and requested to submit them back to the author to be shared with the diagnostic physicist community at large.

Diagnostic Imaging↗
PubMed1982

Optical disk technology and information.

The optical video disk, spawned by the home entertainment industry, and its counterpart, the optical digital disk, both hold great promise for information storage and retrieval and the scientific enterprise. Optical digital disks for computer mass storage are currently under development by many firms. In addition, efforts are under way to allow encoding of digital information on video disks. This is desirable as an inexpensive publication medium for machine-readable data as well as a means of obtaining both video and digital information on one disk. Potential applications of this technology include inexpensive on-line storage, random access graphics to complement on-line information systems, hybrid network architectures, office automation systems, and archival storage.

Computers↗
PubMed1998

A clinical image library using photo CD.

In a move to update a collection of medical slide images and improve access to high-quality medical images for postgraduate teachers at the Institute of Child Health and Great Ormond Street Hospital for Children, a new collection of scanned slide images was created on Kodak Photo CD discs. Each image was available in five different resolutions. The images were catalogued in an image database by diagnosis, date, patient registration number, and anatomical view. Images could be accessed using simple search protocols and output to digital files, slides or prints.

CD-ROM↗
PubMed2000

Pathfinder: multiresolution region-based searching of pathology images using IRM.

The fast growth of digitized pathology slides has created great challenges in research on image database retrieval. The prevalent retrieval technique involves human-supplied text annotations to describe slide contents. These pathology images typically have very high resolution, making it difficult to search based on image content. In this paper, we present Pathfinder, an efficient multiresolution region-based searching system for high-resolution pathology image libraries. The system uses wavelets and the IRM (Integrated Region Matching) distance. Experiments with a database of 70,000 pathology image fragments have demonstrated high retrieval accuracy and high speed. The algorithm can be combined with our previously developed wavelet-based progressive pathology image transmission and browsing algorithm and is expandable for medical image databases.

Abstracting and Indexing↗
PubMed1976

Application of a spectrophotometric method to the determination of the composition of oligonucleotides obtained from cysteine transfer ribonucleic acid.

1. The applications of methods for determining the composition of oligonucleotides from u.v.-absorption spectra is described. 2. In the first method absorbances at selected wave-lengths were read from the spectra of oligonucleotides in solution in 7 M-urea which had been recorded at acid and alkaline pH values. 3. In the second method absorbances were sampled automatically at regular time-intervals during scans at acid and alkaline pH of each spectrum, converted into digital signals and recorded on paper take for computer processing. The holmium spectrum in the region of the holmium peak at 333.7 nm was superimposed on each nucleotide spectrum. The position of this peak maximum was used as a standard reference point in the computer-based analysis. 4. By using either method the composition was calculated by a least-squares procedure by using a library of values for five standard nucelotides obtained in a similar manner. 5. The methods gave satisfactory compositions for mixtures of mononucleotides as well as for five dinucleoside monophosphates. 6. Methods of minimizing the effects on the nucleotide composition of spectural changes due to base stacking are discussed. 7. The compositions of some oligonucleotides obtained during an investigation of the nucleotide sequence of tRNA (Cys) were determined and agreed with the sequences found by other methods.

Base Sequence↗
PubMed1993

Image Engine: an object-oriented multimedia database for storing, retrieving and sharing medical images and text.

This paper describes Image Engine, an object-oriented, microcomputer-based, multimedia database designed to facilitate the storage and retrieval of digitized biomedical still images, video, and text using inexpensive desktop computers. The current prototype runs on Apple Macintosh computers and allows network database access via peer to peer file sharing protocols. Image Engine supports both free text and controlled vocabulary indexing of multimedia objects. The latter is implemented using the TView thesaurus model developed by the author. The current prototype of Image Engine uses the National Library of Medicine's Medical Subject Headings (MeSH) vocabulary (with UMLS Meta-1 extensions) as its indexing thesaurus.

Abstracting and Indexing↗
PubMed2003

Protein micro- and macroarrays: digitizing the proteome.

The early applications of microarrays and detection technologies have been centered on DNA-based applications. The application of array technologies to proteomics is now occurring at a rapid rate. Numerous researchers have begun to develop technologies for the creation of microarrays of protein-based screening tools. The stability of antibody molecules when bound to surfaces has made antibody arrays a starting point for proteomic microarray technology. To minimize disadvantages due to size and availability, some researchers have instead opted for antibody fragments, antibody mimics or phage display technology to create libraries for protein chips. Even further removed from antibodies are libraries of aptamers, which are single-stranded oligonucleotides that express high affinity for protein molecules. A variation on the theme of protein chips arrayed with antibody mimics or other protein capture ligand is that of affinity MS where the protein chips are directly placed in a mass spectrometer for detection. Other approaches include the creation of intact protein microarrays directly on glass slides or chips. Although many of the proteins may likely be denatured, successful screening has been demonstrated. The investigation of protein-protein interactions has formed the basis of a technique called yeast two-hybrid. In this method, yeast "bait" proteins can be probed with other yeast "prey" proteins fused to DNA binding domains. Although the current interpretation of protein arrays emphasizes microarray grids of proteins or ligands on glass slides or chips, 2-D gels are technically macroarrays of authentic proteins. In an innovative departure from the traditional concept of protein chips, some researchers are implementing microfluidic printing of arrayed chemistries on individual protein spots blotted onto membranes. Other researchers are using in-jet printing technology to create protein microarrays on chips. The rapid growth of proteomics and the active climate for new technology is driving a new generation of companies and academic efforts that are developing novel protein microarray techniques for the future.

Protein Array Analysis↗
PubMed2006

An interactive three-dimensional virtual body structures system for anatomical training over the internet.

The Visible Human digital datasets make it possible to develop computer-based anatomical training systems that use virtual anatomical models (virtual body structures-VBS). Medical schools are combining these virtual training systems and classical anatomy teaching methods that use labeled images and cadaver dissection. In this paper we present a customizable web-based three-dimensional anatomy training system, W3D-VBS. W3D-VBS uses National Library of Medicine's (NLM) Visible Human Male datasets to interactively locate, explore, select, extract, highlight, label, and visualize, realistic 2D (using axial, coronal, and sagittal views) and 3D virtual structures. A real-time self-guided virtual tour of the entire body is designed to provide detailed anatomical information about structures, substructures, and proximal structures. The system thus facilitates learning of visuospatial relationships at a level of detail that may not be possible by any other means. The use of volumetric structures allows for repeated real-time virtual dissections, from any angle, at the convenience of the user. Volumetric (3D) virtual dissections are performed by adding, removing, highlighting, and labeling individual structures (and/or entire anatomical systems). The resultant virtual explorations (consisting of anatomical 2D/3D illustrations and animations), with user selected highlighting colors and label positions, can be saved and used for generating lesson plans and evaluation systems. Tracking users' progress using the evaluation system helps customize the curriculum, making W3D-VBS a powerful learning tool. Our plan is to incorporate other Visible Human segmented datasets, especially datasets with higher resolutions, that make it possible to include finer anatomical structures such as nerves and small vessels.

Anatomy↗
PubMed1988

Operational radiologic image archive on digital optical disks.

A digital optical disk archive for storage of computed radiographic, computed tomographic, magnetic resonance, ultrasonographic, and digitized film radiographic images was installed. In the system, digital images enter a minicomputer, are temporarily stored on magnetic disks, and are archived onto write-once read-many optical disks at their full resolution. A pictorial index of minified images is maintained for each patient. After 8 months of operation, 49,400 megabytes of images had been retained on 19 optical disks stored, after January 1987, in a mechanical jukebox-style optical disk library. The success rate for archival capture of images during the initial period was 96.6%. The failures were due to overfilling of the magnetic disk, a problem addressed through the addition of a second magnetic disk unit. There were no medium-related image errors during the early period. Problems resulting from the slow speed of optical disk systems were addressed operationally by initiating recall of a patient's archived images from the optical to the faster magnetic disk as soon as the system received a request to acquire a new image. Also, optical disk retrieval times are expected to improve with technologic development.

Electronic Data Processing↗
PubMed2005

Evidence-Based Practice: a new paradigm brings new opportunities for health sciences librarians.

It is questionable whether the Evidence-Based Health Care model, whereby end users appraise all potentially pertinent information, is sustainable. A shift to an Evidence-Based Practice model, featuring a new medical knowledge base infrastructure facilitating rapid translation of clinical research into practice should be embraced. This shift would offer new opportunities for health sciences librarians. In this article, the authors: (1) review milestones in the evolution of the health sciences knowledge base; (2) review the evolution of the Evidence- Based Health Care/Practice model of health information utilization; and (3) discuss the significance and implications for health sciences librarians of trends towards an increasingly digital health information environment. The authors suggest new roles for health sciences librarians: partnering to integrate advanced information management technologies into the clinical enterprise and integration into the processes for developing these technologies.

Evidence-Based Medicine↗
PubMed1988

Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes.

Chromosome aberrations in two glioma cell lines were analyzed using biotinylated DNA library probes that specifically decorate chromosomes 1, 4, 7, 18 and 22 from pter to qter. Numerical changes, deletions and rearrangements of these chromosomes were readily visualized in metaphase spreads, as well as in early prophase and interphase nuclei. Complete chromosomes, deleted chromosomes and segments of translocated chromosomes were rapidly delineated in very complex karyotypes. Simultaneous hybridizations with additional subregional probes were used to further define aberrant chromosomes. Digital image analysis was used to quantitate the total complement of specific chromosomal DNAs in individual metaphase and interphase cells of each cell line. In spite of the fact that both glioma lines have been passaged in vitro for many years, an under-representation of chromosome 22 and an over-representation of chromosome 7 (specifically 7p) were observed. These observations agree with previous studies on gliomas. In addition, sequences of chromosome 4 were also found to be under-represented, especially in TC 593. These analyses indicate the power of these methods for pinpointing chromosome segments that are altered in specific types of tumors.

Biotin↗
PubMed1999

Enhancing availability of the electronic image record for patients and caregivers during follow-up care.

PURPOSE: To develop a personal computer (PC)-based software package that allows portability of the electronic imaging record. To create custom software that enhances the transfer of images in two fashions. Firstly, to an end user, whether physician or patient, provide a browser capable of viewing digital images on a conventional personal computer. Second, to provide the ability to transfer the archived Digital Imaging and Communications in Medicine (DICOM) images to other institutional picture archiving and communications systems (PACS) through a transfer engine. METHOD/MATERIALS: Radiologic studies are provided on a CD-ROM. This CD-ROM contains a copy of the browser to view images, a DICOM-based engine to transfer images to the receiving institutional PACS, and copies of all pertinent imaging studies for the particular patient. The host computer system in an Intel based Pentium 90 MHz PC with Microsoft Windows 95 software (Microsoft Inc, Seattle, WA). The system has 48 MB of random access memory, a 3.0 GB hard disk, and a Smart and Friendly CD-R 2006 CD-ROM recorder (Smart and Friendly Inc, Chatsworth, CA). RESULTS: Each CD-ROM disc can hold 640 MB of data. In our experience, this houses anywhere from, based on Table 1, 12 to 30 computed tomography (CT) examinations, 24 to 80 magnetic resonance (MR) examinations, 60 to 128 ultrasound examinations, 32 to 64 computed radiographic examinations, 80 digitized x-rays, or five digitized mammography examinations. We have been able to successfully transfer DICOM images from one DICOM-based PACS to another DICOM-based PACS. This is accomplished by inserting the created CD-ROM onto a CD drive attached to the receiving PACS and running the transfer engine application. CONCLUSIONS: Providing copies of radiologic studies performed to the patient is a necessity in every radiology department. Conventionally, film libraries have provided copies to the patient generating issues of cost of loss of film, as well as mailing costs. This software package saves costs and loss of studies, as well as improving patient care by enabling the patient to maintain an archive of their electronic imaging record.

CD-ROM↗
PubMed1990

Common standards for quantitative electrocardiography: goals and main results. CSE Working Party.

Computer processing of electrocardiograms (ECGs) has over the last 15 years increased rapidly. Still, there are at present no standards for computer ECG interpretation. Different techniques are used not only for measurement and interpretation, but also for transmission and storage of data. In order to fill these gaps, a large international project, sponsored by the European Commission, was launched in 1980 to develop "Common Standards for Quantitative Electrocardiography (CSE)". The main objective of the first CSE study was to reduce the wide variation in wave measurements currently obtained by ECG computer programs. The second study was started in 1985 and aimed at the assessment and improvement of diagnostic classification of ECG interpretation programs. To this end reference libraries of well documented ECGs have been developed and comprehensive reviewing schemes devised for the visual and computer analysis of ECGs. This task was performed by a board of cardiologists in a Delphi review process, and by 9 VCG and 10 standard 12-lead programs developed by university research groups and by industry. A third action was started in June 1989 to harmonize acquisition, encoding, interchange and storing of digital ECG data. The action thus performed have become internationally recognized milestones for the standardization of quantitative electrocardiography.

Algorithms↗
PubMed2005

Life and death on the coral reef: an ecological perspective on scholarly publishing in the health sciences.

OBJECTIVE: Reflecting patterns evident in past Janet Doe lectures, the 2004 address draws on the foundations of biology to provide a model that offers insights into the advent of electronic publications and choices for the future. SETTING: The lecture sketches a picture of the fragile relationships found in complex ecosystems and illustrates how such interdependencies function in the environment of the coral reef. ANALYSIS: Deriving lessons from the marine world, the lecture then shifts to a description of similarities in the realm of scholarly publishing, the impact of digital innovations in the marketplace, and the controversies and choices inherent in open access publications. CONCLUSIONS: Lessons from ecology and publishing lead to the conclusion that librarians must take action and risks in this time of dramatic environmental change.

Ecosystem↗
PubMed2000

Systems of evidence-based healthcare and personalised health information: some international and national trends.

In Europe, North America and elsewhere, growing interest has focussed on evidence-based healthcare systems, incorporating the deployment of practice guidelines, as a field of application for health telematics. The clinical benefit and technical feasibility of common European approaches to this task has recently been demonstrated. In Europe it is likely that, building on recent progress in electronic health record architecture (EHRA) standards, a sufficient state of maturity can be reached to justify initiation within CEN TC251 of a prestandards process on guideline content formats during the current 5th Framework of EC RT&D activity. There is now a similar impetus to agree standards for this field in North America. Thanks to fruitful EC-USA contacts during the 4th Framework programme, there is now a chance, given well-planned coordination, to establish a global consensus optimally suited to serve the world-wide delivery and application of evidence-based medicine. This review notes three factors which may accelerate progress to convergence: (1) revolutionary changes in the knowledge basis of professional/patient/public healthcare partnerships, involving the key role of the Web as a health knowledge resource for citizens, and a rapidly growing market for personalised health information and advice; (2) the emergence at national levels of digital warehouses of clinical guidelines and EBM knowledge resources, agencies which are capable of brokering common mark-up and interchange media definitions between knowledge providers, industry and healthcare organizations; (3) the closing gap in knowledge management technology, with the advent of XML and RDF, between approaches and services based respectively on text mark-up and knowledge-base paradigms. A current project in the UK National Health Service (the National electronic Library of Health) is cited as an example of a national initiative designed to harness these trends.

Artificial Intelligence↗