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PubMed1996

Redundant array of independent disks: practical on-line archiving of nuclear medicine image data.

While various methods for long-term archiving of nuclear medicine image data exist, none support rapid on-line search and retrieval of information. We assembled a 90-Gbyte redundant array of independent disks (RAID) system using 10-, 9-Gbyte disk drives. The system was connected to a personal computer and software was used to partition the array into 4-Gbyte sections. All studies (50,000) acquired over a 7-year period were archived in the system. Based on patient name/number and study date, information could be located within 20 seconds and retrieved for display and analysis in less than 5 seconds. RAID offers a practical, redundant method for long-term archiving of nuclear medicine studies that supports rapid on-line retrieval.

CD-ROM↗

PubMed1997

CD-based image archival and management on a hybrid radiology intranet.

This article describes the design and implementation of a low-cost image archival and management solution on a radiology network consisting of UNIX, IBM personal computer-compatible (IBM, Purchase, NY) and Macintosh (Apple Computer, Cupertino, CA) workstations. The picture archiving and communications system (PACS) is modular, scaleable and conforms to the Digital Imaging and Communications in Medicine (DICOM) 3.0 standard for image transfer, storage and retrieval. Image data is made available on soft-copy reporting workstations by a work-flow management scheme and on desktop computers through a World Wide Web (WWW) interface. Data archival is based on recordable compact disc (CD) technology and is automated. The project has allowed the radiology department to eliminate the use of film in magnetic resonance (MR) imaging, computed tomography (CT) and ultrasonography.

Compact Disks↗

PubMed1999

Benchmark testing the Digital Imaging Network-Picture Archiving and Communications System proposal of the Department of Defense.

The Department of Defense issued a Request for Proposal (RFP) for its next generation Picture Archiving and Communications System in January of 1997. The RFP was titled Digital Imaging Network-Picture Archiving and Communications System (DIN-PACS). Benchmark testing of the proposed vendors' systems occurred during the summer of 1997. This article highlights the methods for test material and test system organization, the major areas tested, and conduct of actual testing. Department of Defense and contract personnel wrote test procedures for benchmark testing based on the important features of the DIN-PACS Request for Proposal. Identical testing was performed with each vendor's system. The Digital Imaging and Communications in Medicine (DICOM) standard images used for the Benchmark Testing included all modalities. The images were verified as being DICOM standard compliant by the Mallinckrodt Institute of Radiology, Electronic Radiology Laboratory. The Johns Hopkins University Applied Physics Laboratory prepared the Unix-based server for the DICOM images and operated it during testing. The server was loaded with the images and shipped to each vendor's facility for on-site testing. The Defense Supply Center, Philadelphia (DSCP), the Department of Defense agency managing the DIN-PACS contract, provided representatives at each vendor site to ensure all tests were performed equitably and without bias. Each vendor's system was evaluated in the following nine major areas: DICOM Compliance; System Storage and Archive of Images; Network Performance; Workstation Performance; Radiology Information System Performance; Composite Health Care System/Health Level 7 communications standard Interface Performance; Teleradiology Performance; Quality Control; and Failover Functionality. These major sections were subdivided into workable test procedures and were then scored. A combined score for each section was compiled from this data. The names of the involved vendors and the scoring for each is contract sensitive and therefore can not be discussed. All of the vendors that underwent the benchmark testing did well. There was no one vendor that was markedly superior or inferior. There was a typical bell shaped curve of abilities. Each vendor had their own strong points and weaknesses. A standardized benchmark protocol and testing system for PACS architectures would be of great value to all agencies planning to purchase a PACS. This added information would assure the purchased system meets the needed functional requirements as outlined by the purchasers PACS Request for Proposal.

Benchmarking↗

PubMed2001

Electronic teaching files: seven-year experience using a commercial picture archiving and communication system.

With the advent of electronic imaging and the internet, the ability to create, search, access, and archive digital imaging teaching files has dramatically improved. Despite the fact that a picture archival and communication system (PACS) has the potential to greatly simplify the creation of, archival, and access to a department or multifacility teaching file, this potential has not yet been satisfactorily realized in our own and most other PACS installations. Several limitations of the teaching file tools within our PACS have become apparent over time. These have, at our facility, resulted in a substantially reduced role of the teaching file tools for conferences, daily teaching, and research purposes. With the PACS at our institution, academic folders can only be created by the systems engineer, which often serves as an impediment to the teaching process. Once these folders are created, multiple steps are required to identify the appropriate folders, and subsequently save images. Difficulties exist for those attempting to search for the teaching file images. Without pre-existing knowledge of the folder name and contents, it is difficult to query the system for specific images. This is due to the fact that there is currently no fully satisfactory mechanism for categorizing, indexing, and searching cases using the PACS. There is currently no easy mechanism to save teaching, research, or clinical files onto a CD or other removable media or to automatically strip demographic or other patient information from the images. PACS vendors should provide much more sophisticated tools to create and annotate teaching file images in an easy to use but standard format (possibly Radiological Society of North America's Medical Image Resource Center [MIRC] format) that could be exchanged with other sites and other vendors' PAC systems. The privilege to create teaching or conference files should be given to the individual radiologists, technologists, and other users, and an audit should be kept of who has created these files, as well as keep track of who has accessed the files. Vendors should maintain a local PACS library of image quality phantoms, normal variants, and interesting cases and should have the capability of accessing central image repositories such as the RSNA's MIRC images. Commercial PAC systems should utilize a standard lexicon to facilitate the creation and categorization of images, as well as to facilitate sharing of images and related text with other sites. This should be combined with a very easy to use mechanism to write images and related text when appropriate onto removable media (while maintaining a high level of security and confidentiality) to make it easier to share images for teaching, research, or clinical purposes.

Computer-Assisted Instruction↗

PubMed1997

[Analysis of the publication spectrum of 4 German-language medical specialty periodicals "Der Chirurg", "Der Unfallchirurg", "Langenbecks Archiv für Chirurgie" and "Medizinische Klinik"].

All 1994 publications of four leading journals in surgery, orthopedics and internal medicine in Germany (Der Chirurg, Der Unfallchirurg, Langenbecks Archiv für Chirurgie, Medizinische Klinik) were reviewed by means of a structured analysis. The type of article, authorship, number of references, geographical location, quality, and main conclusion (positive; neutral; negative) of each article were documented. The journals focused on clinical studies (32.2-59.6%), case reports (11.0-26.1%) and reviews (6.4-40.9%). Articles about surgical techniques were mainly found in Der Chirurg (16.9%), experimental studies in Der Unfallchirurg (14.7%) and Langenbecks Archiv für Chirurgie (25.7%). Most articles were written by university clinic personnel (62.6-81.4%). In 11.0-22.6% of all articles, the head of a clinic was the first author and the co-author in 36.5-58.7%. Women were found to be first author in 4% in surgery, and in 10.4% in internal medicine. Of a total of 495 publications, 53.9% were written in Northrhine-Westphalia, Bavaria or Baden-Württemberg and only 1.6% in the five new federal states. Of all articles 16.4% were by foreign authors, with 10.5% originating from German-speaking countries. The portion of controlled randomized trials ranged between 4.9% (Der Unfallchirurg) and 11.3% (Der Chirurg) of all published studies. Studies and case reports with negative results were found to be more evident in Der Chirurg and Langenbecks Archiv für Chirurgie (ca. 20%) as compared to Der Unfallchirurg and Medizinische Klinik (ca. 6%). All journals provided good general information about the actual developments in a variety of topics to the reader. However, some improvement concerning international contributions, participation of the new federal states, and the quality of studies is recommended.

Authorship↗

PubMed2006

[Digital photography and video archives in ENT].

Digital media have become standard documentation tools in modern ENT clinics. To date, multiple formats are generated by variable data sources. Old fashioned archiving techniques with numerous print-outs, hard copies or even slides would soon generate an unmanageable data flood and require costly manpower for proper and precise maintenance. It has become obvious that data archiving is the prime challenge for modern hospital information technology. Multiple computerized multimedia archives exist and offer promising solutions for collecting and managing these data. From a clinical point of view, not only data centralisation but also interactions with existing network components and hospital information technology systems have to be made available. Here, we describe variable data sources and formats, centralisation techniques, networking options and discuss available digital documentation solutions.

Computer Communication Networks↗

PubMed2003

Detection of HER2/neu gene amplification in archival paraffin-embedded breast cancer tissues by fluorescence in situ hybridization.

We evaluated HER2/neu gene amplification by fluorescence in situ hybridization (FISH) in archival paraffin-embedded breast cancer tissues. Tumors from 63 human invasive breast cancers were categorized into two groups depending on whether the paraffin-embedded tissue blocks had been stored for more or less than 12 months duration. These were subjected to routine and modified FISH protocols. As microwave oven formalin fixation of tissues was carried out in the majority of the older archived specimens, the effect of this fixation method was also analyzed. FISH signals were obtained in all 13 archival specimens stored for less than 12 months. However, in 50 specimens stored for more than 12 months duration, the procedure was successful in only 10 specimens (20%), for which the pretreatment procedure had to be individually optimized for each specimen. There was no significant difference in the detection of FISH signals between microwave oven and routinely fixed specimens.

Breast Neoplasms↗

PubMed2001

A hierarchical storage management (HSM) scheme for cost-effective on-line archival using lossy compression.

A hierarchical storage management (HSM) scheme for cost-effective on-line archival of image data using lossy compression is described. This HSM scheme also provides an off-site tape backup mechanism and disaster recovery. The full-resolution image data are viewed originally for primary diagnosis, then losslessly compressed and sent off site to a tape backup archive. In addition, the original data are wavelet lossy compressed (at approximately 25:1 for computed radiography, 10:1 for computed tomography, and 5:1 for magnetic resonance) and stored on a large RAID device for maximum cost-effective, on-line storage and immediate retrieval of images for review and comparison. This HSM scheme provides a solution to 4 problems in image archiving, namely cost-effective on-line storage, disaster recovery of data, off-site tape backup for the legal record, and maximum intermediate storage and retrieval through the use of on-site lossy compression.

Algorithms↗

PubMed1996

Fluorescence in situ hybridization for the detection of aneuploidy from archived fetal cells.

BACKGROUND: In perinatal settings, fluorescence in situ hybridization has the potential to provide specific chromosome evaluation when full karyotype analysis is not possible because there are no dividing cells. CASE: Based on clinical features, cases of fetal and neonatal demise were selected for evaluation with chromosome-specific probes. Sources of nondividing cells included deparaffinated tissue sections, disaggregated tissue biopsies, and archived, Giemsa-stained slides. CONCLUSION: Diagnostic information was obtained by fluorescence in situ hybridization in three settings: 1) postmortem trisomy 21 identification from paraffin sections following unsuccessful tissue culture, 2) postmortem trisomy 18 confirmation in disaggregated cells from macerated fetal tissues, and 3) retrospective documentation of a cryptic deletion (22q-) in archived metaphase spreads. We encourage familiarity by obstetricians with fluorescence in situ hybridization for chromosomal assessment using archived fetal material.

Abnormalities, Multiple↗

PubMed1993

Improved predictive carrier testing for familial adenomatous polyposis using DNA from a single archival specimen and polymorphic markers with multiple alleles.

Familial adenomatous polyposis (FAP) is an autosomal dominant inherited condition caused by mutations in a candidate tumor suppressor gene, adenomatous polyposis coli. Predictive carrier testing for FAP can be accomplished by DNA linkage or mutation detection analysis. In many FAP families all affected individuals are deceased. Archival tissue specimens, if available from such patients, are a useful source of DNA for molecular analysis. We investigated the carrier risk of a presymptomatic 5-year-old girl with a family history of FAP. An archival specimen of normal colonic tissue was only available from the proband's affected deceased father. We screened DNA extracted from this specimen with dinucleotide repeat (CA/GT)n polymorphic marker (D5S346) linked to the adenomatous polyposis coli gene and established that the proband is at more than 99% risk of developing FAP. The proband's increased risk status was subsequently confirmed by identification of a germline adenomatous polyposis coli gene mutation consisting of a 5 base pair deletion at codon 1061. This strategy of using DNA from archival specimens of affected, unavailable FAP patients will increase the number of at-risk individuals that can be diagnosed presymptomatically.

Adenomatous Polyposis Coli↗

PubMedDate not supplied

Picture archiving and communications systems (PACS).

Although there has been a recent increase in interest in picture archiving and communications systems (PACS) topics, little has been published to assist the non-technical person in understanding the complexities of the technologies required for a PACS implementation. This issue of Current Problems in Radiology defines each PACS component and explains why each is important in a system design. PACS installations at the University of Florida are used as examples to tie the concepts together. The infrastructure required for PACS consists of the information system interfaces, networks, and databases. Information system interfaces guarantee consistent patient data across all platforms and reduce labor requirements by eliminating duplicate data entry. Data networks move information from the originating location to users around the hospital, clinic, campus, city, or world. In the PACS environment, the data consist of patient and study information as well as images and information about these images. Databases organize the data from multiple sources into a coherent package that can be queried for many different purposes, such as retrieving images, reviewing patient and study information, studying practice statistics, and performing outcomes analysis. PACS components consist of acquisition nodes, archives, and output devices. Acquisition nodes may include "digital modalities" such as CT, MRI, nuclear medicine, and computed radiography (CR), along with devices to convert from analog to digital, such as digitizers and frame grabbers. Options for archives are discussed along with configuration schemes. Output devices include both hard copy (film and paper prints) and soft copy (workstations for display and diagnosis). Finally, a description of the PACS installations at the University of Florida is presented, with comments on some of the difficulties and complexities encountered. A discussion of the cost and benefits of PACS is included, along with a forecast of the future of PACS.

Computer Systems↗

PubMedDate not supplied

Selective archiving of radiologic images.

The increasing number of radiographic images is a problem in most radiology departments. The problem will be emphasized with the introduction of digital acquisition and storage of radiographs. Changes in image management strategies will therefore become necessary. Such strategies will have great technologic and financial impact and will probably determine the applicability and success of digital radiography. Based on the experience that not all radiographs are equally important and on the assumption that not every image in a radiology archive can be maintained on-line, we investigated the effect of storing only selected, clinically informative radiographs; i.e., clinical data compression. In 165 routine examinations (77 barium enemas, 16 barium meals and 72 urographies) 2433 films were used (14.7 films per examination). We archived only the 461 films (19%) which were considered to be of future informative value. During a one-year follow-up period none of the 1972 removed films was requested. This indicates that a considerable number of films and a considerable amount of image data can be removed from the archive without affecting the clinical work.

Humans↗

PubMedDate not supplied

Implementation of a large-scale picture archiving and communication system.

This paper describes the implementation of a large-scale picture archiving and communication system (PACS) in a clinical environment. The system consists of a PACS infrastructure, composed of a PACS controller, a database management system, communication networks, and optical disk archive. It connects to three MR units, four CT scanners, three computed radiography systems, and two laser film digitizers. Seven display stations are on line 24 h/day, 7 days/wk in genitourinary radiology (2K), pediatric radiology in-patient (1K and 2K) and outpatient (2K), neuroradiology (2K), pediatric ICU (1K), coronary care unit (1K), and one laser film printing station. The PACS is integrated with the hospital information system and the radiology information system. The system has been in operation since February 1992. We have integrated this PACS as a clinical component in daily radiology practice. It archives an average of 2.0-gigabyte image data per workday. A 3-mo system performance of various components are tabulated. The deployment of this large-scale PACS signifies a milestone in our PACS research and development effort. Radiologists, fellows, residents, and clinicians use it for case review, conferences, and occasionally for primary diagnosis. With this large-scale PACS in place, it will allow us to investigate the two critical issues raised when PACS research first started 10 yrs ago: system performance and cost effectiveness between a digital-based and a film-based system.

Computer Communication Networks↗

PubMed2006

Flashback to the 1960s: utility of archived sera to explore the origin and evolution of Plasmodium falciparum chloroquine resistance in the Pacific.

The increasing frequencies of Plasmodium falciparum strains that are resistant to chloroquine (CQ) and other antimalarials are resulting in a global resurgence of malaria morbidity and mortality. CQ resistance (CQR) is associated with multiple mutations in the P. falciparum chloroquine resistance transporter (pfcrt) gene. The mode and tempo of the accumulation of substitutions leading to these complex CQR haplotypes remain speculative due to the dearth of samples temporally spanning the evolution of drug resistance. The origin and evolution of the CQR alleles of Papua New Guinea (PNG) is particularly ambiguous. It remains unclear whether the pfcrt haplotype in PNG resulted from an independent origin of a CQR haplotype identical in sequence to the South American haplotype, or if this haplotype originated in South America and recombined into a Southeast Asian-derived genome. We sequenced a segment of pfcrt exon 2 from 398 plasmid clones derived from archival human sera collected in the Pacific before and after the first reported cases of CQ treatment failure (n=251) and modern samples (n=147). None of the 251 pfcrt plasmid clones from nine archival samples displayed the C72S or the K76T mutations that are characteristic of CQR strains. In contrast, these two amino acid substitutions were present in all 147 pfcrt plasmid clones from five samples collected between 2001 and 2003; thus, the archival samples represent the baseline parasite genetic diversity before the evolution of CQR strains. We are currently expanding our analyses to include additional samples from the series described here and from series collected in the 1970s and the 1980s to evaluate the geographic origin of CQR strains in the Pacific and the validity of the sequential point mutation accumulation model of CQR evolution.

Amino Acid Sequence↗

PubMed2006

Multiple strand displacement amplification of DNA isolated from human archival plasma/serum: identification of cytokine polymorphism by pyrosequencing analysis.

BACKGROUND: DNA isolation from formalin-fixed paraffin-embedded tissue appears to be problematic due to degradation caused by fixative. Our aim was to investigate if the isolated genomic DNA from archival plasma/serum, combined with multiple strand displacement amplification (MDA) can be used for genotyping. METHODS: Nine archival plasma/serum samples and freshly frozen gastric biopsies from the same nine H. pylori-infected subjects were used for DNA isolation. Subsequently, MDA-DNA derived from the plasma/serum samples and DNA isolated from the antrum biopsies were analyzed by PCR amplification and pyrosequencing for the presence of interleukin-1beta gene (IL-1B) single nucleotide polymorphism (SNP). In addition, Southern blot and pyrosequencing analysis of H. pylori-specific PCR amplicons were performed. RESULTS: IL-1B SNP profiles obtained from the plasma/serum MDA-DNA and antrum biopsy DNA were identical. A C/C genotype was observed in 7 of 9 samples, and 2 of 9 revealed a C/T genotype for IL-1B -511. Similarly, 7 of 9 had a T/T, and 2 of 9 had a C/T genotype for IL-1B -31; 4 of 9 had a C/C, 4 of 9 had a C/T, and 1 of 9 had a T/T genotype, respectively, for IL-1B +3954. Moreover, pyrosequencing analysis revealed the presence of H. pylori 26695 and J99-like 16S rDNA variable V3 region sequence motifs in the antrum biopsies but not in the plasma/serum samples. CONCLUSIONS: We conclude that MDA combined with pyrosequencing enables a rapid and accurate molecular typing of cytokine single nucleotide polymorphisms from archival plasma/serum samples.

Base Sequence↗

PubMed2004

Assaying particle-bound polycyclic aromatic hydrocarbons from archived PM2.5 filters.

Airborne particulate matter contains numerous organic species, including several polycyclic aromatic hydrocarbons (PAHs) that are known or suspected carcinogens. Existing methods for measuring airborne PAHs are complex and costly, primarily because they are designed to collect both gas-phase and particle-phase PAH constituents. Here, we report an assay for measuring particle-bound PAHs in archived filters from the network of U.S. monitoring stations for particles less than 2.5 microm in diameter (PM2.5), without the need for deploying specialized samplers. PAHs are extracted from Teflon filters with dichloromethane, concentrated, and measured at trace levels using gas chromatography-mass spectrometry. Although PAHs with 3-6 aromatic rings can be assayed, results are only unambiguously accurate for compounds with 5- or 6-rings, due to variable vaporization losses of the more volatile 3- and 4-ring compounds during sampling and/or storage. The method was evaluated for sensitivity, recovery, precision, and agreement of paired air samples, using PM2.5 samplers locally in Chapel Hill, NC. Additionally, three sets of archived samples were analyzed from a study of PM2.5 in the Czech Republic. Levels of some 4-ring and all 5- and 6-ring PAHs in both the local and Czech samples were consistent with published results from investigations employing PAH-specific air samplers. This work strongly suggests that assessment of particle-bound 5- and 6-ring PAHs from archived PM2.5 filters is quantitatively robust. The assay may also be useful for selected 4-ring compounds, notably chrysene and benzo(a)anthracene, if PM2.5 filters are stored under refrigeration.

Filtration↗

PubMed2006

Validation of XP-C pathogenic variations in archival material from a live XP patient.

Xeroderma pigmentosum (XP) genetic complementation group C (XP-C) is the most common form of the disease worldwide. Thirty-four distinct genetic defects have been identified in 45 XP-C patients. Further identification of such defects and the frequency of their occurrence offers the potential of generating diagnostic and prognostic molecular screening panels. Archival material (such as formalin-fixed paraffin embedded skin) may be useful for the identification of novel genetic variations and for documenting the frequency of individual genetic defects in patients who are no longer available for study. However, the use of archival material precludes direct analysis of changes in the mRNA resulting from genomic changes. The serendipitous reacquisition of an XP individual in whom genetic defects were previously characterized in archival material allowed confirmation of the defects as well as a direct analysis of the consequences of these defects on mRNA, mRNA expression and on cellular phenotypes.

Cell Survival↗

PubMed2004

Microdissection genotyping of archival fixative treated tissue for Gaucher disease.

The genetic diagnosis of Gaucher disease by molecular methods is complicated by the existence of a highly homologous transcribed pseudogene (96% identity) that is found in close proximity to the true gene on chromosome 1q21. In addition, the pseudogene sequence can mimic disease-causing mutations in the true gene. Selective polymerase chain reaction (PCR) amplification of the true gene can be accomplished in extracted DNA from fresh-frozen samples by designing oligonucleotide primers to hybridize to defined regions that are not present in the pseudogene. This standard molecular approach, which entails amplification of relatively long segments of intact DNA, is not feasible in archival, paraffin-embedded, solid-tissue specimens in which the negative effects of chemical fixation result in DNA strand scission and breakdown of nucleic acid. A novel approach, specifically created for use with archival, fixative-treated tissue specimens, was developed for detection and characterization of common mutations of Gaucher disease. Three separate robust PCR reactions were formulated, 2 for selective amplification of portions of only the true gene exons 2 and 9, with a third reaction targeting exon 10, wherein both the true and pseudogene were coamplified. In the latter, DNA sequencing was used to determine the presence of true and pseudogene allele content in addition to identification of base sequence alterations. This method, requiring a single, 4-microm-thick histologic section, was successfully applied to archival paraffin block tissue specimens that had been in storage for up to 75 years. It was capable of accurately genotyping common Gaucher disease mutations as well as discovering a novel mutation and genetic polymorphism. We recommend our approach when only fixative-treated tis sue is available for molecular genotyping.

DNA Primers↗