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At least 109 records · Page 6Linked to original sources
PubMed2001

Diagnosis of aneuploidy in archival, paraffin-embedded pregnancy-loss tissues by comparative genomic hybridization.

OBJECTIVE: To evaluate the detection of aneuploidy in archival tissues from miscarriages by a method that uses microdissection and DNA extraction of villus cells from paraffin blocks, followed by universal DNA amplification and comparative genomic hybridization (CGH). DESIGN: Retrospective analysis. SETTING: Academic medical center. PATIENT(S): Nine archival tissues from cases of spontaneous abortion with trisomy 16 (two cases), trisomy 21 (three cases), trisomy 22 (two cases), triploidy (one case), and monosomy X (one case). INTERVENTION(S): Villus DNA was extracted from microdissected, formalin-fixed, paraffin-embedded tissues. Aneuploidy was detected by CGH after universal amplification of the DNA with the use of degenerate oligonucleotide-primed polymerase chain reaction. MAIN OUTCOME MEASURE(S): Detection of aneuploidy in archival pregnancy-loss tissues using CGH. RESULT(S): In all nine cases, DNA was successfully extracted from the microdissected tissues and was of sufficient quantity and quality for evaluation by CGH. In six of nine cases, the chromosomal abnormality detected by conventional cytogenetic analysis was identified by CGH: trisomy 16 (2/2), trisomy 21 (3/3), and trisomy 22 (1/2). One case of each of the following was not detectable: triploidy (1/1), monosomy X (1/1), and trisomy 22 (1/2). CONCLUSION(S): We propose CGH as a method for determination of aneuploidy in pregnancy-loss archival tissues when conventional cytogenetic analysis is unsuccessful or when it was not performed when fresh tissue was available.

Abortion, Spontaneous↗
PubMed2002

The Protein Data Bank: unifying the archive.

The Protein Data Bank (PDB; http://www.pdb.org/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the progress that has been made in validating all data in the PDB archive and in releasing a uniform archive for the community. We have now produced a collection of mmCIF data files for the PDB archive (ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/). A utility application that converts the mmCIF data files to the PDB format (called CIFTr) has also been released to provide support for existing software.

Amino Acid Sequence↗
PubMed2004

The European Radiobiology Archives (ERA), present state and future developments.

The European Radiobiology Archives (ERA) aims to collect most of the information still available in Europe on long-term animal experiments--including some selected human studies suitable for comparison with animal data--and to make them available to the scientific community for further analysis. ERA cooperates with the US (National Radiobiology Archives, NRA) and Japan (Japanese Radiobiology Archives, JRA) in the International Radiobiology Archives (IRA).

Animals↗
PubMed2001

Motor vehicle crash involvement and moving violations: convergence of self-report and archival data.

In the crash involvement literature, it is generally assumed that archival and other "objective" criterion data are superior to self-reports of crash involvement. Using 394 participants (mean age = 36.23 years), the present study assessed the convergence of archival and self-report measures of motor vehicle crash involvement and moving violations. We also sought to determine whether predictor/criterion relationships would vary as a function of criterion type (i.e., archival vs. self-report), and if a combination of both criteria would result in better prediction than would either by itself. The degree of agreement between the two criterion sources was low, with participants self-reporting more crashes and tickets than were found in their state records. Different predictor/criterion relationships were also found for the two criterion types; stronger effects were obtained for self-report data. Combining the two criteria did not result in relationships stronger than those obtained for self-reports alone. Our findings suggest that self-report data are not inherently inferior to archival data and, furthermore, that the two sources of data cannot be used interchangeably. Actual or potential applications include choosing the appropriate criterion to use, which, as the finding of this study reveals, may depend on the purpose of the investigation.

Accidents, Traffic↗
PubMed2000

Archiving of care related information in XML-format.

Patient related care information is important over long periods of time. Thus it cannot be stored in running systems handling day by day information exchange. In the future, when the demands arise to use patient related information, neither the programmes nor the databases, in which the information once was fed, will be available. These facts imply that electronically stored patient related information must be electronically accessible and searchable and thus the information must be stored in a time-invariant way. In future use of patient related information it is of extraordinary importance both nationally, in the EU and internationally to use a standardised way to handle and access archived patient related information. Already in 1995 the search for a solution of these issues was initialised at the Health Informatics Department at Spri--the Swedish National Institute for Health Services Development. A number of internal reports have been produced as background information. Further work has to be carried out at relevant organisational levels in order to structure and logically harmonise an archiving format. The basic XML-format has been preliminary tested by a Spri project and found suitable. Spri has advised the Swedish National Board of Health and Welfare and the Swedish National Archive to issue directives concerning the use of XML as the archive-format for EHCR (Electronic Health Care Record) information.

Archives↗
PubMed1998

Documentation of the history of malaria in Italy at the Rockefeller Archive Center.

The Rockefeller Archive Center holds approximately 50,000 pages of archival documents pertaining to the history of anti-malaria programs in Italy in the 20th century. Reports on the status of public health in Italy occur in the archives dating from 1915, but there was no sustained Rockefeller commitment to anti-malaria work in Italy until 1924. The article presents a brief description of the sources for the study of the history of malaria in Italy that are held at the Rockefeller Archive Center.

Archives↗
PubMed1990

Flow cytometric DNA ploidy analysis of soft tissue sarcomas. A comparative study of preoperative fine needle aspirates and postoperative fresh tissues and archival material.

Flow cytometric (FCM) DNA ploidy measurements on frozen fresh samples of soft tissue sarcomas were compared with the corresponding analyses on preoperative fine needle aspirates and postoperative formalin-fixed archival tissues from the same tumors. A concordance in ploidy status (diploid versus non-diploid) was obtained for 63% of the fresh tissue-fine needle aspiration (FNA) sample comparisons and for 85% of the fresh tissue-archival material comparisons. The majority of discordances in the fresh tissue-FNA sample comparisons could be explained by FNA sampling errors. In the remaining discordant cases (3 of 27 FNA sample comparisons and 6 of 40 archival material comparisons), sampling errors could not explain the differences in ploidy status. The discordant cases were evenly distributed among the different sampling methods. Method reproducibility was not responsible for the differences in ploidy determinations; tumor heterogeneity may be an explanation for the discrepancies. This study showed that archival soft tissue sarcoma samples are as well suited for DNA ploidy analysis as are fresh frozen tissues.

Archives↗
PubMed1984

Building an archives in a medical library.

In 1979 the University of Medicine and Dentistry of New Jersey established an archives to collect, preserve, and retrieve important documentation related to its history. This paper examines various steps in building an archives and the development of a coherent collection policy, including potential sources for archival material. Problems and possible solutions concerning what to preserve from the vast quantities of material generated by an institution are considered. The relationship between the archives and the medical library and the requirements of the physical plant are discussed, including the storage and preservation of materials.

Archives↗
PubMed1994

Caveats in the use of archival cell material for DNA ploidy analysis by image cytometry.

Monolayer preparation from paraffin-embedded tissue from archival biopsy specimens older than 10 years was shown in this study to be more difficult to deal with than recent biopsies. We have studied the disseminative effect of several enzymes on archival biopsies from laryngeal epithelium, as well as mechanical dissemination. Thirty minutes incubation in protease 0.5% in 37 degrees C without syringing provided the best cell yield. Hydrolysis and Schiff staining conditions were also studied. Cell loss was calculated by stereological methods and found to be high in most cases. Cell loss during various steps in monolayer production was examined and we found no proof of selective cell loss. Large variations in Feulgen-Schiff staining intensities were observed, especially in biopsy specimens older than 10 years. The use of reliable internal (intrinsic) control cells is advocated since interspecimen variations in the diploid integrated optical density (IOD) can be expected. Although DNA measurements on archival biopsy material should be treated with caution, we demonstrate that meticulous studies of the preparation procedures will make it possible to obtain reliable histograms from old, archival biopsies.

Archives↗
PubMed2004

Move over ANOVA: progress in analyzing repeated-measures data and its reflection in papers published in the Archives of General Psychiatry.

BACKGROUND: The analysis of repeated-measures data presents challenges to investigators and is a topic for ongoing discussion in the Archives of General Psychiatry. Traditional methods of statistical analysis (end-point analysis and univariate and multivariate repeated-measures analysis of variance [rANOVA and rMANOVA, respectively]) have known disadvantages. More sophisticated mixed-effects models provide flexibility, and recently developed software makes them available to researchers. OBJECTIVES: To review methods for repeated-measures analysis and discuss advantages and potential misuses of mixed-effects models. Also, to assess the extent of the shift from traditional to mixed-effects approaches in published reports in the Archives of General Psychiatry. DATA SOURCES: The Archives of General Psychiatry from 1989 through 2001, and the Department of Veterans Affairs Cooperative Study 425. STUDY SELECTION: Studies with a repeated-measures design, at least 2 groups, and a continuous response variable. DATA EXTRACTION: The first author ranked the studies according to the most advanced statistical method used in the following order: mixed-effects model, rMANOVA, rANOVA, and end-point analysis. DATA SYNTHESIS: The use of mixed-effects models has substantially increased during the last 10 years. In 2001, 30% of clinical trials reported in the Archives of General Psychiatry used mixed-effects analysis. CONCLUSIONS: Repeated-measures ANOVAs continue to be used widely for the analysis of repeated-measures data, despite risks to interpretation. Mixed-effects models use all available data, can properly account for correlation between repeated measurements on the same subject, have greater flexibility to model time effects, and can handle missing data more appropriately. Their flexibility makes them the preferred choice for the analysis of repeated-measures data.

Analysis of Variance↗
PubMed2000

Simulation of disaster recovery of a picture archiving and communications system using off-site hierarchal storage management.

The purpose of this communication is to report on the testing of the disaster recovery capability of our hierarchical storage management (HSM) system. Disaster recovery implementation is a requirement of every mission-critical information technology project. Picture archiving and communications systems (PACS) certainly falls into this category, even though the counterpart, conventional film archive, has no protection against fire, for example. We have implemented a method for hierarchical storage with wavelet technology that maximizes on-site case storage (using lossy compression), retains bit-preserved image data for legal purposes, provides an off-site backup (lossless bit-preserving wavelet transform), and provides for disaster recovery. Recovery from a natural (earthquake and subsequent fire) or technical (system crash and data loss) disaster was simulated by attempting to restore from the off-site image and database backup to clean core PACS components. The only existing loaded software was the operating system. The database application was reloaded locally, and then the database contents and image store were loaded from the off-site component of the HSM system. The following measurements were analyzed: (1) the ability to recover all data; (2) the integrity of the recovered database and image data; (3) the time to recover the database relative to the number of studies and age of the archive, as well as bandwidth between the local and remote site; and (4) the time to recover image data relative to compression ratio, number of studies, number of images, and time depth of the archive. This HSM system, which maximizes on-site storage, maintains a legal record, and provides off-site backup, also facilitates disaster recovery for a PACS.

Computer Storage Devices↗
PubMed2000

Effects of a large-scale deployment of soft-copy devices for picture archiving and communication systems viewing.

A study was developed to investigate several aspects of deployment of stand-alone computers and a web-based server for displaying digital images. The costs associated with installation, upgrades, training, and maintenance of both systems were documented, as well as patterns of usage and preferences of physicians for the two types of systems. A clinical archive was created to store relevant images with a web-based front end. Users were classified according to their imaging requirements and were given access to images from either the diagnostic archive (full study sets) or the clinical archive. The range of functionality of the web-based system was significantly lower than that of the stand-alone system; however, the costs associated with the administration of the stand-alone systems were far higher than those associated with a web server. A clinical archive was created to store relevant images with a web-based front end. This study illustrates the different approaches to distribution of images to clinicians with the costs of administration of each system.

Computer Storage Devices↗
PubMed1996

Large picture archiving and communication systems of the world--Part 2.

A survey of 82 institutions worldwide was done in 1995 to identify large picture archiving and communication systems (PACS) in clinical operation. A continuing strong trend toward the creation and operation of large PACS was identified. In the 15 months since the first such survey the number of clinical large PACS went from 13 to 23, almost a doubling in that short interval. New systems were added in Asia, Europe, and North America. A strong move to primary interpretation from soft copy was identified, and filmless radiology has become a reality. Workstations for interpretation reside mainly within radiology, but one-third of reporting PACS have more than 20 workstations outside of radiology. Fiber distributed data interface networks were the most numerous, but a variety of networks was reported to be in use. Replies on various display times showed surprisingly good, albeit diverse, speeds. The planned archive length of many systems was 60 months, with usually more than 1 year of data on-line. The main large archive and off-line storage media for these systems were optical disks and magneto-optical disks. Compression was not used before interpretation in most cases, but many systems used 2.5:1 compression for on-line, interpreted cases and 10:1 compression for longer-term archiving. A move to digital imaging and communication in medicine interface usage was identified.

Asia↗
PubMed2001

The Digital Imaging and Communications in Medicine (DICOM) archive is a dynamic component of a clinician image-related workflow solution.

The authors investigated clinician transactions against the Digital Imaging and Communications in Medicine (DICOM) archive within a clinical image management system (CIMS) in support of patient care. A Neurosurgical Oncology practice was audited for image utilization. There were 400 requests for 233 image studies during 297 sessions. Fifty percent were for current studies, and 50% were for historical studies. Current studies alone were requested in 37% of the sessions, current plus historical in 31%, and historical alone in 32% of the sessions. Seventy percent of studies were within 8 weeks old and were rapidly available from the CIMS disk cache without an archive image transaction. Conversely, 30% were older than 8 weeks, requiring a clinician transaction against the archive for image retrieval. Approximately 25% of studies were older than 3 months and 10% older than 6 months. Clinician image needs are complex and any CIMS solution must include a DICOM archive that can support clinician-based transactions.

Database Management Systems↗
PubMed2002

Enterprise utilization of "always on-line" diagnostic study archive.

To meet demands for enterprise image distribution, an "always on-line" image storage archive architecture was implemented before soft copy interpretation. It was presumed that instant availability of historical diagnostic studies would elicit a substantial utilization. Beginning November 1, 2000 an enterprise distribution archive was activated (Stentor, SanFrancisco, CA). As of August 8, 2001, 83,052 studies were available for immediate access without the need for retrieval from long-term archive. Image storage and retrieval logs for the period from June 12, 2001 to August 8, 2001 were analyzed. A total of 41,337 retrieval requests were noted for the 83,052 studies available as August 8, 2001. Computed radiography represented 16.8% of retrieval requests; digital radiography, 16.9%; computed tomography (CT), 44.5%; magnetic resonance (MR), 19.2%; and ultrasonography, 2.6%. A total of 51.5% of study retrievals were for studies less than 72 hours old. Study requests for cases greater than 100 days old represented 9.9% of all accessions, 9.7% of CT accessions, and 15.4% of MR accessions. Utilization of the archive indicates a substantial proportion of study retrievals for studies less than 72 hours after study completion. However, significant interest in historical CT and MR examinations was shown.

Online Systems↗
PubMed2005

Electronic signatures for long-lasting storage purposes in electronic archives.

Communication and co-operation in healthcare and welfare require a certain set of trusted third party (TTP) services describing both status and relation of communicating principals as well as their corresponding keys and attributes. Additional TTP services are needed to provide trustworthy information about dynamic issues of communication and co-operation such as time and location of processes, workflow relations, and system behaviour. Legal and ethical requirements demand securely stored patient information and well-defined access rights. Among others, electronic signatures based on asymmetric cryptography are important means for securing the integrity of a message or file as well as for accountability purposes including non-repudiation of both origin and receipt. Electronic signatures along with certified time stamps or time signatures are especially important for electronic archives in general, electronic health records (EHR) in particular, and especially for typical purposes of long-lasting storage. Apart from technical storage problems (e.g. lifetime of the storage devices, interoperability of retrieval and presentation software), this paper identifies mechanisms of e.g. re-signing and re-stamping of data items, files, messages, sets of archived items or documents, archive structures, and even whole archives.

Computer Security↗
PubMed2004

Optimisation and validation of methods to assess single nucleotide polymorphisms (SNPs) in archival histological material.

BACKGROUND AND PURPOSE: An increasing amount of evidence indicates that single nucleotide polymorphisms (SNPs) may affect a variety of oncology related phenotypes. Occasionally, it is convenient to base studies addressing genotype-phenotype relationships on historical patient cohorts, from which only archival specimens are available. This study was conducted to validate protocols optimised for assessment of SNPs based on paraffin embedded, formalin fixed tissue samples. PATIENTS AND METHODS: In 137 breast cancer patients, three TGFB1 SNPs were assessed based on archival histological specimens. In 37 of these patients, the SNPs were also assessed using cultured fibroblasts and the assays were validated by direct comparison of the results. From the remaining 100 patients, only archival material was available. In these patients, the existence of a genetic linkage pattern between the assessed TGFB1 SNPs was used to provide an indirect validation of the genotyping results. Furthermore, two different methods for DNA extraction were compared (semi-automatic DNA extraction using the ABI Prism 6100 Nucleic Acid PrepStation versus Proteinase K digestion for 5 days followed by boiling and DNA precipitation). RESULTS: Assessment of SNPs based on archival histological material is encumbered by a number of obstacles and pitfalls. However, these can be widely overcome by careful optimisation of the methods used for sample selection, DNA extraction and PCR. Within 130 samples that fulfil the criteria for analysis a highly reliable SNP assessment was observed. The study demonstrated that different 'down-stream applications' ('single nucleotide primer extension' or 'TaqMan-based' real-time PCR) could be used as genotyping procedure. CONCLUSIONS: Reliable assessment of SNPs in formalin-fixed paraffin-embedded specimens is possible but a number of precautions should be carefully taken.

Biological Specimen Banks↗
PubMed2006

Expression analysis of mRNA in formalin-fixed, paraffin-embedded archival tissues by mRNA in situ hybridization.

Gene expression in diseased tissues can indicate the contribution to a disease process and potentially guide therapeutic decision-making. Archival tissues with associated clinical outcome may be useful to discover or validate the role of a candidate gene in a disease process or the response to therapy. Such archival tissues are commonly formalin-fixed and paraffin-embedded, restricting the methods available for gene expression analysis. Obviously, the detection of proteins in tissues requires adaptation for each protein and the detection of secreted proteins can prove difficult or of reduced value since the protein detected may not reflect the total amount produced. Thus, we describe here a reliable method for the detection of mRNA in archival tissues. The method for mRNA in situ hybridization (ISH) was adapted by us for >15 different genes and applied to several hundred tissue microarrays (TMAs) and full sections generating >10,000 expression data points. We also discuss the utility of TMAs to simultaneously analyze several hundred tissue samples on one slide to minimize variability and preserve valuable tissue samples. Experimental protocols are provided that can be implemented without major hurdles in a typical molecular pathology laboratory and we discuss quantitative analysis as well as advantages and limitations of ISH with a special focus on secreted proteins. We conclude that ISH is a reliable and cost effective approach to gene expression analysis in archival tissues that is amenable to screening of series of tissues or of genes of interest.

Animals↗