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PubMed2002

Improved detection of apoptotic cells in archival paraffin sections: immunohistochemistry using antibodies to cleaved caspase 3.

Apoptosis has gained central importance in the study of many biological processes, including neoplasia, neurodegenerative diseases, and development. One of the limitations of many studies is the difficulty of specifically identifying individual apoptotic cells. Of the many specific methods developed to detect apoptotic cells, most are not applicable to histological sections of archival paraffin-embedded tissues. Recently, advances in the understanding of the molecular events in apoptosis have led to the realization that caspase activation is by far the most specific indicator of this cell suicide mechanism. Several publications have reported the development of antibodies directed at neoepitopes that are generated in various substrates through the action of caspases. One of these is that present on activated caspase 3, a ubiquitously distributed caspase that is a main effector caspase of the apoptotic cascade within cells. This study demonstrates the utility of using a recently commercially available antibody to cleaved caspase 3 in archival paraffin sections, suggesting that this may be a highly specific and sensitive method generally applicable to many studies of archival material.

Antibodies↗

PubMed1998

Detection of human papillomavirus in archival tissues. Comparison of in situ hybridization and polymerase chain reaction.

Formalin-fixed, paraffin-embedded tissues in pathology archives are an important resource for molecular epidemiology studies. Use of these tissues requires that assays be optimized to account for inevitable variations in tissue fixation and processing that occur in the performance of routine histology. We compared results of colorimetric in situ hybridization (ISH) to L1 consensus polymerase chain reaction (PCR) for detection and typing of human papillomavirus (HPV) in 180 blocks of archival tissues (up to 9 years in storage) from cervical cancer patients. Fifteen samples could not be amplified by PCR, but assays were concordant in 75.1% (124/165) of samples that could be analyzed by both methods. Similar numbers of ISH+/PCR- (23) and ISH-/PCR+ (18) cases were found. Eight of the 18 ISH-/PCR+ cases were attributable to PCR detection of HPV types not included in the ISH assay. This degree of concordance required individual optimization of assay conditions for each block. ISH and PCR assays for HPV yield complementary results, and both can be successfully applied to archival tissues.

Female↗

PubMed1993

Prototype system for archiving and transmitting digitized radiographs.

A prototype system for archiving and transmitting digitized dental radiographs is described. The system uses a CCD video camera, IBM compatible personal computer with a frame-grabber and a high resolution VGA monitor. All archived images were compressed lossless by a factor of about 3. Digitized radiographs were archived together with their exposure data and assembled in an examination with a unique identifier and date of examination, together with the patient's history and reason for radiological examination. A radiological report with a list of differential diagnoses could be attached. Each examination could contain 50 digitized radiographs which could be converted to a tagged image file (TIFF) and printed halftone with a laser printer. Users of the system could receive examinations from the network-server and share the images in a local area network.

Humans↗

PubMed2005

RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain.

microRNAs (miRNAs) are small (approximately 22 nucleotide) regulatory RNAs which play fundamental roles in many biological processes. Recent studies have shown that the expression of many miRNAs is altered in various human tumors and some miRNAs may function as oncogenes or tumor suppressor genes. However, with the exception of glioblastoma multiforme, the expression of miRNAs in brain tumors is unknown. Furthermore, methods to profile miRNAs from formalin-fixed, paraffin-embedded (FFPE) archival tissues or to study their cellular and subcellular localization in FFPE tissues have been lacking. Here we report the coordinated miRNA expression analysis from the tissue level to the subcellular level, using the RAKE (RNA-primed, array-based, Klenow Enzyme) miRNA microarray platform in conjunction with Locked Nucleic Acid (LNA)-based in situ hybridization (LNA-ISH) on archival FFPE human brains and oligodendroglial tumors. The ability to profile miRNAs from archival tissues at the tissue level, by RAKE microarrays, and at the cellular level by LNA-ISH, will accelerate studies of miRNAs in human diseases.

Brain↗

PubMed1994

Cloning and sequencing of genomic DNA extracted from archival human temporal bone sections.

Cloning techniques allow the engineering and production of highly purified DNA. Further advances in molecular biology have provided the means to identify DNA sequences in a rapid fashion. Sequencing methods can identify mutations, deletions, polymorphisms, or confirm a known genetic sequence. The use of these techniques in clinical medicine has made it possible to accurately diagnose infectious diseases and determine the molecular etiology of many genetic disorders and malignancies. In this study, DNA extracted from archival, celloidin-embedded temporal bone sections has been cloned and sequenced using these techniques. We amplified, cloned, and sequenced varicella-zoster viral DNA extracted from archival temporal bone sections from patients who had herpes zoster oticus. The application of cloning and sequencing techniques to DNA extracted from archival temporal bones provides the methodology to study temporal bone pathology at the molecular level.

Base Sequence↗

PubMed2005

Detection of CX3CR1 single nucleotide polymorphism and expression on archived eyes with age-related macular degeneration.

There is a significant genetic component in age-related macular degeneration (AMD). CX3CR1, which encodes the fractalkine (chemokine, CX3CL1) receptor, has two single nucleotide polymorphisms (SNPs): V249I and T280M. These SNPs are correlated with other aged-related diseases such as atherosclerosis. We have reported an association of CX3CR1 SNP and AMD. In this study we examined CX3CR1 SNP frequencies and protein expression on archived sections of AMD and normal eyes. We microdissected non-retinal, peripheral retinal and macular cells from archived slides of eyes of AMD patients and normal subjects. CX3CR1 SNP typing was conducted by PCR and restriction fragment length polymorphism analysis. CX3CR1 transcripts from retinal cells were also measured using RT-PCR. CX3CR1 protein expression was evaluated using avidin-biotin complex immunohistochemistry. We successfully extracted DNA from 32/40 AMD cases and 2/2 normal eyes. Among the 32 AMD cases, 18 had neovascular AMD and 14 had non-neovascular AMD. The M280 allele was detected in 19/64 (32 cases x2) with a frequency of 29.7%, which was significantly higher as compared to the frequency in the normal population (11.2%). We detected CX3CR1 expression in the various retinal cells. CX3CR1 transcript and protein levels were diminished in the macular lesions. This study successfully analyzed CX3CR1 SNP and transcript expression in microdissected cells from archived paraffin fixed slides. Our data suggest that the M280 allele, a SNP resulting in aberrant CX3CR1 and CX3CL1 interaction, as well as lowered expression of macular CX3CR1, may contribute to the development of AMD.

Age Factors↗

PubMed2004

Natural sound archives: past, present and future.

Recordings of wild animals were first made in the Palearctic in 1900, in the Nearctic in 1929, in Antarctica in 1934, in Asia in 1937, and in the Neotropics in the 1940s. However, systematic collecting did not begin until the 1950s. Collections of animal sound recordings serve many uses in education, entertainment, science and nature conservation. In recent years, technological developments have transformed the ways in which sounds can be sampled, stored and accessed. Now the largest collections between them hold altogether around 0.5 million recordings with their associated data. The functioning of a major archive will be described with reference to the British Library Sound Archive. Preserving large collections for the long term is a primary concern in the digital age. While digitization and digital preservation has many advantages over analogue methods, the rate of technology change and lack of standardization are a serious problem for the world's major audio archives. Another challenge is to make collections more easily and widely accessible via electronic networks. On-line catalogues and access to the actual sounds via the internet are already available for some collections. Case studies describing the establishment and functioning of sound libraries in Mexico, Colombia and Brazil are given in individually authored sections in an Appendix.

Analog-Digital Conversion↗

PubMed1994

Accessing picture archiving and communication system text and image information through personal computers.

Recent advances in storage technology have made possible the archiving of tremendous amounts of text and image information within a picture archiving and communication system (PACS). However, a radiologist's access to this information typically has been limited to viewing workstations designed primarily to support clinical activities. Unfortunately, these workstations often overlook the benefits of PACS in teaching and research applications, which are of significant importance in an academic institution. To support such activities at our own institution, we have included two major objectives in our second-generation PACS development: (1) to provide access to text and image information archived within our PACS in an environment that is easily accessible to and comfortable for our radiologists, namely, their own Macintosh (Apple Computer, Cupertino, CA) personal computers; and (2) to provide this information in standard Macintosh formats, so that tools with which radiologists are already familiar can be used in frequently performed teaching activities--the production of slides and prints, the maintenance of personal teaching and research files, and specialized image analysis and processing.

Computer Communication Networks↗

PubMedDate not supplied

A package for cost and critical analysis of picture archiving and communication indicating its true yield (CAPACITY).

The hospital-wide use of picture archiving and communication systems (PACS) promises a number of advantages in the future. These benefits will only be obtained at considerable costs, however. In view of the rapidly developing technology the costs of hardware can be expected to decrease. The ideas about the expected moment when the benefits will exceed the costs show wide variation. In order to get a better view on the cost comparison between PACS and the classical film-based system and also to stimulate discussions on this topic, a software package called CAPACITY (cost and critical analysis of picture archiving and communication indicating its true yield) has been developed by BAZIS within the scope of its IMAGIS (image information system) project. CAPACITY calculates the costs in the year of introduction for both situations, conventional and PACS, based on the consumption or use of the various resources (e.g. film, optical disks, manpower in the archive, operators, network, workstations etc.) needed for the production of the radiological department. These two costs are calculated for a series of years, thus giving an indication for the moment of breakeven. User-supplied data is interrelated and checked for plausibility against a number of expert given rules of thumb by CAPACITY's critique module. The first results and experiences acquired during a pilot study using a prototype version of the package will be discussed. The CAPACITY package is available for evaluation and trial (only distribution costs will be charged if experiences and results are returned).

Computer Simulation↗

PubMed2006

Digital video recording and archiving in ophthalmic surgery.

Currently most ophthalmic operating rooms are equipped with an analog video recording system [analog Charge Couple Device camera for video grabbing and a Video Cassette Recorder for recording)]. We discuss the various advantages of a digital video capture device, its archiving capabilities and our experience during the transition from analog to digital video recording and archiving. The basic terminology and concepts related to analog and digital video, along with the choice of hardware, software and formats for archiving are discussed.

Computer Storage Devices↗

PubMed1999

Image analysis software for automatic DNA ploidy assessment of archival solid tumours.

BACKGROUND: Image cytometry has proved to provide a good alternative to flow cytometry for DNA ploidy measurement of archival tumors. However, when interactively done this technique is unable to give statistically valuable results within an acceptable time for clinical oncology. METHODS: An image cytometer was developed for fully automatic DNA ploidy quantitation, focusing efforts on speed and accuracy. Software functionalities include systematic acquisition of fields on a microscopic slide, detection, localization and sorting of nuclei, computation of the DNA content together with post-processing tools, for a deeper analysis of the DNA ploidy diagram. RESULTS: DNA ploidy analysis of archival breast carcinoma samples illustrates the accuracy of DNA ploidy measurements and the sensitivity in the detection of DNA ploidy abnormalities as a result of cell sorting. CONCLUSIONS: Fully automatic image cytometry is able to combine qualities of flow cytometry (automatic analysis of a statistically significant collection of cell nuclei) with additional advantages: sorting of unwanted events (debris, stromal and inflammatory cell nuclei) and facilities for an a posteriori control of the quality of cell selection. This method is well suited to DNA ploidy analysis of archival cancer samples.

Aneuploidy↗

PubMed1999

In situ RT-PCR allows the detection of ornithine decarboxylase mRNA in paraffin embedded archival human hyperplastic breast tissues.

Expression of ornithine decarboxylase (ODC) is induced by c-Myc oncoprotein and is required for cell proliferation and tumour growth. We have studied the expression of ODC mRNA by in situ hybridisation and in situ RT-PCR in archival human hyperplastic breast tissues. A very low signal was detected by in situ hybridisation, while the in situ RT-PCR on human breast archival tissues demonstrated an over-expression of ODC mRNA in epithelial cells characterised by some degree of hyperplasia, maintaining the morphology of the archival tissue intact despite the multiple steps of fixation, permeabilization and thermal cycling.

Breast↗

PubMed2002

Legal, ethical and human-rights issues related to the storage of oral history interviews in archives.

This paper provides some personal reflections that explore the legal, ethical and human rights issues of conducting oral history interviews with elderly retired nurses. The interviews are part of a research study into the history of nursing in the West Yorkshire towns of Halifax and Huddersfield, UK, between 1870-1960. The merit of this research is that it provides a unique account of the development of nursing and can enrich our understanding of the implications for present-day practice within the fast changing world of the 21st century. A literature review identified a 'gap in knowledge' of how and why local nursing developed. This study proposes to bridge this gap and provide an investigative account of the important issues for local nursing. The two methodological approaches are analysis of the primary and secondary documentary archival sources, and oral history interviewing of retired nurses. 'Word of mouth' or snowball sampling identified over 300 potential interviewees ranging from 65-97 years old. A final sample of 21 representative of location, age and career experience was selected to ensure a strategic purposive sample. The resultant audiotapes and transcripts will be stored in the university's archives. The main focus of the paper will be the legal, ethical and human rights issues of storing interviewees tapes/transcripts in archives. Reflections on these problems and attempts to overcome them have been provided. These are centred on the issue of whether to edit the tapes and/or transcripts. Arguments are provided for and against editing and potential practical solutions to some of the practical issues are identified. The main aim is to identify methods that will enable the protection of those who may be harmed in anyway by the tapes or transcripts been open to public access.

England↗

PubMed1992

Analysis of gene amplification in archival tissue by differential polymerase chain reaction.

Oncogene amplification is found in many human tumors, and its detection may have important prognostic value. However, analysis of gene amplification may be hampered by inadequate tissue or poor DNA quality. We have previously described a polymerase chain reaction (PCR)-based procedure called differential PCR that can detect variations in gene dosage using miniscule amounts of tumor DNA [Frye, R.A., Benz, C.C. & Liu, E. (1989). Oncogene, 4, 1153-1157]. We now report the optimization of this technique for the analysis of oncogene amplification in paraffin-embedded archival tissues. We find that differential PCR is able to detect amplification of the HER2 (c-erbB-2) and the epidermal growth factor receptor (EGFR) genes and can be used to arrive at a semiquantitative estimate of gene dosage. Furthermore, our approach can determine gene amplification in samples in which the DNA is significantly degraded. Using differential PCR on paraffin-embedded tissues from cases previously investigated by standard DNA extraction and dot-blot procedures, good correlation between the two methods was found. Approaches are described to overcome technical problems posed by factors that affect the differential PCR, including the method of DNA extraction and extreme fragmentation of the DNA (less than 200 base pairs). Furthermore, the resulting analytical algorithm reported herein has proved effective in detecting oncogene amplification in archival breast cancer specimens from standard pathology laboratories. Thus, differential PCR will be particularly helpful in the analysis of tumor specimens that are archived, small in size or rare in occurrence.

Algorithms↗

PubMed2004

[Isolation of free DNA from archived serum samples suitable for molecular genetic studies].

INTRODUCTION: Collected and archived serum samples could be important sources for genetic studies, once DNA suitable for molecular genetic studies could be obtained from them. METHODS: DNA was isolated from 54 archived sera samples, collected previously from the participants of a Hungarian allergy study, with commercially available isolation kit. The authors have determined the concentration of the isolated DNA (81.88 +/- 52.36 ng/ml) and the size of the isolated fragments was estimated using semiquantitative real-time PCR. Two primers were used producing two different fragment size, for the phospholipase 2A and the actin beta genes, and melting curve analyses was performed as quality control. RESULTS: The concentration of the phospholipase 2A product was 2.9798 +/- 5.4454 microg/microl and the actin beta gene was 0.0015 +/- 0.0011 microg/microl. The melting curve analysis served as a quality control for the determination of the size of PCR products. In the case of the phospholipase 2A all samples produced the 133 bp PCR fragments, except one, while in the case of actin beta gene only six sample showed the expected 178 bp product, all the others samples had smaller fragments. CONCLUSIONS: These results confirm the suitability of the DNA isolated from archived sera samples for further molecular biological studies (SNP analysis, mutation detection) and give an estimate for the product size of the isolated DNA. Sera samples have been collected years ago can be a good source of genetic information on different diseases.

Actins↗

PubMed2006

From a philanthropic idea to building of civic hospital in Split in light of new archival evidence.

We investigated the circumstances of building of the Civic Hospital in Split in the light of new archival evidence. The study necessitated a thorough review of the older historiography and previously unpublished archival sources kept in the State Archives in Venice and Zadar. The findings showed that construction of the hospital building finished in 1797, ie, five years later than officially cited. The topographical plan and the original project of the Split Civic Hospital were found, as well as the name of the project's author and the building supervisor. The data on the earliest efforts of Ergovac brothers to acquire land and building permission were corrected. The study revealed a recognizable pattern in the attitude of the authorities toward the establishment of a hospital at the end of 18th century.

Croatia↗

PubMed1990

[The definition and realization of a computerized archive for radiological data of scientific interest].

The general requirements are analyzed of a system designed to acquire and manage radiological data of scientific interest. These requirements consist in: easy implementation, to develop the system in the same environment where it is going to be used; easy use, to avoid excessive needs and resources for the system to be managed in practice; reduced implementation cost, in terms of resources required for its implementation; user-oriented approach, in the sense of meeting the radiologists' requirements, and flexibility, for the system to be an effective tool for the widest range of possible applications. Two actual applications of this general approach are then discussed, one relative to breast investigations data, and the other to digital procedures (US, CT, DSA, MR) data. For each application the software tools employed are analyzed, together with the archive structures and the used codes, the collecting data procedures and the programs. For the breast investigations archive the possibility of obtaining standard periodic reports is pointed out. These reports summarize the global department activity in this area during selected periods (six months-one year). They allow interesting clinical conclusions to be drawn. As for the digital procedures archive, the possibility is stressed of searching different combinations of scientific data out of tens of thousands of cases in just a few minutes.

Computer Systems↗

PubMed1988

[Electrophotographic microfilming for archiving roentgenograms and electroroentgenograms].

A method of electrophotographic microfilming was proposed for keeping radiograms and electroradiograms in archives. Some experimental studies on microfilming positive and negative electroradiograms of phantom materials and various body tissues were carried out using the Soviet AE-1524 camera. An attempt was made to set up a scientific archive of electroradiograms and radiograms on electrographic microreels. Obvious advantages of the method of electrographic microfilming in setting up compact and convenient archives of X-ray images were shown.

Hospital Information Systems↗