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At least 487 records · Page 27Linked to original sources
PubMedDate not supplied

Improved technique for investigations on archival formalin-fixed, paraffin-embedded tumors by interphase in-situ hybridisation.

In-situ hybridisation techniques are powerful tools for the analysis of chromosomes in a variety of specimens. Due to hybridisation problems caused by extensive formalin-fixation in tissue samples mainly isolated nuclei were used for chromosomal analysis. In archival tissue, for sections to retain both an optimum of well preserved morphology and hybridisation efficiency a large-scale adjustment of protease digestion steps for each tissue block was required. We sought to develop an easy, reproducible technique by pretreatment in a 90 degrees C glycerol solution and subsequent denaturation in an autoclave 1 bar for 10 minutes. Our experiments were performed on eight up to ten years old human bladder cancer tissue blocks. Comparison with established pretreatment techniques did not reveal hybridisation differences while the morphology of tissue sections kept intact. This technique facilitates retrospective interphase cytogenetic analyses and is a reliable method for detection of chromosomal anomalies in formalin-fixed archival tumors.

Centromere↗
PubMed1998

Six-year-old archival chromosome preparations are still good biological reagents for repeated primed in situ labelling (rPRINS).

Six-year-old chromosome preparations of Eulemur coronatus were used for in situ localization of highly repetitive DNA sequences. The application of the repeated primed in situ labelling (rPRINS) technique allowed the detection of positive signals whereas conventional fluorescence in situ hybridization gave negative results on the same archival preparations. This paper reveals the possibility of rescuing archival chromosome preparations for both clinical and comparative cytogenetics. Moreover, the chromosomal localization of the ECO-SAT 503 bp highly repetitive DNA sequences were found to localize in the pericentromeric region of every chromosome, with the exception of chromosome 9.

Animals↗
PubMed1998

Single cell multiple biomarker analysis in archival breast fine-needle aspiration specimens: quantitative fluorescence image analysis of DNA content, p53, and G-actin as breast cancer biomarkers.

Fine-needle aspiration (FNA) is a sensitive and cost-effective method for evaluating breast lesions. However, the diagnosis of early premalignant lesions is less reliable by FNA because of a lack of distinctive cytological features. Accurately defining the risk of such lesions at the individual level may have significant impact in breast cancer prevention and management. The main objective of this preliminary study was to develop a method to study multiple biomarkers on archival FNA slides using quantitative fluorescence image analysis (QFIA). Biomarkers p53, G-actin, and DNA content were labeled with an immunofluorescence technique and measured by QFIA simultaneously on a single cell basis. QFIA allows the labeling and measurement procedures to be carried out in situ, without the need to remove cells from the slide while preserving the morphology of the cells. FNA slides from 72 incident patients were obtained for this study. Fifty-six cases had an adequate number of cells for the actual analysis (25 benign breast lesions, 14 proliferative breast diseases with nuclear atypia, and 17 malignant lesions). The DNA content (> or = 5c) and G-actin (average gray mean, > 90) were positive in 81% and 88% of malignant lesions, respectively. These were significantly higher than the corresponding positive rates in benign lesions (7% and 15%, respectively; P <0.01 for both). None of the benign cases were positive for G-actin and DNA simultaneously, and none of the malignant cases were negative for G-actin and DNA together. p53 was positive in 33% of malignant lesions and 8% of benign lesions (P >0.05). Our study demonstrates the feasibility of evaluating multiple biomarkers by QFIA on archival FNA-fixed specimens. The G-actin and DNA content assayed by QFIA may be potential intermediate end point markers for breast cancer individual risk assessment.

Actins↗
PubMed2000

An assessment of the long-term preservation of the DNA of a bacterial pathogen in ethanol-preserved archival material.

To examine the potential for DNA recovery from spirit-preserved medical material, a set of specimens from the Hunterian Collection of the Royal College of Surgeons was investigated. Using a range of DNA extraction techniques and the PCR, no replicable positive amplifications were made from this material of either human or Helicobacter DNA. Experiments with modern stomach biopsies of H. pylori-positive patients suggest that the bacterial DNA is typically present in a much lower concentration (10(3)-fold) than that of the host. The potential for recovery of this organism from spirit specimens is therefore low. The absence of DNA in this material is probably due to several factors, chiefly the incomplete fixation of the specimen by the ethanol storage fluid. Studies such as this demonstrate the need for a good understanding of specimen history when working with archival material.

Archives↗
PubMed1992

Detection of HPV DNA in archival specimens of cervical cancer using in situ hybridisation and the polymerase chain reaction.

An archival survey of 98 cervical cancer specimens dating from the 1920s to the 1980s was undertaken to determine whether changes had occurred in the prevalence of human papilloma-virus (HPV) DNA. HPV DNA was detected in paraffin sections of cancers fixed in 10% formalin by in situ hybridisation (ISH) using HPV 6, 11, 16, and 18 32P-labelled DNA probes under conditions of high stringency; and by the polymerase chain reaction (PCR) using 20-mer oligonucleotide primers to amplify 109 bases of the E6 region of HPV 16. In 30 instances results obtained from Southern blot hybridisations which had been carried out on specimens of fresh tissue from the same cancers collected during the 1980s were available for comparison. The rates of HPV DNA detection in cervical cancers ranged from 83% (by Southern or PCR) and 70% (by ISH) on specimens from the 1980s, to 50% and 63% (by ISH and PCR, respectively) on specimens from the 1920s. HPV 16 was by far the most common type, being identified by Southern or ISH in approximately 92% of HPV DNA-positive specimens. No significant change in the prevalence of HPV DNA, or of HPV types, in cervical cancers was found over the 65 year period examined.

Archives↗
PubMed1994

Serological and nucleic acid analyses for HIV and HTLV infection on archival human plasma samples from Zaire.

In order to better understand the genomic diversity and molecular phylogeny of the human retroviruses, the plasmas from 250 Zairean patients collected in 1969 were tested for antibodies to human T-cell lymphoma and human immunodeficiency viruses (HTLV or HIV) using ELISA and confirmatory Western blots and for viral nucleic acids by reverse transcriptase-directed PCR (RT-PCR). Interestingly, none of the patients was confirmed positive for HIV, even though this region is now endemic for HIV-1. However, 74 (30%) and 3 (1%) of the samples were positive for antibodies to HTLV-I and II, respectively. Forty-four of 74 (59%) Western blot-positive Zairean samples were RT-PCR positive for HTLV-I, while 1 of 3 (33%) of HTLV-II-seropositive samples was RT-PCR positive. On the contrary, none of the Western blot-negative or indeterminate samples were RT-PCR positive for either HTLV-I or HTLV-II. We have cloned and sequenced 140 bp of the pol gene flanked by SK110/SK111 from 8 HTLV-I- and 1 HTLV-II-positive archival samples from Zaire. The HTLV-I isolates from Zaire cluster together as a phylogenetic group, diverging from the prototype Japanese HTLV-I (ATK) by a range of 1.4 to 3.6%. Their close homology to some African STLV-I isolates suggests relatively recent interspecies transmission. The Zairean HTLV-II isolate is closely grouped with the HTLV-II substrain of isolates found in Paleo-Amerindians of the New World, making it unlikely that it represents an endemic African strain.

Antibodies, Viral↗
PubMed1994

Demonstration of gene-amplification by PCR in archival paraffin-embedded breast cancer tissue.

The polymerase chain reaction (PCR) is a powerful tool to examine genetic alterations in tumor samples. We describe a simple, rapid, nonisotopic PCR method to semi-quantitatively determine the number of gene copies in human formalin-fixed paraffin-embedded tissue. The procedure is exemplified by analysis of 15 years old breast cancer samples to determine the presence of amplification of c-erb-B2. The samples were obtained from routine specimens kept in pathological archives. Patients with amplified samples showed a poor prognosis, both for recurrences and death in breast cancer.

Archives↗
PubMed2003

[The determination of the point of time in processing archived X-ray films].

The point of time, in which archived X-ray films were processed, can be proved with the determination of the remaining content of thiosulphate. The methylene blue method of DIN 19069 (equivalent to ISO 18917) was adapted to X-ray films. The range of time is in about two and a half year,in which the remaining content of thiosulphate is correlatable to the point of time in processing. This range of time covers the range, in which "radiological bodies" control the results of constancy testing. This method brings the "radiological bodies" in a better position to decide wether the recommended time of processing is true or not, when test images according DIN 6868-3 and/or the sensitometric step wedges according DIN 6868-2 are checked.

Archives↗
PubMed2006

An archival analysis of actual cases of historic child sexual abuse: A comparison of jury and bench trials.

Logistic regression analyses were used to predict verdicts from 466 Canadian jury and 644 Canadian judge-alone criminal trials involving delayed or historic allegations of child sexual abuse. Variables in regard to the complainant and offence were selected from the legal, clinical, and experimental literatures, including mock juror research. Of six variables that had been related to decisions reached in mock juror research concerning delayed allegations of child sexual abuse (i.e., repressed memory testimony, involvement in therapy, length of delay, age of complainant, presence of experts, and frequency of abuse) two (age of complainant and presence of expert) predicted verdicts. An additional five variables (duration, severity, complainant-accused relationship, threats, and complainant gender) were also examined: of these, threats and the complainant-accused relationship reliably predicted jury verdicts. For judge-alone trials, five variables predicted verdict: length of the delay, offence severity, claims of repression, the relationship between complainant and accused, and presence of an expert. Implications of the jurors' and judges' differential sensitivity to these variables for future simulation and archival research are discussed.

Archives↗
PubMed1985

Archival exploration of anorexia nervosa.

This study explores the use of hospital archives to establish a wider view of the history of anorexia nervosa and similar symptomatic presentations in the nineteenth and early twentieth centuries. The research incorporates a detailed investigation of admission registers and case records relating to over 36 000 admissions to two general infirmaries and four asylums. In addition, an extensive search has been made of printed medical sources for this period. The study clarifies both the range and limitations of information derived from hospital records and gives perspective to the accepted nineteenth century accounts of anorexia nervosa.

Anorexia Nervosa↗
PubMed1988

Cost-effectiveness prospects of picture archiving and communication systems.

PAC (picture archiving and communication) systems are widely discussed and promoted as the organizational solution to digital image management in a radiology department. For approximately two decades digital imaging has increasingly been used for such diagnostic modalities as CT, DSA, MRI, DR (Digital Radiography) and others. PACS are seen as a step toward high technology integration and more efficient management. Although the acquisition of such technology is investment intensive, there are well-founded projections that prolonged operation will prove cost justified. Such justification can only partly be derived from cost reduction through PAC with respect to present department management--the major justification is preparation for future economic pressures which could make survival of a department without modern technology difficult. Especially in the United States the political climate favors 'competitive medicine' and reduced government support. Seen in this context PACS promises to speed the transition of Health Care Services into a business with tight resource management, cost accounting and marketing. The following paper analyzes cost and revenue in a typical larger Radiology Department, projects various scenarios of cost reduction by means of digital technology and concludes with cautious optimism that the investment expenses for a PACS will be justified in the near future by prudent utilization of high technology.

Archives↗
PubMedDate not supplied

Top-down design of a picture archiving and communications system (PACS) by means of simulation.

The development of picture archiving and communications systems (PACS) for medical applications can be regarded as a challenging field in medical informatics. Since 1982, several projects have been started into this direction worldwide. The Dutch IMAGIS (Image Information System) project, started in 1984, is one of them. Within this project, a top-down design strategy is chosen, with the following first steps: (1) A thorough information analysis for a Radiology Department, in which both qualitative and quantitative aspects are included. Such an analysis can be used to estimate the workload on a future PACS system. (2) The construction of a flexible performance prediction tool, based on discrete even simulation. Such a tool can be used to predict the performance of a certain computer system configuration under a certain workload. Based on the information analysis, and using the performance prediction tool, a PACS system is drafted for the thorax section of the Diagnostic Radiology Department of the Leiden University Hospital. In this first design attempt, the assumption was made that current working procedures concerning images will be maintained as much as possible.

Archives↗
PubMed2005

Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology.

Three-dimensional electron microscopy (3DEM) has made significant contributions to structural biology. To accomplish this feat, many image-processing software packages were developed by various laboratories. The independent development of methods naturally implied the adoption of dissimilar conventions-penalizing users who want to take advantage of the wealth of algorithms from different packages. In addition, a public repository of 3DEM research results, the EM Data Bank, is now established. In an era where information exchange is important, standardizing conventions is a necessity. The 3DEM field requires a consistent set of conventions. We propose a set of common conventions named the "3DEM Image Conventions." They are designed as a standardized approach to image interpretation and presentation. In this regard, the conventions serve as a first step on which to build data-exchange solutions among existing software packages and as a vehicle for homogenous data representation in data archives, such as the EM Data Bank.

Algorithms↗
PubMed2000

Chromogenic in situ hybridization: a practical alternative for fluorescence in situ hybridization to detect HER-2/neu oncogene amplification in archival breast cancer samples.

Determination of HER-2/neu oncogene amplification has become necessary for selection of breast cancer patients for trastuzumab (Herceptin) therapy. Fluorescence in situ hybridization (FISH) is currently regarded as a gold standard method for detecting HER-2/neu amplification, but it is not very practical for routine histopathological laboratories. We evaluated a new modification of in situ hybridization, the chromogenic in situ hybridization (CISH), which enables detection of HER-2/neu gene copies with conventional peroxidase reaction. Archival formalin-fixed paraffin-embedded tumor tissue sections were pretreated (by heating in a microwave oven and using enzyme digestion) and hybridized with a digoxigenin-labeled DNA probe. The probe was detected with anti-digoxigenin fluorescein, anti-fluorescein peroxidase, and diaminobenzidine. Gene copies visualized by CISH could be easily distinguished with a x40 objective in hematoxylin-stained tissue sections. HER-2/neu amplification typically appeared as large peroxidase-positive intranuclear gene copy clusters. CISH and FISH (according to Vysis, made from frozen pulverized tumor samples) correlated well in a series of 157 breast cancers (kappa coefficient, 0.81). The few different classifications were mostly because of low-level amplifications by FISH that were negative by CISH and immunohistochemistry with monoclonal antibody CB-11. We conclude that CISH, using conventional bright-field microscopy in evaluation, is a useful alternative for determination of HER-2/neu amplification in paraffin-embedded tumor samples, especially for confirming the immunohistochemical staining results.

Archives↗
PubMed2002

Identification and ranking of genetic and laboratory environment factors influencing a behavioral trait, thermal nociception, via computational analysis of a large data archive.

Laboratory conditions in biobehavioral experiments are commonly assumed to be 'controlled', having little impact on the outcome. However, recent studies have illustrated that the laboratory environment has a robust effect on behavioral traits. Given that environmental factors can interact with trait-relevant genes, some have questioned the reliability and generalizability of behavior genetic research designed to identify those genes. This problem might be alleviated by the identification of the most relevant environmental factors, but the task is hindered by the large number of factors that typically vary between and within laboratories. We used a computational approach to retrospectively identify and rank sources of variability in nociceptive responses as they occurred in a typical research laboratory over several years. A machine-learning algorithm was applied to an archival data set of 8034 independent observations of baseline thermal nociceptive sensitivity. This analysis revealed that a factor even more important than mouse genotype was the experimenter performing the test, and that nociception can be affected by many additional laboratory factors including season/humidity, cage density, time of day, sex and within-cage order of testing. The results were confirmed by linear modeling in a subset of the data, and in confirmatory experiments, in which we were able to partition the variance of this complex trait among genetic (27%), environmental (42%) and genetic x environmental (18%) sources.

Animals↗
PubMed2000

Identification of the primary auditory field in archival human brain tissue via immunocytochemistry of parvalbumin.

Using parvalbumin (PV)-immunocytochemistry, we identified the human primary auditory field (PAF) for the first time. The first gyrus of the right Heschl was identified, and a serial perpendicular cut to the gyrus was made. PV-immunoreactive neuropils delineated four zones, as have been described in monkeys. Unlike with conventional staining, zone 1, characterized by intense immunostaining, corresponded to the koniocortex (PAF), while zone 2, characterized by moderate immunostaining around zone 1, to the parakoniocortex. PV-immunocytochemistry was a useful way to identify PAF in formaline-fixed archival human brain tissue.

Aged↗
PubMed2002

London home for Crick archive.

Unprecedented access to the archives of Francis Crick, just before the 50th anniversary next year of his famous paper co-authored with James Watson on the proposed double helix structure of DNA, looks set to go ahead. Nigel Williams reports.

Archives↗
PubMed2002

Determination of cyclin D1 and CD20 mRNA levels by real-time quantitative RT-PCR from archival tissue sections of mantle cell lymphoma and other non-Hodgkin's lymphomas.

Cyclin D1 overexpression is a valuable marker for the diagnosis of mantle cell lymphoma (MCL). We used a real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) method to quantify levels of cyclin D1, CD20, and cyclophilin A mRNA in manually microdissected, paraffin-embedded tissue sections using an ABI 7700 qRT-PCR system. The study group included 21 cases of MCL and 37 cases of other types of B-cell non-Hodgkin's lymphoma. Cyclin D1 mRNA copy number was normalized to CD20 and cyclophilin A mRNA and evaluated statistically by analysis of variance. The relative cyclin D1 levels were similar whether normalized to CD20 or cyclophilin A, indicating that CD20 levels are stable and can be used as a B-cell-specific normalizer. Statistically significant differences were found in the median levels of cyclin D1 mRNA (expressed as % CD20 mRNA) among cases of MCL (87.6), small lymphocytic lymphoma (9.9), follicular lymphoma (2.4), diffuse large B-cell lymphoma (5.9), marginal zone B-cell lymphoma (39.8), and Burkitt lymphoma (7.1) (P < 0.05). We conclude that qRT-PCR can be used to quantify cyclin D1 mRNA levels in archival tissue sections. Normalization of cyclin D1 to a B-cell-specific marker more accurately reflects overexpression by MCL than other methods that normalize using constitutively expressed mRNA species.

Adolescent↗