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At least 793 records · Page 44Linked to original sources
PubMed2004

In situ detection of apolipoprotein E epsilon 4 in archival human brain.

A monoclonal antibody specific to apolipoprotein E 4 (apoE4) was applied immunohistochemically to archival human brain tissue. The examined 30 cases comprised four epsilon/epsilon4, 10 epsilon3/epsilon4, one epsilon2/epsilon4, 10 epsilon3/epsilon3 and five epsilon2/epsilon3 genotypes. The anti apoE4 antibody visualized senile plaques, neurofibrillary tangles and reactive astrocytes, as well as serum in the blood vessels and vascular smooth muscle cells in the cases of epsilon4. Moreover, the staining intensity was stronger in the cases carrying the epsilon4 homozygosity than in those cases of epsilon4 heterozygosity. Specific immunoreactivity was not obtained in those cases not carrying the epsilon4 allele. This method will allow in situ detection of apoE epsilon4 and contribute to studies of the effect of epsilon4 on Alzheimer's disease.

Alleles↗
PubMed2000

A picture archival and communication system shortens delays in obtaining radiographic information in a medical intensive care unit.

OBJECTIVE: To assess whether variables such as unit occupancy and aggregate severity of illness that reflect increased work demands on physicians in medical intensive care units (MICU) are associated with increased delays in their obtaining information about nonroutine chest radiographic examinations. To determine whether the presence of a picture archiving and communication system (PACS) workstation in the MICU shortens those delays. DESIGN: A prospective cohort study stratified for presence or absence of PACS. SETTING: MICU of a university hospital. PATIENTS: A total of 118 patients admitted to the MICU who had nonroutine bedside chest radiographs. MEASUREMENTS AND MAIN RESULTS: Multivariate analyses were conducted to determine how unit occupancy, patient acuity, the time of day the examination was taken, and the presence of a PACS workstation influenced the time from radiographic examination completion to the time when MICU physicians first obtained image information. In a multivariate analysis, patient acuity, unit occupancy, the aggregate level of severity of illness in the study cohort, whether the examination was taken at night or day, and the presence of a PACS workstation were significant predictors of the elapsed time from examination completion until review by MICU physicians. Without the PACS workstation, higher occupancy, higher aggregate severity of illness, and examinations taken during the day were associated with longer delays. Overall, the multivariate analysis showed a 24-min decrease in the elapsed time to obtain information during periods with the PACS workstation compared with periods without the workstation (p = .03). CONCLUSIONS: A PACS workstation significantly decreased the delays in obtaining image information that occurred with high unit occupancy and high aggregate severity of illness and may improve unit efficiency under conditions of high physician workload.

APACHE↗
PubMed1992

Image preprocessing for a picture archiving and communication system.

OBJECTIVES AND RATIONALE: In a picture archiving and communication system (PACS), images are acquired from multiple modalities and displayed on an electronic workstation. Each modality has different image characteristics. This variability must be addressed before the image is displayed. METHODS: The authors developed methods to automatically process magnetic resonance (MR), computed tomographic (CT), and computed radiography (CR) images before display and subjectively evaluated their effectiveness. RESULTS: Unwanted background successfully was automatically removed from 89.5% of 615 CR images. Of 803 chest, abdomen, and hand images 93% were automatically rotated to the correct orientation. CONCLUSIONS: Automated preprocessing of PACS images can be performed successfully, improving speed and convenience for the radiologist interpreting images at an electronic workstation.

Image Processing, Computer-Assisted↗
PubMed1983

Data compression techniques for CT image archiving.

Large digital files are inherent to computed tomography (CT) image data. The CT installations that routinely archive patient data are penalized computer time, technologist's time, tape, purchase, and file space. This paper introduces compression techniques that reduce the amount of tape needed to store image data and the amount of computer time to do so. The benefits delivered by this technique have also been applied to CT disk systems in which limited on-line memory requires compact file storage. Typical reductions of 40 to 50% of original file space are reported.

Computers↗
PubMed1993

Molecular genetics of pediatric brain stem gliomas. Application of PCR techniques to small and archival brain tumor specimens.

Brain stem gliomas are pediatric astrocytomas that histologically resemble adult supratentorial astrocytomas such as glioblastomas multiforme (GBM). Our molecular genetic studies have suggested that adult GBM can be divided into two genetic subsets: tumors with p53 tumor suppressor gene mutations and chromosome 17p loss that occur more commonly in younger patients; and tumors with epidermal growth factor receptor (EGFR) gene amplification that occur more commonly in older patients. Brain stem gliomas have not been studied since biopsies of these tumors are rare and extremely small. We investigated the molecular genetic composition of seven brain stem glioblastomas (two small biopsies, five autopsies) using polymerase chain reaction (PCR) assays for chromosomal loss, gene mutation and gene amplification. Four cases lost portions of chromosome 17p that included the p53 gene. These four cases and one additional case had mutations in the p53 gene. None of the cases showed amplification of the EGFR gene. Allelic losses of the long arm of chromosome 10 were noted in four cases. These results suggest similarities between pediatric brain stem glioblastomas and those GBM that occur in younger adult patients, and confirm the utility of PCR-based means of studying small and archival brain tumor specimens.

Adolescent↗
PubMed1998

Picture archiving communication system does not decrease the number of radiographs needed to evaluate the trauma patient.

BACKGROUND: Picture Archiving Communication System (PACS) is a sophisticated software and hardware package that enables clinicians to retrieve, review, and digitally manipulate radiographs from computer workstations throughout the hospital. PACS was instituted at Brooke Army Medical Center in July 1993. METHODS: Fifty consecutive trauma and 50 consecutive motor vehicle crash (MVC) trauma admissions to an urban trauma center were reviewed before PACS (January 1993) and 18 months after PACS was instituted (January 1995). Patients were compared by the number of radiographs needed during the initial evaluation by type and total. The trauma groups were subdivided by mechanism and also compared. Demographic and physiologic data were collected for each patient. RESULTS: There are no differences in the demographic and physiologic data between groups. For the 50 consecutive trauma admissions, only two areas of statistical difference were found: more chest films were obtained in the MVC PACS group and more pelvis films were obtained in the gunshot wound pre-PACS group. For the 50 consecutive MVC trauma admissions, the PACS group had more chest and total radiographs per patient than the pre-PACS group. More computed tomographic scans of the neck were obtained in the PACS group. CONCLUSION: PACS did not decrease the number of radiographs needed to adequately and fully evaluate the trauma patient.

Accidents, Traffic↗
PubMed1995

Polymerase chain reaction detection of immunoglobulin gene rearrangement and bcl-2 translocation in archival glass slides of cytologic material.

Cytologic evaluation of lymph node fine-needle aspirates and serous effusions is a rapid and useful means for establishing the diagnosis of a variety of lymphoproliferative disorders. However, in some instances, cytologic findings are not sufficient to establish a diagnosis of lymphoma, thus necessitating the use of ancillary procedures, the most frequent of which is immunophenotyping. In this respect, the usefulness of molecular markers, such as clonal immunoglobulin gene rearrangements or chromosomal translocations, have been less well evaluated. Follicular lymphoma constitutes an interesting disease for such a study because these tumors possess characteristic histopathologic features and contain two potential molecular markers, that is, a clonal immunoglobulin gene rearrangement and a bcl-2 gene translocation [t(14;18)]. In the present study, we evaluated, retrospectively, the cytologic material from four lymph node fine-needle aspirates and one pleural effusion of five patients with biopsy-proven follicular lymphoma. In four of the cases, definitive diagnosis of lymphoma had not been possible solely from cytologic evaluation. DNA was isolated from archival air-dried samples present on glass slides and amplified by the polymerase chain reaction (PCR) for detection of either a clonal immunoglobulin heavy chain gene rearrangement or bcl-2 translocation (major breakpoint region). An immunoglobulin heavy chain gene rearrangement was detected in four of five patients, and two patients had the bcl-2 translocation by PCR. The effusion case was identical by gel electrophoresis with product amplified from a lymph node biopsy of the same patient and DNA extracted directly from fresh pleural effusion cells.(ABSTRACT TRUNCATED AT 250 WORDS)

B-Lymphocytes↗
PubMed1996

Detection of p53 gene abnormality by sequence analysis of archival paraffin tissue. A comparison with fresh-frozen specimens.

This parallel study was designed to compare the sensitivity and specificity of detection of point mutations in fresh-frozen and formalin-fixed, paraffin-embedded breast cancer tissue. Sequence analysis of exon 5 of p53 gene was performed on polymerase chain reaction-amplified DNA from 25 infiltrating ductal carcinomas of the breast. Four tumor showed mutations with identical base substitutions in their respective codons of both frozen and paraffin-embedded specimens. We conclude that subtle genetic alterations can be detected in archival paraffin tissue with an accuracy comparable to that of fresh-frozen histologic samples.

Breast Neoplasms↗
PubMed1997

Efficiency of single-cell polymerase chain reaction from stained histologic slides and integrity of DNA in archival tissue.

Molecular analysis of isolated single cells is a powerful tool for studying heterogeneity within a population of cells and for clarifying issues of cell origin and clonality. Here, we investigate the applicability of molecular techniques at a single-cell level by using routinely processed archival tissue. An ultraviolet laser in conjunction with a computer-controlled micromanipulator and a microscope were used for the contamination-free isolation of single tumor cells from stained sections of diffuse-type gastric cancer. A total of 1,328 single cells and 654 clusters of 10-30 cells each, taken from specimens of 14 patients, were analyzed for parts of the E-cadherin gene by the polymerase chain reaction (PCR). With increasing length in base pairs (bp) of the amplified fragments, the efficiency of single-cell PCR as measured by the rate of detectable amplification products declined from approximately 25% (156, 213, and 228 bp) to 14% (246 bp) and 11% (264 and 296 bp). For groups of 10-30 cells, a similar effect was seen at a higher level at 33% (246 bp), 31% (264 bp), and 26% (296 bp), respectively. To our knowledge, this is the first report that has studied the outcome of single-cell PCR on a large systematic scale. The average degree of DNA disintegration in paraffin-embedded, stained tissues was estimated to be approximately 100 bp when the aforementioned data were used in a mathematical model. This study provides evidence that in order to obtain reasonable sensitivity with single-cell PCR, short fragments, preferably < 200 bp long, should be used. Furthermore, whenever applicable, pooling of cells of interest may be another favorable option.

DNA↗
PubMed1998

Detection of tyrosinase mRNA in formalin-fixed, paraffin-embedded archival sections of melanoma, using the reverse transcriptase in situ polymerase chain reaction.

Most studies of the reverse transcriptase in situ polymerase chain reaction technique have reported results from assessments of cultured cells, frozen sections, and cytospin preparations. For application to routine diagnosis, it will be necessary to adapt the technique for use with formalin-fixed, paraffin-embedded tissues, the materials that are generally available. We have evaluated the feasibility of such an approach, using surgical pathology archival material from 25 UCLA patients: 15 tissues from primary and metastatic melanoma, 7 from nonmelanocytic tumors, including cancer of the lung, colon, kidney and skin and a thyroid adenoma, and 3 nontumorous tissues. Seven of 15 melanoma tissues gave a strong positive signal, 5 gave a weak signal, and 3 were negative. None of the 10 nonmelanoma tissues gave a positive signal. The specific reaction product was mainly located in the cytoplasm. None of the nonmelanocytic tumors or normal tissues demonstrated this pattern of cytoplasmic staining. Some nonspecific nuclear staining was observed in melanocytic and nonmelanocytic tumors and must not be overread as a true positive result. It is possible to detect tyrosinase mRNA in formalin-fixed, paraffin-embedded tissue sections of melanoma, but the technique remains too demanding for routine application.

Formaldehyde↗
PubMed1998

Detection of TLS/FUS-CHOP fusion transcripts in myxoid and round cell liposarcomas by nested reverse transcription-polymerase chain reaction using archival paraffin-embedded tissues.

The reciprocal translocation t(12;16)(q13;p11) has been shown to be highly characteristic of myxoid and round cell subtypes of liposarcoma, and the TLS/FUS-CHOP fusion gene that resulted from the translocation is expected to be a diagnostic molecular marker of these sarcomas. In this study, we conducted a nested reverse transcription-polymerase chain reaction (RT-PCR)-based assay to detect the TLS/FUS-CHOP fusion gene transcripts using archival formalin-fixed, paraffin-embedded tumor specimens. Of 18 paraffin-embedded specimens from 16 myxoid and round cell liposarcoma cases, the fusion transcripts could be identified in 16 (89%) specimens from 15 (94%) cases. A sequence analysis using the PCR products confirmed that the detected messages were derived from either type I or type II TLS/FUS-CHOP fusion gene, the latter of which was predominant (80%). The results were consistent in primary and recurrent lesions of the same patients and in paraffin-embedded and snap-frozen samples from the same tumors. In two negative specimens, transcripts of the beta-actin gene could not be detected by RT-PCR, and intact mRNA including the fusion messages might have been degraded. No fusion transcripts were detected in snap-frozen or paraffin-embedded material of other types of tumors with myxoid morphology (seven myxoid malignant fibrous histiocytomas and four lipomas with myxoid change). These results indicate that this molecular assay can be applied to formalin-fixed, paraffin-embedded tumor tissues as a diagnostic aid for these subtypes of liposarcoma.

Adolescent↗
PubMed1999

Optimizing the APC gene mutation analysis in archival colorectal tumor tissue.

Critical steps in the methodology of mutation analysis on routinely fixed, paraffin-embedded samples have been evaluated, including extraction and purification of DNA, amplification of gene fragments in various sizes, and screening for mutations. The DNA was extracted from tissue sections with proteinase K, using various procedures, and purified. The mutation cluster region of the APC gene was amplified with polymerase chain reaction to generate either two large or four small overlapping DNA fragments. The GC-clamped fragments were screened for mutations with temperature gradient gel electrophoresis, and mutations were identified with sequencing. The DNA was easily amplified as large fragments from fresh or unfixed-frozen samples. However, DNA amplification of large fragments from archival samples was successful in only 40 of the 114 tumor specimens analyzed (35%). Prolonged extraction, either at 55 degrees C or at 37 degrees C, gave no better results. Polymerase chain reaction of smaller fragments, with sizes between 200 and 270 base pairs (bp), was successful for 97% of the amplification reactions when using DNA that was purified with silica. Screening with temperature gradient gel electrophoresis was reproducible and sensitive with a detection limit of 5% mutated DNA in the presence of an excess of wild-type DNA.

Adenocarcinoma↗
PubMed1995

Screening for p53 gene mutations in archived tumors of workers occupationally exposed to carcinogens: examples from analysis of bladder tumors.

Point mutations in the p53 tumor suppressor gene are the most common genetic alterations in human cancers. The nature and location of these mutations can be informative in assessing the importance of putative carcinogenic agents. Potential associations between a given carcinogen and a specific mutation pattern can be substantiated when the exposure history of the patients is known. While the past exposure to environmental risk factors is often difficult to determine, documented occupational exposure to carcinogens presents a unique situation for evaluating this approach. Analysis usually involves working with paraffin-embedded tissues, fixed under conditions suboptimal for genetic analysis and stored for many years, since frozen tissues are not available in sufficient numbers. The particular methodological problems encountered with fixed samples are discussed here, using as illustration an ongoing study of oncogene and tumor suppressor gene mutations in archived bladder tumors of workers exposed to aromatic amines and nonexposed patients.

Base Sequence↗
PubMed2003

Alcohol availability as a predictor of youth drinking and driving: a hierarchical analysis of survey and archival data.

BACKGROUND: Much attention has recently been directed toward developing preventive interventions to reduce drinking and driving through efforts to limit the numbers and locations of alcohol outlets at the community level. Although evaluations of these efforts have suggested linkages between alcohol outlets and problem outcomes, they have not addressed the linkage between outlets and drinking and driving among youth. The analysis reported here investigates the relationship between alcohol outlet densities and underage drinking and driving as self-reported on two telephone surveys conducted in California. METHODS: These analyses were based on data obtained from two telephone surveys conducted by the Prevention Research Center and archival data collected by the California Department of Alcoholic Beverage Control and the US Census Bureau. The sample for the first survey consisted of 15- to 20-year-old adolescents and young adults contacted by telephone, using a random digit dialing of exchanges in the greater San Francisco Bay Area. A second set of survey data was similarly collected by a random sample of households throughout California, and the Bay Area subset was also used for this analysis. RESULTS: At the individual level, older respondents were more likely to report drinking and driving and riding with drinking drivers, whereas females and Asians were less so. At the aggregate or city-level, alcohol outlet density, as measured by the number of on- and off-premises establishments licensed to sell alcohol, was associated with both drinking and driving and riding with drinking drivers. These effects were moderated by a number of individual level effects, with younger respondents and females more likely to be affected by outlet densities. CONCLUSIONS: The findings here provide support for the implementation of policies targeting alcohol outlet density reductions. Areas with large numbers of such outlets provide ample opportunities to youth for alcohol purchases.

Adolescent↗
PubMed2002

An efficient method for the assessment of DNA quality of archival microdissected specimens.

There will be an increasing need of methods for assessing the suitability of specimens for genetic-based assays as DNA markers become an integral part of molecular diagnosis. The targeting of specimens for specific analyses will require the ability to rapidly screen for DNA quality. Conventional methods such as Southern analysis and gene specific-polymerase chain reaction (PCR) often require quantities of material that represent a significant portion of the specimen, especially in microdissected samples. Here we describe a novel application of a commonly used PCR-based DNA-fingerprinting technology that requires minimal quantities of DNA to simultaneously assess multiple regions throughout the genome for DNA quality. Randomly amplified polymorphic DNA (RAPD) PCR generates DNA fragments of a broad size range with the product size reflecting the degree of sample fragmentation. Fourteen DNA samples extracted from cells microdissected from seven formalin-fixed, paraffin-embedded oral cancer biopsies were assessed for DNA quality using gene-specific PCR and RAPD-PCR. Although the more conventional assay required 2-ng DNA (or 300-cell equivalents) to examine DNA quality at a single locus, RAPD-PCR provided a more informative profile of DNA quality from the same microdissected archival specimens.

Carcinoma, Squamous Cell↗
PubMed2007

Early archives of genetically-restricted proviral DNA in the female genital tract after heterosexual transmission of HIV-1.

OBJECTIVES AND METHOD: In order to characterize human immunodeficiency virus type 1 (HIV-1) variants that are transmitted in women via heterosexual intercourse, the env V1-V3 sequences of HIV-1 provirus (DNA) and free virus (RNA) in paired samples of blood and cervicovaginal secretions of untreated chronically and primary infected African women were compared. RESULTS: Env RNA sequences retrieved from plasma and genital compartments formed a single cluster in primary infection. In contrast, env RNA sequences from these two compartments were distinct in chronically infected women. Analysis of proviral DNA of primary infected women showed that most HIV-1 sequences derived from the genital epithelia form independent clusters from HIV-1 sequences of DNA from peripheral blood mononuclear cells and RNA recovered from plasma and genital secretions. Similarly, the analysis of proviral DNA in the genital compartment of chronically infected women showed the persistence of genetically-restricted cluster of HIV-1. CONCLUSIONS: These observations indicate that a viral subpopulation is archived as proviral DNA in the female genital tract early in primary infection, and suggest that HIV-1 variants from the male donor are selected in the female mucosal site during male to female transmission of HIV-1.

Acute Disease↗
PubMed2007

Genotypic resistance of archived and circulating viral strains in the blood of treated HIV-infected individuals.

The aim of this study was to evaluate patterns of antiretroviral resistance of HIV-1 in peripheral blood mononuclear cells (PBMCs) and in the plasma of patients whose therapeutic regimen is failing. Plasma and PBMC samples were collected from 95 HIV-infected patients undergoing long-term treatment. Genotyping of the reverse transcriptase (RT) and protease genes of HIV-1 was undertaken using the fluorescent dideoxy-terminator method. Comparison of the amino acid sequence of the RT and protease genes in cell-associated variants of HIV-1 with that of the plasma revealed that 62 of the 95 patients' samples tested exhibited different genotypic resistance patterns (discordant samples [DSs]). In 27% of samples, the patterns of resistance detected were concordant in both compartments. In 51% of DSs, the greatest number of mutations was found in plasma; however, in 37% of DSs, greater numbers of mutations were found in PBMC DNA. The HIV mutation patterns detected in plasma do not necessarily reflect those found in the cell-associated compartment. The observation that the cellular compartment may contain an archive of the resistance variant makes this reservoir an interesting substrate for analysis of the "resistance potential" in a given patient.

Anti-HIV Agents↗
PubMed2003

Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod (Gadus morhua).

Despite increasing evidence that current exploitation rates can contribute to shifts in life-history traits and the collapse of marine fish stocks, few empirical studies have investigated the likely evolutionary impacts. Here, we used DNA recovered from a temporal series of archived North Sea cod (Gadus morhua) otoliths, to investigate genetic diversity within the Flamborough Head population between 1954 and 1998, during which time the population underwent two successive declines. Microsatellite data indicated a significant reduction in genetic diversity between 1954 and 1970 (total number of alleles: 1954, 46; 1960, 42; 1970, 37), and a subsequent recovery between 1970 and 1998 (total number of alleles: 1970, 37; 1981, 42; 1998, 45). Furthermore, estimates of genetic differentiation (F(ST) and R(ST)) showed a significant divergence between 1998 and earlier samples. Data are consistent with a period of prolonged genetic drift, accompanied by a replacement of the Flamborough Head population through an increased effective migration rate that occurred during a period of high exploitation and appreciable demographic and phenotypic change. Other studies indicate that diversity at neutral microsatellite loci may be correlated with variability at selected genes, thus compromising a population's subsequent recovery and adaptive potential. Such effects are especially pertinent to North Sea cod, which are threatened by continuing exploitation and rising sea temperatures.

Animals↗