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At least 703 records · Page 39Linked to original sources
PubMed1993

Correlation between [3H]thymidine and proliferating cell nuclear antigen (PCNA)/cyclin indices in archival, formaldehyde-fixed human colorectal tissues.

Sections were obtained from archival colorectal tissue samples preserved in paraffin since 1974, after an in vitro incubation with [3H]thymidine and fixation in formaldehyde. These sections were submitted to immunohistochemical staining with the 19A2 monoclonal antibody against proliferating cell nuclear antigen (PCNA) (i.e. the PCNA identified as the auxiliary protein to DNA polymerase delta), followed by autoradiography. Analysis of this double-labelled material revealed an excess of PCNA-labelled over 3H-labelled nuclei, as expected from our previous studies with this fixative. On the other hand, PCNA positive nuclei showed the same overall topographical distribution as the [3H]thymidine-labelled ones, eventually revealing the same heterogeneity or abnormality in the spatial distribution of proliferative cells. Finally, there was a highly significant correlation (r = 0.898; P < 0.0001) between the [3H]thymidine labelling index (TLI) and the proportion of PCNA-positive nuclei (PCNAF-LI). PCNA immunostaining after formaldehyde fixation thus appears as a valid approach for mapping the proliferative compartment and demonstrating tumour heterogeneity or abnormalities in the distribution of proliferative cells. The excellent correlation between the PCNAF-LI and the TLI also makes PCNA immunostaining a simple tool for retrospective or prospective studies on pathological material aimed at evaluating the potential relevance of proliferative indices to clinical prognosis or prediction of cancer risk.

Adenocarcinoma↗
PubMed1996

Multiple drug resistance-related messenger RNA expression in archival formalin-fixed paraffin-embedded human breast tumour tissue.

A method is described by which RNA, suitable for reverse transcriptase-polymerase chain reaction (RT-PCR) analysis, can be extracted from formalin-fixed paraffin-embedded (FFPE) tissues and subsequently used for detecting the expression of several genes. Using this technique, RNA can be extracted from specimens, quantified, reverse transcribed and regions of interest amplified and analysed within 36 h. The tissue specimens included in this study were from human breast carcinoma, investigating a range of genes associated with the development and/or maintenance of multiple drug resistance (MDR). This technique, applied to archival tissues, offers great potential for increasing our understanding of alterations in expression levels of genes associated with MDR. The method developed is also applicable to studies on expression of other genes in paraffin-embedded tissues.

Adult↗
PubMed2005

Misuse of statistical tests in Archives of Clinical Neuropsychology publications.

This article reviews the (mis)use of statistical tests in neuropsychology research studies published in the Archives of Clinical Neuropsychology in the years 1990-1992 and 1996-2000, and 2001-2004, prior to, commensurate with the internet-based and paper-based release, and following the release of the American Psychological Association's Task Force on Statistical Inference. The authors focused on four statistical errors: inappropriate use of null hypothesis tests, inappropriate use of P-values, neglect of effect size, and inflation of Type I error rates. Despite the recommendations of the Task Force on Statistical Inference published in 1999, the present study recorded instances of these statistical errors both pre- and post-APA's report, with only the reporting of effect size increasing after the release of the report. Neuropsychologists involved in empirical research should be better aware of the limitations and boundaries of hypothesis testing as well as the theoretical aspects of research methodology.

Bibliometrics↗
PubMed2004

Multi-detector computed tomography and 3-dimensional imaging in a multi-vendor picture archiving and communications systems (PACS) environment.

RATIONALE AND OBJECTIVES: To show the impact of the introduction of multi-detector computed tomography (CT) on radiologic workflow and to demonstrate how this reflects on picture archiving and communications systems (PACS) requirements. MATERIALS AND METHODS: Production measurements were obtained from different CT scanners (first two single-slice CT scanners; from December 2001 single and 4-slice CT; from April 2002 single and 16-slice CT) in number of patients from the radiologic information system. Implications on our PACS were recorded in terms of images and studies stored. Furthermore, our PACS design was made so that optimal use of 3-dimensional imaging within the radiologic workflow was possible. Finally, the number of non-diagnosed studies were recorded every day since the start of the transition to a filmless radiology department. RESULTS: This PACS design achieved a high level of integration between simple viewing and advanced 3-dimensional imaging and is optimized for handling large amounts of data. Overall increase of patients scanned with CT from January 2002-December 2003 was 54%. The number of series increased by 286% from December 2001-April 2003 and by 130% from April 2002-December 2003. From January 2002-February 2003, the number of images per patient increased from 175 to 450 (157%). Non-diagnosed studies decreased from about 100-120 before to practically zero after PACS implementation. CONCLUSION: PACS significantly increases productivity because of availability of the images and elimination of certain manual tasks. These results show that although the amount of examinations increases significantly with the introduction of MDCT, simultaneous introduction of PACS and filmless operation allows radiologists to handle the growth in workload.

Efficiency↗
PubMed2005

Assessment of bony resection margins in oral cancer using elastic scattering spectroscopy: a study on archival material.

Oral squamous cell carcinoma has been shown to infiltrate local bone necessitating either a local or segmental resection for clearance. The current decalcification process takes several weeks before histological examination of the margins is possible. The aim of this study was to determine whether elastic scattering spectroscopy (ESS) could be used to identify bone resection margins positive for tumour. We used an ESS biopsy (optical biopsy) system to assess formalin fixed bone margins resected for squamous cell carcinoma of the oral cavity and compared the results with the histopathological diagnosis. Archival specimens obtained in oral cancer resections over the last 10 years were used, the ESS spectra were obtained from residual resection margins immediately adjacent to the area from which sections were cut and the results correlated with the histopathological diagnosis. Three hundred and forty-one spectra were used in this study taken from the mandibular specimens of 21 patients, of which 231 spectra were taken from histologically positive sites and the rest were of normal tissue. Two different sets of spectra were obtained and using a linear discriminant analysis, a sensitivity of 87% and a specificity of 80% were obtained. These results suggest that ESS may identify tumour involvement of resection margins. This study, on formalin fixed tissue, was shown to be reliable and may significantly reduce pathology workload. If these findings can be applied in vivo, this would be an accurate and instant mechanism for assessment of margins in clinical practice.

Carcinoma, Squamous Cell↗
PubMed2006

Extraction of RNA from archival tissues and measurement of thrombospondin-1 mRNA in normal, dysplastic, and malignant oral tissues.

Thrombospondin-1 (TSP-1) is an extracellular matrix glycoprotein implicated in the regulation of angiogenesis and tumour development. Our objectives were to ascertain the quantity and quality of RNA extracted from archival, formalin-fixed, paraffin embedded, oral tissues and their application in measuring the concentrations of TSP-1 mRNA in these tissues. We compared three techniques of isolation of RNA as well as related experimental variables. TSP-1 mRNA was measured in specimens of normal, dysplastic, and malignant oral tissues by real-time reverse transcriptase polymerase chain reaction (RT-PCR). RNA suitable for analysis by real-time RT-PCR was obtained by the three techniques tested, although the yield varied depending on the protocol used (range 0.2-3.6 microg/mm(3)). The mean (S.D.) concentrations of TSP-1 mRNA relative to 18S were 21.1 (7.2) in normal oral tissues (n=9), 11.0 (8.2) in dysplastic tissue (n=8) and 7.3 (5.3) in carcinomatous tissue (n=17). The difference between normal and carcinomatous specimens was significant (p=0.01). This reduction in expression of TSP-1 mRNA from normal to dysplasia to carcinoma may favour the angiogenic drive that accompanies the development of oral tumours.

Carcinoma, Squamous Cell↗
PubMed2005

Detection of mRNA levels for the estrogen alpha, estrogen beta and androgen nuclear receptor genes in archival breast cancer tissue.

Previous studies in our laboratory have shown association of nuclear receptor expression and histological breast cancer grade. To further investigate these findings, it was the objective of this study to determine if expression levels of the estrogen alpha, estrogen beta and androgen nuclear receptor genes varied in different breast cancer grades. RNA extracted from paraffin embedded archival breast tumour tissue was converted into cDNA and cDNA underwent PCR to enable quantitation of mRNA expression. Expression data was normalised against the 18S ribosomal gene multiplex and analysed using ANOVA. Analysis indicated a significant alteration of expression for the androgen receptor in different cancer grades (P=0.014), as well as in tissues that no longer possess estrogen receptor alpha proteins (P=0.025). However, expression of estrogen receptors alpha and beta did not vary significantly with cancer grade (P=0.057 and 0.622, respectively). Also, the expression of estrogen receptor alpha or beta did not change, regardless of the presence of estrogen receptor alpha protein in the tissue (P=0.794 and 0.716, respectively). Post-hoc tests indicate that the expression of the androgen receptor is increased in estrogen receptor negative tissue as well as in grade 2 and grade 3 tumours, compared to control tissue. This increased expression in late stage breast tumours may have implications to the treatment of breast tumours, particularly those lacking expression of other nuclear receptor genes.

Breast Neoplasms↗
PubMed2006

Halogenated organic compounds in archived whale oil: a pre-industrial record.

To provide additional evidence that several halogenated organic compounds (HOCs) found in environmental samples are natural and not industrially produced, we analyzed an archived whale oil sample collected in 1921 from the last voyage of the whaling ship Charles W. Morgan. This sample, which pre-dates large-scale industrial manufacture of HOCs, contained two methoxylated polybrominated diphenyl ethers (MeO-PBDEs), five halogenated methyl bipyrroles (MBPs), one halogenated dimethyl bipyrrole (DMBP), and tentatively one dimethoxylated polybrominated biphenyl (diMeO-PBB). This result indicates, at least in part, a natural source of the latter compounds.

Animals↗
PubMed2005

Detection of human papillomavirus from archival tissues in cervical cancer patients in Mauritius.

BACKGROUND: Around half a million new cases of cervical cancer are diagnosed worldwide each year, accounting for almost 300,000 deaths. Development of cervical cancer can be multi-factorial, but high-risk human papillomaviruses (HPV) have been associated with the aetiology of cervical cancer. It is believed that HPV DNA integrates into the host DNA causing abnormal cell growth with cells becoming carcinogenic and spreading metastatically. In Mauritius, cervical cancer account for 65% of gynaecological cancers and 3.4% of the cervical cancers are diagnosed at the stage of carcinoma in situ. OBJECTIVES: To determine the prevalence of HPV in histological samples from patients with cervical cancer in Mauritius. STUDY DESIGN: DNA from archival cervical samples from a cohort of 65 patients suffering from cervical cancer and controls from Mauritius were tested for the presence of HPV using MY09/11 and GP5+/6+ primer sets. RESULTS: In a cohort of 65 patients from Mauritius, diagnosed with cervical cancer in the year 2000, 19% of cervical histology sections were found to be positive for the presence of high-grade HPV, exclusively HPV18 using MY09 and MY11 primers. Only 15% of the Mauritian population is over 50 years of age, whereas 66% (35) of the diagnosed cases of cervical cancer were seen in patients above 50 years with 50% (5) affected with HPV. These findings suggest that for an infection with HPV to develop into cancer may take years if not decades. Differences were noted using two different primer sets, MY09/11 and GP5+/6+. The latter produce a much smaller amplicon (150bp) compared to the former ( approximately 450bp). Seven additional positive cases were detected with the GP5+/6+ primer set, resulting in an apparent prevalence of 32% as compared to the 19% seen with the MY09/11 primer set. This may indicate that some degradation of the target DNA has occurred during processing and storage of histological samples. CONCLUSION: Using primer sets MY09/11 and GP5+/6+, only HPV type 18 was found in the Mauritian cohort with a prevalence of 32%.

Cervix Uteri↗
PubMed2006

Microwave-assisted antigen retrieval and incubation with cox-2 antibody of archival paraffin-embedded human oligodendroglioma and astrocytomas.

Immunohistochemistry is an important tool that is often used for the diagnosis of pathologies; however, the length of time required to process the tissue is relatively long. Furthermore, the quality and sensitivity of immunohistochemical staining is affected by formalin fixation which results in variable loss of antigenicity, known as masking effect. Here we assess the effect of microwave irradiation on the incubation time required to obtain high quality immunohistochemical staining for cox-2 using archival formalin-fixed, paraffin-embedded human oligodendrogliomas and astrocytomas. The results show that intermittent microwave irradiation during the incubation with the primary antibody reduced the time requirement to 5 min while the staining quality was indistinguishable from 1 or 24 h long incubations. Thus, the use of this procedure results in a significant saving of time which is important for a timely diagnosis of pathological conditions that await treatment.

Antigens, Neoplasm↗
PubMed2006

A simple method for detection of rabies viral sequences in 16-year old archival brain specimens with one-week fixation in formalin.

Archival formalin-fixed and paraffin-embedded brain tissues are important source for diagnosis and molecular analysis. However, nucleic acids are particularly vulnerable to degradation during tissue processing. The brain cutting process usually is performed after 1 week of brain storage in formalin followed by embedding of each particular neuro-anatomical specimen in paraffin. A simple method of deparaffinization, proteinase K digestion and RNA extraction using the Boom technique to obtain rabies RNA in unbuffered, formalin-fixed and paraffin-embedded brain tissues kept at 30 degrees C for 16 years is described. Reverse transcription-polymerase chain reaction (RT-PCR) can be used to identify rabies viral N gene sequences of 150 bases in length in all patients, but not from every immunohistochemical (IHC)-positive specimen. Direct sequencing of 301bp of N gene was achieved in 4 of 7 patients. Results of sequencing a single sample of 1432 bases of N gene from a 24h processed formalin-fixed and paraffin-embedded rabies infected brain tissue after 1 month storage were in accord with those from frozen specimen analysis. It is strongly suggested that for further molecular analysis, a piece of fresh brain tissue should be saved prior to the brain sectioning process and stored no longer than 24h in formalin before embedding.

Animals↗
PubMed2004

Re-evaluation of archival material for neuronal cell injury produced by L-2-chloropropionic acid in the rat brain.

Previous studies have shown that L-2-chloropropionic acid (L-CPA) produces necrosis to cerebellar granule cells with some associated Purkinje cell damage in the rat. We have re-evaluated the neuropathology using the original sections and fresh sections from archived brain material from rats treated with L-CPA at different ages, times after dosing and the following prior treatment with the N-methyl-D-aspartate (NMDA) receptor antagonist, MK-801. In addition we have determined the lobular distribution of cerebellar granule cell necrosis produced by L-CPA. Using Fluoro-Jade staining to detect degenerating neurons, we have identified three new brain regions that show neuronal cell necrosis as a result of exposure to L-CPA, these are the medial habenular nucleus, pontine gray and inferior olivary nucleus. The neuronal cell degeneration was confirmed in conventional haematoxylin and eosin stained sections and in some cases by glial fibrillary acidic protein staining for reactive gliosis. The neuronal cell necrosis at these new sites was both time and dose dependent; young 22-day-old rats, which are refractory to L-CPA-induced cerebellar granule cell necrosis, did however show some neuronal cell degeneration in the medial habenular, pontine gray and inferior olivary nuclei. Treatment of rats with MK-801 30 min prior to L-CPA, afforded complete protection against the neuronal cell injury in the medial habenular, pontine gray and inferior olivary nuclei, similar to that previously reported for the cerebellum, supporting an excitotoxic mechanism of neuronal cell death. In the cerebellum the lobular distribution of the granule cell loss was not uniform, more severe granule cell loss occurring in lobules 1-4 and 9a + b. This localization exactly mirrors that seen previously in the cerebellum of rats given L-CPA and examined by magnetic resonance imaging (MRI). The basis for the neuronal cell loss in the medial habenular nucleus, pontine gray and inferior olivary nucleus, in addition to the major site in the cerebellum, and the sensitivity of particular cerebellar lobes is not currently understood. Anatomical connections between the sites of injury and their likely neurotransmitter use are discussed.

Age Factors↗
PubMed2004

House dust mites (Der p 1, Der f 1), cat (Fel d 1) and cockroach (Bla g 2) allergens in indoor work-places (offices and archives).

BACKGROUND: Exposure to indoor allergens has already been shown to occur in many public places, including workplaces, in several countries. Aim of this study was to measure the levels of house dust mites, cat and cockroach allergens in indoor workplaces (offices and archives) in Italy and to evaluate the possible relationships between allergen levels and building characteristics, type of ventilation, indoor relative humidity and temperature. METHODS: Der f 1 and Der p 1, Fel d 1, Bla g 2 were measured by ELISA in dust samples collected from floors or upholstered seats of 160 workplaces. RESULTS: Detectable Der p 1 levels were found in 86 (54%) workplaces Der f 1 in 87 (55%), Fel d 1 in 86 (54%) and Bla g 2 in 3 (1.9%). Der p 1 allergen concentrations expressed per weight were higher than the proposed sensitization thresholds in 7 samples, Der f 1 in 5, Fel d 1 in 6 and Bla g 2 in 3. The highest allergen levels were detected in samples from upholstered seats. A significant correlation was found between Der f 1 level on floors, expressed per surface, and indoor temperature (r = 0.39; P < 0.01). CONCLUSIONS: In our study we found that upholstered seats in workplaces in Italy may constitute a significant reservoir both of house dust mites and cat allergens. Exposure to these allergens in workplaces may represent a risk factor for elicitation of symptoms and/or induction/maintenance of inflammation in allergic individuals and might also constitute a risk factor for sensitization.

Antigens, Dermatophagoides↗
PubMed1990

NucNet: a single-vendor clinical picture archiving and communication system--description and reflections.

In 1984 to 1985, work commenced at the University of Michigan to develop, in cooperation with commercial vendors, a picture archiving and communication system capable of handling all clinical imaging in the division of nuclear medicine. The guiding features of NucNet are the optimization of the system for perceived, rather than actual speed, and the use of technology appropriate to the majority of clinical activity rather than to the entirety. This has resulted in a cost-effective system that has been easy to use and well accepted for routine clinical work. A new image management system currently being developed at William Beaumont Hospital is based on these principles but uses the latest generation of powerful microcomputers to perform most of the actions currently performed by larger computers on NucNet. It is anticipated that, using current technology, the key functionality of NucNet can be obtained for a fraction of its original cost.

Costs and Cost Analysis↗
PubMed2002

Telomere length assessment in human archival tissues: combined telomere fluorescence in situ hybridization and immunostaining.

A method was developed to assess human telomere lengths at the individual cell level in tissue sections from standard formalin-fixed paraffin-embedded tissues. We coupled this method with immunofluorescence to allow the simultaneous identification of specific cell types. Validation of this in situ quantification method showed excellent agreement with the commonly used telomere repeat fragment-Southern blot method. The assay requires very few cells ( approximately 10 to 15). Thus, small tissue samples, including clinical biopsies, can be easily accommodated. In addition, the cells under study need not be actively cycling and there is no requirement for tissue disaggregation or cell culture. This method provides a more accurate assessment of telomere lengths than Southern blotting because confounding contributions from undesired cell types within tissue samples are avoided. Using this technique, we were able to perform the first comparison of relative telomere lengths in matched tumor versus normal epithelial cells within archival human prostate tissues.

Animals↗
PubMed1999

A high frequency of sequence alterations is due to formalin fixation of archival specimens.

Genomic analysis of archival tissues fixed in formalin is of fundamental importance in biomedical research, and numerous studies have used such material. Although the possibility of polymerase chain reaction (PCR)-introduced artifacts is known, the use of direct sequencing has been thought to overcome such problems. Here we report the results from a controlled study, performed in parallel on frozen and formalin-fixed material, where a high frequency of nonreproducible sequence alterations was detected with the use of formalin-fixed tissues. Defined numbers of well-characterized tumor cells were amplified and analyzed by direct DNA sequencing. No nonreproducible sequence alterations were found in frozen tissues. In formalin-fixed material up to one mutation artifact per 500 bases was recorded. The chance of such artificial mutations in formalin-fixed material was inversely correlated with the number of cells used in the PCR-the fewer cells, the more artifacts. A total of 28 artificial mutations were recorded, of which 27 were C-T or G-A transitions. Through confirmational sequencing of independent amplification products artifacts can be distinguished from true mutations. However, because this problem was not acknowledged earlier, the presence of artifacts may have profoundly influenced previously reported mutations in formalin-fixed material, including those inserted into mutation databases.

Base Sequence↗
PubMed2001

A simple comet assay for archived sperm correlates DNA fragmentation to reduced hyperactivation and penetration of zona-free hamster oocytes.

OBJECTIVE: To correlate sperm variables with sperm DNA fragmentation, as assessed by using a modified alkaline comet assay for sperm smears. DESIGN: The comet assay was adapted for fixed sperm smears (59 cases), and the level of DNA fragmentation was determined. SETTING: Clinical and academic research environment. PATIENT(S): 59 patients undergoing fertility treatment. INTERVENTION(S): Sperm samples leftover from IVF procedures were fixed and processed for the comet assay. MAIN OUTCOME MEASURE(S): Sperm head DNA density and sperm variables. RESULT(S): A correlation was observed between increased sperm head DNA fragmentation and decreased penetration of zona-free hamster oocytes. Heat-induced hyperactive motility decreased as DNA fragmentation increased. The DNA fragmentation did not correlate with percentages of intact acrosome, normality, maturity, and strict normal morphology. CONCLUSION(S): The advantages of the comet assay for archived cells include simplicity, low intraassay coefficient of variation, and low performance cost; in addition, DNA analysis can be carried out at leisure. Low DNA damage was associated with higher hyperactivation and oocyte penetration, suggesting that failed fertilization was linked to compromised DNA integrity in the sperm. Exploration of compounds to repair damaged DNA is warranted.

Acridine Orange↗
PubMed1996

Guidelines for cost-effective implementation of Picture Archiving and Communication Systems. An approach building on practical experiences in three European hospitals.

This paper describes a comprehensive approach for the assessment of the impact of (partial) Picture Archiving and Communication Systems (PACS). The approach is developed, based on actual clinical experience in three European hospitals and tested in these environments. The approach departs from a thorough analysis of the working procedures and information flows before implementation, both descriptive and quantitative. On the basis of this analysis, quantitative (and hence testable) objectives of the implementation are defined. The implementation strategy is defined after comparison of various scenarios, taking costs and effects for both the final and the transition phases into account. The approach is supported by a comprehensive evaluation protocol and a software package (PACER). The approach is demonstrated in this paper by applying it on a hypothetical PACS implementation for CT, ultrasound and for the part of the radiology department serving ICU. The objectives of this PACS are: (1)--to shorten the turn around time between the radiology department and ICU from 4 h to 30 min, (2)--to save 2000 m2 of film per year and (3)--to save personnel time. In this case the PACS is introduced in three phases and completed after three years. The cost analysis shows that, if started in 1995, a financial break even point is reached after 6 years, when comparing costs for the film-based system with those of the PACS. Experiences in the three sites show that the approach helps to harvest potential benefits, allowing a cost-effective implementation of PACS.

Cost-Benefit Analysis↗