WorldWideScience

Sample records for paraffin embedded sections

  1. Optimization of Glial Fibrillary Acidic Protein Immunoreactivity in Formalin-fixed, Paraffin-Embedded Guinea Pig Brain Sections

    Science.gov (United States)

    2003-09-01

    fixed, paraffin-embedded guinea pig brain sections using a variety of commercially available GFAP antibody clones. Of the 7 clones tested for cross...determining neuropathological consequences in the guinea pig following exposure to chemical warfare nerve agent.

  2. Combined in situ zymography, immunofluorescence, and staining of iron oxide particles in paraffin-embedded, zinc-fixed tissue sections.

    Science.gov (United States)

    Haeckel, Akvile; Schoenzart, Lena; Appler, Franziska; Schnorr, Joerg; Taupitz, Matthias; Hamm, Bernd; Schellenberger, Eyk

    2012-01-01

    Superparamagnetic iron oxide particles are used as potent contrast agents in magnetic resonance imaging. In histology, these particles are frequently visualized by Prussian blue iron staining of aldehyde-fixed, paraffin-embedded tissues. Recently, zinc salt-based fixative was shown to preserve enzyme activity in paraffin-embedded tissues. In this study, we demonstrate that zinc fixation allows combining in situ zymography with fluorescence immunohistochemistry (IHC) and iron staining for advanced biologic investigation of iron oxide particle accumulation. Very small iron oxide particles, developed for magnetic resonance angiography, were applied intravenously to BALB/c nude mice. After 3 hours, spleens were explanted and subjected to zinc fixation and paraffin embedding. Cut tissue sections were further processed to in situ zymography, IHC, and Prussian blue staining procedures. The combination of in situ zymography as well as IHC with subsequent Prussian blue iron staining on zinc-fixed paraffin-embedded tissues resulted in excellent histologic images of enzyme activity, protease distribution, and iron oxide particle accumulation. The combination of all three stains on a single section allowed direct comparison with only moderate degradation of fluorescein isothiocyanate-labeled substrate. This protocol is useful for investigating the biologic environment of accumulating iron oxide particles, with excellent preservation of morphology.

  3. In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections.

    Science.gov (United States)

    Ellison, Mitchell A; McMahon, Michael B; Bonde, Morris R; Palmer, Cristi L; Luster, Douglas G

    2016-01-01

    Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here. To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues. This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.

  4. Staining of E-selectin ligands on paraffin-embedded sections of tumor tissue.

    Science.gov (United States)

    Carrascal, Mylène A; Talina, Catarina; Borralho, Paula; Gonçalo Mineiro, A; Henriques, Ana Raquel; Pen, Cláudia; Martins, Manuela; Braga, Sofia; Sackstein, Robert; Videira, Paula A

    2018-05-02

    The E-selectin ligands expressed by cancer cells mediate adhesion of circulating cancer cells to endothelial cells, as well as within tissue microenvironments important for tumor progression and metastasis. The identification of E-selectin ligands within cancer tissue could yield new biomarkers for patient stratification and aid in identifying novel therapeutic targets. The determinants of selectin ligands consist of sialylated tetrasaccharides, the sialyl Lewis X and A (sLe X and sLe A ), displayed on protein or lipid scaffolds. Standardized procedures for immunohistochemistry make use of the antibodies against sLe X and/or sLe A . However, antibody binding does not define E-selectin binding activity. In this study, we developed an immunohistochemical staining technique, using E-selectin-human Ig Fc chimera (E-Ig) to characterize the expression and localization of E-selectin binding sites on paraffin-embedded sections of different cancer tissue. E-Ig successfully stained cancer cells with high specificity. The E-Ig staining show high reactivity scores in colon and lung adenocarcinoma and moderate reactivity in triple negative breast cancer. Compared with reactivity of antibody against sLe X/A , the E-Ig staining presented higher specificity to cancer tissue with better defined borders and less background. The E-Ig staining technique allows the qualitative and semi-quantitative analysis of E-selectin binding activity on cancer cells. The development of accurate techniques for detection of selectin ligands may contribute to better diagnostic and better understanding of the molecular basis of tumor progression and metastasis.

  5. Detection of Streptococcus suis by in situ hybridization, indirect immunofluorescence, and peroxidase-antiperoxidase assays in formalin-fixed, paraffin-embedded tissue sections from pigs

    DEFF Research Database (Denmark)

    Boye, Mette; Feenstra, Anne Avlund; Tegtmeier, Conny

    2000-01-01

    and the immunohistochemical methods were used for detection of S. suis in formalin-fixed, paraffin-embedded tissue sections of brain, endocardium, and lung from pigs infected with S. suis. The methods developed were able to detect single cells of S. suis in situ in the respective samples, whereas no signal was observed from...

  6. Identification of 5-hydroxytryptamine-producing cells by detection of fluorescence in paraffin-embedded tissue sections

    Directory of Open Access Journals (Sweden)

    Y. Kaneko

    2016-09-01

    Full Text Available 5-Hydroxytryptamine (5-HT produced by enterochromaffin (EC cells is an important enteric mucosal signaling ligand and has been implicated in several gastrointestinal diseases, including inflammatory bowel disease and functional disorders such as irritable bowel syndrome. The present study reports a new, simple and rapid visualization method of 5-HT-producing EC cells utilizing detection of autofluorescence in paraffin-embedded tissue sections after formalin fixation. In human samples, there was a high incidence of autofluorescence+ cells in the 5-HT+ cells in the pyloric, small intestinal and colonic glands, while co-localization was lacking between autofluorescence+ and gastrin+ cells in the pyloric and small intestinal glands. Autofluorescence+ EC cells were detected in the colon of mice and rats. Autofluorescence+ cells were also observed in 5-HT+ β cells in the pancreatic islets of Langerhans in pregnant mice, while non-pregnant mouse pancreatic islet cells showed no 5-HT immunoreactivity or autofluorescence. These results suggest that autofluorescence+ cells are identical to 5-HT+ cells, and the source of autofluorescence may be 5-HT itself or molecules related to its synthesis or degradation. This autofluorescence signal detection method may be applicable for monitoring of inflammatory status of inflammatory bowel diseases in both the experimental and clinical settings.

  7. Fluorescence in situ hybridization on formalin-fixed and paraffin-embedded tissue

    DEFF Research Database (Denmark)

    Laub Petersen, Bodil; Zeuthen, Mette Christa; Pedersen, Sanni

    2004-01-01

    , such as quantitation of signals as in triploidy, it is possible to isolate nuclei from paraffin-embedded tissue. However, using formalin-fixed paraffin-embedded tissue, either in thin sections or as isolated nuclei, one encounters a range of technical problems, paralleling those met in immunohistochemistry. Variations...... nuclei and tissue sections from formalin-fixed, paraffin-embedded tissue....

  8. Replacing xylene with n-heptane for paraffin embedding.

    Science.gov (United States)

    Stockert, J C; López-Arias, B; Del Castillo, P; Romero, A; Blázquez-Castro, A

    2012-10-01

    In standard histological technique, aromatic solvents such as xylene and toluene are used as clearing agents between ethanol dehydration and paraffin embedding. In addition, these solvents are used for de-waxing paraffin sections. Unfortunately, these solvents are harmful and therefore adequate substitutes would be useful. We suggest the use of n-heptane as a convenient substitute for xylene. Paraffin sections of rat tissues processed with n-heptane and stained with hematoxylin-eosin or Masson's trichrome showed proper embedment, well preserved morphology and excellent staining.

  9. Rapid, sensitive, type specific PCR detection of the E7 region of human papillomavirus type 16 and 18 from paraffin embedded sections of cervical carcinoma

    DEFF Research Database (Denmark)

    Lesnikova, Iana; Lidang, Marianne; Hamilton-Dutoit, Stephen Jacques

    2010-01-01

    ABSTRACT: Human papillomavirus (HPV) infection, and in particularly infection with HPVs 16 and 18 is a central carcinogenic factor in the uterine cervix. We established and optimized a PCR assay for the detection and discrimination of HPV types 16 and 18 in archival formaldehyde fixed and paraffin...... embedded (FFPE) sections of cervical cancer. Tissue blocks from 35 cases of in situ or invasive cervical squamouscell carcinoma and surrogate FFPE sections containing the cell lines HeLa and SiHa were tested for HPV 16 and HPV18 and for the housekeeping gene beta-actin by conventional PCR using type...

  10. Rapid, sensitive, type specific PCR detection of the E7 region of human papillomavirus type 16 and 18 from paraffin embedded sections of cervical carcinoma

    DEFF Research Database (Denmark)

    Lesnikova, Iana; Lidang, Marianne; Hamilton-Dutoit, Steven

    2010-01-01

    ABSTRACT: Human papillomavirus (HPV) infection, and in particularly infection with HPVs 16 and 18, is a central carcinogenic factor in the uterine cervix. We established and optimized a PCR assay for the detection and discrimination of HPV types 16 and 18 in archival formaldehyde fixed and paraffin...... embedded (FFPE) sections of cervical cancer.Tissue blocks from 35 cases of in situ or invasive cervical squamous cell carcinoma and surrogate FFPE sections containing the cell lines HeLa and SiHa were tested for HPV 16 and HPV18 by conventional PCR using type specific primers, and for the housekeeping gene...

  11. Antigen retrieval prior to on-tissue digestion of formalin-fixed paraffin-embedded tumour tissue sections yields oxidation of proline residues.

    Science.gov (United States)

    Djidja, Marie-Claude; Claude, Emmanuelle; Scriven, Peter; Allen, David W; Carolan, Vikki A; Clench, Malcolm R

    2017-07-01

    MALDI-mass spectrometry imaging (MALDI-MSI) has been shown to allow the study of protein distribution and identification directly within formalin-fixed paraffin-embedded (FFPE) tissue sections. However, direct protein identification from tissue sections remains challenging due to signal interferences and/or existing post-translational or other chemical modifications. The use of antigen retrieval (AR) has been demonstrated for unlocking proteins prior to in situ enzymatic digestion and MALDI-MSI analysis of FFPE tissue sections. In the work reported here, the identification of proline oxidation, which may occur when performing the AR protocol, is described. This facilitated and considerably increased the number of identified peptides when adding proline oxidation as a variable modification to the MASCOT search criteria. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Differential N-glycan patterns identified in lung adenocarcinoma by N-glycan profiling of formalin-fixed paraffin-embedded (FFPE) tissue sections.

    Science.gov (United States)

    Wang, Xiaoning; Deng, Zaian; Huang, Chuncui; Zhu, Tong; Lou, Jiatao; Wang, Lin; Li, Yan

    2018-02-10

    N-glycan profiling is a powerful approach for analyzing the functional relationship between N-glycosylation and cancer. Current methods rely on either serum or fresh tissue samples; however, N-glycan patterns may differ between serum and tissue, as the proteins of serum originate from a variety of tissues. Furthermore, fresh tissue samples are difficult to ship and store. Here, we used a profiling method based on formalin-fixed paraffin-embedded (FFPE) tissue sections from lung adenocarcinoma patients. We found that our method was highly reproducible. We identified 58 N-glycan compositions from lung adenocarcinoma FFPE samples, 51 of which were further used for MS n -based structure prediction. We show that high mannose type N-glycans are upregulated, while sialylated N-glycans are downregulated in our FFPE lung adenocarcinoma samples, compared to the control samples. Our receiver operating characteristic (ROC) curve analysis shows that high mannose type and sialylated N-glycans are useful discriminators to distinguish between lung adenocarcinoma and control tissue. Together, our results indicate that expression levels of specific N-glycans correlate well with lung adenocarcinoma, and strongly suggest that our FFPE-based method will be useful for N-glycan profiling of cancer tissues. Glycosylation is one of the most important post-translational protein modifications, and is associated with several physiopathological processes, including carcinogenesis. In this study, we tested the feasibility of using formalin-fixed paraffin-embedded (FFPE) tissue sections to identify changes in N-glycan patterns and identified the differentially expressed N-glycans of lung adenocarcinoma. Our study shows that the FFPE-based N-glycan profiling method is useful for clinical diagnosis as well as identification of potential biomarkers, and our data expand current knowledge of differential N-glycan patterns of lung adenocarcinoma. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Diagnostic accuracy of morphologic identification of filamentous fungi in paraffin embedded tissue sections: Correlation of histological and culture diagnosis

    Directory of Open Access Journals (Sweden)

    Sundaram Challa

    2014-01-01

    Full Text Available Aims and Objectives: The aim was to investigate the correlation between histological and culture diagnosis of filamentous fungi. Materials and Methods: Tissue sections from biopsy samples stained with Hematoxylin and Eosin and special stains from samples of chronic invasive/noninvasive sinusitis and intracranial space occupying lesions during 2005-2011 diagnosed to have infection due to filamentous fungi were reviewed. The histopathology and culture diagnoses were analyzed for correlation and discrepancy. Results: There were 125 samples positive for filamentous fungi on biopsy. Of these 76 (60.8% were submitted for culture and fungi grew in 30 (39.97% samples. There was a positive correlation between histological and culture diagnosis in 25 (83.33% samples that included Aspergillus species (16/19, Zygomycetes species (8/10 and dematiaceous fungi (1/1. The negative yield of fungi was more in Zygomycetes species (20/30 when compared to Aspergillus species (25/44. There was a discrepancy in diagnosis in 5/30 (16.67% samples which included probable dual infection in two, and dematiaceous fungi being interpreted as Aspergillus species in three samples. Conclusion: Histopathology plays a major role in the diagnosis of infection due to filamentous fungi, especially when cultures are not submitted or negative. The discrepancy between histological and culture diagnosis was either due to dematiaceous fungi being interpreted as Aspergillus species or probable dual infection.

  14. RT-PCR amplification of RNA extracted from formalin-fixed, paraffin-embedded oral cancer sections: analysis of p53 pathway.

    Science.gov (United States)

    Tachibana, Masatsugu; Shinagawa, Yasuhiro; Kawamata, Hitoshi; Omotehara, Fumie; Horiuchi, Hideki; Ohkura, Yasuo; Kubota, Keiichi; Imai, Yutaka; Fujibayashi, Takashi; Fujimori, Takahiro

    2003-01-01

    We present a new approach towards the detection of the mRNAs in formalin-fixed, paraffin-embedded samples using a reverse transcriptase (RT)-polymerase chain reaction (PCR). The total RNAs were extracted from 10-micron-thick sections and were reverse-transcribed, then the RT-products were subjected to PCR amplification of GAPDH mRNA for screening the mRNA degradation. Next, nested PCR was performed for examining the expression of p53-related genes, p21WAF1, MDM2, p33ING1 and p14ARF. GAPDH mRNA expression was detectable in 12 out of 21 oral squamous cell carcinoma (SCC) samples. p21WAF1 mRNA expression was detectable in 5 out of 12 SCC samples, MDM2 mRNA expression was detectable in 5 our of 12 SCC samples and p33ING1 mRNA expression was detectable in 6 out of 12 SCC samples. However, the expression of p14ARF mRNA was not detectable in any of the samples. Seven out of 12 oral SCC samples showed abnormal nuclear accumulation of p53 protein by immunohistochemical staining, whereas 5 out of 12 oral SCCs showed negative staining for p53 protein. Of of p33ING1 mRNA. One of these was a verrucous carcinoma in which the p53 gene products might be inactivated by the oncoprotein E6 of human papilloma virus. Thus, the p53 tumor suppressor pathway was disrupted in most oral SCCs at the cellular levels, due to either an abnormality in p53 itself or loss of expression of p53 regulatory factors. This method would assist in making diagnosis, determining therapeutic strategy and predicting the prognosis of various cancers including oral SCCs.

  15. RNA analysis of inner ear cells from formalin fixed paraffin embedded (FFPE) archival human temporal bone section using laser microdissection--a technical report.

    Science.gov (United States)

    Kimura, Yurika; Kubo, Sachiho; Koda, Hiroko; Shigemoto, Kazuhiro; Sawabe, Motoji; Kitamura, Ken

    2013-08-01

    Molecular analysis using archival human inner ear specimens is challenging because of the anatomical complexity, long-term fixation, and decalcification. However, this method may provide great benefit for elucidation of otological diseases. Here, we extracted mRNA for RT-PCR from tissues dissected from archival FFPE human inner ears by laser microdissection. Three human temporal bones obtained at autopsy were fixed in formalin, decalcified by EDTA, and embedded in paraffin. The samples were isolated into spiral ligaments, outer hair cells, spiral ganglion cells, and stria vascularis by laser microdissection. RNA was extracted and heat-treated in 10 mM citrate buffer to remove the formalin-derived modification. To identify the sites where COCH and SLC26A5 mRNA were expressed, semi-nested RT-PCR was performed. We also examined how long COCH mRNA could be amplified by semi-nested RT-PCR in archival temporal bone. COCH was expressed in the spiral ligament and stria vascularis. However, SLC26A5 was expressed only in outer hair cells. The maximum base length of COCH mRNA amplified by RT-PCR was 98 bp in 1 case and 123 bp in 2 cases. We detected COCH and SLC26A5 mRNA in specific structures and cells of the inner ear from archival human temporal bone. Our innovative method using laser microdissection and semi-nested RT-PCR should advance future RNA study of human inner ear diseases. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. A single simple procedure for dewaxing, hydration and heat-induced epitope retrieval (HIER) for immunohistochemistry in formalin fixed paraffin-embedded tissue

    DEFF Research Database (Denmark)

    Paulsen, I M S; Dimke, H; Frische, S

    2015-01-01

    Heat-induced epitope retrieval (HIER) is widely used for immunohistochemistry on formalin fixed paraffin-embedded tissue and includes temperatures well above the melting point of paraffin. We therefore tested whether traditional xylene-based removal of paraffin is required on sections from paraff...... of dewaxing in xylene. In conclusion, the HIER procedure described and tested can be used as a single procedure enabling dewaxing, hydration and epitope retrieval for immunohistochemistry in formalin fixed paraffin-embedded tissue....

  17. Measurement of Gene Expression in Archival Paraffin-Embedded Tissues

    Science.gov (United States)

    Cronin, Maureen; Pho, Mylan; Dutta, Debjani; Stephans, James C.; Shak, Steven; Kiefer, Michael C.; Esteban, Jose M.; Baker, Joffre B.

    2004-01-01

    Throughout the last decade many laboratories have shown that mRNA levels in formalin-fixed and paraffin-embedded (FPE) tissue specimens can be quantified by reverse transcriptase-polymerase chain reaction (RT-PCR) techniques despite the extensive RNA fragmentation that occurs in tissues so preserved. We have developed RT-PCR methods that are sensitive, precise, and that have multianalyte capability for potential wide use in clinical research and diagnostic assays. Here it is shown that the extent of fragmentation of extracted FPE tissue RNA significantly increases with archive storage time. Probe and primer sets for RT-PCR assays based on amplicons that are both short and homogeneous in length enable effective reference gene-based data normalization for cross comparison of specimens that differ substantially in age. A 48-gene assay used to compare gene expression profiles from the same breast cancer tissue that had been either frozen or FPE showed very similar profiles after reference gene-based normalization. A 92-gene assay, using RNA extracted from three 10-μm FPE sections of archival breast cancer specimens (dating from 1985 to 2001) yielded analyzable data for these genes in all 62 tested specimens. The results were substantially concordant when estrogen receptor, progesterone receptor, and HER2 receptor status determined by RT-PCR was compared with immunohistochemistry assays for these receptors. Furthermore, the results highlight the advantages of RT-PCR over immunohistochemistry with respect to quantitation and dynamic range. These findings support the development of RT-PCR analysis of FPE tissue RNA as a platform for multianalyte clinical diagnostic tests. PMID:14695316

  18. A SIMPLE PARAFFIN EMBEDDED PROTOCOL FOR FISH EGG, EMBRYO, AND LARVAE

    Directory of Open Access Journals (Sweden)

    Gratiana Eka Wijayanti

    2017-06-01

    Full Text Available This paper describes a simple protocol of paraffin-embedded histological section for fish eggs, embryo and larvae of the hard-lipped barb and the giant gourami. The specimens were fixed in Bouin solution, washed in 70% ethanol, then were dehydrated in a series of ethanol solution of increasing concentration until absolute ethanol was reached. The specimens were cleared in graded xylene and were infiltrated with liquid paraffin then were embedded in pure paraffin. Upon sectioning, at 4–5 µm thick the specimens were attached to the gelatin-coated glass slide and let to dry at room temperature or 37°C overnight. The specimens were deparaffinized in xylene, rehydrated then were stained with hematoxylin and eosin. After being dehydrated in graded ethanol, the specimens were cleared in xylene and were mounted with an organic mounting agent. Any step in preparing histological section including samples collection, fixation, dehydration, infiltration and embedding might contribute to the quality of histological features. A proper knowledge of the tissues beeing processed, fixative solution and the histological techniques is essential to gain good results. Bouin fixative is preferable to fix fish larvae and produce a good histological feature. Decalcification is necessary to produce a good histological section on the specimens containing bone.

  19. Molecular diagnosis of skin infections using paraffin-embedded tissue - review and interdisciplinary consensus.

    Science.gov (United States)

    Sunderkötter, Cord; Becker, Karsten; Kutzner, Heinz; Meyer, Thomas; Blödorn-Schlicht, Norbert; Reischl, Udo; Nenoff, Pietro; Geißdörfer, Walter; Gräser, Yvonne; Herrmann, Mathias; Kühn, Joachim; Bogdan, Christian

    2018-02-01

    Nucleic acid amplification techniques (NATs), such as PCR, are highly sensitive and specific methods that have become valuable supplements to culture and serology in the diagnosis of infectious disorders. However, especially when using formalin-fixed and paraffin-embedded tissue, these techniques are associated with both false-negative and false-positive results, a pitfall that is frequently misjudged. Representatives of the German Society of Hygiene and Microbiology (DGHM) and the German Society of Dermatology (DDG) therefore set out to develop a consensus - in the form of a review article - on the appropriate indications for NATs using paraffin-embedded tissue, its contraindications, and the key points to be considered in the pre- and post-analytical phase. Given that fresh, naive tissue is preferably to be used in the workup of a suspected infection, PCR analysis on paraffin sections represents an exception. The latter may be considered if an infection is suspected at a later point in time and fresh tissue has not been preserved or can no longer be obtained. Potential indications include confirmation of histologically suspected infections with Leishmania spp., Bartonella spp., Rickettsia spp., or in case of ecthyma contagiosum. Infections with, for example, mycobacteria or RNA viruses, on the other hand, are not considered useful indications for NATs using paraffin sections. In order to avoid misinterpretation of test results, it is essential that laboratory reports on NATs using paraffin-embedded tissue contain information on the indication/diagnostic circumstances, the required and chosen pre-analytical steps, the limitations of the method, and on diagnostic alternatives. © 2018 Deutsche Dermatologische Gesellschaft (DDG). Published by John Wiley & Sons Ltd.

  20. Analysis of hepcidin expression: in situ hybridization and quantitative polymerase chain reaction from paraffin sections.

    Science.gov (United States)

    Sakuraoka, Yuhki; Sawada, Tokihiko; Shiraki, Takayuki; Park, Kyunghwa; Sakurai, Yuhichiro; Tomosugi, Naohisa; Kubota, Keiichi

    2012-07-28

    To establish methods for quantitative polymerase chain reaction (PCR) for hepcidin using RNAs isolated from paraffin-embedded sections and in situ hybridization of hepatocellular carcinoma (HCC). Total RNA from paraffin-embedded sections was isolated from 68 paraffin-embedded samples of HCC. Samples came from 54 male and 14 female patients with a mean age of 66.8 ± 7.8 years. Quantitative PCR was performed. Immunohistochemistry and in situ hybridization for hepcidin were also performed. Quantitative PCR for hepcidin using RNAs isolated from paraffin-embedded sections of HCC was performed successfully. The expression level of hepcidin mRNA in cancer tissues was significantly higher than that in non-cancer tissues. A method of in situ hybridization for hepcidin was established successfully, and this demonstrated that hepcidin mRNA was expressed in non-cancerous tissue but absent in cancerous tissue. We have established novel methods for quantitative PCR for hepcidin using RNAs isolated from paraffin-embedded sections and in situ hybridization of HCC.

  1. A new technique for Gram staining paraffin-embedded tissue.

    Science.gov (United States)

    Engbaek, K; Johansen, K S; Jensen, M E

    1979-01-01

    Five techniques for Gram staining bacteria in paraffin sections were compared on serial sections of pulmonary tissues from eight bacteriological necropsies. Brown and Hopp's method was the most satisfactory for distinguishing Gram-positive and Gram-negative bacteria. However, this method cannot be recommended as the preparations were frequently overstained, and the Gram-negative bacteria were stained indistinctly. A modification of Brown and Hopps' method was developed which stains larger numbers of Gram-negative bacteria and differentiates well between different cell types and connective tissue, and there is no risk of overstaining. PMID:86548

  2. Detection of apoptotic cells in tumour paraffin sections

    International Nuclear Information System (INIS)

    Pizem, J.; Coer, A.

    2003-01-01

    Apoptosis is a distinct form of cell death characterised by specific morphological features and regulated by complex molecular mechanisms. Its deregulation is fundamental for tumour growth and progression and, moreover, anticancer therapies suppress tumour growth mainly by induction of apoptosis. Since the extent of apoptosis in a tumour may have prognostic as well as therapeutic implications, much effort has been invested in developing specific methods that can be routinely used to detect apoptotic cells in archival formalin- fixed paraffin-embedded tissue. Complex molecular pathways are involved in the regulation of apoptosis. Pro-apoptotic signals trigger activation of caspases that specifically cleave target proteins. Cleavage of proteins (caspase substrates) is responsible for morphological changes of apoptotic cells and DNA fragmentation. In the last decade, detection of apoptotic cells in formalin-fixed tumour tissue sections has been based mainly on morphology and characteristic DNA fragmentation. Recently, specific antibodies to activated caspases and cleaved target proteins (including cytokeratin 18, actin and PARP) have been produced that enable accurate detection of apoptosis in paraffin sections. (author)

  3. Evaluation of a fluorescence-labelled oligonucleotide tide probe targeting 23S rRNA for in situ detection of Salmonella serovars in paraffin-embedded tissue sections and their rapid identification in bacterial smears

    DEFF Research Database (Denmark)

    Nordentoft, Steen; Christensen, H.; Wegener, Henrik Caspar

    1997-01-01

    with the probe. The probe did not hybridize to serovars from subspecies IIIa (S. arizonae) or to S. bongori. No cross-reaction to 64 other strains of the family Enterobacteriaceae or 18 other bacterial strains outside this family was observed. The probe was tested with sections of formalin-fixed, paraffin...

  4. Relative shrinkage of adipocytes by paraffin in proportion to plastic embedding in human adipose tissue before and after weight loss.

    Science.gov (United States)

    Verhoef, Sanne P M; van Dijk, Paul; Westerterp, Klaas R

    2013-01-01

    Adipocyte size is a major modulator of endocrine functioning of adipose tissue and methods allowing accurate determination of adipocyte size are important to study energy metabolism. The aim of this study was to assess the relative shrinkage of adipocytes before and after weight loss by comparing adipose tissue from the same subjects embedded in paraffin and plastic. 18 healthy subjects (5 males and 13 females) aged 20-50 y with a BMI of 28-38 kg/m² followed a very low energy diet for 8 weeks. Adipose tissue biopsies were taken prior to and after weight loss and were processed for paraffin and plastic sections. Parameters of adipocyte size were determined with computer image analysis. Mean adipocyte size was smaller in paraffin compared to plastic embedded tissue both before (66 ± 4 vs. 103 ± 5 μm, P paraffin embedded tissue in proportion to plastic embedded tissue was not significantly different before and after weight loss (73 and 69%, respectively). Shrinkage due to the type of embedding of the adipose tissue can be ignored when comparing before and after weight loss. Plastic embedding of adipose tissue provides more accurate and sensitive results. © 2013 Asian Oceanian Association for the Study of Obesity . Published by Elsevier Ltd. All rights reserved.

  5. Light microscopic identification and semiquantification of polyethylene particles in methylmethacrylate and paraffin-embedded experimental bone implant specimens

    DEFF Research Database (Denmark)

    Rahbek, O; Kold, S; Overgaard, S

    2005-01-01

    The aim of this study was to evaluate the identification of polyethylene (PE) particles in relatively thick methylmethacrylate (MMA) sections widely used in bone implant research. The sensitivity and specificity were compared between decalcified paraffin-embedded oil red O (ORO) stained and MMA-e...

  6. PrPSc detection in formalin-fixed paraffin-embedded tissue by ELISA

    Directory of Open Access Journals (Sweden)

    Nicholson Eric M

    2011-10-01

    Full Text Available Abstract Background Formalin-fixed paraffin-embedded tissue is regularly employed in the diagnosis of transmissible spongiform encephalopathies (TSE by immunohistochemistry (IHC, the standard by which all other TSE diagnostic protocols are judged. While IHC affords advantages over diagnostic approaches that typically utilize fresh or frozen tissue, such as Western blot and ELISA, the process of fixing, staining, and analyzing individual sections by hand does not allow for rapid or high throughput screening. However, preservation of tissues in formalin is not dependent upon the availability of refrigeration. Findings Formalin-fixed paraffin-embedded tissues from TSE transmission studies of scrapie in sheep, chronic wasting disease in white-tailed deer or transmissible mink encephalopathy in cattle were cut at 5 μm thickness. Samples containing the tissue equivalent of as little as one 5 μm section can be used to readily discriminate positive from negative samples. Conclusions This approach cannot replace IHC but may be used along with IHC as both a more rapid and readily high throughput screen where fresh or frozen tissues are not available or impractical.

  7. Automated Analysis of Protein Expression and Gene Amplification within the Same Cells of Paraffin-Embedded Tumour Tissue

    Directory of Open Access Journals (Sweden)

    Timo Gaiser

    2010-01-01

    Full Text Available Background: The simultaneous detection of protein expression and gene copy number changes in patient samples, like paraffin-embedded tissue sections, is challenging since the procedures of immunohistochemistry (IHC and Fluorescence in situ Hybridization (FISH negatively influence each other which often results in suboptimal staining. Therefore, we developed a novel automated algorithm based on relocation which allows subsequent detection of protein content and gene copy number changes within the same cell.

  8. Cellular localization of 2-[3H]deoxy-D-glucose from paraffin-embedded brains

    International Nuclear Information System (INIS)

    Durham, D.; Woolsey, T.A.; Kruger, L.

    1981-01-01

    Results of experiments in which regional neuronal activity is revealed by a 2-[ 3 H]deoxy-D-glucose ( 3 H-2-DG)-paraffin section-emulsion autoradiography method are described. The trigeminal pathway of freely behaving mice was activated differentially by selective patterns of whisker removal. One hour after injection of concentrated 3 H-2-DG, the animals were perfused systemically with a periodate/lysine/paraformaldehyde mixture the brains were embedded in paraffin, and serial sections were taken and coated with emulsion for autoradiography. Diffusion of the isotope out of the tissue was assessed visually and by liquid scintillation counting. While substantial loss of 3 H isotope into the embedding fluids (about 95%) was found, the scintillation counts and the autoradiograms showed good fixation of the isotope in situ, no evidence of isotope movement into the emulsion, and no gradients of diffusion in the sectioned material. Patterns of regional labeling were similar to those reported from brains prepared by conventional 2-[ 14 C]deoxy-D-glucose ( 14 C-2-DG) autoradiography; Trigeminal structures associated with the intact (stimulated) whiskers were labeled relatively heavily, indicating that label uptake is specific with respect to neuronal activity. In the cortex, the patterns of label corresponded directly and precisely to those barrels known to receive inputs from the intact whiskers. Distribution of silver grains in the cortex and in the brainstem was correlated directly with neuronal profiles. Clearly, this approach offers considerable technical advantages, in particular, the ease with which the histological material is prepared. The resolution of the autoradiograms and the quality of the histology are excellent

  9. Amplification of chromosomal translocation junctions from paraffin-embedded tissues of follicular lymphoma patients

    International Nuclear Information System (INIS)

    Nambiar, Mridula; Raghavan, Sathees C; Choudhary, Bibha; Rao, Clementina R

    2008-01-01

    Follicular lymphoma is associated with the t(14;18) translocation, which is one of the most common chromosomal translocations in cancer. Generally, tissues from such patients are preserved as formalin-fixed and paraffin-embedded samples. Most of the time, retrieving the molecular information from such samples is hampered due to quality of preservation, extraction procedures and reaction conditions. In the present study, we isolate the chromosomal DNA from the paraffin-embedded nodal tissues of lymphoma patients and use a highly sensitive nested PCR approach to detect t(14;18) translocation. Our studies show that despite the sheared DNA obtained, appropriate modification of PCR reaction conditions can help in obtaining the desired amplifications. The DNA extraction protocol from paraffin-embedded nodal tissues and modifications in the PCR conditions are discussed. This study would contribute to the successful use of archival tissue samples in obtaining valuable information for cancer research

  10. Amplification of chromosomal translocation junctions from paraffin-embedded tissues of follicular lymphoma patients

    Energy Technology Data Exchange (ETDEWEB)

    Nambiar, Mridula; Raghavan, Sathees C [Department of Biochemistry, Indian Institute of Science, Bangalore-560 012 (India); Choudhary, Bibha [Manipal Institute of Regenerative Medicine, Manipal University, Bangalore-560 071 (India); Rao, Clementina R [Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore-560 029 (India)], E-mail: sathees@biochem.iisc.ernet.in

    2008-09-01

    Follicular lymphoma is associated with the t(14;18) translocation, which is one of the most common chromosomal translocations in cancer. Generally, tissues from such patients are preserved as formalin-fixed and paraffin-embedded samples. Most of the time, retrieving the molecular information from such samples is hampered due to quality of preservation, extraction procedures and reaction conditions. In the present study, we isolate the chromosomal DNA from the paraffin-embedded nodal tissues of lymphoma patients and use a highly sensitive nested PCR approach to detect t(14;18) translocation. Our studies show that despite the sheared DNA obtained, appropriate modification of PCR reaction conditions can help in obtaining the desired amplifications. The DNA extraction protocol from paraffin-embedded nodal tissues and modifications in the PCR conditions are discussed. This study would contribute to the successful use of archival tissue samples in obtaining valuable information for cancer research.

  11. Diagnosis of lymphoma in paraffin wax sections by nested PCR and immunohistochemistry.

    OpenAIRE

    Kitamura, Y; Nanba, E; Inui, S; Tanigawa, T; Ichihara, K

    1996-01-01

    AIMS: To investigate whether nested polymerase chain reaction (PCR) and immunohistochemistry can be used to diagnose malignant lymphoma. METHODS: Paraffin wax embedded tissue sections from 31 patients with malignant lymphoma were analysed by nested PCR and immunohistochemistry using standard protocols. RESULTS: Nested PCR amplification of 1 pg DNA confirmed monoclonality in B cell lymphoma; PCR amplification of 10 pg DNA confirmed monoclonality in T cell lymphoma. Twenty seven (87%) samples w...

  12. STR typing of formalin-fixed paraffin embedded (FFPE) aborted foetal tissue in criminal paternity cases.

    Science.gov (United States)

    Reshef, Ayeleth; Barash, Mark; Voskoboinik, Lev; Brauner, Paul; Gafny, Roni

    2011-03-01

    Sexual assault or rape cases occasionally result in unwanted pregnancies. In almost all such cases the foetus is aborted. A forensic laboratory may receive the foetus, the placenta, or paraffin embedded abortion material for paternity testing. Obtaining a foetal profile DNA from a foetus or placenta may not be successful due to the age or condition of the tissue. Moreover, maternal contamination of placental material will invariably result in a mixed DNA profile. However, the use of properly screened abortion material from paraffin blocks will almost always result in obtaining a foetal DNA profile. Furthermore, foetal tissue fixed in paraffin blocks does not require special conditions for submission and storage as required to preserve fresh foetal or placental tissue. As hospitals routinely prepare foetal tissue in paraffin blocks, which should be readily obtainable by forensic laboratories, these samples would appear to be the preferred choice for paternity testing. 2010 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

  13. Real-time quantitative PCR of microdissected paraffin-embedded breast carcinoma

    DEFF Research Database (Denmark)

    Gjerdrum, Lise Mette; Sorensen, Boe Sandahl; Kjeldsen, Eigil

    2004-01-01

    We studied the feasibility of using real-time quantitative PCR to determine HER-2 DNA amplification and mRNA expression in microdissected formalin-fixed, paraffin-embedded breast tumors and compared this with standard immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) methods...

  14. Detection of apoptosis in paraffin embedded tissues: the influence of tissue type and fixation

    Czech Academy of Sciences Publication Activity Database

    Matalová, Eva; Dubská, L.; Míšek, Ivan

    2002-01-01

    Roč. 71, č. 4 (2002), s. 529-533 ISSN 0001-7213 R&D Projects: GA ČR GP204/02/P112; GA AV ČR KSK6005114 Keywords : apoptosis * TUNEL test * paraffin embedded tissues Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.370, year: 2002

  15. Virus characterization and discovery in formalin-fixed paraffin-embedded tissues

    NARCIS (Netherlands)

    Bodewes, Rogier; van Run, Peter R W A; Schürch, Anita C; Koopmans, Marion P G; Osterhaus, Albert D M E; Baumgärtner, Wolfgang; Kuiken, Thijs; Smits, Saskia L

    2015-01-01

    Detection and characterization of novel viruses is hampered frequently by the lack of properly stored materials. Especially for the retrospective identification of viruses responsible for past disease outbreaks, often only formalin-fixed paraffin-embedded (FFPE) tissue samples are available.

  16. Evaluating Quality of Aged Archival Formalin-Fixed Paraffin-Embedded Samples for RNA-Sequencing

    Science.gov (United States)

    Archival formalin-fixed paraffin-embedded (FFPE) samples offer a vast, untapped source of genomic data for biomarker discovery. However, the quality of FFPE samples is often highly variable, and conventional methods to assess RNA quality for RNA-sequencing (RNA-seq) are not infor...

  17. Comparison of Different Double Immunostaining Protocols for Paraffin Embedded Liver Tissue

    Directory of Open Access Journals (Sweden)

    Alexander Schütz

    1999-01-01

    Full Text Available Most of the double immunostaining protocols that have been introduced so far have been developed for application on fresh frozen material or based on different species antibodies. In liver tissue, general problems of double immunostaining techniques are further complicated by tissue‐specific difficulties, such as necrosis or high intracellular protein content. To assess a reliable double immunostaining protocol for archived, paraffin embedded liver tissue, different protocols based on the use of same species primary antibodies were evaluated in terms of sensitivity, specificity and non‐specific background staining in pathological liver specimens. We compared peroxidase–anti‐peroxidase, alkaline phosphatase–anti‐alkaline phosphatase (PAP/APAP, labelled‐avidin–biotin (LAB/LAB and digoxigenin–anti‐digoxigenin (dig–a‐dig/PAP techniques using different cytokeratin antibodies and an antibody against PCNA. Comparison of the double immunostaining techniques revealed a high sensitivity and specificity in all procedures. Sections, which were stained employing PAP/APAP‐technique, displayed a higher background staining compared to sections which were treated with the LAB/LAB or dig–a‐dig/PAP protocol. In contrast to the dig–a‐dig/PAP protocol, the LAB/LAB technique provides a better time/cost relationship. Therefore, we would like to recommend a modified LAB/LAB protocol for simultaneous detection of different antigens in archived liver tissue.

  18. Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

    DEFF Research Database (Denmark)

    Bjerg Bennike, Tue; Kastaniegaard, Kenneth; Padurariu, Simona

    2016-01-01

    Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving...... samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control ("Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples" [1]). We here report the data from the analysis...

  19. A single simple procedure for dewaxing, hydration and heat-induced epitope retrieval (HIER for immunohistochemistry in formalin fixed paraffin-embedded tissue

    Directory of Open Access Journals (Sweden)

    I.M.S. Paulsen

    2015-11-01

    Full Text Available Heat-induced epitope retrieval (HIER is widely used for immunohistochemistry on formalin fixed paraffin-embedded tissue and includes temperatures well above the melting point of paraffin. We therefore tested whether traditional xylene-based removal of paraffin is required on sections from paraffin-embedded tissue, when HIER is performed by vigorous boiling in 10 mM Tris/0.5 mM EGTA-buffer (pH=9. Immunohistochemical results using HIER with or without prior dewaxing in xylene were evaluated using 7 primary antibodies targeting proteins located in the cytosol, intracellular vesicles and plasma membrane. No effect of omitting prior dewaxing was observed on staining pattern. Semiquantitative analysis did not show HIER to influence the intensity of labelling consistently. Consequently, quantification of immune labelling intensity using fluorescent secondary antibodies was performed at 5 dilutions of primary antibody with and without prior dewaxing in xylene. No effect of omitting prior dewaxing on signal intensity was detectable indicating similar immunoreactivity in dewaxed and non-dewaxed sections. The intensity of staining the nucleus with the DNA-stain ToPro3 was similarly unaffected by omission of dewaxing in xylene. In conclusion, the HIER procedure described and tested can be used as a single procedure enabling dewaxing, hydration and epitope retrieval for immunohistochemistry in formalin fixed paraffin-embedded tissue.

  20. Advantages of infrared transflection micro spectroscopy and paraffin-embedded sample preparation for biological studies

    Science.gov (United States)

    Yao, Jie; Li, Qian; Zhou, Bo; Wang, Dan; Wu, Rie

    2018-04-01

    Fourier-Transform Infrared micro-spectroscopy is an excellent method for biological analyses. In this paper, series metal coating films on ITO glass were prepared by the electrochemical method and the different thicknesses of paraffin embedding rat's brain tissue on the substrates were studied by IR micro-spetroscopy in attenuated total reflection (ATR) mode and transflection mode respectively. The Co-Ni-Cu alloy coating film with low cost is good reflection substrates for the IR analysis. The infrared microscopic transflection mode needs not to touch the sample at all and can get the IR spectra with higher signal to noise ratios. The Paraffin-embedding method allows tissues to be stored for a long time for re-analysis to ensure the traceability of the sample. Also it isolates the sample from the metal and avoids the interaction of biological tissue with the metals. The best thickness of the tissues is 4 μm.

  1. Protein extraction from methanol fixed paraffin embedded tissue blocks: A new possibility using cell blocks

    Science.gov (United States)

    Kokkat, Theresa J.; McGarvey, Diane; Patel, Miral S.; Tieniber, Andrew D.; LiVolsi, Virginia A.; Baloch, Zubair W.

    2013-01-01

    Background: Methanol fixed and paraffin embedded (MFPE) cellblocks are an essential cytology preparation. However, MFPE cellblocks often contain limited material and their relatively small size has caused them to be overlooked in biomarker discovery. Advances in the field of molecular biotechnology have made it possible to extract proteins from formalin fixed and paraffin embedded (FFPE) tissue blocks. In contrast, there are no established methods for extracting proteins from MFPE cellblocks. We investigated commonly available CHAPS (3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate) buffer, as well as two commercially available Qiagen® kits and compared their effectiveness on MFPE tissue for protein yields. Materials and Methods: MFPE blocks were made by Cellient™ automated system using human tissue specimens from normal and malignant specimens collected in ThinPrep™ Vials. Protein was extracted from Cellient-methanol fixed and paraffin embedded blocks with CHAPS buffer method as well as FFPE and Mammalian Qiagen® kits. Results: Comparison of protein yields demonstrated the effectiveness of various protein extraction methods on MFPE cellblocks. Conclusion: In the current era of minimally invasive techniques to obtain minimal amount of tissue for diagnostic and prognostic purposes, the use of commercial and lab made buffer on low weight MFPE scrapings obtained by Cellient® processor opens new possibilities for protein biomarker research. PMID:24403950

  2. Polymerase chain reaction detection of retinoblastoma gene deletions in paraffin-embedded mouse lung adenocarcinomas

    International Nuclear Information System (INIS)

    Churchill, M.E.; Gemmell, M.A.; Woloschak, G.E.

    1991-01-01

    A Polymerase chain reaction (PCR) technique was used to detect deletions in the mouse retinoblastoma (mRb) gene using microtomed sections from paraffin-embedded radiation-induced and spontaneous tumors as the DNA source. Six mRb gene exon fragments were amplified in a 40-cycle, 3-temperature PCR protocol. Absence of any of these fragments relative to control PCR products on a Southern blot indicated a deletion of that portion of the mRb gene. Tumors chosen for analysis were lung adenocarcinomas that were judged to be the cause of death. Spontaneous tumors as well as those from irradiated mice (569 cGy of 60 Co γ rays or 60 cGy of JANUS neutrons) were analyzed. Tumors in six neutron-irradiated mice also had no mRb deletions. However, one of six tumors from γ-irradiated mice and 6 of 18 spontaneous tumors from unirradiated mice showed a deletion in one or both mRb alleles. All deletions detected were in the 5' region of the mRb gene

  3. Virus characterization and discovery in formalin-fixed paraffin-embedded tissues.

    Science.gov (United States)

    Bodewes, Rogier; van Run, Peter R W A; Schürch, Anita C; Koopmans, Marion P G; Osterhaus, Albert D M E; Baumgärtner, Wolfgang; Kuiken, Thijs; Smits, Saskia L

    2015-03-01

    Detection and characterization of novel viruses is hampered frequently by the lack of properly stored materials. Especially for the retrospective identification of viruses responsible for past disease outbreaks, often only formalin-fixed paraffin-embedded (FFPE) tissue samples are available. Although FFPE tissues can be used to detect known viral sequences, the application of FFPE tissues for detection of novel viruses is currently unclear. In the present study it was shown that sequence-independent amplification in combination with next-generation sequencing can be used to detect sequences of known and unknown viruses, although with relatively low sensitivity. These findings indicate that this technique could be useful for detecting novel viral sequences in FFPE tissues collected from humans and animals with disease of unknown origin, when other samples are not available. In addition, application of this method to FFPE tissues allows to correlate with the presence of histopathological changes in the corresponding tissue sections. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Complete solubilization of formalin-fixed, paraffin-embedded tissue may improve proteomic studies.

    Science.gov (United States)

    Shi, Shan-Rong; Taylor, Clive R; Fowler, Carol B; Mason, Jeffrey T

    2013-04-01

    Tissue-based proteomic approaches (tissue proteomics) are essential for discovering and evaluating biomarkers for personalized medicine. In any proteomics study, the most critical issue is sample extraction and preparation. This problem is especially difficult when recovering proteins from formalin-fixed, paraffin-embedded (FFPE) tissue sections. However, improving and standardizing protein extraction from FFPE tissue is a critical need because of the millions of archival FFPE tissues available in tissue banks worldwide. Recent progress in the application of heat-induced antigen retrieval principles for protein extraction from FFPE tissue has resulted in a number of published FFPE tissue proteomics studies. However, there is currently no consensus on the optimal protocol for protein extraction from FFPE tissue or accepted standards for quantitative evaluation of the extracts. Standardization is critical to ensure the accurate evaluation of FFPE protein extracts by proteomic methods such as reverse phase protein arrays, which is now in clinical use. In our view, complete solubilization of FFPE tissue samples is the best way to achieve the goal of standardizing the recovery of proteins from FFPE tissues. However, further studies are recommended to develop standardized protein extraction methods to ensure quantitative and qualitative reproducibility in the recovery of proteins from FFPE tissues. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Detection of p62 on Paraffin Sections by Immunohistochemistry.

    Science.gov (United States)

    Watson, Alexander S; Soilleux, Elizabeth J

    2015-08-03

    The study of autophagy in human disease is a rapidly expanding field. Diagnostic paraffin sections of a variety of patient tissues, including bone marrow, are available to researchers-yet are unsuitable for traditional autophagy quantification methods such as western blot or electron microscopy. This protocol outlines the immunohistochemical detection of the protein p62 (sequestosome-1, encoded by the gene SQSTM1)-an indicator of autophagic degradative activity-in slide-mounted paraffin sections such as bone marrow samples cut by a trephine. The p62 protein is an autophagic cargo adaptor, capable of binding to ubiquitylated proteins as well as autophagosome membrane proteins (LC3B and GABA(A) receptor-associated protein [GABARAP] family members) and hypothesized thus to target protein aggregates for lysosomal degradation. p62 itself is degraded by autophagy, remaining at low levels when autophagy is induced, and has been shown to accumulate when autophagy is deficient. Qualitative assessment and comparison of p62 staining between healthy and disease sections or disease subtypes will help target further investigation into the potential roles for autophagy in a variety of disorders. © 2015 Cold Spring Harbor Laboratory Press.

  6. Reliable PCR quantitation of estrogen, progesterone and ERBB2 receptor mRNA from formalin-fixed, paraffin-embedded tissue is independent of prior macro-dissection

    DEFF Research Database (Denmark)

    Tramm, Trine; Hennig, Guido; Kyndi, Marianne

    2013-01-01

    Gene expression analysis on messenger RNA (mRNA) purified from formalin-fixed, paraffin-embedded tissue is increasingly used for research purposes. Tissue heterogeneity may question specificity and interpretation of results from mRNA isolated from a whole slide section, and thresholds for minimal...... tumor content in the paraffin block or macrodissection are used to avoid contamination from non-neoplastic tissue. The aim was to test if mRNA from tissue surrounding breast cancer affected quantification of estrogen receptor α (ESR1), progesterone receptor (PGR) and human epidermal growth factor...... receptor 2 (ERBB2), by comparing gene expression from whole slide and tumor-enriched sections, and correlating gene expression from whole slide sections with corresponding immunohistochemistry. Gene expression, based on mRNA extracted from a training set (36 paraffin blocks) and two validation sets (133...

  7. A method to evaluate genome-wide methylation in archival formalin-fixed, paraffin-embedded ovarian epithelial cells.

    Directory of Open Access Journals (Sweden)

    Qiling Li

    Full Text Available The use of DNA from archival formalin and paraffin embedded (FFPE tissue for genetic and epigenetic analyses may be problematic, since the DNA is often degraded and only limited amounts may be available. Thus, it is currently not known whether genome-wide methylation can be reliably assessed in DNA from archival FFPE tissue.Ovarian tissues, which were obtained and formalin-fixed and paraffin-embedded in either 1999 or 2011, were sectioned and stained with hematoxylin-eosin (H&E.Epithelial cells were captured by laser micro dissection, and their DNA subjected to whole genomic bisulfite conversion, whole genomic polymerase chain reaction (PCR amplification, and purification. Sequencing and software analyses were performed to identify the extent of genomic methylation. We observed that 31.7% of sequence reads from the DNA in the 1999 archival FFPE tissue, and 70.6% of the reads from the 2011 sample, could be matched with the genome. Methylation rates of CpG on the Watson and Crick strands were 32.2% and 45.5%, respectively, in the 1999 sample, and 65.1% and 42.7% in the 2011 sample.We have developed an efficient method that allows DNA methylation to be assessed in archival FFPE tissue samples.

  8. Establishment of a Pcr Technique for Determination of Htlv-1 Infection in Paraffin-Embedded Tissues

    Directory of Open Access Journals (Sweden)

    M Rastin

    2007-04-01

    Full Text Available Introduction: HTLV-1 , the first known human retrovirus belongs to oncovirus subfamily of retroviruses. The major characteristic of HTLV-1 is its highly restricted geographic prevalence. Northern part of Khorasan is an endemic region of HTLV-1 infection. Epidemiological studies can help in designing preventive programs for HTLV-1 infection. The aim of this study was the establishment of a PCR technique for determination of HTLV-1 infection in paraffin-embedded tissues. Methods: In this experimental laboratory study for establishment of a technique, PCR was initially optimized using Beta-actin primers on various formalin fixed paraffin-embedded tissues from liver, spleen, skin and lymph nodes. The optimized concentration of Mgcl2 was 2mm, primer was 8 pmol. Optimized concentration of DNA was different according to the kind of tissue. HTLV-1 infection was determined by applying tax, pol, env and LTR primers on 50 paraffin-embedded lymph node tissues . The reporoducibility of this technique was shown for skin and lymph node tissues infected with HTLV-1. Resuls: In 50 lymph node tissues, one case with pathologic diagnosis of NHL was positive with all 5 sets of primers (tax, Pol, env and LTR primers and the other case was positive with only two sets of tax primers but was negative with pol, env and LTR primers. The prevalence of infection was 2% among lymph node specimens. (1 of 50 specimens and if the second case is considered, the prevalence would be 4%. Conclusion: Comparison of the results of this study with another study on blood specimens (seroprevalence2.3% was not statistically significant thus confirming the results of one another. (P=0.883

  9. Real-time quantitative PCR of microdissected paraffin-embedded breast carcinoma

    DEFF Research Database (Denmark)

    Gjerdrum, Lise Mette; Sorensen, Boe Sandahl; Kjeldsen, Eigil

    2004-01-01

    We studied the feasibility of using real-time quantitative PCR to determine HER-2 DNA amplification and mRNA expression in microdissected formalin-fixed, paraffin-embedded breast tumors and compared this with standard immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) methods...... tumors as being amplified. Interestingly, all these scored 2+ with the HercepTest, but were negative using FISH. We believe that real-time quantitative PCR analysis of HER-2 DNA amplification following microdissection represents a useful supplementary or perhaps even an alternative technique...

  10. Immunohistochemical detection of SWC3, CD2, CD3, CD4 and CD8 antigens in paraformaldehyde fixed and paraffin embedded porcine lymphoid tissue

    DEFF Research Database (Denmark)

    Tingstedt, Jens Erik; Tornehave, Ditte; Lind, Peter

    2003-01-01

    Identification of the different cell types of the immune system is important for in situ studies on the pathogenesis of infectious diseases in various animals, including the pig. Unfortunately, many monoclonal anti-leukocyte antibodies are only useful for staining frozen tissue sections with inhe......Identification of the different cell types of the immune system is important for in situ studies on the pathogenesis of infectious diseases in various animals, including the pig. Unfortunately, many monoclonal anti-leukocyte antibodies are only useful for staining frozen tissue sections...... with inherent poor tissue morphology, and are not readily adapted to formaldehyde fixed and paraffin embedded tissue with well preserved morphology. Seven well characterised monoclonal antibodies against porcine leukocyte antigens were tested on neutral buffered paraformaldehyde fixed and paraffin embedded...

  11. Diagnosis of Nocardia paucivorans central nervous system infection by DNA sequencing from paraffin-embedded tissue.

    Science.gov (United States)

    Schiaroli, Elisabetta; Pasticci, Maria Bruna; De Carolis, Elena; Mello, Enrica; Pallotto, Carlo; Leli, Christian; De Socio, Giuseppe Vittorio; Baldelli, Franco; Sanguinetti, Maurizio; Mencacci, Antonella

    2016-06-01

    Infections by Nocardia spp. are generally regarded as opportunistic diseases in immunocompromised patients, but can also affect immunocompetent subjects. Such infections represent an important diagnostic challenge for clinicians and microbiologists, and diagnosis is frequently delayed or even conducted post mortem. A 54-year-old man was admitted to our hospital because of ventriculitis and relapsing brain abscess. Five months prior, this patient had undergone external ventricular drain and surgery for a cerebellar abscess. Histopathology demonstrated pyogenic inflammatory reaction, microbiologic investigations proved negative and empiric antimicrobial therapy was administered for a total of eight weeks. Six weeks later, the patient developed relapsing neurologic manifestations. On reviewing the patient's clinical history it emerged that the patient had suffered pneumonia two months prior to neurosurgery, treated with amoxicillin/clavulanate 3g a day and levofloxacin 500mg a day for three weeks. On the CNS relapsing manifestations, nocardiosis was suspected and DNA sequencing from the formalin-fixed paraffin-embedded cerebellar tissue collected during neurosurgery allowed diagnosis of Nocardia paucivorans infection. The patient received medical therapy for 11 months. At follow-up, eight months after treatment was discontinued, the patient was aymptomatic. Nocardia spp. infections need to be suspected not only in immunocompromised, but also in immunocompetent patients. Proper samples need to be collected for proper microbiologic investigations. Paraffin-embedded tissue genomic sequencing can be a useful tool for diagnosis of nocardiosis.

  12. A simple osmium post-fixation paraffin-embedment technique to identify lipid accumulation in fish liver using medaka (Oryziaslatipes) eggs and eleutheroembryos as lipid rich models

    International Nuclear Information System (INIS)

    Mondon, J.A.; Howitt, J.; Tosiano, M.; Kwok, K.W.H.; Hinton, D.E.

    2011-01-01

    Highlights: → Hepatic lipidosis in fish liver is often misdiagnosed or overlooked. → Specific histological fat stains and cryostat sections are not commonly used. → Standard paraffin processing removes lipid leaving vacuoles of unknown origin. → Osmium post-fixed paraffin-embedment is a cost effective alternative. → Medaka trials show suitability for lipid visualization in tissues from egg to adult. - Abstract: Hepatic lipidosis is a non-specific biomarker of effect from pollution exposure in fish. Fatty liver is often misdiagnosed or overlooked in histological assessments due to the decreasing application of specific fat procedures and stains. For example, ethanol dehydration in standard paraffin processing removes lipids, leaving vacuoles of which the precise nature is unknown. Lipids can be identified using osmium post-fixation in semi-thin resin sections or transmission electron microscopy. However, both are expensive and technically demanding procedures, often not available for routine environmental risk assessment and monitoring programs. The current emphasis to reduce and refine animal toxicity testing, requires refinement of the suite of histopathological techniques currently available to maximize information gained from using fish for toxicity testing and as bio-indicators of environmental quality. This investigation has successfully modified an osmium post-fixation technique to conserve lipids in paraffin-embedded tissues using medaka (Oryzias latipes) eleutheroembryos and eggs (embryos) as lipid rich models.

  13. Terahertz spectroscopy for the study of paraffin-embedded gastric cancer samples

    Science.gov (United States)

    Wahaia, Faustino; Kasalynas, Irmantas; Seliuta, Dalius; Molis, Gediminas; Urbanowicz, Andrzej; Carvalho Silva, Catia D.; Carneiro, Fatima; Valusis, Gintaras; Granja, Pedro L.

    2015-01-01

    Terahertz (THz) spectroscopy constitute promising technique for biomedical applications as a complementary and powerful tool for diseases screening specially for early cancer diagnostic. The THz radiation is not harmful to biological tissues. As increased blood supply in cancer-affected tissues and consequent local increase in tissue water content makes THz technology a potentially attractive. In the present work, samples of healthy and adenocarcinoma-affected gastric tissue were analyzed using transmission time-domain THz spectroscopy (THz-TDS). The work shows the capability of the technique to distinguish between normal and cancerous regions in dried and paraffin-embedded samples. Plots of absorption coefficient α and refractive index n of normal and cancer affected tissues, are presented and the conditions for discrimination between normal and affected tissues are discussed.

  14. Limited numbers of apoptotic cells in fresh paraffin embedded bone marrow samples of patients with myelodysplastic syndrome

    NARCIS (Netherlands)

    Brada, SJL; van de Loosdrecht, AA; Koudstaal, J; de Wolf, JTM; Vellenga, E

    In myelodysplasia (MDS) the precise mechanism of ineffective erythropoiesis is not fully elucidated, but it is suggested that apoptosis may contribute to this process. We performed TdT-mediated dUTP-nick end labelling (TUNEL) staining of paraffin embedded bone marrow specimens to assess the amount

  15. New comprehensive denaturing-gradient-gel-electrophoresis assay for KRAS mutation detection applied to paraffin-embedded tumours

    NARCIS (Netherlands)

    Hayes, VM; Westra, JL; Verlind, E; Bleeker, W; Plukker, JT; Hofstra, RMW; Buys, CHCM

    2000-01-01

    A comprehensive mutation detection assay is presented for the entire coding region and all splice site junctions of the KRAS oncogene. The assay is based on denaturing gradient gel electrophoresis and applicable to archival paraffin-embedded tumour material. All KRAS amplicons are analysed within

  16. Investigation of archived formalin-fixed paraffin-embedded pancreatic tissue with whole-genome gene expression microarray

    DEFF Research Database (Denmark)

    Michelsen, Nete Vinstrup; Brusgaard, Klaus; Tan, Qihua

    2011-01-01

    The use of formalin-fixed, paraffin-embedded (FFPE) tissue overcomes the most prominent issues related to research on relatively rare diseases: limited sample size, availability of control tissue, and time frame. The use of FFPE pancreatic tissue in GEM may be especially challenging due to its very...

  17. Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Kastaniegaard, Kenneth; Padurariu, Simona

    2016-01-01

    Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described.Human colon mucosal biopsies were extracted from the sigmoideum...

  18. Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples.

    Science.gov (United States)

    Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-sequencing offers a promising way to address this problem. Here we evaluated transcriptomic dose responses us...

  19. Digital dewaxing of Raman signals: discrimination between nevi and melanoma spectra obtained from paraffin-embedded skin biopsies.

    Science.gov (United States)

    Tfayli, Ali; Gobinet, Cyril; Vrabie, Valeriu; Huez, Regis; Manfait, Michel; Piot, Olivier

    2009-05-01

    Malignant melanoma (MM) is the most severe tumor affecting the skin and accounts for three quarters of all skin cancer deaths. Raman spectroscopy is a promising nondestructive tool that has been increasingly used for characterization of the molecular features of cancerous tissues. Different multivariate statistical analysis techniques are used in order to extract relevant information that can be considered as functional spectroscopic descriptors of a particular pathology. Paraffin embedding (waxing) is a highly efficient process used to conserve biopsies in tumor banks for several years. However, the use of non-dewaxed formalin-fixed paraffin-embedded tissues for Raman spectroscopic investigations remains very restricted, limiting the development of the technique as a routine analytical tool for biomedical purposes. This is due to the highly intense signal of paraffin, which masks important vibrations of the biological tissues. In addition to being time consuming and chemical intensive, chemical dewaxing methods are not efficient and they leave traces of the paraffin in tissues, which affects the Raman signal. In the present study, we use independent component analysis (ICA) on Raman spectral images collected on melanoma and nevus samples. The sources obtained from these images are then used to eliminate, using non-negativity constrained least squares (NCLS), the paraffin contribution from each individual spectrum of the spectral images of nevi and melanomas. Corrected spectra of both types of lesion are then compared and classified into dendrograms using hierarchical cluster analysis (HCA).

  20. DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks.

    Science.gov (United States)

    Guyard, Alice; Boyez, Alice; Pujals, Anaïs; Robe, Cyrielle; Tran Van Nhieu, Jeanne; Allory, Yves; Moroch, Julien; Georges, Odette; Fournet, Jean-Christophe; Zafrani, Elie-Serge; Leroy, Karen

    2017-10-01

    Formalin-fixed paraffin-embedded (FFPE) tissue blocks are widely used to identify clinically actionable molecular alterations or perform retrospective molecular studies. Our goal was to quantify degradation of DNA occurring during mid to long-term storage of samples in usual conditions. We selected 46 FFPE samples of surgically resected carcinomas of lung, colon, and urothelial tract, of which DNA had been previously extracted. We performed a second DNA extraction on the same blocks under identical conditions after a median period of storage of 5.5 years. Quantitation of DNA by fluorimetry showed a 53% decrease in DNA quantity after storage. Quantitative PCR (qPCR) targeting KRAS exon 2 showed delayed amplification of DNA extracted after storage in all samples but one. The qPCR/fluorimetry quantification ratio decreased from 56 to 15% after storage (p DNA analyzable by qPCR represented only 11% of the amount obtained at first extraction. Maximal length of amplifiable DNA fragments assessed with a multiplex PCR was reduced in DNA extracted from stored tissue, indicating that DNA fragmentation had increased in the paraffin blocks during storage. Next-generation sequencing was performed on 12 samples and showed a mean 3.3-fold decrease in library yield and a mean 4.5-fold increase in the number of single-nucleotide variants detected after storage. In conclusion, we observed significant degradation of DNA extracted from the same FFPE block after 4 to 6 years of storage. Better preservation strategies should be considered for storage of FFPE biopsy specimens.

  1. Gelatin in situ zymography on fixed, paraffin-embedded tissue: zinc and ethanol fixation preserve enzyme activity.

    Science.gov (United States)

    Hadler-Olsen, Elin; Kanapathippillai, Premasany; Berg, Eli; Svineng, Gunbjørg; Winberg, Jan-Olof; Uhlin-Hansen, Lars

    2010-01-01

    In situ zymography is a method for the detection and localization of enzymatic activity in tissue sections. This method is used with frozen sections because routine fixation of tissue in neutral-buffered formalin inhibits enzyme activity. However, frozen sections present with poor tissue morphology, making precise localization of enzymatic activity difficult to determine. Ethanol- and zinc-buffered fixative (ZBF) are known to preserve both morphological and functional properties of the tissue well, but it has not previously been shown that these fixatives preserve enzyme activity. In the present study, we show that in situ zymography can be performed on ethanol- and ZBF-fixed paraffin-embedded tissue. Compared with snap-frozen tissue, ethanol- and ZBF-fixed tissue showed stronger signals and superior morphology, allowing for a much more precise detection of gelatinolytic activity. Gelatinolytic enzymes could also be extracted from both ethanol- and ZBF-fixed tissue. The yield, as analyzed by SDS-PAGE gelatin zymography and Western blotting, was influenced by the composition of the extraction buffer, but was generally lower than that obtained from unfixed tissue.

  2. Influence of parasite density and sample storage time on the reliability of Entamoeba histolytica-specific PCR from formalin-fixed and paraffin-embedded tissues.

    Science.gov (United States)

    Frickmann, Hagen; Tenner-Racz, Klara; Eggert, Petra; Schwarz, Norbert G; Poppert, Sven; Tannich, Egbert; Hagen, Ralf M

    2013-12-01

    We report on the reliability of polymerase chain reaction (PCR) for the detection of Entamoeba histolytica from formalin-fixed, paraffin-embedded tissue in comparison with microscopy and have determined predictors that may influence PCR results. E. histolytica-specific and Entamoeba dispar-specific real-time PCR and microscopy from adjacent histologic sections were performed using a collection of formalin-fixed, paraffin-embedded tissue specimens obtained from patients with invasive amebiasis. Specimens had been collected during the previous 4 decades. Association of sample age, parasite density, and reliability of PCR was analyzed. E. histolytica PCR was positive in 20 of 34 biopsies (58.8%); 2 of these 20 were microscopically negative for amebae in neighboring tissue sections. PCR was negative in 9 samples with visible amebae in neighboring sections and in 5 samples without visible parasites in neighboring sections. PCR was negative in all specimens that were older than 3 decades. Low parasite counts and sample ages older than 20 years were predictors for false-negative PCR results. All samples were negative for E. dispar DNA. PCR is suitable for the detection of E. histolytica in formalin-fixed, paraffin-embedded tissue samples that are younger than 2 decades and that contain intermediate to high parasite numbers. Negative results in older samples were due to progressive degradation of DNA over time as indicated by control PCRs targeting the human 18S rRNA gene. Moreover, our findings support previous suggestions that only E. histolytica but not E. dispar is responsible for invasive amebiasis.

  3. Multi-Center Evaluation of the Fully Automated PCR-Based Idylla™ KRAS Mutation Assay for Rapid KRAS Mutation Status Determination on Formalin-Fixed Paraffin-Embedded Tissue of Human Colorectal Cancer

    DEFF Research Database (Denmark)

    Solassol, Jérôme; Vendrell, Julie; Märkl, Bruno

    2016-01-01

    , was assessed on archived formalin-fixed paraffin-embedded (FFPE) tissue sections by comparing its results with the results previously obtained by routine reference approaches for KRAS genotyping. In case of discordance, samples were assessed further by additional methods. Among the 374 colorectal cancer FFPE...

  4. Molecular Markers for Prostate Cancer in Formalin-Fixed Paraffin-Embedded Tissues

    Directory of Open Access Journals (Sweden)

    Tamara Sequeiros

    2013-01-01

    Full Text Available Prostate cancer (PCa is the most frequently diagnosed type of cancer in developed countries. The decisive method of diagnosis is based on the results of biopsies, morphologically evaluated to determine the presence or absence of cancer. Although this approach leads to a confident diagnosis in most cases, it can be improved by using the molecular markers present in the tissue. Both miRNAs and proteins are considered excellent candidates for biomarkers in formalin-fixed paraffin-embedded (FFPE tissues, due to their stability over long periods of time. In the last few years, a concerted effort has been made to develop the necessary tools for their reliable measurement in these types of samples. Furthermore, the use of these kinds of markers may also help in establishing tumor grade and aggressiveness, as well as predicting the possible outcomes in each particular case for the different treatments available. This would aid clinicians in the decision-making process. In this review, we attempt to summarize and discuss the potential use of microRNA and protein profiles in FFPE tissue samples as markers to better predict PCa diagnosis, progression, and response to therapy.

  5. Multi-elemental imaging of paraffin-embedded human samples by laser-induced breakdown spectroscopy

    Science.gov (United States)

    Moncayo, S.; Trichard, F.; Busser, B.; Sabatier-Vincent, M.; Pelascini, F.; Pinel, N.; Templier, I.; Charles, J.; Sancey, L.; Motto-Ros, V.

    2017-07-01

    Chemical elements play central roles for physiological homeostasis in human cells, and their dysregulation might lead to a certain number of pathologies. Novel imaging techniques that improve the work of pathologists for tissue analysis and diagnostics are continuously sought. We report the use of Laser-Induced Breakdown Spectroscopy (LIBS) to perform multi-elemental images of human paraffin-embedded skin samples on the entire biopsy scale in a complementary and compatible way with microscope histopathological examination. A specific instrumental configuration is proposed in order to detect most of the elements of medical interest (i.e. P, Al, Mg, Na, Zn, Si, Fe, and Cu). As an example of medical application, we selected and analysed skin biopsies, including healthy skin tissue, cutaneous metastasis of melanoma, Merkel-cell carcinoma and squamous cell carcinoma. Clear distinctions in the distribution of chemical elements are observed from the different samples investigated. This study demonstrates the high complementarity of LIBS elemental imaging with conventional histopathology, opening new opportunities for any medical application involving metals.

  6. Improved protein extraction and protein identification from archival formalin-fixed paraffin-embedded human aortas.

    Science.gov (United States)

    Fu, Zongming; Yan, Kun; Rosenberg, Avraham; Jin, Zhicheng; Crain, Barbara; Athas, Grace; Heide, Richard S Vander; Howard, Timothy; Everett, Allen D; Herrington, David; Van Eyk, Jennifer E

    2013-04-01

    Evaluate combination of heat and elevated pressure to enhance protein extraction and quality of formalin-fixed (FF), and FF paraffin-embedded (FFPE) aorta for proteomics. Proteins were extracted from fresh frozen aorta at room temperature (RT). FF and FFPE aortas (3 months and 15 years) were extracted at RT, heat alone, or a combination of heat and high pressure. Protein yields were compared, and digested peptides from the extracts were analyzed with MS. Combined heat and elevated pressure increased protein yield from human FF or FFPE aorta compared to matched tissues with heat alone (1.5-fold) or at RT (8.3-fold), resulting in more proteins identified and with more sequence coverage. The length of storage did adversely affect the quality of proteins from FF tissue. For long-term storage, aorta was preserved better with FFPE than FF alone. Periostin and MGF-E8 were demonstrated suitable for MRM assays from FFPE aorta. Combination of heat and high pressure is an effective method to extract proteins from FFPE aorta for downstream proteomics. This method opens the possibility for use of archival and often rare FFPE aortas and possibly other tissues available to proteomics for biomarker discovery and quantification. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Biomedical analysis of formalin-fixed, paraffin-embedded tissue samples: The Holy Grail for molecular diagnostics.

    Science.gov (United States)

    Donczo, Boglarka; Guttman, Andras

    2018-06-05

    More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics. The aim of this review is to critically evaluate the omics options for FFPE tissue sample analysis in the molecular diagnostics field. Copyright © 2018. Published by Elsevier B.V.

  8. Analytical validation of a melanoma diagnostic gene signature using formalin-fixed paraffin-embedded melanocytic lesions.

    Science.gov (United States)

    Warf, M Bryan; Flake, Darl D; Adams, Doug; Gutin, Alexander; Kolquist, Kathryn A; Wenstrup, Richard J; Roa, Benjamin B

    2015-01-01

    These studies were to validate the analytical performance of a gene expression signature that differentiates melanoma and nevi, using RNA expression from 14 signature genes and nine normalization genes that generates a melanoma diagnostic score (MDS). Formalin-fixed paraffin-embedded melanocytic lesions were evaluated in these studies. The overall SD of the assay was determined to be 0.69 MDS units. Individual amplicons within the signature had an average amplification efficiency of 92% and a SD less than 0.5 CT. The MDS was reproducible across a 2000-fold dilution range of input RNA. Melanin, an inhibitor of PCR, does not interfere with the signature. These studies indicate this signature is robust and reproducible and is analytically validated on formalin-fixed paraffin-embedded melanocytic lesions.

  9. Evaluation of two methods DNA extraction from formalin-fixed, paraffin-embedded tissues on non-optimal conditions

    International Nuclear Information System (INIS)

    Bustamante, Javier Andres; Astudillo, Miryam; Pazos, Alvaro Jairo; Bravo, Luis Eduardo

    2011-01-01

    Paraffin wax embedded tissues are an invaluable material for retrospective studies requiring the application of molecular analysis. Multiple methods are available to extract DNA from these kinds of samples. However, the most common methods are slow and the reagents often contribute to the fragmentation of genetic material. In order to optimize the procedure, two methods for DNA extraction from paraffin embedded tissue non-optimal conditions were used. 47 blocks containing paraffin-embedded biopsies of pleura, lung and pericardium from 24 patients (66.6% males) older than 18 years, with biopsy proven chronic granulomatous inflammation referred to the department of pathology at University Hospital of Valle between 2002 and 2007 were selected. Each sample was subjected to 10 cuts and was to two methods of DNA extraction: 1. conventional and 2. QIAamp - DNA mini kit. The efficiency of the extracted DNA was assessed by spectrophotometry and PCR amplification of a fragment of the housekeeping gene GAPDH. The concentration of DNA samples extracted by the conventional method was of 65.52 ng/Mu l ± 11.47 (mean ± SE) and the 260/280 absorbance ratio ranged between 0.52 and 2.30 the average concentration of DNA of the samples extracted by the commercial method was 60.89 ng/Mu l ± 6.02 (mean ± SE), with an absorbance that fluctuated between 0 and 2.64. The DNA obtained was amplified by PCR, of 47 samples extracted by methods, 25 and 23 respectively the GAPDH gene amplified successfully. The methods used to obtain DNA showed similar performance, highlighting the potential utility of both extraction methods for the retrospective studies from paraffin embedded tissues in unsuitable conditions.

  10. Validation of putative reference genes for normalization of Q-RT-PCR data from paraffin-embedded lymphoid tissue

    DEFF Research Database (Denmark)

    Green, Tina Marie; de Stricker, Karin; Møller, Michael Boe

    2009-01-01

    Normalization of quantitative reverse transcription-PCR (Q-RT-PCR) data to appropriate tissue-specific reference genes is an essential part of interpreting the results. This study aimed to determine the most appropriate reference genes for normalizing gene expressions in lymphatic tissue...... was 0.93 (Pnormalization with the appropriate reference genes. Thus, we show that formalin-fixed, paraffin-embedded lymphoid samples are suitable for Q-RT-PCR when using thoroughly validated reference genes....

  11. Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Kastaniegaard, Kenneth; Padurariu, Simona

    2016-01-01

    Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving...... throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD002029....

  12. Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

    Directory of Open Access Journals (Sweden)

    Tue Bjerg Bennike

    2016-03-01

    Full Text Available Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control (“Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples” [1]. We here report the data from the analysis. The comparative analysis was performed on 24 colon mucosa biopsies, extracted from the sigmoideum of two gastroenterologically healthy participants for the purpose of this study. A set of biopsies were additionally stored for 30 min at room temperature prior to formalin-fixation. The samples were analyzed by high throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002029. Keywords: Human, Colon, Mucosa, RNAlater, FFPE, Snap-frozen, Stability, LC–MS, Proteomics

  13. Polymerase chain reaction analysis for viruses in paraffin-embedded myocardium from dogs with dilated cardiomyopathy or myocarditis.

    Science.gov (United States)

    Maxson, T R; Meurs, K M; Lehmkuhl, L B; Magnon, A L; Weisbrode, S E; Atkins, C E

    2001-01-01

    To perform polymerase chain reaction (PCR) analysis on paraffin-embedded myocardium from dogs with dilated cardiomyopathy (DCM) and dogs with myocarditis to screen for canine parvovirus, adenovirus types 1 and 2, and herpesvirus. Myocardial specimens from 18 dogs with an antemortem diagnosis of DCM and 9 dogs with a histopathologic diagnosis of myocarditis were evaluated. Paraffin-embedded myocardial specimens were screened for viral genome by PCR analysis. Positive-control specimens were developed from cell cultures as well as paraffin-embedded tissue specimens from dogs with clinical and histopathologic diagnoses of viral infection with canine parvovirus, adenovirus types 1 and 2, and herpesvirus. The histologic characteristics of all myocardial specimens were classified regarding extent, location, and type of inflammation and fibrosis. Canine adenovirus type 1 was amplified from 1 specimen from a dog with DCM. Canine parvovirus, adenovirus type 2, and herpesvirus were not amplified from any myocardial specimens. Histologic analysis of specimens from dogs with DCM revealed variable amounts of fibrosis; myocardial inflammation was observed in 1 affected dog. Histopathologic analysis of specimens from dogs with myocarditis disclosed variable degrees of inflammation and fibrosis. Viral agents canine parvovirus, adenovirus types 1 and 2, and herpesvirus are not commonly associated with DCM or active myocarditis in dogs. Additional studies evaluating for nucleic acid from viruses that less commonly affect dogs or different types of infectious agents may be warranted to gain insight into the cause of DCM and myocarditis in dogs.

  14. An Optimized Method of Metabolite Extraction from Formalin-Fixed Paraffin-Embedded Tissue for GC/MS Analysis.

    Science.gov (United States)

    Wojakowska, Anna; Marczak, Łukasz; Jelonek, Karol; Polanski, Krzysztof; Widlak, Piotr; Pietrowska, Monika

    2015-01-01

    Formalin-fixed paraffin-embedded (FFPE) tissue specimens constitute a highly valuable source of clinical material for retrospective molecular studies. However, metabolomic assessment of such archival material remains still in its infancy. Hence, there is an urgent need for efficient methods enabling extraction and profiling of metabolites present in FFPE tissue specimens. Here we demonstrate the methodology for isolation of primary metabolites from archival tissues; either fresh-frozen, formalin-fixed or formalin-fixed and paraffin-embedded specimens of mouse kidney were analysed and compared in this work. We used gas chromatography followed by mass spectrometry (GC/MS approach) to identify about 80 metabolites (including amino acids, saccharides, carboxylic acids, fatty acids) present in such archive material. Importantly, about 75% of identified compounds were detected in all three types of specimens. Moreover, we observed that fixation with formalin itself (and their duration) did not affect markedly the presence of particular metabolites in tissue-extracted material, yet fixation for 24h could be recommended as a practical standard. Paraffin embedding influenced efficiency of extraction, which resulted in reduced quantities of several compounds. Nevertheless, we proved applicability of FFPE specimens for non-targeted GS/MS-based profiling of tissue metabolome, which is of great importance for feasibility of metabolomics studies using retrospective clinical material.

  15. Predicting response to primary chemotherapy: gene expression profiling of paraffin-embedded core biopsy tissue.

    Science.gov (United States)

    Mina, Lida; Soule, Sharon E; Badve, Sunil; Baehner, Fredrick L; Baker, Joffre; Cronin, Maureen; Watson, Drew; Liu, Mei-Lan; Sledge, George W; Shak, Steve; Miller, Kathy D

    2007-06-01

    Primary chemotherapy provides an ideal opportunity to correlate gene expression with response to treatment. We used paraffin-embedded core biopsies from a completed phase II trial to identify genes that correlate with response to primary chemotherapy. Patients with newly diagnosed stage II or III breast cancer were treated with sequential doxorubicin 75 mg/M2 q2 wks x 3 and docetaxel 40 mg/M2 weekly x 6; treatment order was randomly assigned. Pretreatment core biopsy samples were interrogated for genes that might correlate with pathologic complete response (pCR). In addition to the individual genes, the correlation of the Oncotype DX Recurrence Score with pCR was examined. Of 70 patients enrolled in the parent trial, core biopsies samples with sufficient RNA for gene analyses were available from 45 patients; 9 (20%) had inflammatory breast cancer (IBC). Six (14%) patients achieved a pCR. Twenty-two of the 274 candidate genes assessed correlated with pCR (p < 0.05). Genes correlating with pCR could be grouped into three large clusters: angiogenesis-related genes, proliferation related genes, and invasion-related genes. Expression of estrogen receptor (ER)-related genes and Recurrence Score did not correlate with pCR. In an exploratory analysis we compared gene expression in IBC to non-inflammatory breast cancer; twenty-four (9%) of the genes were differentially expressed (p < 0.05), 5 were upregulated and 19 were downregulated in IBC. Gene expression analysis on core biopsy samples is feasible and identifies candidate genes that correlate with pCR to primary chemotherapy. Gene expression in IBC differs significantly from noninflammatory breast cancer.

  16. Unmasking of complements using proteinase-K in formalin fixed paraffin embedded renal biopsies

    Directory of Open Access Journals (Sweden)

    R Nada

    2016-01-01

    Full Text Available Renal biopsy interpretation requires histopathology, direct immunofluorescence (DIF and electron microscopy. Formalin-fixed, paraffin-embedded tissue (FFPE sent for light microscopy can be used for DIF after antigen retrieval. However, complement staining has not been satisfactory. We standardized DIF using proteinase-K for antigen retrieval in FFPE renal biopsies. A pilot study was conducted on known cases of membranous glomerulonephritis (MGN, membranoproliferative type-1 (MPGN-1, immunoglobulin A nephropathy (IgAN, and anti-glomerular basement disease (anti-GBM. Immunofluorescence panel included fluorescein isothiocyanate (FITC conjugated IgG, IgA, IgM, complements (C3 and C1q, light chains (kappa, lambda and fibrinogen antibodies. After standardization of the technique, 75 renal biopsies and 43 autopsies cases were stained. Out of 43 autopsy cases, immune-complex mediated glomerulonephritis (GN was confirmed in 18 cases (Lupus nephritis-11, IgAN-6, MGN-1, complement-mediated dense deposit disease (DDD-1 and monoclonal diseases in 4 cases (amyloidosis-3, cast nephropathy-1. Immune-mediated injury was excluded in 17 cases (focal segmental glomerulosclerosis -3, crescentic GN-6 [pauci-immune-3, anti-GBM-3], thrombotic microangiopathy-5, atherosclerosis-3. Renal biopsies (n-75 where inadequate or no frozen sample was available; this technique classified 52 mesangiocapillary pattern as MPGN type-1-46, DDD-2 and (C3GN-4. Others were diagnosed as IgAN-3, lupus nephritis-2, MGN-4, diffuse proliferative glomerulonephritis (DPGN-1, Non-IC crescentic GN-1, monoclonal diseases-3. In nine cases, DIF on FFPE tissue could not help in making diagnosis. Proteinase-K enzymatic digestion of FFPE renal biopsies can unmask complements (both C3 and C1q in immune-complexes mediated and complement-mediated diseases. This method showed good results on autopsy tissues archived for as long as 15 years.

  17. Single-Nucleotide Polymorphism-Microarray Ploidy Analysis of Paraffin-Embedded Products of Conception in Recurrent Pregnancy Loss Evaluations.

    Science.gov (United States)

    Maslow, Bat-Sheva L; Budinetz, Tara; Sueldo, Carolina; Anspach, Erica; Engmann, Lawrence; Benadiva, Claudio; Nulsen, John C

    2015-07-01

    To compare the analysis of chromosome number from paraffin-embedded products of conception using single-nucleotide polymorphism (SNP) microarray with the recommended screening for the evaluation of couples presenting with recurrent pregnancy loss who do not have previous fetal cytogenetic data. We performed a retrospective cohort study including all women who presented for a new evaluation of recurrent pregnancy loss over a 2-year period (January 1, 2012, to December 31, 2013). All participants had at least two documented first-trimester losses and both the recommended screening tests and SNP microarray performed on at least one paraffin-embedded products of conception sample. Single-nucleotide polymorphism microarray identifies all 24 chromosomes (22 autosomes, X, and Y). Forty-two women with a total of 178 losses were included in the study. Paraffin-embedded products of conception from 62 losses were sent for SNP microarray. Single-nucleotide polymorphism microarray successfully diagnosed fetal chromosome number in 71% (44/62) of samples, of which 43% (19/44) were euploid and 57% (25/44) were noneuploid. Seven of 42 (17%) participants had abnormalities on recurrent pregnancy loss screening. The per-person detection rate for a cause of pregnancy loss was significantly higher in the SNP microarray (0.50; 95% confidence interval [CI] 0.36-0.64) compared with recurrent pregnancy loss evaluation (0.17; 95% CI 0.08-0.31) (P=.002). Participants with one or more euploid loss identified on paraffin-embedded products of conception were significantly more likely to have an abnormality on recurrent pregnancy loss screening than those with only noneuploid results (P=.028). The significance remained when controlling for age, number of losses, number of samples, and total pregnancies. These results suggest that SNP microarray testing of paraffin-embedded products of conception is a valuable tool for the evaluation of recurrent pregnancy loss in patients without prior fetal

  18. Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization.

    Directory of Open Access Journals (Sweden)

    Heike Horn

    Full Text Available Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH, especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs. We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL and six malignant mesothelioma (MM samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches.

  19. Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples.

    Directory of Open Access Journals (Sweden)

    Craig April

    2009-12-01

    Full Text Available We have developed a gene expression assay (Whole-Genome DASL, capable of generating whole-genome gene expression profiles from degraded samples such as formalin-fixed, paraffin-embedded (FFPE specimens.We demonstrated a similar level of sensitivity in gene detection between matched fresh-frozen (FF and FFPE samples, with the number and overlap of probes detected in the FFPE samples being approximately 88% and 95% of that in the corresponding FF samples, respectively; 74% of the differentially expressed probes overlapped between the FF and FFPE pairs. The WG-DASL assay is also able to detect 1.3-1.5 and 1.5-2 -fold changes in intact and FFPE samples, respectively. The dynamic range for the assay is approximately 3 logs. Comparing the WG-DASL assay with an in vitro transcription-based labeling method yielded fold-change correlations of R(2 approximately 0.83, while fold-change comparisons with quantitative RT-PCR assays yielded R(2 approximately 0.86 and R(2 approximately 0.55 for intact and FFPE samples, respectively. Additionally, the WG-DASL assay yielded high self-correlations (R(2>0.98 with low intact RNA inputs ranging from 1 ng to 100 ng; reproducible expression profiles were also obtained with 250 pg total RNA (R(2 approximately 0.92, with approximately 71% of the probes detected in 100 ng total RNA also detected at the 250 pg level. When FFPE samples were assayed, 1 ng total RNA yielded self-correlations of R(2 approximately 0.80, while still maintaining a correlation of R(2 approximately 0.75 with standard FFPE inputs (200 ng.Taken together, these results show that WG-DASL assay provides a reliable platform for genome-wide expression profiling in archived materials. It also possesses utility within clinical settings where only limited quantities of samples may be available (e.g. microdissected material or when minimally invasive procedures are performed (e.g. biopsied specimens.

  20. [Comparison of two different real-time PCR systems in postmortem diagnosis of tuberculosis in paraffin-embedded tissues].

    Science.gov (United States)

    Yağmur, Gülhan; Albayrak, Nurhan; Daş, Taner; Yıldırım, Muzaffer; Ozgün, Ayşe; Büyük, Yalçın

    2014-10-01

    Tuberculosis (TB) is one of those infections with high morbidity and mortality in all around the world. Hundreds of people died from this disease without diagnosed or due to resistant strains in Turkey. Therefore, it is important to identify postmortem cases who have died from tuberculosis. Molecular methods have been widely used as well as conventional methods in the diagnosis of tuberculosis. The aim of this study was to compare the two different real-time polymerase chain reaction (Rt-PCR) system in the postmortem diagnosis of Mycobacterium tuberculosis infections in paraffin-embedded tissues. A total of 40 paraffin-embedded tissue samples [lung (n= 35), brain (n= 2), heart (n= 2), lymph node (n= 1)] in which histopathologic findings consistent with TB (necrotizing granulomatous inflammation, gelatinous caseous pneumonia, necrotic fibrous nodul) obtained from 37 autopsy cases (31 male, 6 female; age range: 25-85 yrs) were included in the study. Paraffin-embedded tissues were deparafinized with xylene and ethyl alcohol and then DNA isolation was done with QIAsymphony DSP Virus/Pathogen Midi kit in the QIAsymphony device. DNA amplification process was performed by Rt-PCR using the kit Artus® M. tuberculosis RG-PCR in the Rotor-Gene® Q device (Qiagen, Germany). Likewise, after deparafinization process, samples placed in the cartridge and isolation and Rt-PCR was performed by Xpert® MTB/RIF (Cepheid, USA) system, simultaneosly. Seventeen and 20 out of the 40 paraffin-embedded tissues yielded positive results with Qiagen and Xpert system, respectively. M.tuberculosis DNA was found positive in 13 (32.5%) and negative in 16 (40%) of the samples by both of the systems, exhibiting 72.5% (29/40) of concordance. On the other hand, seven (17.5%) samples that were positive with Xpert system yielded negative result with the Qiagen, while four (10%) samples that were positive with Qiagen yielded negative result with the Xpert system. Of the 20 positive cases detected with

  1. A gene-protein assay for human epidermal growth factor receptor 2 (HER2: brightfield tricolor visualization of HER2 protein, the HER2 gene, and chromosome 17 centromere (CEN17 in formalin-fixed, paraffin-embedded breast cancer tissue sections

    Directory of Open Access Journals (Sweden)

    Nitta Hiroaki

    2012-05-01

    Full Text Available Abstract Background The eligibility of breast cancer patients for human epidermal growth factor receptor 2 (HER2-directed therapies is determined by the HER2 gene amplification and/or HER2 protein overexpression status of the breast tumor as determined by in situ hybridization (ISH or immunohistochemistry (IHC, respectively. Our objective was to combine the US Food and Drug Administration (FDA-approved HER2 & chromosome 17 centromere (CEN17 brightfield ISH (BISH and HER2 IHC assays into a single automated HER2 gene-protein assay allowing simultaneous detection of all three targets in a single tissue section. Methods The HER2 gene-protein assay was optimized using formalin-fixed, paraffin-embedded (FFPE samples of the xenograft tumors MCF7 [HER2 negative (non-amplified gene, protein negative] and Calu-3 [HER2 positive (amplified gene, protein positive]. HER2 IHC was performed using a rabbit monoclonal anti-HER2 antibody (clone 4B5 and a conventional 3,3'-diaminobenzidine IHC detection. The HER2 & CEN17 BISH signals were visualized using horseradish peroxidase-based silver and alkaline phosphatase-based red detection systems, respectively with a cocktail of 2,4-dinitrophenyl-labeled HER2 and digoxigenin-labeled CEN17 probes. The performance of the gene-protein assay on tissue microarray slides containing 189 randomly selected FFPE clinical breast cancer tissue cores was compared to that of the separate HER2 IHC and HER2 & CEN17 BISH assays. Results HER2 protein detection was optimal when the HER2 IHC protocol was used before (rather than after the BISH protocol. The sequential use of HER2 IHC and HER2 & CEN17 BISH detection steps on FFPE xenograft tumor sections appropriately co-localized the HER2 protein, HER2 gene, and CEN17 signals after mitigating the silver background staining by using a naphthol phosphate-containing hybridization buffer for the hybridization step. The HER2 protein and HER2 gene status obtained using the multiplex HER2 gene

  2. The effect of aging of formalin-fixed paraffin-embedded tissues on the in situ hybridization and immunohistochemistry signals in cervical lesions.

    Science.gov (United States)

    Nuovo, Allison J; Garofalo, Michela; Mikhail, Alexandria; Nicol, Alcina F; Vianna-Andrade, Cecilia; Nuovo, Gerard J

    2013-09-01

    Formalin-fixed, paraffin-embedded tissues are widely used in biomedical research but little is known about the effect of the age of the block or unstained slides on the in situ hybridization or immunohistochemistry signal. We compared the in situ-based and immunohistochemistry-based signals for cervical intraepithelial neoplasia samples that ranged from 0 to 15 years of age. There was a progressive and statistically significant decrease in the strength of the p16 signal when comparing tissues prepared from recent unstained slides (0 to 1 y old, mean score of 92%) to those of intermediate age (5 to 7 y old, mean score of 49%) to old unstained slides (cut 13 to 15 y ago, mean score of 10%). Equivalent, progressive, and significant decreases in the intensity of the signals for microRNAs, CD45, and human papillomavirus DNA were seen in tissues stored on slides from 5 to 7 years and 13 to 15 years, respectively. However, the diminution of signal was much less, although still statistically significant, if the sections from the 13- to 15-year-old paraffin blocks were prepared in 2012. The data likely does not represent degradation of the targets as extraction of several microRNA from the old blocks showed no detectable degradation, despite the markedly weakened in situ hybridization signal. It is concluded that in situ-based signal for DNA, microRNAs, and proteins in paraffin-embedded tissues are significantly reduced over time, especially when stored long term on glass slides which, in turn, can lead to a significant underestimation of the amount and presence of the nucleic acid or protein target.

  3. The effects of age-in-block on RNA-seq analysis of archival formalin-fixed paraffin-embedded (FFPE) samples

    Science.gov (United States)

    Archival samples represent a vast resource for identification of chemical and pharmaceutical targets. Previous use of formalin-fixed paraffin-embedded (FFPE) samples has been limited due to changes in RNA introduced by fixation and embedding procedures. Recent advances in RNA-seq...

  4. Optimization of Single- and Dual-Color Immunofluorescence Protocols for Formalin-Fixed, Paraffin-Embedded Archival Tissues.

    Science.gov (United States)

    Kajimura, Junko; Ito, Reiko; Manley, Nancy R; Hale, Laura P

    2016-02-01

    Performance of immunofluorescence staining on archival formalin-fixed paraffin-embedded human tissues is generally not considered to be feasible, primarily due to problems with tissue quality and autofluorescence. We report the development and application of procedures that allowed for the study of a unique archive of thymus tissues derived from autopsies of individuals exposed to atomic bomb radiation in Hiroshima, Japan in 1945. Multiple independent treatments were used to minimize autofluorescence and maximize fluorescent antibody signals. Treatments with NH3/EtOH and Sudan Black B were particularly useful in decreasing autofluorescent moieties present in the tissue. Deconvolution microscopy was used to further enhance the signal-to-noise ratios. Together, these techniques provide high-quality single- and dual-color fluorescent images with low background and high contrast from paraffin blocks of thymus tissue that were prepared up to 60 years ago. The resulting high-quality images allow the application of a variety of image analyses to thymus tissues that previously were not accessible. Whereas the procedures presented remain to be tested for other tissue types and archival conditions, the approach described may facilitate greater utilization of older paraffin block archives for modern immunofluorescence studies. © 2016 The Histochemical Society.

  5. Multicenter Evaluation of a Novel Automated Rapid Detection System of BRAF Status in Formalin-Fixed, Paraffin-Embedded Tissues.

    Science.gov (United States)

    Schiefer, Ana-Iris; Parlow, Laura; Gabler, Lisa; Mesteri, Ildiko; Koperek, Oskar; von Deimling, Andreas; Streubel, Berthold; Preusser, Matthias; Lehmann, Annika; Kellner, Udo; Pauwels, Patrick; Lambin, Suzan; Dietel, Manfred; Hummel, Michael; Klauschen, Frederick; Birner, Peter; Möbs, Markus

    2016-05-01

    The mutated BRAF oncogene represents a therapeutic target in malignant melanoma. Because BRAF mutations are also involved in the pathogenesis of other human malignancies, the use of specific BRAF inhibitors might also be extended to other diseases in the future. A prerequisite for the clinical application of BRAF inhibitors is the reliable detection of activating BRAF mutations in routine histopathological samples. In a multicenter approach, we evaluated a novel and fully automated PCR-based system (Idylla) capable of detecting BRAF V600 mutations in formalin-fixed, paraffin-embedded tissue within 90 minutes with high sensitivity. We analyzed a total of 436 samples with the Idylla system. Valid results were obtained in 421 cases (96.56%). Its performance was compared with conventional methods (pyrosequencing or Sanger sequencing). Concordant results were obtained in 406 cases (96.90%). Reanalysis of eight discordant samples by next-generation sequencing and/or pyrosequencing with newly extracted DNA and the BRAF RGQ Kit confirmed the Idylla result in seven cases, resulting in an overall agreement of 98.57%. In conclusion, the Idylla system is a highly reliable and sensitive platform for detection of BRAF V600 mutations in formalin-fixed, paraffin-embedded material, providing an efficient alternative to conventional diagnostic methods, particularly for routine diagnostics laboratories with limited experience in molecular pathology. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  6. Matrix-comparative genomic hybridization from multicenter formalin-fixed paraffin-embedded colorectal cancer tissue blocks

    Directory of Open Access Journals (Sweden)

    Köhne Claus-Henning

    2007-04-01

    Full Text Available Abstract Background The identification of genomic signatures of colorectal cancer for risk stratification requires the study of large series of cancer patients with an extensive clinical follow-up. Multicentric clinical studies represent an ideal source of well documented archived material for this type of analyses. Methods To verify if this material is technically suitable to perform matrix-CGH, we performed a pilot study using macrodissected 29 formalin-fixed, paraffin-embedded tissue samples collected within the framework of the EORTC-GI/PETACC-2 trial for colorectal cancer. The scientific aim was to identify prognostic genomic signatures differentiating locally restricted (UICC stages II-III from systemically advanced (UICC stage IV colorectal tumours. Results The majority of archived tissue samples collected in the different centers was suitable to perform matrix-CGH. 5/7 advanced tumours displayed 13q-gain and 18q-loss. In locally restricted tumours, only 6/12 tumours showed a gain on 13q and 7/12 tumours showed a loss on 18q. Interphase-FISH and high-resolution array-mapping of the gain on 13q confirmed the validity of the array-data and narrowed the chromosomal interval containing potential oncogenes. Conclusion Archival, paraffin-embedded tissue samples collected in multicentric clinical trials are suitable for matrix-CGH analyses and allow the identification of prognostic signatures and aberrations harbouring potential new oncogenes.

  7. Evaluation of three methods of DNA extraction from paraffin-embedded material for the amplification of genomic DNA by means of the PCR technique

    Directory of Open Access Journals (Sweden)

    MESQUITA Ricardo Alves

    2001-01-01

    Full Text Available There are several protocols reported in the literature for the extraction of genomic DNA from formalin-fixed paraffin-embedded samples. Genomic DNA is utilized in molecular analyses, including PCR. This study compares three different methods for the extraction of genomic DNA from formalin-fixed paraffin-embedded (inflammatory fibrous hyperplasia and non-formalin-fixed (normal oral mucosa samples: phenol with enzymatic digestion, and silica with and without enzymatic digestion. The amplification of DNA by means of the PCR technique was carried out with primers for the exon 7 of human keratin type 14. Amplicons were analyzed by means of electrophoresis in an 8% polyacrylamide gel with 5% glycerol, followed by silver-staining visualization. The phenol/enzymatic digestion and the silica/enzymatic digestion methods provided amplicons from both tissue samples. The method described is a potential aid in the establishment of the histopathologic diagnosis and in retrospective studies with archival paraffin-embedded samples.

  8. Effective melanin depigmentation of human and murine ocular tissues: an improved method for paraffin and frozen sections.

    Directory of Open Access Journals (Sweden)

    Caroline Manicam

    Full Text Available PURPOSE: The removal of excessive melanin pigments that obscure ocular tissue morphology is important to address scientific questions and for differential diagnosis of ocular tumours based on histology. Thus, the goal of the present study was to establish an effective and fast melanin bleaching method for paraffin and frozen mouse and human ocular tissues. METHODS: Paraffin-embedded and frozen ocular specimens from mice and human donors were subjected to bleaching employing two methods. The first employed potassium permanganate (KMnO4 with oxalic acid, and the second 10% hydrogen peroxide (H2O2. To determine optimal bleaching conditions, depigmentation was carried out at various incubation times. The effect of diluents used for 10% H2O2 was assessed using phosphate-buffered saline (PBS, and deionized water. Three different slide types and two fixatives, which were ice-cold acetone with 80% methanol, and 4% paraformaldehyde (PFA were used to determine the optimal conditions for better tissue adherence during bleaching. All tissues were stained in hematoxylin and eosin for histological evaluation. RESULTS: Optimal bleaching was achieved using warm 10% H2O2 diluted in PBS at 65°C for 120 minutes. Chromium-gelatin-coated slides prevented tissue detachment. Adherence of cryosections was also improved with post-fixation using 4% PFA and overnight air-drying at RT after cryosectioning. Tissue morphology was preserved under these conditions. Conversely, tissues bleached in KMnO4/oxalic acid demonstrated poor depigmentation with extensive tissue damage. CONCLUSIONS: Warm dilute H2O2 at 65°C for 120 minutes rapidly and effectively bleached both cryo- and paraffin sections of murine and human ocular tissues.

  9. Effective melanin depigmentation of human and murine ocular tissues: an improved method for paraffin and frozen sections.

    Science.gov (United States)

    Manicam, Caroline; Pitz, Susanne; Brochhausen, Christoph; Grus, Franz H; Pfeiffer, Norbert; Gericke, Adrian

    2014-01-01

    The removal of excessive melanin pigments that obscure ocular tissue morphology is important to address scientific questions and for differential diagnosis of ocular tumours based on histology. Thus, the goal of the present study was to establish an effective and fast melanin bleaching method for paraffin and frozen mouse and human ocular tissues. Paraffin-embedded and frozen ocular specimens from mice and human donors were subjected to bleaching employing two methods. The first employed potassium permanganate (KMnO4) with oxalic acid, and the second 10% hydrogen peroxide (H2O2). To determine optimal bleaching conditions, depigmentation was carried out at various incubation times. The effect of diluents used for 10% H2O2 was assessed using phosphate-buffered saline (PBS), and deionized water. Three different slide types and two fixatives, which were ice-cold acetone with 80% methanol, and 4% paraformaldehyde (PFA) were used to determine the optimal conditions for better tissue adherence during bleaching. All tissues were stained in hematoxylin and eosin for histological evaluation. Optimal bleaching was achieved using warm 10% H2O2 diluted in PBS at 65°C for 120 minutes. Chromium-gelatin-coated slides prevented tissue detachment. Adherence of cryosections was also improved with post-fixation using 4% PFA and overnight air-drying at RT after cryosectioning. Tissue morphology was preserved under these conditions. Conversely, tissues bleached in KMnO4/oxalic acid demonstrated poor depigmentation with extensive tissue damage. Warm dilute H2O2 at 65°C for 120 minutes rapidly and effectively bleached both cryo- and paraffin sections of murine and human ocular tissues.

  10. Progesterone receptor isoform analysis by quantitative real-time polymerase chain reaction in formalin-fixed, paraffin-embedded canine mammary dysplasias and tumors

    DEFF Research Database (Denmark)

    Guil-Luna, S.; Stenvang, Jan; Brünner, Nils

    2014-01-01

    and its isoforms in formalin-fixed, paraffin-embedded tissue samples from canine mammary lesions (4 dysplasias, 10 benign tumors, and 46 carcinomas) using 1-step SYBR Green quantitative real-time polymerase chain reaction (RT-qPCR). Progesterone receptor was expressed in 75% of dysplasias, all benign...... in the expression of isoform A versus B. Analysis of progesterone receptor mRNA isoforms by RT-qPCR was successful in routinely formalin-fixed, paraffin-embedded tissue samples and enabled the distribution of isoforms A and B to be identified for the first time in dysplasias, benign tumors, and malignant tumors...

  11. Analysis of formalin-fixed, paraffin-embedded (FFPE) tissue via proteomic techniques and misconceptions of antigen retrieval.

    Science.gov (United States)

    O'Rourke, Matthew B; Padula, Matthew P

    2016-01-01

    Since emerging in the late 19(th) century, formaldehyde fixation has become a standard method for preservation of tissues from clinical samples. The advantage of formaldehyde fixation is that fixed tissues can be stored at room temperature for decades without concern for degradation. This has led to the generation of huge tissue banks containing thousands of clinically significant samples. Here we review techniques for proteomic analysis of formalin-fixed, paraffin-embedded (FFPE) tissue samples with a specific focus on the methods used to extract and break formaldehyde crosslinks. We also discuss an error-of-interpretation associated with the technique known as "antigen retrieval." We have discovered that this term has been mistakenly applied to two disparate molecular techniques; therefore, we argue that a terminology change is needed to ensure accurate reporting of experimental results. Finally, we suggest that more investigation is required to fully understand the process of formaldehyde fixation and its subsequent reversal.

  12. Molecular identification of Coccidioides immitis in formalin-fixed, paraffin-embedded (FFPE) tissues from a Colombian patient.

    Science.gov (United States)

    Canteros, Cristina E; Vélez H, Alejandro; Toranzo, Adriana I; Suárez-Alvarez, Roberto; Tobón O, Ángela; Jimenez A, María del Pilar; Restrepo M, Ángela

    2015-06-01

    Coccidioides immitis and C. posadasii are the etiologic agents of coccidioidomycosis, an endemic fungal disease of the Americas. In Colombia, this mycosis is uncommon, and only five cases, two of them imported, have been documented.By means of DNA sequencing, C. immitis was identified in formalin-fixed, paraffin-embedded archival tissues samples from the 5th Colombian patient diagnosed in 1997. The patient was born in Pinto, Department of Magdalena, and had never visited other geographic regions, a reason to consider that the mycosis had been acquired locally.This species is primarily found in California although it has been occasionally reported in other geographic areas such as Mexico and Brazil. This is the first indigenous report of C. immitis-associated coccidioidomycosis in a Colombian patient. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.

  13. Ewing's Sarcoma: An Analysis of miRNA Expression Profiles and Target Genes in Paraffin-Embedded Primary Tumor Tissue.

    Science.gov (United States)

    Parafioriti, Antonina; Bason, Caterina; Armiraglio, Elisabetta; Calciano, Lucia; Daolio, Primo Andrea; Berardocco, Martina; Di Bernardo, Andrea; Colosimo, Alessia; Luksch, Roberto; Berardi, Anna C

    2016-04-30

    The molecular mechanism responsible for Ewing's Sarcoma (ES) remains largely unknown. MicroRNAs (miRNAs), a class of small non-coding RNAs able to regulate gene expression, are deregulated in tumors and may serve as a tool for diagnosis and prediction. However, the status of miRNAs in ES has not yet been thoroughly investigated. This study compared global miRNAs expression in paraffin-embedded tumor tissue samples from 20 ES patients, affected by primary untreated tumors, with miRNAs expressed in normal human mesenchymal stromal cells (MSCs) by microarray analysis. A miRTarBase database was used to identify the predicted target genes for differentially expressed miRNAs. The miRNAs microarray analysis revealed distinct patterns of miRNAs expression between ES samples and normal MSCs. 58 of the 954 analyzed miRNAs were significantly differentially expressed in ES samples compared to MSCs. Moreover, the qRT-PCR analysis carried out on three selected miRNAs showed that miR-181b, miR-1915 and miR-1275 were significantly aberrantly regulated, confirming the microarray results. Bio-database analysis identified BCL-2 as a bona fide target gene of the miR-21, miR-181a, miR-181b, miR-29a, miR-29b, miR-497, miR-195, miR-let-7a, miR-34a and miR-1915. Using paraffin-embedded tissues from ES patients, this study has identified several potential target miRNAs and one gene that might be considered a novel critical biomarker for ES pathogenesis.

  14. Feasibility of using tissue microarray cores of paraffin-embedded breast cancer tissue for measurement of gene expression: a proof-of-concept study.

    Science.gov (United States)

    Drury, Suzanne; Salter, Janine; Baehner, Frederick L; Shak, Steven; Dowsett, Mitch

    2010-06-01

    To determine whether 0.6 mm cores of formalin-fixed paraffin-embedded (FFPE) tissue, as commonly used to construct immunohistochemical tissue microarrays, may be a valid alternative to tissue sections as source material for quantitative real-time PCR-based transcriptional profiling of breast cancer. Four matched 0.6 mm cores of invasive breast tumour and two 10 microm whole sections were taken from eight FFPE blocks. RNA was extracted and reverse transcribed, and TaqMan assays were performed on the 21 genes of the Oncotype DX Breast Cancer assay. Expression of the 16 recurrence-related genes was normalised to the set of five reference genes, and the recurrence score (RS) was calculated. RNA yield was lower from 0.6 mm cores than from 10 microm whole sections, but was still more than sufficient to perform the assay. RS and single gene data from cores were highly comparable with those from whole sections (RS p=0.005). Greater variability was seen between cores than between sections. FFPE sections are preferable to 0.6 mm cores for RNA profiling in order to maximise RNA yield and to allow for standard histopathological assessment. However, 0.6 mm cores are sufficient and would be appropriate to use for large cohort studies.

  15. Detection of hepatitis C viral RNA sequences in fresh and paraffin-embedded liver biopsy specimens of non-A, non-B hepatitis patients

    NARCIS (Netherlands)

    Bresters, D.; Cuypers, H. T.; Reesink, H. W.; Chamuleau, R. A.; Schipper, M. E.; Boeser-Nunnink, B. D.; Lelie, P. N.; Jansen, P. L.

    1992-01-01

    In this study methods of HCV-RNA detection in fresh frozen and formalin-fixed, paraffin-embedded liver biopsies are described. Of 22 untreated chronic non-A, non-B hepatitis patients and 6 control patients, a plasma sample and part of a liver biopsy were freshly frozen for hepatitis C virus (HCV)

  16. Development and independent validation of a prognostic assay for stage II colon cancer using formalin-fixed paraffin-embedded tissue.

    LENUS (Irish Health Repository)

    Kennedy, Richard D

    2011-12-10

    Current prognostic factors are poor at identifying patients at risk of disease recurrence after surgery for stage II colon cancer. Here we describe a DNA microarray-based prognostic assay using clinically relevant formalin-fixed paraffin-embedded (FFPE) samples.

  17. Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue.

    Science.gov (United States)

    Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for genomic research into the molecular basis of disease. However, use of FFPE samples in gene expression studies has been limited by technical challenges resulting from degradation...

  18. MicroRNA expression in melanocytic nevi: the usefulness of formalin-fixed, paraffin-embedded material for miRNA microarray profiling

    DEFF Research Database (Denmark)

    Glud, M.; Klausen, M.; Gniadecki, R.

    2009-01-01

    surgical specimens are formalin fixed and paraffin embedded (FFPE). To explore whether FFPE material would be suitable for miRNA profiling in melanocytic lesions, we compared miRNA expression patterns in FFPE versus fresh frozen samples, obtained from 15 human melanocytic nevi. Out of microarray data, we...

  19. Comparison between single PCR and nested PCR in detection of human papilloma viruses in paraffin-embedded OSCC and fresh oral mucosa.

    Science.gov (United States)

    Jalouli, Miranda; Jalouli, Jamshid; Ibrahim, Salah O; Hirsch, Jan-Michaél; Sand, Lars

    2015-01-01

    Infection with human papilloma virus (HPV) has been implicated as one of the risk factors for the development of oropharyngeal cancer. Many different HPV tests exist, and information regarding their specific technical, analytical, and clinical properties is increasing. This study aimed to compare the level of detection of HPV using two reliable polymerase chain reaction (PCR) methods, nested PCR (NPCR) and single PCR (SPCR), in archival paraffin-embedded oral squamous cell carcinoma (OSCC) samples and fresh oral mucosa specimens. The presence of HPV genome in two groups of tissue samples was analyzed: (i) 57 paraffin-embedded OSCC samples from Sudan and (ii) eight healthy fresh oral mucosal samples from Swedish volunteers. The specimens were tested by SPCR with primer pair MY9/MY11 and NPCR using GP5+/GP6+ primer sets. Eighteen (32%) out of the 57 paraffin-embedded OSCC samples, and five (62%) out of the eight fresh clinically healthy samples were found to be HPV-positive with NPCR. With SPCR, four (7%) out of the paraffin-embedded OSCC samples were HPV-positive. A statistically significant difference between HPV-positive and -negative samples was found when comparing NPCR and SPCR in OSCC and fresh oral mucosa (pnested PCR increased the positivity rate, efficiency rate and sensitivity of HPV detection in oral samples significantly and should be considered as the method of choice. Copyright © 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  20. Detection of Tropical Fungi in Formalin-Fixed, Paraffin-Embedded Tissue: Still an Indication for Microscopy in Times of Sequence-Based Diagnosis?

    Directory of Open Access Journals (Sweden)

    Hagen Frickmann

    2015-01-01

    Full Text Available Introduction. The aim of the study was the evaluation of panfungal PCR protocols with subsequent sequence analysis for the diagnostic identification of invasive mycoses in formalin-fixed, paraffin-embedded tissue samples with rare tropical mycoses. Materials and Methods. Five different previously described panfungal PCR/sequencing protocols targeting 18S and 28S ribosomal RNA gene fragments as well as internal transcribed spacer 1 and 2 fragments were evaluated with a collection of 17 formalin-fixed, paraffin-embedded tissue samples of patients with rare and/or tropical invasive mycoses, comprising chromoblastomycosis, coccidioidomycosis, cryptococcosis, histoplasmosis, mucormycosis, mycetoma/maduromycosis, and rhinosporidiosis, in a proof-of-principle analysis. Results. The primers of the panfungal PCRs readily and predominantly reacted with contaminating environmental fungi that had deposited on the paraffin blocks. Altogether three sequence results of histoplasmosis and mycetoma samples that matched the histological assessment were associated with sample age <10 years and virtually without PCR inhibition. Conclusions. The high risk of amplifying environmental contaminants severely reduces the usefulness of the assessed panfungal PCR/sequencing protocols for the identification of rare and/or tropical mycoses in stored formalin-fixed, paraffin-embedded tissues. Histological assessment remains valuable for such indications if cultural differentiation is impossible from inactivated sample material.

  1. A case report of Anisakis pegreffii (Nematoda, Anisakidae) identified from archival paraffin sections of a Croatian patient.

    Science.gov (United States)

    Mladineo, Ivona; Popović, Marijana; Drmić-Hofman, Irena; Poljak, Vedran

    2016-02-01

    This is the first report of anisakiasis in a Croatian patient, evidenced from an archival paraffin-embedded and hematoxylin-eosin stained tissue section. Anisakiasis has been only suspected in the country based on previously detected anti-Anisakis IgE seroprevalence in the healthy coastal population, as well as an acute case where pathohistological and serological findings suggested the diseases, but the migrating larva has not been retrieved. Seventy years-old female, operated in 1998 for pulmonary carcinoma, was admitted to the General hospital Šibenik, Croatia in 2003, because of gastric pain and nausea that lasted for couple of days. She was showing good general condition, full mobility and lucidity, subfebrile status. Abdominal palpation inferred acute pain in paraumbilical and ileocecal region. Exploratory right pararectal laparotomy revealed a hardened, 5 cm-long structure, located intraluminally in the sigmoid colon, not perforating colon serosa. The process has been dissected and sent for patohistological diagnosis. Results showed a 2 mm-long whitish nematode spiralised in muscular layer of colon mucosa surrounded by granulomatous inflammation. After genomic DNA isolation of the nematode from the histological section, and amplification at the mitochondrial cytochrome oxidase 2 locus, etiological agent has been identified as Anisakis pegreffii. Used methodology suggests that screening of archival suspicious sections is feasible in order to study epidemiology of this zoonotic disease poorly recognised in Croatia.

  2. Improved method for extraction and detection of Helicobacter pylori DNA in formalin-fixed paraffin embedded gastric biopsies using laser micro-dissection.

    Science.gov (United States)

    Loayza, María Fernanda; Villavicencio, Fernando Xavier; Santander, Stephanie Carolina; Baldeón, Manuel; Ponce, Lourdes Karina; Salvador, Iván; Vivar Díaz, Nicolás

    2015-01-01

    To assess the molecular events exerted by Helicobacter pylori interacting directly with gastric epithelial cells, an improved procedure for microbial DNA isolation from stained hematoxilin-eosin gastric biopsies was developed based on laser micro-dissection (LM) [1]. Few articles have described the use of LM to select and detect H. pylori genome from formalin-fixed paraffin embedded gastric tissue [2]. To improve the yield and quality of DNA isolated from H. pylori contacting intestinal epithelial cells, the following conditions were established after modification of the QIAamp DNA Micro kit. •Use of at least 25 cut sections of 10-20 μm of diameter and 3 μm thick with more than 10 bacteria in each cut.•Lysis with 30 μL of tissue lysis buffer and 20 μL of proteinase K (PK) with the tube in an upside-down position.•The use of thin purification columns with 35 μL of elution buffer. The mean of DNA concentration obtained from 25 LM cut sections was 1.94± 0 .16 ng/μL, and it was efficiently amplified with qPCR in a Bio Rad iCycler instrument. The LM can improve the sample selection and DNA extraction for molecular analysis of H. pylori associated with human gastric epithelium.

  3. Molecular genotyping of Echinococcus granulosus using formalin-fixed paraffin-embedded preparations from human isolates in unusual tissue sites.

    Science.gov (United States)

    Hizem, A; M'rad, S; Oudni-M'rad, M; Mestiri, S; Hammedi, F; Mezhoud, H; Zakhama, A; Mokni, M; Babba, H

    2016-07-01

    Cystic echinococcosis (CE) caused by Echinococcus granulosus remains a serious problem worldwide for issues relating to public health and the economy. The most predominantly affected sites are the liver and the lungs, but other organs such as the heart, the spleen and the peritoneum can also be infected. Access to cysts from uncommon sites has limited genomic and molecular investigations. In the present study, genotypes of E. granulosus sensu lato were identified from formalin-fixed paraffin-embedded tissues (FF-PETs) implicated in human CE. Tissue samples were obtained from 57 patients with histologically confirmed CE. DNA samples were analysed using Egss 1 polymerase chain reaction (PCR) specific to the mitochondrial 12S rRNA gene of E. granulosus sensu stricto. All cysts were typed as E. granulosus sensu stricto with up to 35% of the liver and 16.6% of lungs being the most frequently infected, and up to 48.4% of samples being from rare sites. No correlation was found between cyst site and either the gender or the age of patients. This study demonstrates the possibility of exploiting atypical cysts using FF-PET samples and highlights the predominance of E. granulosus sensu stricto species in the Tunisian population, even in unusual infection sites.

  4. KLC1-ALK: a novel fusion in lung cancer identified using a formalin-fixed paraffin-embedded tissue only.

    Directory of Open Access Journals (Sweden)

    Yuki Togashi

    Full Text Available The promising results of anaplastic lymphoma kinase (ALK inhibitors have changed the significance of ALK fusions in several types of cancer. These fusions are no longer mere research targets or diagnostic markers, but they are now directly linked to the therapeutic benefit of patients. However, most available tumor tissues in clinical settings are formalin-fixed and paraffin-embedded (FFPE, and this significantly limits detailed genetic studies in many clinical cases. Although recent technical improvements have allowed the analysis of some known mutations in FFPE tissues, identifying unknown fusion genes by using only FFPE tissues remains difficult. We developed a 5'-rapid amplification of cDNA ends-based system optimized for FFPE tissues and evaluated this system on a lung cancer tissue with ALK rearrangement and without the 2 known ALK fusions EML4-ALK and KIF5B-ALK. With this system, we successfully identified a novel ALK fusion, KLC1-ALK. The result was confirmed by reverse transcription-polymerase chain reaction and fluorescence in situ hybridization. Then, we synthesized the putative full-length cDNA of KLC1-ALK and demonstrated the transforming potential of the fusion kinase with assays using mouse 3T3 cells. To the best of our knowledge, KLC1-ALK is the first novel oncogenic fusion identified using only FFPE tissues. This finding will broaden the potential value of archival FFPE tissues and provide further biological and clinical insights into ALK-positive lung cancer.

  5. Detection of Mycobacterium tuberculosis Complex in Paraffin-Embedded Tissues by the New Automated Abbott RealTime MTB Assay.

    Science.gov (United States)

    Fu, Yung-Chieh; Liao, I-Chuang; Chen, Hung-Mo; Yan, Jing-Jou

    2016-07-01

    The Abbott RealTime MTB assay, launched in June 2014, has been shown to have a competitive performance in the detection of the Mycobacterium tuberculosis (MTB) complex in respiratory specimens. The present study was conducted to investigate the usefulness of the Abbott MTB Realtime assay in the detection of MTB in formalin-fixed paraffin-embedded (FFPE) tissues. A total of 96 FFPE specimens obtained from microbiologically proven MTB cases (N=60) and nontuberculous Mycobacterium cases (N=36) were analyzed. The performance of the Abbott MTB Realtime assay was compared with that of the Roche Cobas TaqMan MTB assay. The overall sensitivity and specificity of the Abbott assay were 63.3% and 97.2%, respectively, compared with 11.7% and 100% for the Cobas assay. The detection rate of the Abbott assay was much higher among 37 acid-fast-positive specimens than among 23 acid-fast-negative specimens (89.3% versus 21.7%, respectively). The detection rate of the assay was higher among 29 resection specimens than among 31 small biopsy specimens (86.2% versus 41.9%, respectively). Our results suggest that the Abbott RealTime MTB assay can be used to differentiate MTB from nontuberculous mycobacterial infections in acid-fast-positive FFPE tissues. © 2016 by the Association of Clinical Scientists, Inc.

  6. Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue.

    Science.gov (United States)

    Thompson, Seonaid M; Craven, Rachel A; Nirmalan, Niroshini J; Harnden, Patricia; Selby, Peter J; Banks, Rosamonde E

    2013-04-01

    Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples.

    Science.gov (United States)

    Moens, Lotte N J; Falk-Sörqvist, Elin; Ljungström, Viktor; Mattsson, Johanna; Sundström, Magnus; La Fleur, Linnéa; Mathot, Lucy; Micke, Patrick; Nilsson, Mats; Botling, Johan

    2015-11-01

    In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomolecular analyses. We evaluated the HaloPlex target enrichment system for somatic mutation detection in 80 tissue fractions derived from 20 clinical cancer cases with paired tumor and normal tissue available in both FFPE and fresh-frozen format. Several modifications to the standard method were introduced, including a reduced target fragment length and two strand capturing. We found that FFPE material can be used for HaloPlex-based target enrichment and next-generation sequencing, even when starting from small amounts of DNA. By specifically capturing both strands for each target fragment, we were able to reduce the number of false-positive errors caused by FFPE-induced artifacts and lower the detection limit for somatic mutations. We believe that the HaloPlex method presented here will be broadly applicable as a tool for somatic mutation detection in clinical cancer settings. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  8. A new classification method for MALDI imaging mass spectrometry data acquired on formalin-fixed paraffin-embedded tissue samples.

    Science.gov (United States)

    Boskamp, Tobias; Lachmund, Delf; Oetjen, Janina; Cordero Hernandez, Yovany; Trede, Dennis; Maass, Peter; Casadonte, Rita; Kriegsmann, Jörg; Warth, Arne; Dienemann, Hendrik; Weichert, Wilko; Kriegsmann, Mark

    2017-07-01

    Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) shows a high potential for applications in histopathological diagnosis, and in particular for supporting tumor typing and subtyping. The development of such applications requires the extraction of spectral fingerprints that are relevant for the given tissue and the identification of biomarkers associated with these spectral patterns. We propose a novel data analysis method based on the extraction of characteristic spectral patterns (CSPs) that allow automated generation of classification models for spectral data. Formalin-fixed paraffin embedded (FFPE) tissue samples from N=445 patients assembled on 12 tissue microarrays were analyzed. The method was applied to discriminate primary lung and pancreatic cancer, as well as adenocarcinoma and squamous cell carcinoma of the lung. A classification accuracy of 100% and 82.8%, resp., could be achieved on core level, assessed by cross-validation. The method outperformed the more conventional classification method based on the extraction of individual m/z values in the first application, while achieving a comparable accuracy in the second. LC-MS/MS peptide identification demonstrated that the spectral features present in selected CSPs correspond to peptides relevant for the respective classification. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Application of the FICTION technique for the simultaneous detection of immunophenotype and chromosomal abnormalities in routinely fixed, paraffin wax embedded bone marrow trephines

    Science.gov (United States)

    Korać, P; Jones, M; Dominis, M; Kušec, R; Mason, D Y; Banham, A H; Ventura, R A

    2005-01-01

    The use of interphase fluorescence in situ hybridisation (FISH) to study cytogenetic abnormalities in routinely fixed paraffin wax embedded tissue has become commonplace over the past decade. However, very few studies have applied FISH to routinely fixed bone marrow trephines (BMTs). This may be because of the acid based decalcification methods that are commonly used during the processing of BMTs, which may adversely affect the suitability of the sample for FISH analysis. For the first time, this report describes the simultaneous application of FISH and immunofluorescent staining (the FICTION technique) to formalin fixed, EDTA decalcified and paraffin wax embedded BMTs. This technique allows the direct correlation of genetic abnormalities to immunophenotype, and therefore will be particularly useful for the identification of genetic abnormalities in specific tumour cells present in BMTs. The application of this to routine clinical practice will assist diagnosis and the detection of minimal residual disease. PMID:16311361

  10. Applying a Real-Time PCR Assay for Histoplasma capsulatum to Clinically Relevant Formalin-Fixed Paraffin-Embedded Human Tissue

    Science.gov (United States)

    Koepsell, Scott A.; Hinrichs, Steven H.

    2012-01-01

    A real-time PCR assay to detect Histoplasma capsulatum in formalin-fixed, paraffin-embedded (FFPE) tissue is described. The assay had an analytical sensitivity of 6 pg/μl of fungal DNA, analytical specificity of 100%, and clinical sensitivity of 88.9%. This proof-of-concept study may aid in the diagnosis of histoplasmosis from FFPE tissue. PMID:22855519

  11. Zoonotic onchocerciasis in Hiroshima, Japan, and molecular analysis of a paraffin section of the agent for a reliable identification

    Directory of Open Access Journals (Sweden)

    Fukuda M.

    2011-05-01

    Full Text Available Japan is a country of high specific diversity of Onchocerca with eight species, the adults of two not yet known. Onchocerca dewittei japonica, a common filarial parasite of wild boar, had been proved to be the agent of five zoonotic onchocerciasis in Kyushu island with morphological and molecular studies. The sixth case, at Hiroshima in the main island, was identified to the same Onchocerca species, based on adult characters observed on histological sections. To consolidate the identification, mitochondrial cytochrome c oxidase subunit 1 (CO1 gene analysis was attempted with the formalin-fixed, paraffin-embedded parasite specimen. The sequence (196 bp of a CO1 gene fragment of the parasite successfully PCR-amplified agreed well with those of O. dewittei japonica registered in GenBank, confirming the morphological identification. Moreover a comparison with the CO1 gene sequences of six other Onchocerca species in GenBank excluded the possibility that Onchocerca sp. from wild boar and Onchocerca sp. type A from cattle in Japan, were the causative agents in this case. Mitochondrial DNA analysis proved to be a valuable tool to support the morphological method for the discrimination of zoonotic Onchocerca species in a histological specimen.

  12. Non-hazardous organic solvents in the paraffin-embedding technique

    DEFF Research Database (Denmark)

    Holm, Inger Lindebo; Lyon, Hans; Prentø, Poul

    1995-01-01

    The aim of this study was to substitute hazardous compounds, used in tissue processing and dewaxing, with compounds having lowest possible toxicity and inflammability without impairing the morphology, staining characteristics, or diagnostic value of the tissue sections. All aromatic compounds...... and aliphatic hydrocarbons (e.g. alkanes, isoparaffins, petroleum distillates, etc.) were rejected, primarily due to their high vapour pressure. Based on a theoretical study of compounds used for clearing, a number of non-hazardous potential substitutes were chosen. The following experimental study narrowed...... the group to three unbranched, saturated, aliphatic monoesters containing 12-14 carbon atoms. On large-scale testing of these compounds, we found butyldecanoate to be the closest to an ideal substitute for aromatic and aliphatic hydrocarbons in the histology department: the section quality is at least equal...

  13. Modified paraffin wax for improvement of histological analysis efficiency.

    Science.gov (United States)

    Lim, Jin Ik; Lim, Kook-Jin; Choi, Jin-Young; Lee, Yong-Keun

    2010-08-01

    Paraffin wax is usually used as an embedding medium for histological analysis of natural tissue. However, it is not easy to obtain enough numbers of satisfactory sectioned slices because of the difference in mechanical properties between the paraffin and embedded tissue. We describe a modified paraffin wax that can improve the histological analysis efficiency of natural tissue, composed of paraffin and ethylene vinyl acetate (EVA) resin (0, 3, 5, and 10 wt %). Softening temperature of the paraffin/EVA media was similar to that of paraffin (50-60 degrees C). The paraffin/EVA media dissolved completely in xylene after 30 min at 50 degrees C. Physical properties such as the amount of load under the same compressive displacement, elastic recovery, and crystal intensity increased with increased EVA content. EVA medium (5 wt %) was regarded as an optimal composition, based on the sectioning efficiency measured by the numbers of unimpaired sectioned slices, amount of load under the same compressive displacement, and elastic recovery test. Based on the staining test of sectioned slices embedded in a 5 wt % EVA medium by hematoxylin and eosin (H&E), Masson trichrome (MT), and other staining tests, it was concluded that the modified paraffin wax can improve the histological analysis efficiency with various natural tissues. (c) 2010 Wiley-Liss, Inc.

  14. Evaluation of a panel of antibodies for the immunohistochemical identification of immune cells in paraffin-embedded lymphoid tissues of new- and old-world camelids.

    Science.gov (United States)

    Uhde, Ann-Kathrin; Lehmbecker, Annika; Baumgärtner, Wolfgang; Spitzbarth, Ingo

    2017-02-01

    Different species of camelids play an important role in the epidemiology of various emerging infectious diseases such as Middle East respiratory syndrome. For precise investigations of the immunopathogenesis in these host species, appropriate immunohistochemical markers are highly needed in order to phenotype distinct immune cells populations in camelids. So far, specific immunohistochemical markers for camelid immune cells are rarely commercially available, and cross-reactivity studies are restricted to the use of frozen dromedary tissues. To bridge this gap, 14 commercially available primary antibodies were tested for their suitability to demonstrate immune cell populations on formalin fixed paraffin-embedded (FFPE) tissue sections of dromedaries, Bactrian camels, llamas, and alpacas in the present study. Out of these, 9 antibodies directed against CD3, CD20, CD79α, HLA-DR, Iba-1, myeloid/histiocyte antigen, CD204, CD208, and CD68 antigen exhibited distinct immunoreaction patterns to certain camelid immune cell subsets. The distribution of these antigens was comparatively evaluated in different anatomical compartments of thymus, spleen, mesenteric, and tracheobronchial lymph nodes. The presented results will provide a basis for further investigations in camelids, especially with respect to the role of the immune response in certain infectious diseases, which harbor a considerable risk to spill over to other species. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. MALDI imaging mass spectrometry profiling of N-glycans in formalin-fixed paraffin embedded clinical tissue blocks and tissue microarrays.

    Science.gov (United States)

    Powers, Thomas W; Neely, Benjamin A; Shao, Yuan; Tang, Huiyuan; Troyer, Dean A; Mehta, Anand S; Haab, Brian B; Drake, Richard R

    2014-01-01

    A recently developed matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) method to spatially profile the location and distribution of multiple N-linked glycan species in frozen tissues has been extended and improved for the direct analysis of glycans in clinically derived formalin-fixed paraffin-embedded (FFPE) tissues. Formalin-fixed tissues from normal mouse kidney, human pancreatic and prostate cancers, and a human hepatocellular carcinoma tissue microarray were processed by antigen retrieval followed by on-tissue digestion with peptide N-glycosidase F. The released N-glycans were detected by MALDI-IMS analysis, and the structural composition of a subset of glycans could be verified directly by on-tissue collision-induced fragmentation. Other structural assignments were confirmed by off-tissue permethylation analysis combined with multiple database comparisons. Imaging of mouse kidney tissue sections demonstrates specific tissue distributions of major cellular N-linked glycoforms in the cortex and medulla. Differential tissue distribution of N-linked glycoforms was also observed in the other tissue types. The efficacy of using MALDI-IMS glycan profiling to distinguish tumor from non-tumor tissues in a tumor microarray format is also demonstrated. This MALDI-IMS workflow has the potential to be applied to any FFPE tissue block or tissue microarray to enable higher throughput analysis of the global changes in N-glycosylation associated with cancers.

  16. Gene Expression Analysis of Immunostained Endothelial Cells Isolated from Formaldehyde-fixated Paraffin Embedded Tumors Using Laser Capture Microdissection – a Technical Report

    Science.gov (United States)

    Kaneko, Tomoatsu; Okiji, Takashi; Kaneko, Reika; Suda, Hideaki; Nör, Jacques E.

    2009-01-01

    Laser capture microdissection (LCM) allows microscopic procurement of specific cell types from tissue sections that can then be used for gene expression analysis. In conventional LCM, frozen tissues stained with hematoxylin are normally used to the molecular analysis. Recent studies suggested that it is possible to carry out gene expression analysis of formaldehyde-fixated paraffin embedded (FFPE) tissues that were stained with hematoxylin. However, it is still unclear if quantitative gene expression analyses can be performed from LCM cells from FFPE tissues that were subjected to immunostaining to enhance identification of target cells. In this proof-of-principle study, we analyzed by RT-PCR and real time PCR the expression of genes in factor VIII immunostained human endothelial cells that were dissected from FFPE tissues by LCM. We observed that immunostaining should be performed at 4°C to preserve the mRNA from the cells. The expression of Bcl-2 in the endothelial cells was evaluated by RT-PCR and by real time PCR. GAPDH and 18S were used as house keeping genes for RT-PCR and real time PCR, respectively. This report unveils a method for quantitative gene expression analysis in cells that were identified by immunostaining and retrieved by LCM from FFPE tissues. This method is ideally suited for the analysis of relatively rare cell types within a tissue, and should improve on our ability to perform differential diagnosis of pathologies as compared to conventional LCM. PMID:19425073

  17. Confirmation of immunoglobulin heavy chain rearrangement by polymerase chain reaction using surgically obtained, paraffin-embedded samples to diagnose primary palate mucosa-associated lymphoid tissue lymphoma: A case study

    Directory of Open Access Journals (Sweden)

    Shigehiro Abe

    2015-01-01

    Conclusion: We suggest that, if histological examination is ambiguous or fresh material is insufficient, PCR can be performed using paraffin-embedded materials to definitively diagnose low-grade lymphomas, such as MALT lymphoma.

  18. Superresolution Imaging of Aquaporin-4 Cluster Size in Antibody-Stained Paraffin Brain Sections.

    Science.gov (United States)

    Smith, Alex J; Verkman, Alan S

    2015-12-15

    The water channel aquaporin-4 (AQP4) forms supramolecular clusters whose size is determined by the ratio of M1- and M23-AQP4 isoforms. In cultured astrocytes, differences in the subcellular localization and macromolecular interactions of small and large AQP4 clusters results in distinct physiological roles for M1- and M23-AQP4. Here, we developed quantitative superresolution optical imaging methodology to measure AQP4 cluster size in antibody-stained paraffin sections of mouse cerebral cortex and spinal cord, human postmortem brain, and glioma biopsy specimens. This methodology was used to demonstrate that large AQP4 clusters are formed in AQP4(-/-) astrocytes transfected with only M23-AQP4, but not in those expressing only M1-AQP4, both in vitro and in vivo. Native AQP4 in mouse cortex, where both isoforms are expressed, was enriched in astrocyte foot-processes adjacent to microcapillaries; clusters in perivascular regions of the cortex were larger than in parenchymal regions, demonstrating size-dependent subcellular segregation of AQP4 clusters. Two-color superresolution imaging demonstrated colocalization of Kir4.1 with AQP4 clusters in perivascular areas but not in parenchyma. Surprisingly, the subcellular distribution of AQP4 clusters was different between gray and white matter astrocytes in spinal cord, demonstrating regional specificity in cluster polarization. Changes in AQP4 subcellular distribution are associated with several neurological diseases and we demonstrate that AQP4 clustering was preserved in a postmortem human cortical brain tissue specimen, but that AQP4 was not substantially clustered in a human glioblastoma specimen despite high-level expression. Our results demonstrate the utility of superresolution optical imaging for measuring the size of AQP4 supramolecular clusters in paraffin sections of brain tissue and support AQP4 cluster size as a primary determinant of its subcellular distribution. Copyright © 2015 Biophysical Society

  19. MicroRNA expression profiles of multiple system atrophy from formalin-fixed paraffin-embedded samples.

    Science.gov (United States)

    Wakabayashi, Koichi; Mori, Fumiaki; Kakita, Akiyoshi; Takahashi, Hitoshi; Tanaka, Shinya; Utsumi, Jun; Sasaki, Hidenao

    2016-12-02

    MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression. Recently, we have shown that informative miRNA data can be derived from archived formalin-fixed paraffin-embedded (FFPE) samples from postmortem cases of amyotrophic lateral sclerosis and normal controls. miRNA analysis has now been performed on FFPE samples from affected brain regions in patients with multiple system atrophy (MSA) and the same areas in neurologically normal controls. We evaluated 50 samples from patients with MSA (n=13) and controls (n=13). Twenty-six samples were selected for miRNA analysis on the basis of the criteria reported previously: (i) a formalin fixation time of less than 4 weeks, (ii) a total RNA yield per sample of more than 500ng, and (iii) sufficient quality of the RNA electrophoresis pattern. These included 11 cases of MSA and 5 controls. Thus, the success rate for analysis of RNA from FFPE samples was 52% (26 of 50). For MSA, a total of 395 and 383 miRNAs were identified in the pons and cerebellum, respectively; 5 were up-regulated and 33 were down-regulated in the pons and 5 were up-regulated and 18 were down-regulated in the cerebellum. Several miRNAs down-regulated in the pons (miR-129-2-3p and miR-129-5p) and cerebellum (miR-129-2-3p, miR-129-5p and miR-132-3p) had already been identified in frozen cerebellum from MSA patients. These findings suggest that archived FFPE postmortem samples can be a valuable source for miRNA profiling in MSA. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  20. [Histopathological Diagnosis of Invasive Fungal Infections in Formalin-Fixed and Paraffin-Embedded Tissues in Conjunction with Molecular Methods].

    Science.gov (United States)

    Shinozaki, Minoru; Tochigi, Naobumi; Sadamoto, Sota; Yamagata Murayama, Somay; Wakayama, Megumi; Nemoto, Tetsuo

    2018-01-01

    The main objective of this study was to evaluate the relationship between histopathology, polymerase chain reaction (PCR), and in situ hybridization (ISH) for the identification of causative fungi in formalin-fixed and paraffin-embedded (FFPE) tissue specimens. Since pathogenic fungi in tissue specimens can be difficult to identify morphologically, PCR and ISH have been usually employed as auxiliary procedures. However, little comparison has been made on the sensitivity and specificity of PCR and ISH using FFPE specimens. Therefore, to compare and clarify the reproducibility and usefulness of PCR and ISH as auxiliary procedures for histological identification, we performed histopathological review, PCR assays, and ISH to identify pathogenic fungi in 59 FFPE tissue specimens obtained from 49 autopsies. The following are the main findings for this retrospective review: i) even for cases classified as "mold not otherwise specified" (MNOS), two cases could be identified as Aspergillus species by molecular methods; ii) all cases classified as non-zygomycetes mold (NZM) were Aspergillus species and were not identified by molecular methods as other fungi; iii) all 3 cases classified as zygomycetes mold (ZM) could be identified by molecular methods as Mucorales; iv) except for 1 case identified by molecular methods as Trichosporon spp., 5 cases were originally identified as dimorphic yeast (DY). As a measure of nucleic acid integrity, PCR and ISH successfully detected human and fungal nucleic acids in approximately 60% of the specimens. Detection of Aspergillus DNA by nested PCR assay and by ISH against the A. fumigatus ALP gene were similarly sensitive and significant (pmolecular methods such as ISH and PCR on FFPE specimens with pathological diagnosis should improve diagnostic accuracy of fungal infection.

  1. Elevated pressure improves the extraction and identification of proteins recovered from formalin-fixed, paraffin-embedded tissue surrogates.

    Directory of Open Access Journals (Sweden)

    Carol B Fowler

    2010-12-01

    Full Text Available Proteomic studies of formalin-fixed paraffin-embedded (FFPE tissues are frustrated by the inability to extract proteins from archival tissue in a form suitable for analysis by 2-D gel electrophoresis or mass spectrometry. This inability arises from the difficulty of reversing formaldehyde-induced protein adducts and cross-links within FFPE tissues. We previously reported the use of elevated hydrostatic pressure as a method for efficient protein recovery from a hen egg-white lysozyme tissue surrogate, a model system developed to study formalin fixation and histochemical processing.In this study, we demonstrate the utility of elevated hydrostatic pressure as a method for efficient protein recovery from FFPE mouse liver tissue and a complex multi-protein FFPE tissue surrogate comprised of hen egg-white lysozyme, bovine carbonic anhydrase, bovine ribonuclease A, bovine serum albumin, and equine myoglobin (55∶15∶15∶10∶5 wt%. Mass spectrometry of the FFPE tissue surrogates retrieved under elevated pressure showed that both the low and high-abundance proteins were identified with sequence coverage comparable to that of the surrogate mixture prior to formaldehyde treatment. In contrast, non-pressure-extracted tissue surrogate samples yielded few positive and many false peptide identifications. Studies with soluble formalin-treated bovine ribonuclease A demonstrated that pressure modestly inhibited the rate of reversal (hydrolysis of formaldehyde-induced protein cross-links. Dynamic light scattering studies suggest that elevated hydrostatic pressure and heat facilitate the recovery of proteins free of formaldehyde adducts and cross-links by promoting protein unfolding and hydration with a concomitant reduction in the average size of the protein aggregates.These studies demonstrate that elevated hydrostatic pressure treatment is a promising approach for improving the recovery of proteins from FFPE tissues in a form suitable for proteomic analysis.

  2. Elevated Pressure Improves the Extraction and Identification of Proteins Recovered from Formalin-Fixed, Paraffin-Embedded Tissue Surrogates

    Science.gov (United States)

    Fowler, Carol B.; Chesnick, Ingrid E.; Moore, Cedric D.; O'Leary, Timothy J.; Mason, Jeffrey T.

    2010-01-01

    Background Proteomic studies of formalin-fixed paraffin-embedded (FFPE) tissues are frustrated by the inability to extract proteins from archival tissue in a form suitable for analysis by 2-D gel electrophoresis or mass spectrometry. This inability arises from the difficulty of reversing formaldehyde-induced protein adducts and cross-links within FFPE tissues. We previously reported the use of elevated hydrostatic pressure as a method for efficient protein recovery from a hen egg-white lysozyme tissue surrogate, a model system developed to study formalin fixation and histochemical processing. Principal Findings In this study, we demonstrate the utility of elevated hydrostatic pressure as a method for efficient protein recovery from FFPE mouse liver tissue and a complex multi-protein FFPE tissue surrogate comprised of hen egg-white lysozyme, bovine carbonic anhydrase, bovine ribonuclease A, bovine serum albumin, and equine myoglobin (55∶15∶15∶10∶5 wt%). Mass spectrometry of the FFPE tissue surrogates retrieved under elevated pressure showed that both the low and high-abundance proteins were identified with sequence coverage comparable to that of the surrogate mixture prior to formaldehyde treatment. In contrast, non-pressure-extracted tissue surrogate samples yielded few positive and many false peptide identifications. Studies with soluble formalin-treated bovine ribonuclease A demonstrated that pressure modestly inhibited the rate of reversal (hydrolysis) of formaldehyde-induced protein cross-links. Dynamic light scattering studies suggest that elevated hydrostatic pressure and heat facilitate the recovery of proteins free of formaldehyde adducts and cross-links by promoting protein unfolding and hydration with a concomitant reduction in the average size of the protein aggregates. Conclusions These studies demonstrate that elevated hydrostatic pressure treatment is a promising approach for improving the recovery of proteins from FFPE tissues in a form

  3. Bisulfite-Based DNA Methylation Analysis from Recent and Archived Formalin-Fixed, Paraffin Embedded Colorectal Tissue Samples.

    Science.gov (United States)

    Kalmár, Alexandra; Péterfia, Bálint; Hollósi, Péter; Wichmann, Barnabás; Bodor, András; Patai, Árpád V; Schöller, Andrea; Krenács, Tibor; Tulassay, Zsolt; Molnár, Béla

    2015-09-01

    We aimed to test the applicability of formalin-fixed and paraffin-embedded (FFPE) tissue samples for gene specific DNA methylation analysis after using two commercially available DNA isolation kits. Genomic DNA was isolated from 5 colorectal adenocarcinomas and 5 normal adjacent tissues from "recent", collected within 6 months, and "archived", collected more than 5 years ago, FFPE tissues using either High Pure FFPET DNA Isolation kit or QIAamp DNA FFPE Tissue kit. DNA methylation analysis of MAL, SFRP1 and SFRP2 genes, known to be hypermethylated in CRC, was performed using methylation-sensitive high resolution melting (MS-HRM) analysis and sequencing. QIAamp (Q) method resulted in slightly higher recovery in archived (HP: 1.22 ± 3.18 μg DNA; Q: 3.00 ± 4.04 μg DNA) and significantly (p < 0.05) higher recovery in recent samples compared to High Pure method (HP) (HP: 4.10 ± 2.91 μg DNA; Q: 11.51 ± 7.50 μg DNA). Both OD260/280 and OD260/230 ratios were lower, but still high in the High Pure isolated archived and recent samples compared to those isolated with QIAamp. Identical DNA methylation patterns were detected for all 3 genes tested by MS-HRM with both isolation kits in the recent group. However, despite of higher DNA recovery in QIAamp slightly more reproducible methylation results were obtained from High Pure isolated archived samples. Sequencing confirmed DNA hypermethylation in CRCs. In conclusion, reproducible DNA methylation patterns were obtained from recent samples using both isolation kits. However, long term storage may affect the reliability of the results leading to moderate differences between the efficiency of isolation kits.

  4. Simultaneous phenotyping and genotyping (FICTION-methodology) on paraffin sections and cytologic specimens: a comparison of 2 different protocols

    DEFF Research Database (Denmark)

    Bzorek, M.Sr.; Hansen, L.; Petersen, Bodil Laub

    2008-01-01

    for the investigation of neoplasms)]. However, few studies have been applied to the technical problems posed by antigen retrieval and accessibility of genetic probes to target-DNA, using formalin-fixed, paraffin-embedded tissue. In this study, we compared 2 immunofluorescence detection systems, the 3-step IF (TIF......) method against the Tyramide Signal Amplification techniques (TSA). The FICTION-TSA technique significantly improved the sensitivity for detection of the immunophenotypic markers without influencing specific probe hybridization to target-DNA, compared with the results obtained with the TIF method....... The reaction product of the TSA system was robust to the following FISH procedure in contrast to the TIF technique. The TSA technique used also allowed synchronous detection of nuclear antigens and FISH signals using both fusion (IgH/CCND1) and break-apart (CCND1) probes on formalin-fixed paraffin...

  5. Quantitative PCR for HTLV-1 provirus in adult T-cell leukemia/lymphoma using paraffin tumor sections.

    Science.gov (United States)

    Kato, Junki; Masaki, Ayako; Fujii, Keiichiro; Takino, Hisashi; Murase, Takayuki; Yonekura, Kentaro; Utsunomiya, Atae; Ishida, Takashi; Iida, Shinsuke; Inagaki, Hiroshi

    2016-11-01

    Detection of HTLV-1 provirus using paraffin tumor sections may assist the diagnosis of adult T-cell leukemia/lymphoma (ATLL). For the detection, non-quantitative PCR assay has been reported, but its usefulness and limitations remain unclear. To our knowledge, quantitative PCR assay using paraffin tumor sections has not been reported. Using paraffin sections from ATLLs and non-ATLL T-cell lymphomas, we first performed non-quantitative PCR for HTLV-1 provirus. Next, we determined tumor ratios and carried out quantitative PCR to obtain provirus copy numbers. The results were analyzed with a simple regression model and a novel criterion, cut-off using 95 % rejection limits. Our quantitative PCR assay showed an excellent association between tumor ratios and the copy numbers (r = 0.89, P paraffin tumor sections may be useful for the screening of ATLL cases, especially in HTLV-1 non-endemic areas where easy access to serological testing for HTLV-1 infection is limited. © 2016 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

  6. Improved clonality detection in Hodgkin lymphoma using a semi-nested modification of the BIOMED-2 PCR assay for IGH and IGK rearrangements: A paraffin-embedded tissue study.

    Science.gov (United States)

    Han, Shusen; Masaki, Ayako; Sakamoto, Yuma; Takino, Hisashi; Murase, Takayuki; Iida, Shinsuke; Inagaki, Hiroshi

    2018-05-01

    The BIOMED-2 PCR protocols targeting IGH and IGK genes may be useful for detecting clonality in Hodgkin lymphoma (HL). The clonality detection rates, however, have not been very high with these methods using paraffin-embedded tumor sections. We previously described the usefulness of the semi-nested BIOMED-2 IGH assay in B-cell malignancies. In this study, we devised a novel semi-nested BIOMED-2 IGK assay. Employing 58 cases of classical HL, we carried out the standard BIOMED-2, BIOMED-2 followed by BIOMED-2 re-amplification, and BIOMED-2 followed by semi-nested BIOMED-2, all targeting IGH and IGK, using paraffin-embedded tissues. In both IGH and IGK assays, semi-nested assays yielded significantly higher clonality detection rates than the standard assays and re-amplification assays. Clonality was detected in 13/58 (22.4%) classical HL cases using the standard IGH/IGK assays while it was detected in 38/58 (65.5%) cases using semi-nested IGH/IGK assays. The detection rates were not associated with the HL subtypes, CD30-positive cell density, CD20-positive cell density, or Epstein-Barr virus (EBV) positivity. In conclusion, tumor clonality was detected in nearly two-thirds of classical HL cases using semi-nested BIOMED-2 IGH/IGK assays using paraffin tumor sections. These semi-nested assays may be useful when the standard IGH/IGK assays fail to detect clonality in histopathologically suspected HLs. © 2018 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

  7. Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

    International Nuclear Information System (INIS)

    Sadi, Al Muktafi; Wang, Dong-Yu; Youngson, Bruce J; Miller, Naomi; Boerner, Scott; Done, Susan J; Leong, Wey L

    2011-01-01

    The ability of gene profiling to predict treatment response and prognosis in breast cancers has been demonstrated in many studies using DNA microarray analyses on RNA from fresh frozen tumor specimens. In certain clinical and research situations, performing such analyses on archival formalin fixed paraffin-embedded (FFPE) surgical specimens would be advantageous as large libraries of such specimens with long-term follow-up data are widely available. However, FFPE tissue processing can cause fragmentation and chemical modifications of the RNA. A number of recent technical advances have been reported to overcome these issues. Our current study evaluates whether or not the technology is ready for clinical applications. A modified RNA extraction method and a recent DNA microarray technique, cDNA-mediated annealing, selection, extension and ligation (DASL, Illumina Inc) were evaluated. The gene profiles generated from FFPE specimens were compared to those obtained from paired fresh fine needle aspiration biopsies (FNAB) of 25 breast cancers of different clinical subtypes (based on ER and Her2/neu status). Selected RNA levels were validated using RT-qPCR, and two public databases were used to demonstrate the prognostic significance of the gene profiles generated from FFPE specimens. Compared to FNAB, RNA isolated from FFPE samples was relatively more degraded, nonetheless, over 80% of the RNA samples were deemed suitable for subsequent DASL assay. Despite a higher noise level, a set of genes from FFPE specimens correlated very well with the gene profiles obtained from FNAB, and could differentiate breast cancer subtypes. Expression levels of these genes were validated using RT-qPCR. Finally, for the first time we correlated gene expression profiles from FFPE samples to survival using two independent microarray databases. Specifically, over-expression of ANLN and KIF2C, and under-expression of MAPT strongly correlated with poor outcomes in breast cancer patients. We

  8. Temperature-dependent thermal properties of a paraffin phase change material embedded with herringbone style graphite nanofibers

    International Nuclear Information System (INIS)

    Warzoha, Ronald J.; Weigand, Rebecca M.; Fleischer, Amy S.

    2015-01-01

    Highlights: • The thermal properties of a PCM with nanofibers are determined. • The solid-phase thermal conductivity scales exponentially with volume fraction. • The liquid-phase thermal conductivity is only enhanced beyond a critical percolation threshold. • The nanoscale interface resistance depends on the nanoparticle’s dimensionality. • The thermal diffusivity and volumetric heat capacity of the nanoenhanced PCMs are found. - Abstract: In many studies, carbon nanoparticles with high values of thermal conductivity (10–3000 W/m K) have been embedded into phase change thermal energy storage materials (PCMs) in order to enhance their bulk thermal properties. While a great deal of work to date has focused on determining the effect of these nanoparticles on a PCM’s solid phase thermal properties, little is known about their effect on its liquid phase thermal properties. Thus, in this study, the effect of implanting randomly oriented herringbone style graphite nanofibers (HGNF, average diameter = 100 nm, average length = 20 μm) on the bulk thermal properties of an organic paraffin PCM (IGI 1230A, T melt = 329.15 K) in both the solid and liquid phase is quantified. The bulk thermal conductivity, volumetric heat capacity and thermal diffusivity of HGNF/PCM nanocomposites are obtained as a function of temperature and HGNF volume loading level. It is found that the property enhancement varies significantly depending on the material phase. In order to explain the difference between solid and liquid phase thermal properties, heat flow at the nanoparticle–PCM and nanoparticle–nanoparticle interfaces is examined as a function of HGNF loading level and temperature. To do this, the solid and liquid phase thermal boundary resistances (TBRs) between the nanoparticles and the surrounding PCM and/or between contacting nanoparticles are found. Results suggest that the TBR at the HGNF–PCM interface is nearly double the TBR across the HGNF–HGNF interface in

  9. Detection of feline coronavirus mutations in paraffin-embedded tissues in cats with feline infectious peritonitis and controls.

    Science.gov (United States)

    Sangl, Laura; Matiasek, Kaspar; Felten, Sandra; Gründl, Stefanie; Bergmann, Michele; Balzer, Hans-Jörg; Pantchev, Nikola; Leutenegger, Christian M; Hartmann, Katrin

    2018-03-01

    Objectives The amino acid substitutions M1058L and S1060A in the spike protein of feline coronavirus (FCoV) have been postulated to be responsible for the development of the pathogenic feline infectious peritonitis virus (FIPV), which causes feline infectious peritonitis (FIP). The aim of the following study was to investigate the presence of mutated virus in tissue samples of cats with and without FIP. Methods The study population consisted of 64 cats, 34 of which were diagnosed with FIP and 30 control cats. All cases underwent autopsy, histopathology and immunohistochemistry (IHC) for FCoV. Furthermore, a genotype-discriminating quantitative reverse transcriptase PCR (RT-qPCR) was performed on shavings of paraffin-embedded tissues to discriminate between cats with FIP and controls, and the sensitivity and specificity of this discriminating RT-qPCR were calculated using 95% confidence intervals (CIs). Results Specificity of genotype-discriminating RT-qPCR was 100.0% (95% CI 88.4-100.0), sensitivity was 70.6% (95% CI 52.5-84.9). In cats with FIP, 24/34 cats tested positive for FIPV. In samples of three control cats and in seven cats with FIP, FCoV was found, but genotyping was not possible owing to low FCoV RNA concentrations. Out of the positive samples, 23 showed the amino acid substitution M1058L in the spike protein and none the substitution S1060A. One sample in a cat with FIP revealed a mixed population of non-mutated FCoV and FIPV (mixed genotype). For one sample genotyping was not possible despite high viral load, and two samples were negative for FCoV. Conclusions and relevance As none of the control animals showed FCoV amino acid substitutions previously demonstrated in cats with FIP, it can be presumed that the substitution M1058L correlates with the presence of FIP. FCoV was detected in low concentration in tissues of control animals, confirming the ability of FCoV to spread systemically. The fact that no negative controls were included in the IHC

  10. Droplet digital polymerase chain reaction detection of HER2 amplification in formalin fixed paraffin embedded breast and gastric carcinoma samples.

    Science.gov (United States)

    Zhu, Yazhen; Lu, Dan; Lira, Maruja E; Xu, Qing; Du, Yunzhi; Xiong, Jianghong; Mao, Mao; Chung, Hyun Cheol; Zheng, Guangjuan

    2016-04-01

    Human epidermal growth factor receptor 2 (HER2) is a key driver of tumorigenesis, and over-expression as a result of HER2 gene amplification has been observed in a number of solid tumors. Recently HER2 has become an important biomarker for the monoclonal antibody treatment of HER2-positive metastatic breast and advanced gastric cancer. The HER2 targeting antibody trastuzumab treatment requires accurate measurement of HER2 levels for proper diagnosis. Droplet digital PCR (ddPCR) with highly direct, precise and absolute nucleic acid quantification could be used to detect HER2 amplification levels. Our objective was to evaluate a robust, accurate and less subjective application of ddPCR for HER2 amplification levels and test the assay performance in clinical formalin-fixed paraffin-embedded (FFPE) breast and gastric carcinoma samples. Genomic DNA from HER2 amplified cell line SK-BR-3 was used to set up the ddPCR assays. The copy number of HER2 was compared to the chromosome 17 centromere reference gene (CEP17), expressed as HER2:CEP17 ratio. Genomic DNAs of FFPE specimens from 145 Asian patients with breast and gastric carcinomas were assayed using both standard methods, immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH), and ddPCR. Based on 145 clinical breast and gastric carcinoma cases, our study demonstrated a high concordance of ddPCR results to FISH and IHC. In breast cancer specimens, the ddPCR results had high concordance with FISH and IHC defined HER2 status with a sensitivity of 90.9% (30/33) and a specificity of 100% (77/77). In gastric cancer specimens that were concordant in both FISH and IHC, our assay was 95.5% concordant with FISH and IHC (21/22). ddPCR has the advantage of automation and also allows levels of HER2 amplification to be easily evaluated in large numbers of samples, and presents a potential option to define HER2 status. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Evaluation of different tissue de-paraffinization procedures for infrared spectral imaging.

    Science.gov (United States)

    Nallala, Jayakrupakar; Lloyd, Gavin Rhys; Stone, Nicholas

    2015-04-07

    In infrared spectral histopathology, paraffin embedded tissues are often de-paraffinized using chemical agents such as xylene and hexane. These chemicals are known to be toxic and the routine de-waxing procedure is time consuming. A comparative study was carried out to identify alternate de-paraffinization methods by using paraffin oil and electronic de-paraffinization (using a mathematical computer algorithm) and their effectiveness was compared to xylene and hexane. Sixteen adjacent tissue sections obtained from a single block of a normal colon tissue were de-paraffinized using xylene, hexane and paraffin oil (+ hexane wash) at five different time points each for comparison. One section was reserved unprocessed for electronic de-paraffinization based on a modified extended multiplicative signal correction (EMSC). IR imaging was carried out on these tissue sections. Coefficients based on the fit of a pure paraffin model to the IR images were then calculated to estimate the amount of paraffin remaining after processing. Results indicate that on average xylene removes more paraffin in comparison to hexane and paraffin oil although the differences were small. This makes paraffin oil, followed by a hexane wash, an interesting and less toxic alternative method of de-paraffinization. However, none of the chemical methods removed paraffin completely from the tissues at any given time point. Moreover, paraffin was removed more easily from the glandular regions than the connective tissue regions indicating a form of differential paraffin retention based on the histology. In such cases, the use of electronic de-paraffinization to neutralize such variances across different tissue regions might be considered. Moreover it is faster, reduces scatter artefacts by index matching and enables samples to be easily stored for further analysis if required.

  12. Detection of SYT-SSX mutant transcripts in formalin-fixed paraffin-embedded sarcoma tissues using one-step reverse transcriptase real-time PCR.

    Science.gov (United States)

    Norlelawati, A T; Mohd Danial, G; Nora, H; Nadia, O; Zatur Rawihah, K; Nor Zamzila, A; Naznin, M

    2016-04-01

    Synovial sarcoma (SS) is a rare cancer and accounts for 5-10% of adult soft tissue sarcomas. Making an accurate diagnosis is difficult due to the overlapping histological features of SS with other types of sarcomas and the non-specific immunohistochemistry profile findings. Molecular testing is thus considered necessary to confirm the diagnosis since more than 90% of SS cases carry the transcript of t(X;18)(p11.2;q11.2). The purpose of this study is to diagnose SS at molecular level by testing for t(X;18) fusion-transcript expression through One-step reverse transcriptase real-time Polymerase Chain Reaction (PCR). Formalin-fixed paraffin-embedded tissue blocks of 23 cases of soft tissue sarcomas, which included 5 and 8 cases reported as SS as the primary diagnosis and differential diagnosis respectively, were retrieved from the Department of Pathology, Tengku Ampuan Afzan Hospital, Kuantan, Pahang. RNA was purified from the tissue block sections and then subjected to One-step reverse transcriptase real-time PCR using sequence specific hydrolysis probes for simultaneous detection of either SYT-SSX1 or SYT-SSX2 fusion transcript. Of the 23 cases, 4 cases were found to be positive for SYT-SSX fusion transcript in which 2 were diagnosed as SS whereas in the 2 other cases, SS was the differential diagnosis. Three cases were excluded due to failure of both amplification assays SYT-SSX and control β-2-microglobulin. The remaining 16 cases were negative for the fusion transcript. This study has shown that the application of One-Step reverse transcriptase real time PCR for the detection SYT-SSX transcript is feasible as an aid in confirming the diagnosis of synovial sarcoma.

  13. Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay.

    Science.gov (United States)

    Cronin, Maureen; Pho, Mylan; Dutta, Debjani; Stephans, James C; Shak, Steven; Kiefer, Michael C; Esteban, Jose M; Baker, Joffre B

    2004-01-01

    Throughout the last decade many laboratories have shown that mRNA levels in formalin-fixed and paraffin-embedded (FPE) tissue specimens can be quantified by reverse transcriptase-polymerase chain reaction (RT-PCR) techniques despite the extensive RNA fragmentation that occurs in tissues so preserved. We have developed RT-PCR methods that are sensitive, precise, and that have multianalyte capability for potential wide use in clinical research and diagnostic assays. Here it is shown that the extent of fragmentation of extracted FPE tissue RNA significantly increases with archive storage time. Probe and primer sets for RT-PCR assays based on amplicons that are both short and homogeneous in length enable effective reference gene-based data normalization for cross comparison of specimens that differ substantially in age. A 48-gene assay used to compare gene expression profiles from the same breast cancer tissue that had been either frozen or FPE showed very similar profiles after reference gene-based normalization. A 92-gene assay, using RNA extracted from three 10- micro m FPE sections of archival breast cancer specimens (dating from 1985 to 2001) yielded analyzable data for these genes in all 62 tested specimens. The results were substantially concordant when estrogen receptor, progesterone receptor, and HER2 receptor status determined by RT-PCR was compared with immunohistochemistry assays for these receptors. Furthermore, the results highlight the advantages of RT-PCR over immunohistochemistry with respect to quantitation and dynamic range. These findings support the development of RT-PCR analysis of FPE tissue RNA as a platform for multianalyte clinical diagnostic tests.

  14. Multiplex polymerase chain reaction for the detection of high-risk-human papillomavirus types in formalin-fixed paraffin-embedded cervical tissues

    Directory of Open Access Journals (Sweden)

    Mini P Singh

    2017-01-01

    Full Text Available Detecting high-risk-human papillomavirus (HPV types has become an integral part of the cervical cancer screening programmes. This study aimed to develop a multiplex polymerase chain reaction (PCR for identification of HPV types 16 and 18 along with the beta globin gene in formalin-fixed and paraffin-embedded cervical biopsy specimens. A total of 59 samples from patients with cervical abnormalities were tested. HPV 16 positivity was 50% in cervical cancers and 52.9% in cervical intraepithelial neoplasia. Our multiplex PCR protocol can be used as a simple and cost-effective tool for high-risk-HPV detection in cervical cancer screening programmes.

  15. Comparative investigations of T cell receptor gamma gene rearrangements in frozen and formalin-fixed paraffin wax-embedded tissues by capillary electrophoresis

    DEFF Research Database (Denmark)

    Christensen, M; Funder, A D; Bendix, K

    2006-01-01

    AIM: To compare clonal T cell receptor gamma (TCRgamma) gene rearrangements in frozen and formalin-fixed paraffin wax-embedded (FFPE) tissue, using capillary electrophoresis for use in diagnostics, as T cell lymphomas may be difficult to diagnose by conventional methods.METHODS: The DNA for PCR......% for patient specimens and the specificity 100%. The junctional region between the Vgamma and Jgamma segments was specific for each patient.CONCLUSIONS: Capillary electrophoresis of PCR products from frozen and FFPE tissue is suitable for detecting clonal TCRgamma gene rearrangements. It is important, however...

  16. Characterization of Melanin Radicals in Paraffin-embedded Malignant Melanoma and Nevus Pigmentosus Using X-band EPR and EPR Imaging.

    Science.gov (United States)

    Nakagawa, Kouichi; Minakawa, Satoko; Sawamura, Daisuke; Hara, Hideyuki

    2017-01-01

    Continuous wave electron paramagnetic resonance (CW EPR) and X-band (9 GHz) EPR imaging (EPRI) were used to nondestructively investigate the possible differentiation between malignant melanoma (MM) and nevus pigmentosus (NP) melanin radicals in paraffin-embedded specimens. The EPR spectra of both samples were analyzed using linewidth, spectral pattern, and X-band EPRI. The CW-EPR spectra of the MM showed an additional signal overlap. Eumelanin- and pheomelanin-related radicals were observed in the MM specimens. The EPR results revealed that the peak-to-peak linewidths (ΔH pp ) of paraffin-embedded MM and NP samples were 0.65 ± 0.01 and 0.69 ± 0.01 mT, respectively. The g-value was 2.005 for both samples. Moreover, the two-dimensional (2D) EPRI of the MM showed different signal intensities at the different tumor stages, unlike the NP, which displayed fewer variations in signal intensity. Thus, the present results suggest that EPR and 2D EPRI can be useful for characterization of the two melanin radicals in the MM and for determination of their size and concentration.

  17. Genetic Characterization of Echinococcus granulosus from a Large Number of Formalin-Fixed, Paraffin-Embedded Tissue Samples of Human Isolates in Iran

    Science.gov (United States)

    Rostami, Sima; Torbaghan, Shams Shariat; Dabiri, Shahriar; Babaei, Zahra; Mohammadi, Mohammad Ali; Sharbatkhori, Mitra; Harandi, Majid Fasihi

    2015-01-01

    Cystic echinococcosis (CE), caused by the larval stage of Echinococcus granulosus, presents an important medical and veterinary problem globally, including that in Iran. Different genotypes of E. granulosus have been reported from human isolates worldwide. This study identifies the genotype of the parasite responsible for human hydatidosis in three provinces of Iran using formalin-fixed paraffin-embedded tissue samples. In this study, 200 formalin-fixed paraffin-embedded tissue samples from human CE cases were collected from Alborz, Tehran, and Kerman provinces. Polymerase chain reaction amplification and sequencing of the partial mitochondrial cytochrome c oxidase subunit 1 gene were performed for genetic characterization of the samples. Phylogenetic analysis of the isolates from this study and reference sequences of different genotypes was done using a maximum likelihood method. In total, 54.4%, 0.8%, 1%, and 40.8% of the samples were identified as the G1, G2, G3, and G6 genotypes, respectively. The findings of the current study confirm the G1 genotype (sheep strain) to be the most prevalent genotype involved in human CE cases in Iran and indicates the high prevalence of the G6 genotype with a high infectivity for humans. Furthermore, this study illustrates the first documented human CE case in Iran infected with the G2 genotype. PMID:25535316

  18. Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins.

    Science.gov (United States)

    Wiśniewski, Jacek R; Duś, Kamila; Mann, Matthias

    2013-04-01

    Archival formalin-fixed and paraffin-embedded clinical samples represent a very diverse source of material for proteomic investigation of diseases, often with follow-up patient information. Here, we describe an analytical workflow for analysis of laser-capture microdissected formalin-fixed and paraffin-embedded samples that allows studying proteomes to a depth of 10 000 proteins per sample. The workflow involves lysis of tissue in SDS-containing buffer, detergent removal, and consecutive digestion of the proteins with two enzymes by the multienzyme digestion filter-aided sample preparation method. Resulting peptides are fractionated by pipette-tip based strong anion exchange into six fractions and analyzed by LC-MS/MS on a bench top quadrupole Orbitrap mass spectrometer. Analysis of the data using the MaxQuant software resulted in the identification of 9502 ± 28 protein groups per a 110 nL sample of microdissected cells from human colonic adenoma. This depth of proteome analysis enables systemic insights into the organization of the adenoma cells and an estimation of the abundances of known biomarkers. It also allows the identification of proteins expressed from tumor suppressors, oncogenes, and other key players in the development and progression of the colorectal cancer. Our proteomic platform can be used for quantitative comparisons between samples representing different stages of diseases and thus can be applied to the discovery of biomarkers or drug targets. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Immunohistochemical detection of PGL-1, LAM, 30 kD and 65 kD antigens in leprosy infected paraffin preserved skin and nerve sections

    NARCIS (Netherlands)

    van den Bos, I. C.; Khanolkar-Young, S.; Das, P. K.; Lockwood, D. N.

    1999-01-01

    A panel of lipid, carbohydrate and protein antibodies were optimized for use in detecting M. leprae antigens in paraffin embedded material. Skin and nerve biopsies from 13 patients across the leprosy spectrum were studied. All antibodies detected antigen in tissues with a BI > 1. Phenolic-glycolipid

  20. Improved clonality detection in B-cell lymphoma using a semi-nested modification of the BIOMED-2 PCR assay for IGH rearrangement: A paraffin-embedded tissue study.

    Science.gov (United States)

    Sakamoto, Yuma; Masaki, Ayako; Aoyama, Satsuki; Han, Shusen; Saida, Kosuke; Fujii, Kana; Takino, Hisashi; Murase, Takayuki; Iida, Shinsuke; Inagaki, Hiroshi

    2017-09-01

    The BIOMED-2 PCR protocol for targeting the IGH gene is widely employed for detecting clonality in B-cell malignancies. Unfortunately, the detection of clonality with this method is not very sensitive when paraffin sections are used as a DNA source. To increase the sensitivity, we devised a semi-nested modification of a JH consensus primer. The clonality detection rates of three assays were compared: the standard BIOMED-2, BIOMED-2 assay followed by BIOMED-2 re-amplification, and BIOMED-2 assay followed by semi-nested BIOMED-2. We tested more than 100 cases using paraffin-embedded tissues of various B-cell lymphomas, and found that the clonality detection rates with the above three assays were 63.9%, 79.6%, and 88.0%, respectively. While BIOMED-2 re-amplification was significantly more sensitive than the standard BIOMED-2, the semi-nested BIOMED-2 was significantly more sensitive than both the standard BIOMED-2 and BIOMED-2 re-amplification. An increase in sensitivity was observed in all lymphoma subtypes examined. In conclusion, tumor clonality may be detected in nearly 90% of B-cell lymphoma cases with semi-nested BIOMED-2. This ancillary assay may be useful when the standard BIOMED-2 fails to detect clonality in histopathologically suspected B-cell lymphomas. © 2017 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

  1. The frequency of p53, Ki67, CD99 and Fli-1 protein expression in paraffin-embedded tissue blocks in Ewing’s sarcoma

    Directory of Open Access Journals (Sweden)

    Bagheri Hossein-Abadi Z

    2011-06-01

    Full Text Available "n Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Arial; mso-bidi-theme-font:minor-bidi;} Background: Ewing sarcoma family tumors (ESFTs are among the most malignant tumors in children and young adults. ESFTs include Ewing sarcoma (ES and peripheral primitive neuroectodermal tumors (pPNETs. As there seemed to be few studies on the molecular biology of ESFTs, we investigated the frequency of CD99, Ki67, p53 and Fli-1 protein expression in 15 Iranian patients with ESFTs. In addition, the correlation between expression rate of these proteins and various clinical factors, including age, sex and survival was computed."n"nMethods: The expression of the aforesaid proteins was studied by immunohisto-chemistry in formalin-fixed and paraffin-embedded blocks of 15 ESFTs specimens. Stained sections were classified according to the percentage of stained tumor cells."n"nResults: The results showed the membrane expression of CD99 protein in all of the specimens. The nuclear expression of Fli-1 protein was observed in 86.7% and the over-expression of p53 nuclear protein was seen in 53.3% of the specimens. The expression rate of Ki67 protein was 60%. Although a significant correlation was not shown between the expression levels of Ki67, p53 or Fli-1 proteins with age, sex or survival of the patients, there was a significant

  2. Implementation of formalin-fixed, paraffin-embedded cell line pellets as high-quality process controls in quality assessment programs for KRAS mutation analysis

    DEFF Research Database (Denmark)

    Dijkstra, Jeroen R; Opdam, Frank J M; Boonyaratanakornkit, Jerry

    2013-01-01

    . We assessed a novel synthetic control for formalin-fixed, paraffin-embedded (FFPE) tumor samples in a blind study conducted within nine laboratories across Europe. We show that FFPE material can, at least in part, mimic clinical samples and we demonstrate this control to be a valuable tool....... For a testing laboratory to become accredited to perform such tests, it is essential that they perform reliability testing, but it has not previously been possible to perform this kind of testing on the complete workflow on a large scale without compromising reproducibility or the mimicry of the control sample...... receptor (EGFR)-targeted therapy with increased progression-free survival only if the tumor does not carry a mutation in KRAS. Many different analytical platforms, both those commercially available and those developed in house, have been used within pathology laboratories to assess KRAS mutational status...

  3. Immunohistochemical detection of VHS virus in paraffin-embedded specimens of rainbow trout (Oncorhynchus mykiss); The influence of primary antibody, fixative, and antigen unmasking on method sensitivity

    DEFF Research Database (Denmark)

    Evensen, O.; Olesen, Niels Jørgen

    1997-01-01

    performed on parallel specimens, and the virus titer (TCID50/ml) was determined. Purified nucleocapsid protein (N-protein) of the virus was incorporated in an artificial antigen substrate (polymerized bovine serum albumin), fixed as described above, and embedded in paraffin wax. Microwave unmasking...... was performed an formalin-, PLP-, and Bouin's fluid-fixed specimens. The presence of virus peptides in situ or N-protein in the artificial antigen substrates was Visualized using an immunohistochemical method based on alkaline phosphatase or peroxidase and one polyclonal and five monoclonal polypeptide......-specific antibodies. VHS virus was identified in situ in specimens with high virus titers (10(7-8) TCID50/ml) regardless of the fixative and without the need of an unmasking procedure. A pronounced masking effect was observed for the cross-linking formalin and PLP fixatives. Regardless of the primary antibodies used...

  4. Ewing’s Sarcoma: An Analysis of miRNA Expression Profiles and Target Genes in Paraffin-Embedded Primary Tumor Tissue

    Directory of Open Access Journals (Sweden)

    Antonina Parafioriti

    2016-04-01

    Full Text Available The molecular mechanism responsible for Ewing’s Sarcoma (ES remains largely unknown. MicroRNAs (miRNAs, a class of small non-coding RNAs able to regulate gene expression, are deregulated in tumors and may serve as a tool for diagnosis and prediction. However, the status of miRNAs in ES has not yet been thoroughly investigated. This study compared global miRNAs expression in paraffin-embedded tumor tissue samples from 20 ES patients, affected by primary untreated tumors, with miRNAs expressed in normal human mesenchymal stromal cells (MSCs by microarray analysis. A miRTarBase database was used to identify the predicted target genes for differentially expressed miRNAs. The miRNAs microarray analysis revealed distinct patterns of miRNAs expression between ES samples and normal MSCs. 58 of the 954 analyzed miRNAs were significantly differentially expressed in ES samples compared to MSCs. Moreover, the qRT-PCR analysis carried out on three selected miRNAs showed that miR-181b, miR-1915 and miR-1275 were significantly aberrantly regulated, confirming the microarray results. Bio-database analysis identified BCL-2 as a bona fide target gene of the miR-21, miR-181a, miR-181b, miR-29a, miR-29b, miR-497, miR-195, miR-let-7a, miR-34a and miR-1915. Using paraffin-embedded tissues from ES patients, this study has identified several potential target miRNAs and one gene that might be considered a novel critical biomarker for ES pathogenesis.

  5. Profiling cancer gene mutations in clinical formalin-fixed, paraffin-embedded colorectal tumor specimens using targeted next-generation sequencing.

    Science.gov (United States)

    Zhang, Liangxuan; Chen, Liangjing; Sah, Sachin; Latham, Gary J; Patel, Rajesh; Song, Qinghua; Koeppen, Hartmut; Tam, Rachel; Schleifman, Erica; Mashhedi, Haider; Chalasani, Sreedevi; Fu, Ling; Sumiyoshi, Teiko; Raja, Rajiv; Forrest, William; Hampton, Garret M; Lackner, Mark R; Hegde, Priti; Jia, Shidong

    2014-04-01

    The success of precision oncology relies on accurate and sensitive molecular profiling. The Ion AmpliSeq Cancer Panel, a targeted enrichment method for next-generation sequencing (NGS) using the Ion Torrent platform, provides a fast, easy, and cost-effective sequencing workflow for detecting genomic "hotspot" regions that are frequently mutated in human cancer genes. Most recently, the U.K. has launched the AmpliSeq sequencing test in its National Health Service. This study aimed to evaluate the clinical application of the AmpliSeq methodology. We used 10 ng of genomic DNA from formalin-fixed, paraffin-embedded human colorectal cancer (CRC) tumor specimens to sequence 46 cancer genes using the AmpliSeq platform. In a validation study, we developed an orthogonal NGS-based resequencing approach (SimpliSeq) to assess the AmpliSeq variant calls. Validated mutational analyses revealed that AmpliSeq was effective in profiling gene mutations, and that the method correctly pinpointed "true-positive" gene mutations with variant frequency >5% and demonstrated high-level molecular heterogeneity in CRC. However, AmpliSeq enrichment and NGS also produced several recurrent "false-positive" calls in clinically druggable oncogenes such as PIK3CA. AmpliSeq provided highly sensitive and quantitative mutation detection for most of the genes on its cancer panel using limited DNA quantities from formalin-fixed, paraffin-embedded samples. For those genes with recurrent "false-positive" variant calls, caution should be used in data interpretation, and orthogonal verification of mutations is recommended for clinical decision making.

  6. In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections

    Science.gov (United States)

    Rust fungi infect a wide range of plant species making them of particular interest to plant pathologists. In order to study the interactions between these important pathogenic fungi and their host plants it is useful to be able to differentiate fungal tissue from plant tissue. This can be accomplish...

  7. Detection of Hepatitis B Virus Antigens in Paraffin-embedded Liver Specimens from the Amazon Region, Brazil

    Directory of Open Access Journals (Sweden)

    Simonetti SRR

    2002-01-01

    Full Text Available Hepatic viscerotomy of paraffin-preserved old specimens, collected in the period from 1934 to 1967, were analyzed by immunohistochemical assays to detect hepatitis B, hepatitis D, dengue and yellow fever virus antigens. The material belongs to the Yellow Fever Collection, Department of Pathology, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil and the cases were diagnosed at that time according to clinical aspects and histopathological findings reporting viral hepatitis, yellow fever, focal necrosis and hepatic atrophy. From the 79 specimens, 69 were collected at the Labrea Region and the other 10 in different other localities in the Amazon Region. The five micra thick histological slices were analyzed for the presence of hepatitis B surface antigen (HBsAg and hepatitis B core antigen (HBcAg by immunoperoxidase technique. An immunofluorescence assay was applied to the detection of hepatitis D, yellow fever and dengue virus antigens. Nine (11.4% histological samples were HBsAg reactive and 5 (6.3% were HBcAg reactive. The oldest reactive sample was from 1934. Viral antigens related to the other pathologies were not detected in this study. Our results confirm that the methodology described may be used to elucidate the aetiology of hepatitis diseases even after a long time of conservation of the specimens.

  8. [Application of Immunohistochemistry and Immunofluorescence Staining in Detection of Phospholipase A2 Receptor on Paraffin Section of Renal Biopsy Tissue].

    Science.gov (United States)

    Dong, Hong-rui; Wang, Yan-yan; Wang, Guo-qin; Sun, Li-jun; Cheng, Hong; Chen, Yi-pu

    2015-10-01

    To evaluate the application of immunohistochemistry and fluorescence staining method in the detection of phospholipase A2 receptor (PLA2R) on paraffin section of renal biopsy tissue,and to find an accurate and fast method for the detection of PLA2R in renal tissue. The PLA2R of 193 cases were detected by immunohistochemical staining,and the antigen was repaired by the method of high pressure cooker (HPC) hot repair plus trypsin repair. The 193 samples including 139 cases of idiopathic membranous nephropathy (IMN), 15 cases of membranous lupus nephritis, 8 cases of hepatitis B virus associated membranous nephropathy, 18 cases of IgA nephropathy, and 13 cases of minimal change diseases. To compare the dyeing effects, 22 paraffin sections of renal biopsy tissue of IMN cases with positive PLA2R were stained by using 4 different. of antigen repairing,which included HPC hot repair, HPC hot repair plus trypsin repair, water bath heat repair, and water bath heat repair plus trypsin repair. To compare the dyeing effects, 15 paraffin sections of renal biopsy tissue of IMN cases with positive PLA2R were stained by using 3 different. of antigen repairing,which included water bath heat repair plus trypsin repair, protease K digestion repair, and pepsin digestion repair. In 193 cases, the positive rate of PLA2R in IMN cases was 90.6% (126/139), and the other 54 patients without IMN were negative. Twenty-two IMN patients were positive for PLA2R by using the HPC heat repair plus trypsin repaire or the water bath heat repair plus trypsin repair;while only a few cases of 22 IMN cases were positive by using the HPC hot repair alone or water bath heat repair alone. Fifteen IMN patients were positive for PLA2R by using water bath heat repair plus trypsin repair,protease K digestion repair,and pepsin digestion repair, but the distribution of positive deposits and the background were different. PLA2R immunohistochemical staining can effectively identify IMN and secondary MN. For

  9. The influence of DNA degradation in formalin-fixed, paraffin-embedded (FFPE) tissue on locus-specific methylation assessment by MS-HRM.

    Science.gov (United States)

    Daugaard, Iben; Kjeldsen, Tina E; Hager, Henrik; Hansen, Lise Lotte; Wojdacz, Tomasz K

    2015-12-01

    Readily accessible formalin-fixed paraffin embedded (FFPE) tissues are a highly valuable source of genetic material for molecular analyses in both research and in vitro diagnostics but frequently genetic material in those samples is highly degraded. With locus-specific methylation changes being widely investigated for use as biomarkers in various aspects of clinical disease management, we aimed to evaluate to what extent standard laboratory procedures can approximate the quality of the DNA extracted from FFPE samples prior to methylation analyses. DNA quality in 107 FFPE non-small cell lung cancer (NSCLC) samples was evaluated using spectrophotometry and gel electrophoresis. Subsequently, the quality assessment results were correlated with the results of locus specific methylation assessment with methylation sensitive high resolution melting (MS-HRM). The correlation of template quality with PCR amplification performance and HRM based methylation detection indicated a significant influence of DNA quality on PCR amplification but not on methylation assessment. In conclusion, standard laboratory procedures fairly well approximate DNA degradation of FFPE samples and DNA degradation does not seem to considerably affect locus-specific methylation assessment by MS-HRM. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Detection of c-myc amplification in formalin-fixed paraffin-embedded tumor tissue by chromogenic in situ hybridization (CISH).

    Science.gov (United States)

    Todorović-Raković, Nataša

    2013-01-01

    In situ hybridization (ISH) allows evaluation of genetic abnormalities, such as changes in chromosome number, chromosome translocations or gene amplifications, by hybridization of tagged DNA (or RNA) probes with complementary DNA (or RNA) sequences in interphase nuclei of target tissue. However, chromogenic in situ hybridization (CISH) is also applicable to formalin-fixed, paraffin-embedded (FFPE) tissues, besides metaphase chromosome spreads. CISH is similar to fluorescent in situ hybridization (FISH) regarding pretreatments and hybridization protocols but differs in the way of visualization. Indeed, CISH signal detection is similar to that used in immunohistochemistry, making use of a peroxidase-based chromogenic reaction instead of fluorescent dyes. In particular, tagged DNA probes are indirectly detected using an enzyme-conjugated antibody targeting the tags. The enzymatic reaction of the chromogenic substrate leads to the formation of strong permanent brown signals that can be visualized by bright-field microscopy at 40 × magnification. The advantage of CISH is that it allows the simultaneous observation of gene amplification and tissue morphology and the slides can be stored for a long time.

  11. Validation of tumor markers in central nervous system germ cell tumors by real-time reverse transcriptase polymerase chain reaction using formalin-fixed paraffin-embedded tissues.

    Science.gov (United States)

    Kim, Dowhan; Lee, Da Hye; Choi, Junjeong; Shim, Kyu Won; Kim, Se Hoon

    2013-01-01

    The therapeutic protocols for treatment of germinomas and non-germinomatous germ cell tumors (NGGCTs) are completely different, so it is important to distinguish pure germinomas from NGGCTs. As it can be difficult to diagnose by morphology alone, immunohisto-chemistry (IHC) has been widely used as an ancillary test to improve diagnostic accuracy. However, IHC has limitations due to the misinterpretation of results or the aberrant loss of immunoreactivity. However, real-time RT-PCR has certain advantages over IHC, including its quantitative nature. The aim of our study was to evaluate the usefulness of real-time RT-PCR on formalin-fixed paraffin-embedded (FFPE) tissue blocks for the diagnosis of germ cell tumors of the central nervous system. We selected eight markers of germ cell tumors using a literature search, and validated them using real-time RT-PCR. Among them, POU5F1, NANOG and TGFB2 were statistically significant (P=0.05) in multiple comparisons (MANOVA) of three groups (pure germinomas, mature teratomas and malignant germ cell tumors). Two-group (pure germinomas and NGGCTs) discriminant analysis achieved a 70.0% success rate in cross-validation. We concluded that real-time RT-PCR using FFPE tissue has adequate validating power comparable to IHC in the diagnosis of central nervous system germ cell tumors; therefore, when IHC is not available, not conclusive or not informative, RT-PCR is a potential alternative to a repeat biopsy.

  12. Trypanosoma cruzi Necrotizing Meningoencephalitis in a Venezuelan HIV+-AIDS Patient: Pathological Diagnosis Confirmed by PCR Using Formalin-Fixed- and Paraffin-Embedded-Tissues

    Directory of Open Access Journals (Sweden)

    Marcello Salvatore Rossi Spadafora

    2014-01-01

    Full Text Available Coinfections with human immunodeficiency virus (HIV and infectious agents have been recognized since the early 90s. In the central nervous system (CNS of HIV+ patients, parasitic protozoans like Toxoplasma gondii have been described as responsible for the space occupying lesions (SOL developed. However, the involvement of Trypanosoma cruzi is also described but appears to be less frequent in acquired immunodeficiency syndrome (AIDS and transplant recipients, associated with necrotizing myocarditis and neurological symptoms related to the occurrence of necrotizing pseudotumoral encephalitis (NPE and meningoencephalitis (NME. The present work aims to present a Venezuelan case of NME associated with the coinfection of HIV and a T. cruzi-like trypanosomatid as well as its evolution and diagnosis by histopathological techniques, electron microscopy, and PCR methods using formalin-fixed- (FF- and paraffin-embedded- (PE- tissues. Postmortem cytological studies of leptomeninges imprints reveal the presence of trypomastigotes of Trypanosoma sp. Histopathological and electron microscopy studies allowed us to identify an amastigote stage and to reject the involvement of other opportunistic microorganisms as the etiological agent of the SOL. The definitive confirmation of T. cruzi as the etiological agent was achieved by PCR suggesting that the NME by T. cruzi was due to a reactivation of Chagas’ disease.

  13. A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay

    Directory of Open Access Journals (Sweden)

    Florenza Lüder Ripoli

    2016-05-01

    Full Text Available Mammary neoplasms are the tumors most affecting female dogs and women. Formalin-fixed, paraffin-embedded (FFPE tissues are an invaluable source of archived biological material. Fresh frozen (FF tissue is considered ideal for gene expression analysis. However, strategies based on FFPE material offer several advantages. Branched-DNA assays permit a reliable and fast workflow when analyzing gene expression. The aim of this study was to assess the comparability of the branched-DNA assay when analyzing certain gene expression patterns between FF and FFPE samples in canine mammary tumors. RNA was isolated from 109 FFPE samples and from 93 FF samples of different canine mammary tissues. Sixteen (16 target genes (Tp53; Myc; HMGA1; Pik3ca; Mcl1; MAPK3; FOXO3; PTEN; GATA4; PFDN5; HMGB1; MAPK1; BRCA2; BRCA1; HMGA2; and Her2 were analyzed via branched-DNA assay (b-DNA. ACTB, GAPDH, and HPRT1 were used as data normalizers. Overall, the relative gene expression of the two different origins of samples showed an agreement of 63%. Still, care should be taken, as FFPE specimens showed lower expression of the analyzed targets when compared to FF samples. The fact that the gene expression in FFPE proved to be lower than in FF specimens is likely to have been caused by the effect of storage time. ACTB had the best performance as a data normalizer.

  14. Development of a monoclonal antibody that specifically detects tissue inhibitor of metalloproteinase-4 (TIMP-4) in formalin-fixed, paraffin-embedded human tissues.

    Science.gov (United States)

    Donover, P Scott; Wojciechowski, Brian S; Thirumaran, Rajesh; Zemba-Palko, Vlasta; Prendergast, George C; Wallon, U Margaretha

    2010-08-01

    Overexpression of the extracellular metalloproteinase inhibitor TIMP-4 in estrogen receptor-negative breast cancers was found recently to be associated with a poor prognosis for survival. To pursue exploration of the theranostic applications of TIMP-4, specific antibodies with favorable properties for immunohistochemical use and other clinical assays are needed. Here we report the characterization of a monoclonal antibody (clone 9:4-7) specific for full-length human TIMP-4 with suitable qualities. The antibody was determined to be an IgG(2b) immunoglobulin. In enzyme-linked immunosorbent assay (ELISA) and immunoblotting assays, it did not exhibit any detectable crossreactivity with recombinant forms of the other human TIMPs 1, 2, and 3. In contrast, the antibody displayed high specificity and sensitivity for TIMP-4 including in formalin-fixed and paraffin-embedded specimens of human breast specimens. An analysis of tissue microarrays of human cancer and corresponding normal tissues revealed specific staining patterns with excellent signal-to-noise ratios. This study documents TIMP-4 monoclonal antibody clone 9:4-7 as an effective tool for preclinical and clinical investigations. Published 2010 Wiley-Liss, Inc.

  15. Multiplexed color-coded probe-based gene expression assessment for clinical molecular diagnostics in formalin-fixed paraffin-embedded human renal allograft tissue.

    Science.gov (United States)

    Adam, Benjamin; Afzali, Bahman; Dominy, Katherine M; Chapman, Erin; Gill, Reeda; Hidalgo, Luis G; Roufosse, Candice; Sis, Banu; Mengel, Michael

    2016-03-01

    Histopathologic diagnoses in transplantation can be improved with molecular testing. Preferably, molecular diagnostics should fit into standard-of-care workflows for transplant biopsies, that is, formalin-fixed paraffin-embedded (FFPE) processing. The NanoString(®) gene expression platform has recently been shown to work with FFPE samples. We aimed to evaluate its methodological robustness and feasibility for gene expression studies in human FFPE renal allograft samples. A literature-derived antibody-mediated rejection (ABMR) 34-gene set, comprised of endothelial, NK cell, and inflammation transcripts, was analyzed in different retrospective biopsy cohorts and showed potential to molecularly discriminate ABMR cases, including FFPE samples. NanoString(®) results were reproducible across a range of RNA input quantities (r = 0.998), with different operators (r = 0.998), and between different reagent lots (r = 0.983). There was moderate correlation between NanoString(®) with FFPE tissue and quantitative reverse transcription polymerase chain reaction (qRT-PCR) with corresponding dedicated fresh-stabilized tissue (r = 0.487). Better overall correlation with histology was observed with NanoString(®) (r = 0.354) than with qRT-PCR (r = 0.146). Our results demonstrate the feasibility of multiplexed gene expression quantification from FFPE renal allograft tissue. This represents a method for prospective and retrospective validation of molecular diagnostics and its adoption in clinical transplantation pathology. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Trypanosoma cruzi Necrotizing Meningoencephalitis in a Venezuelan HIV+-AIDS Patient: Pathological Diagnosis Confirmed by PCR Using Formalin-Fixed- and Paraffin-Embedded-Tissues

    Science.gov (United States)

    Rossi Spadafora, Marcello Salvatore; Céspedes, Ghislaine; Romero, Sandra; Fuentes, Isabel; Boada-Sucre, Alpidio A.; Cañavate, Carmen; Flores-Chávez, María

    2014-01-01

    Coinfections with human immunodeficiency virus (HIV) and infectious agents have been recognized since the early 90s. In the central nervous system (CNS) of HIV+ patients, parasitic protozoans like Toxoplasma gondii have been described as responsible for the space occupying lesions (SOL) developed. However, the involvement of Trypanosoma cruzi is also described but appears to be less frequent in acquired immunodeficiency syndrome (AIDS) and transplant recipients, associated with necrotizing myocarditis and neurological symptoms related to the occurrence of necrotizing pseudotumoral encephalitis (NPE) and meningoencephalitis (NME). The present work aims to present a Venezuelan case of NME associated with the coinfection of HIV and a T. cruzi-like trypanosomatid as well as its evolution and diagnosis by histopathological techniques, electron microscopy, and PCR methods using formalin-fixed- (FF-) and paraffin-embedded- (PE-) tissues. Postmortem cytological studies of leptomeninges imprints reveal the presence of trypomastigotes of Trypanosoma sp. Histopathological and electron microscopy studies allowed us to identify an amastigote stage and to reject the involvement of other opportunistic microorganisms as the etiological agent of the SOL. The definitive confirmation of T. cruzi as the etiological agent was achieved by PCR suggesting that the NME by T. cruzi was due to a reactivation of Chagas' disease. PMID:25763312

  17. Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS: Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE Samples

    Directory of Open Access Journals (Sweden)

    Gladys Arreaza

    2016-09-01

    Full Text Available In cancer drug discovery, it is important to investigate the genetic determinants of response or resistance to cancer therapy as well as factors that contribute to adverse events in the course of clinical trials. Despite the emergence of new technologies and the ability to measure more diverse analytes (e.g., circulating tumor cell (CTC, circulating tumor DNA (ctDNA, etc., tumor tissue is still the most common and reliable source for biomarker investigation. Because of its worldwide use and ability to preserve samples for many decades at ambient temperature, formalin-fixed, paraffin-embedded tumor tissue (FFPE is likely to be the preferred choice for tissue preservation in clinical practice for the foreseeable future. Multiple analyses are routinely performed on the same FFPE samples (such as Immunohistochemistry (IHC, in situ hybridization, RNAseq, DNAseq, TILseq, Methyl-Seq, etc.. Thus, specimen prioritization and optimization of the isolation of analytes is critical to ensure successful completion of each assay. FFPE is notorious for producing suboptimal DNA quality and low DNA yield. However, commercial vendors tend to request higher DNA sample mass than what is actually required for downstream assays, which restricts the breadth of biomarker work that can be performed. We evaluated multiple genomics service laboratories to assess the current state of NGS pre-analytical processing of FFPE. Significant differences in pre-analytical capabilities were observed. Key aspects are highlighted and recommendations are made to improve the current practice in translational research.

  18. A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.

    Directory of Open Access Journals (Sweden)

    Anna Esteve-Codina

    Full Text Available The molecular classification of glioblastoma (GBM based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing platforms is rapidly becoming accepted as a tool for measuring gene expression for both research and clinical use. Fresh frozen (FF tissue specimens of GBM are difficult to obtain since tumor tissue obtained at surgery is often scarce and necrotic and diagnosis is prioritized over freezing. After diagnosis, leftover tissue is usually stored as formalin-fixed paraffin-embedded (FFPE tissue. However, RNA from FFPE tissues is usually degraded, which could hamper gene expression analysis. We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. Only three FFPE out of eleven FFPE-FF matched samples yielded informative results. Several quality-control measurements showed that RNA from FFPE samples was highly degraded but maintained transcriptomic similarities to RNA from FF samples. Certain issues regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data that can be used in molecular studies of GBM if the RNA is sufficiently preserved.

  19. A rapid technique for analysis of formalin-fixed, paraffin-embedded tissues by fluorescent in situ hybridization with alpha-satellite probes

    Directory of Open Access Journals (Sweden)

    Nilce Barril

    1998-12-01

    Full Text Available We describe a rapid procedure for preparing archival tissues for interphase FISH analysis. The present protocol differs from others previously described because it allows the obtention of nuclei in satisfactory number and quality without using special equipments, adhesive-treated slides or solutions for chromatin decondensation. The method is of low cost and useful for retrospective analyses of formalin-fixed, paraffin-embedded samples.Descrevemos aqui um procedimento rápido para obtenção de núcleos interfásicos a partir de amostras arquivadas que podem ser utilizados para análise citogenética através da técnica de FISH. Este procedimento difere de outros previamente descritos porque permite a obtenção de núcleos em número e qualidade satisfatórios sem a utilização de equipamentos ou lâminas especiais e soluções para descondensação da cromatina. O método é de baixo custo e possibilita estudos retrospectivos de tecidos fixados em formol e emblocados em parafina.

  20. Utility of the Roche Cobas 4800 for detection of high-risk human papillomavirus in formalin-fixed paraffin-embedded oropharyngeal squamous cell carcinoma.

    Science.gov (United States)

    Pettus, Jason R; Wilson, Terri L; Steinmetz, Heather B; Lefferts, Joel A; Tafe, Laura J

    2017-02-01

    Clinical laboratories are expected to reliably identify human papilloma virus (HPV) associated oropharyngeal squamous cell carcinoma (OPSCC) for prognostic and potential therapeutic applications. In addition to surrogate p16 immunohistochemistry (IHC) testing, DNA-based HPV-specific testing strategies are widely utilized. Recognizing the efficiency of the Roche Cobas 4800 platform for testing gynecological cytology specimens for high-risk HPV, we elected to evaluate the potential utility of this platform for testing formalin-fixed paraffin-embedded (FFPE) OPSCC tissue. Using the Roche Linear Array assay for comparison, we tested twenty-eight samples (16 primary OPSCC, 2 lymph node metastases from primary OPSCC, 1 oral tongue carcinoma, 3 benign squamous papillomas, and 3 non-oropharyngeal carcinoma tissues). Excluding two invalid results, the Roche Cobas 4800 testing resulted in excellent inter-assay concordance (25/26, 96.2%) and 100% concordance for HPV-16/HPV-18 positive samples. This data suggests that the Roche Cobas 4800 platform may be a cost-effective method for testing OPSCC FFPE tissues in a clinical molecular pathology laboratory setting. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. PCR-based clonality analysis of B-cell lymphomas in paraffin-embedded tissues: diagnostic value of immunoglobulin kappa and lambda light chain gene rearrangement investigation.

    Science.gov (United States)

    Amara, Khaled; Trimeche, Mounir; Ziadi, Sonia; Sriha, Badreddine; Mokni, Moncef; Korbi, Sadok

    2006-01-01

    Polymerase chain reaction (PCR)-based analysis, employed for detecting immunoglobulin heavy chain (IgH) gene rearrangements, has become a diagnostic tool widely used in the investigation of B-cell lymphomas, but the overall sensitivity of these methods does not exceed 80%, notably in germinal center (GC) and post-GC B-cell origin lymphomas. Many PCR strategies devised for detecting immunoglobulin light chain (IgL) gene rearrangements have been developed to enhance the clonality detection rates. However, the feasibility of these methods in routine clinical diagnosis using paraffin-embedded tissues has not yet been investigated sufficiently. We studied a large series of 108 cases of B-cell lymphomas, as well as 20 reactive lymphoid tissues using degenerate primers to amplify immunoglobulin kappa (Igkappa) and lambda (Iglambda) light chain genes. B-cell clonality was further investigated using semi-nested PCR for IgH gene rearrangements. B-cell clonality was detected in 74%, 56.5%, and 43.5% of cases using IgH, Igkappa, and Iglambda PCR, respectively. By combining these methods, the clonality detection rate increased to 93.5%. Only polyclonal patterns were noted in reactive lymphoid samples. We concluded that in addition to the established methods for IgH analysis, a PCR-based approach for IgL gene rearrangements analysis improves the clonality detection rate in over 90% of B-cell lymphoma cases using routine histological specimens with poor preservation of the genomic DNA.

  2. Determination of the cell tropism of serotype 1 feline infectious peritonitis virus using the spike affinity histochemistry in paraffin-embedded tissues.

    Science.gov (United States)

    Cham, Tat-Chuan; Chang, Yen-Chen; Tsai, Pei-Shiue; Wu, Ching-Ho; Chen, Hui-Wen; Jeng, Chian-Ren; Pang, Victor Fei; Chang, Hui-Wen

    2017-08-01

    Unlike for serotype II feline coronaviruses (FCoV II), the cellular receptor for serotype I FCoV (FCoV I), the most prevalent FCoV serotype, is unknown. To provide a platform for assessing the pattern by which FCoV I attaches to its host receptor(s), HEK293 cell lines that stably express the ectodomains of the spike (S) proteins derived from a FCoV I feline enteric coronavirus strain UU7 (FECV UU7) and a feline infectious peritonitis virus strain UU4 (FIPV UU4) were established. Using the recombinant S proteins as probes to perform S protein affinity histochemistry in paraffin-embedded tissues, although no tissue or enteric binding of FECV UU7 S protein was detected, it was found that by immunohistochemistry that the tissue distribution of FIPV UU4 S protein-bound cells correlated with that of FIPV antigen-positive cells and lesions associated with FIP and that the affinity binding of FIPV UU4 S protein on macrophages was not affected by enzymatic removal of host cell-surface sialic acid with neuraminidase. These findings suggest that a factor(s) other than sialic acid contribute(s) to the macrophage tropism of FIPV strain UU4. This approach allowed obtaining more information about both virus-host cell interactions and the biological characteristics of the unidentified cellular receptor for FCoV I. © 2017 The Societies and John Wiley & Sons Australia, Ltd.

  3. Molecular glycopathology by capillary electrophoresis: Analysis of the N-glycome of formalin-fixed paraffin-embedded mouse tissue samples.

    Science.gov (United States)

    Donczo, Boglarka; Szarka, Mate; Tovari, Jozsef; Ostoros, Gyorgyi; Csanky, Eszter; Guttman, Andras

    2017-06-01

    Capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection was used to analyze endoglycosidase released and fluorophore-labeled N-glycans from formalin-fixed paraffin-embedded (FFPE) mouse tissue samples of lung, brain, heart, spleen, liver, kidney and intestine. The FFPE samples were first deparaffinized followed by solubilization and glycoprotein retrieval. PNGase F mediated release of the N-linked oligosaccharides was followed by labeling with aminopyrene trisulfonate. After CE-LIF glycoprofiling of the FFPE mouse tissues, the N-glycan pool of the lung specimen was subject to further investigation by exoglycosidase array based carbohydrate sequencing. Structural assignment of the oligosaccharides was accomplished by the help of the GUcal software and the associated database, based on the mobility shifts after treatments with the corresponding exoglycosidase reaction mixtures. Sixteen major N-linked carbohydrate structures were sequenced from the mouse lung FFPE tissue glycome and identified, as high mannose (3) neutral biantennary (3) sialylated monoantennary (1) and sialylated bianennary (9) oligosaccharides. Two of these latter ones also possessed alpha(1-3) linked galactose residues. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Label-free protein profiling of formalin-fixed paraffin-embedded (FFPE) heart tissue reveals immediate mitochondrial impairment after ionising radiation.

    Science.gov (United States)

    Azimzadeh, Omid; Scherthan, Harry; Yentrapalli, Ramesh; Barjaktarovic, Zarko; Ueffing, Marius; Conrad, Marcus; Neff, Frauke; Calzada-Wack, Julia; Aubele, Michaela; Buske, Christian; Atkinson, Michael J; Hauck, Stefanie M; Tapio, Soile

    2012-04-18

    Qualitative proteome profiling of formalin-fixed, paraffin-embedded (FFPE) tissue is advancing the field of clinical proteomics. However, quantitative proteome analysis of FFPE tissue is hampered by the lack of an efficient labelling method. The usage of conventional protein labelling on FFPE tissue has turned out to be inefficient. Classical labelling targets lysine residues that are blocked by the formalin treatment. The aim of this study was to establish a quantitative proteomics analysis of FFPE tissue by combining the label-free approach with optimised protein extraction and separation conditions. As a model system we used FFPE heart tissue of control and exposed C57BL/6 mice after total body irradiation using a gamma ray dose of 3 gray. We identified 32 deregulated proteins (p≤0.05) in irradiated hearts 24h after the exposure. The proteomics data were further evaluated and validated by bioinformatics and immunoblotting investigation. In good agreement with our previous results using fresh-frozen tissue, the analysis indicated radiation-induced alterations in three main biological pathways: respiratory chain, lipid metabolism and pyruvate metabolism. The label-free approach enables the quantitative measurement of radiation-induced alterations in FFPE tissue and facilitates retrospective biomarker identification using clinical archives. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. MicroRNA expression in melanocytic nevi: the usefulness of formalin-fixed, paraffin-embedded material for miRNA microarray profiling.

    Science.gov (United States)

    Glud, Martin; Klausen, Mikkel; Gniadecki, Robert; Rossing, Maria; Hastrup, Nina; Nielsen, Finn C; Drzewiecki, Krzysztof T

    2009-05-01

    MicroRNAs (miRNAs) are small, noncoding RNA molecules that regulate cellular differentiation, proliferation, and apoptosis. MiRNAs are expressed in a developmentally regulated and tissue-specific manner. Aberrant expression may contribute to pathological processes such as cancer, and miRNA may therefore serve as biomarkers that may be useful in a clinical environment for diagnosis of various diseases. Most miRNA profiling studies have used fresh tissue samples. However, in some types of cancer, including malignant melanoma, fresh material is difficult to obtain from primary tumors, and most surgical specimens are formalin fixed and paraffin embedded (FFPE). To explore whether FFPE material would be suitable for miRNA profiling in melanocytic lesions, we compared miRNA expression patterns in FFPE versus fresh frozen samples, obtained from 15 human melanocytic nevi. Out of microarray data, we identified 84 miRNAs that were expressed in both types of samples and represented an miRNA profile of melanocytic nevi. Our results showed a high correlation in miRNA expression (Spearman r-value of 0.80) between paired FFPE and fresh frozen material. The data were further validated by quantitative RT-PCR. In conclusion, FFPE specimens of melanocytic lesions are suitable as a source for miRNA microarray profiling.

  6. Characterization of a Novel Anti-Human HB-EGF Monoclonal Antibody Applicable for Paraffin-Embedded Tissues and Diagnosis of HB-EGF-Related Cancers.

    Science.gov (United States)

    Iwamoto, Ryo; Takagi, Mika; Akatsuka, Jun-Ichi; Ono, Ken-Ichiro; Kishi, Yoshiro; Mekada, Eisuke

    2016-04-01

    Heparin-binding EGF-like growth factor (HB-EGF) is a member of the EGF family of growth factors that bind to and activate the EGF receptor (EGFR/ErbB1) and ErbB4. HB-EGF plays pivotal roles in pathophysiological processes, including cancer. Thus, monoclonal antibodies (mAbs) for HB-EGF detection could be an important tool in the therapeutic diagnosis of HB-EGF-related cancers and other diseases. However, few mAbs, especially those applicable for immunohistochemistry (IHC), have been established to date. In this study, we generated a clone of hybridoma-derived mAb 2-108 by immunizing mice with recombinant human HB-EGF protein expressed by human cells. The mAb 2-108 specifically bound to human HB-EGF but not to mouse HB-EGF and was successful in immunoblotting, even under reducing conditions, immunoprecipitation, and immunofluorescence for unfixed as well as paraformaldehyde-fixed cells. Notably, this mAb was effective in IHC of paraffin-embedded tumor specimens. Epitope mapping analysis showed that mAb 2-108 recognized the N-terminal prodomain in HB-EGF. These results indicate that this new anti-HB-EGF mAb 2-108 would be useful in the diagnosis of HB-EGF-related cancers and would be a strong tool in both basic and clinical research on HB-EGF.

  7. Scores for standardization of on-tissue digestion of formalin-fixed paraffin-embedded tissue in MALDI-MS imaging.

    Science.gov (United States)

    Erich, Katrin; Sammour, Denis A; Marx, Alexander; Hopf, Carsten

    2017-07-01

    On-slide digestion of formalin-fixed and paraffin-embedded human biopsy tissue followed by mass spectrometry imaging of resulting peptides may have the potential to become an additional analytical modality in future ePathology. Multiple workflows have been described for dewaxing, antigen retrieval, digestion and imaging in the past decade. However, little is known about suitable statistical scores for method comparison and systematic workflow standardization required for development of processes that would be robust enough to be compatible with clinical routine. To define scores for homogeneity of tissue processing and imaging as well as inter-day repeatability for five different processing methods, we used human liver and gastrointestinal stromal tumor tissue, both judged by an expert pathologist to be >98% histologically homogeneous. For mean spectra-based as well as pixel-wise data analysis, we propose the coefficient of determination R 2 , the natural fold-change (natFC) value and the digest efficiency DE% as readily accessible scores. Moreover, we introduce two scores derived from principal component analysis, the variance of the mean absolute deviation, MAD, and the interclass overlap, J overlap , as computational scores that may help to avoid user bias during future workflow development. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. [Use of archival formalin-fixed, paraffin-embedded (FFPE) tissue samples for molecular genetic analysis in diffuse large B-cell lymphoma (DLBCL)].

    Science.gov (United States)

    Jarošová, Marie; Kučerová, Jana; Flodr, Patrik; Mikešová, Michaela; Procházka, Vít; Papajík, Tomáš

    2014-04-01

    The currently valid molecular genetic subclassification of patients with diffuse large B-cell lymphoma (DLBCL) into three prognostic subgroups based on expression profiling has been the objective of numerous genetic studies. In routine clinical practice, however, expression profiling technology remains unavailable for the most of centers. Apart from the technology, in some cases molecular genetic laboratories have problems obtaining high-quality material, i.e. fresh tissues, for RNA isolation to determine gene expression. One possibility is to determine the gene expression from RNA obtained by isolation from formalin-fixed, paraffin-embedded (FFPE) tissue. This pilot study aimed at isolating RNA from FFPE in patients diagnosed with DLBCL and verifying the potential use of such RNA for the expression analysis of 7 selected genes. Although the study showed that it is possible to isolate RNA and determine the expression of the selected genes from archival material, the values of relative expression of some genes in the set were too variable to be used for unambiguous prognostic classification. It was confirmed that retrospective analyses of selected genes may be performed with sufficient material obtained, and that properly archived blocks may be used for molecular biology analyses even after 8 years.

  9. Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis.

    Science.gov (United States)

    Mubemba, B; Thompson, P N; Odendaal, L; Coetzee, P; Venter, E H

    2017-05-01

    Rift Valley fever (RVF), caused by an arthropod borne Phlebovirus in the family Bunyaviridae, is a haemorrhagic disease that affects ruminants and humans. Due to the zoonotic nature of the virus, a biosafety level 3 laboratory is required for isolation of the virus. Fresh and frozen samples are the preferred sample type for isolation and acquisition of sequence data. However, these samples are scarce in addition to posing a health risk to laboratory personnel. Archived formalin-fixed, paraffin-embedded (FFPE) tissue samples are safe and readily available, however FFPE derived RNA is in most cases degraded and cross-linked in peptide bonds and it is unknown whether the sample type would be suitable as reference material for retrospective phylogenetic studies. A RT-PCR assay targeting a 490 nt portion of the structural G N glycoprotein encoding gene of the RVFV M-segment was applied to total RNA extracted from archived RVFV positive FFPE samples. Several attempts to obtain target amplicons were unsuccessful. FFPE samples were then analysed using next generation sequencing (NGS), i.e. Truseq ® (Illumina) and sequenced on the Miseq ® genome analyser (Illumina). Using reference mapping, gapped virus sequence data of varying degrees of shallow depth was aligned to a reference sequence. However, the NGS did not yield long enough contigs that consistently covered the same genome regions in all samples to allow phylogenetic analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples

    Directory of Open Access Journals (Sweden)

    Reis Patricia P

    2010-06-01

    Full Text Available Abstract Background MicroRNAs (miRs are non-coding RNA molecules involved in post-transcriptional regulation, with diverse functions in tissue development, differentiation, cell proliferation and apoptosis. miRs may be less prone to degradation during formalin fixation, facilitating miR expression studies in formalin-fixed paraffin-embedded (FFPE tissue. Results Our study demonstrates that the TaqMan Human MicroRNA Array v1.0 (Early Access platform is suitable for miR expression analysis in FFPE tissue with a high reproducibility (correlation coefficients of 0.95 between duplicates, p 35, we show that reproducibility between technical replicates, equivalent dilutions, and FFPE vs. frozen samples is best in the high abundance stratum. We also demonstrate that the miR expression profiles of FFPE samples are comparable to those of fresh-frozen samples, with a correlation of up to 0.87 (p Conclusion Our study thus demonstrates the utility, reproducibility, and optimization steps needed in miR expression studies using FFPE samples on a high-throughput quantitative PCR-based miR platform, opening up a realm of research possibilities for retrospective studies.

  11. Integrated and convenient procedure for protein extraction from formalin-fixed, paraffin-embedded tissues for LC-MS/MS analysis.

    Science.gov (United States)

    Lai, Xianyin; Schneider, Bryan P

    2014-11-01

    Because fresh-frozen tissue samples associated with long-term clinical data and of rare diseases are often unobtainable at the present time, formalin-fixed paraffin-embedded (FFPE) tissue samples are considered a highly valuable resource for researchers. However, protein extraction from FFPE tissues faces challenges of deparaffinization and cross-link reversion. Current procedures for protein extraction from FFPE tissue require separate steps and toxic solvents, resulting in inconvenience in protein extraction. To overcome these limitations, an integrated method was developed using nontoxic solvents in four types of FFPE tissues. The average amount of proteins from three replicates of bladder, kidney, liver, and lung FFPE tissues were 442.6, 728.9, 736.4, and 694.7 μg with CVs of 7.5, 5.8, 2.4, and 4.5%, respectively. Proteomic analysis showed that 348, 417, 607, and 304 unique proteins were identified and quantified without specification of isoform by a least two peptides from bladder, kidney, liver, and lung FFPE tissue samples, respectively. The analysis of individual protein CV demonstrated that 97-99% of the proteins were quantified with a CV ≤ 30%, verifying the reproducibility of the integrated protein extraction method. In summary, the developed method is high-yield, reproducible, convenient, simple, low cost, nonvolatile, nonflammable, and nontoxic. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Stereological comparison of oocyte recruitment and batch fecundity estimates from paraffin and resin sections using spawning albacore (Thunnus alalunga) ovaries as a case study

    Science.gov (United States)

    Saber, Sámar; Macías, David; Ortiz de Urbina, Josetxu; Kjesbu, Olav Sigurd

    2015-01-01

    Traditional histological protocols in marine fish reproductive laboratories using paraffin as the embedding medium are now increasingly being replaced with protocols using resin instead. These procedures entail different degrees of tissue shrinkage complicating direct comparisons of measurement results across laboratories or articles. In this work we selected ovaries of spawning Mediterranean albacore (Thunnus alalunga) as the subject of our study to address the issue of structural changes, by contrasting values on oocyte recruitment and final batch fecundity given from the same tissue samples in both paraffin and resin. A modern stereological method, the oocyte packing density (OPD) theory, was used supported by initial studies on ovarian tissue sampling and measurement design. Examples of differences in the volume fraction of oocyte stages, free space and connective tissue were found between the embedding media. Mean oocyte diameters were smaller in paraffin than in resin with differences ranging between 0.5% in primary growth and 24.3% in hydration (HYD) stage oocytes. Fresh oocyte measurements showed that oocytes shrank as a consequence of the embedding process, reaching the maximal degree of shrinkage for oocytes in the HYD stage (45.8% in paraffin and 26.5% in resin). In order to assess the effect of oocyte shrinkage on the OPD result, and thereby on relative batch fecundity (Fr), oocyte diameters corrected and uncorrected for shrinkage, were used for estimations. Statistical significant differences were found (P based on either oocytes in the germinal vesicle migration stage or HYD stage. As a valuable adjunct, the present use of the OPD theory made it possible to document that the oocyte recruitment of spawning ovaries of Mediterranean albacore followed the typical pattern of an asynchronous oocyte development and indeterminate fecundity.

  13. Automated Extraction of Formalin-Fixed, Paraffin-Embedded Tissue for High-Risk Human Papillomavirus Testing of Head and Neck Squamous Cell Carcinomas Using the Roche Cobas 4800 System.

    Science.gov (United States)

    Kerr, Darcy A; Sweeney, Brenda; Arpin, Ronald N; Ring, Melissa; Pitman, Martha B; Wilbur, David C; Faquin, William C

    2016-08-01

    -Testing for high-risk human papillomavirus (HR-HPV) in head and neck squamous cell carcinomas (HNSCCs) is important for both prognostication and clinical management. Several testing platforms are available for HR-HPV; however, effective alternative automated approaches are needed. -To assess the performance of the automated Roche cobas 4800 HPV real-time polymerase chain reaction-based system on formalin-fixed, paraffin-embedded HNSCC specimens and compare results with standard methods of in situ hybridization (ISH) and p16 immunohistochemistry. -Formalin-fixed, paraffin-embedded samples of HNSCC were collected from archival specimens in the Department of Pathology, Massachusetts General Hospital (Boston), and prepared using the automated system by deparaffinization and dehydration followed by tissue lysis. Samples were integrated into routine cervical cytology testing runs by cobas. Corresponding formalin-fixed, paraffin-embedded samples were evaluated for HR-HPV by ISH and p16 by immunohistochemistry. Discrepant cases were adjudicated by polymerase chain reaction. -Sixty-two HNSCC samples were analyzed using the automated cobas system, ISH, and immunohistochemistry. Fifty-two percent (n = 32 of 62) of formalin-fixed, paraffin-embedded tumors were positive for HR-HPV by cobas. Eighty-eight percent (n = 28 of 32) of cases were the HPV 16 subtype and 12% (n = 4 of 32) were other HR-HPV subtypes. Corresponding testing with ISH was concordant in 92% (n = 57 of 62) of cases. Compared with the adjudication polymerase chain reaction standard, there were 3 false-positive cases by cobas. -Concordance in HNSCC HR-HPV status between cobas and ISH was more than 90%. The cobas demonstrated a sensitivity of 100% and a specificity of 91% for detection of HR-HPV. Advantages favoring cobas include its automation, cost efficiency, objective results, and ease of performance.

  14. Detection of a putative novel adenovirus by PCR amplification, sequencing and phylogenetic characterisation of two gene fragments from formalin-fixed paraffin-embedded tissues of a cat diagnosed with disseminated adenovirus disease.

    Science.gov (United States)

    Lakatos, Béla; Hornyák, Ákos; Demeter, Zoltán; Forgách, Petra; Kennedy, Frances; Rusvai, Miklós

    2017-12-01

    Adenoviral nucleic acid was detected by polymerase chain reaction (PCR) in formalin-fixed paraffin-embedded tissue samples of a cat that had suffered from disseminated adenovirus infection. The identity of the amplified products from the hexon and DNA-dependent DNA polymerase genes was confirmed by DNA sequencing. The sequences were clearly distinguishable from corresponding hexon and polymerase sequences of other mastadenoviruses, including human adenoviruses. These results suggest the possible existence of a distinct feline adenovirus.

  15. Antibody validation and scoring guidelines for ABCG2 immunohistochemical staining in formalin-fixed paraffin-embedded colon cancer tissue

    DEFF Research Database (Denmark)

    Cederbye, Camilla Natasha; Palshof, Jesper Andreas; Hansen, Tine Plato

    2016-01-01

    cancer (CRC), probably because of the use of different antibodies and scoring approaches. In this study, we systematically studied six commercially available anti-ABCG2 antibodies, using cell lines with up-regulation of ABCG2, and selected one antibody for validation in CRC tissue. Furthermore, we...... sections, especially when more than one core was used. In conclusion, here, we provide validated results to guide future studies on the associations between ABCG2 immunoreactivity in tumor cells and the benefits of chemotherapeutic treatment in patients with CRC...

  16. Nested-PCR for the detection of Mycoplasma hyopneumoniae in bronchial alveolar swabs, frozen tissues and formalin-fixed paraffin-embedded swine lung samples: comparative evaluation with immunohistochemical findings and histological features

    Directory of Open Access Journals (Sweden)

    Paula R. Almeida

    2012-08-01

    Full Text Available The diagnosis of Mycoplasma hyopneumoniae infection is often performed through histopathology, immunohistochemistry (IHC and polymerase chain reaction (PCR or a combination of these techniques. PCR can be performed on samples using several conservation methods, including swabs, frozen tissue or formalin-fixed and paraffin-embedded (FFPE tissue. However, the formalin fixation process often inhibits DNA amplification. To evaluate whether M. hyopneumoniae DNA could be recovered from FFPE tissues, 15 lungs with cranioventral consolidation lesions were collected in a slaughterhouse from swine bred in herds with respiratory disease. Bronchial swabs and fresh lung tissue were collected, and a fragment of the corresponding lung section was placed in neutral buffered formalin for 48 hours. A PCR assay was performed to compare FFPE tissue samples with samples that were only refrigerated (bronchial swabs or frozen (tissue pieces. M. hyopneumoniae was detected by PCR in all 15 samples of the swab and frozen tissue, while it was detected in only 11 of the 15 FFPE samples. Histological features of M. hyopneumoniae infection were presented in 11 cases and 7 of these samples stained positive in IHC. Concordance between the histological features and detection results was observed in 13 of the FFPE tissue samples. PCR was the most sensitive technique. Comparison of different sample conservation methods indicated that it is possible to detect M. hyopneumoniae from FFPE tissue. It is important to conduct further research using archived material because the efficiency of PCR could be compromised under these conditions.

  17. Paraffin wax

    Energy Technology Data Exchange (ETDEWEB)

    Elborne, W

    1917-06-16

    Powdered, granulated, or finely divided paraffin is obtained by subjecting paraffin to a grinding, crushing, or disintegrating operation in the presence of an alcohol such as ethyl alcohol, methyl alcohol (wood spirit), or methylated spirit. The alcohol is afterwards removed by a current of air and is recovered. The product can be used in conjunction with a heating-agent for producing smoke or vapor for use in warfare.

  18. A rapid method of reprocessing for electronic microscopy of cut histological in paraffin

    International Nuclear Information System (INIS)

    Hernandez Chavarri, F.; Vargas Montero, M.; Rivera, P.; Carranza, A.

    2000-01-01

    A simple and rapid method is described for re-processing of light microscopy paraffin sections to observe they under transmission electron microscopy (TEM) and scanning electron microscopy (SEM) The paraffin-embedded tissue is sectioned and deparaffinized in toluene; then exposed to osmium vapor under microwave irradiation using a domestic microwave oven. The tissues were embedded in epoxy resin, polymerized and ultrathin sectioned. The method requires a relatively short time (about 30 minutes for TEM and 15 for SEM), and produces a reasonable quality of the ultrastructure for diagnostic purposes. (Author) [es

  19. A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors.

    Science.gov (United States)

    Espinal, Allyson C; Wang, Dan; Yan, Li; Liu, Song; Tang, Li; Hu, Qiang; Morrison, Carl D; Ambrosone, Christine B; Higgins, Michael J; Sucheston-Campbell, Lara E

    2017-02-28

    DNA from archival formalin-fixed and paraffin embedded (FFPE) tissue is an invaluable resource for genome-wide methylation studies although concerns about poor quality may limit its use. In this study, we compared DNA methylation profiles of breast tumors using DNA from fresh-frozen (FF) tissues and three types of matched FFPE samples. For 9/10 patients, correlation and unsupervised clustering analysis revealed that the FF and FFPE samples were consistently correlated with each other and clustered into distinct subgroups. Greater than 84% of the top 100 loci previously shown to differentiate ER+ and ER- tumors in FF tissues were also FFPE DML. Weighted Correlation Gene Network Analyses (WCGNA) grouped the DML loci into 16 modules in FF tissue, with ~85% of the module membership preserved across tissue types. Restored FFPE and matched FF samples were profiled using the Illumina Infinium HumanMethylation450K platform. Methylation levels (β-values) across all loci and the top 100 loci previously shown to differentiate tumors by estrogen receptor status (ER+ or ER-) in a larger FF study, were compared between matched FF and FFPE samples using Pearson's correlation, hierarchical clustering and WCGNA. Positive predictive values and sensitivity levels for detecting differentially methylated loci (DML) in FF samples were calculated in an independent FFPE cohort. FFPE breast tumors samples show lower overall detection of DMLs versus FF, however FFPE and FF DMLs compare favorably. These results support the emerging consensus that the 450K platform can be employed to investigate epigenetics in large sets of archival FFPE tissues.

  20. Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer.

    Science.gov (United States)

    Al-Attas, Asmaa; Assidi, Mourad; Al-Maghrabi, Jaudah; Dallol, Ashraf; Schulten, Hans-Juergen; Abu-Elmagd, Muhammad; Chaudhary, Adeel; Abuzenadah, Adel; Budowle, Bruce; Buhmeida, Abdelbaset; Al-Qahtani, Mohammed

    To date, the conventional formalin-fixed, paraffin-embedded (FFPE) technique is the gold-standard for preserving histomorphology. Once FFPE tissues are stained, slides are routinely archived along with their blocks at biobanks/hospitals. However, the reuse of fixed and stained biospecimens as DNA source is not a common routine practice worldwide and, thus, indicates the need of studies to investigate the feasibility of extracting DNA from already immunohistochemistry (IHC) FFPE-stained slides and its possible reuse in subsequent downstream molecular analyses. FFPE IHC slides from colorectal cancer (CRC) patients were prepared and stored in the CEGMR Biobank. The workflow consists of digitalization of IHC stained slide's image, removing the slide cover-slip, crude dissection and DNA extraction. Following DNA quality assessment, mutation analysis of CTNNB1 and methylation profile of CDH1 were performed. High-quality DNA was obtained allowing 60% concordance between CDH1 methylation and membranous E-cadherin expression pattern. Clean CTNNB1 DNA chromatograms with evenly-spaced peaks were observed. This study is a proof of concept to recycle and reuse DNA from IHC stained slides with suitable concentration and integrity for further downstream molecular applications. These findings will enhance the pathologists' knowledge, attitudes and practices (KAP) towards the use of these biospecimens and support the implementation of this approach in clinical pathology practice. Therefore, the scientific community will benefit from the largest comprehensive database of human fully annotated FFPE biospecimens already available at their disposal in order to demystify the complexity and the heterogeneity of many challenging diseases and foster the transition towards precision medicine. Copyright© 2016, International Institute of Anticancer Research (Dr. John G. Delinasios), All rights reserved.

  1. A simple and cost-effective method of DNA extraction from small formalin-fixed paraffin-embedded tissue for molecular oncologic testing.

    Science.gov (United States)

    Snow, Anthony N; Stence, Aaron A; Pruessner, Jonathan A; Bossler, Aaron D; Ma, Deqin

    2014-01-01

    Extraction of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is a critical step in molecular oncologic testing. As molecular oncology testing becomes more important for prognostic and therapeutic decision making and tissue specimens become smaller due to earlier detection of suspicious lesions and the use of fine needle aspiration methods for tissue collection, it becomes more challenging for the typical molecular pathology laboratory to obtain reliable test results. We developed a DNA extraction method to obtain sufficient quantity and high quality genomic DNA from limited FFPE tissue for molecular oncology testing using a combination of H&E stained slides, a matrix capture method and the Qiagen DNA column. THREE DNA EXTRACTION METHODS WERE COMPARED: our standard procedure of manually scraping tissue from unstained slides followed by DNA extraction using the QIAamp FFPE column (Qiagen, Valencia, CA), a glue capture method (Pinpoint Solution, Zymo Research Corp, Inc) on H&E stained slides followed by DNA extraction using either the QIAamp column or the column included with the Pinpoint kit (Zymo Research). The DNA extraction protocol was optimized. Statistical analysis was performed using the paired two-sample student's t-test. The combination of the matrix capture method with the QIAamp column gave an equivalent amount of DNA as our standard extraction method using the unstained slides and a 4.6-fold higher DNA yield than using the Zymo column included in the Pinpoint Slide Solution kit. Several molecular tests were performed and DNA purified using the new method gave the same results as for the previous methods. Using H&E stained slides allows visual confirmation of tumor cells during microdissection. The Pinpoint solution made removal of specific tissue from the slides easier and reduced the risk of contamination and tissue loss. This DNA extraction method is simple, cost-effective, and blends with our current workflow requiring no additional equipment.

  2. Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE tumor tissues for copy-number- and mutation-analysis.

    Directory of Open Access Journals (Sweden)

    Michal R Schweiger

    Full Text Available BACKGROUND: Cancer re-sequencing programs rely on DNA isolated from fresh snap frozen tissues, the preparation of which is combined with additional preservation efforts. Tissue samples at pathology departments are routinely stored as formalin-fixed and paraffin-embedded (FFPE samples and their use would open up access to a variety of clinical trials. However, FFPE preparation is incompatible with many down-stream molecular biology techniques such as PCR based amplification methods and gene expression studies. METHODOLOGY/PRINCIPAL FINDINGS: Here we investigated the sample quality requirements of FFPE tissues for massively parallel short-read sequencing approaches. We evaluated key variables of pre-fixation, fixation related and post-fixation processes that occur in routine medical service (e.g. degree of autolysis, duration of fixation and of storage. We also investigated the influence of tissue storage time on sequencing quality by using material that was up to 18 years old. Finally, we analyzed normal and tumor breast tissues using the Sequencing by Synthesis technique (Illumina Genome Analyzer, Solexa to simultaneously localize genome-wide copy number alterations and to detect genomic variations such as substitutions and point-deletions and/or insertions in FFPE tissue samples. CONCLUSIONS/SIGNIFICANCE: The application of second generation sequencing techniques on small amounts of FFPE material opens up the possibility to analyze tissue samples which have been collected during routine clinical work as well as in the context of clinical trials. This is in particular important since FFPE samples are amply available from surgical tumor resections and histopathological diagnosis, and comprise tissue from precursor lesions, primary tumors, lymphogenic and/or hematogenic metastases. Large-scale studies using this tissue material will result in a better prediction of the prognosis of cancer patients and the early identification of patients which

  3. Chromosomal aberrations in bladder cancer: fresh versus formalin fixed paraffin embedded tissue and targeted FISH versus wide microarray-based CGH analysis.

    Directory of Open Access Journals (Sweden)

    Elena Panzeri

    Full Text Available Bladder carcinogenesis is believed to follow two alternative pathways driven by the loss of chromosome 9 and the gain of chromosome 7, albeit other nonrandom copy number alterations (CNAs were identified. However, confirmation studies are needed since many aspects of this model remain unclear and considerable heterogeneity among cases has emerged. One of the purposes of this study was to evaluate the performance of a targeted test (UroVysion assay widely used for the detection of Transitional Cell Carcinoma (TCC of the bladder, in two different types of material derived from the same tumor. We compared the results of UroVysion test performed on Freshly Isolated interphasic Nuclei (FIN and on Formalin Fixed Paraffin Embedded (FFPE tissues from 22 TCCs and we didn't find substantial differences. A second goal was to assess the concordance between array-CGH profiles and the targeted chromosomal profiles of UroVysion assay on an additional set of 10 TCCs, in order to evaluate whether UroVysion is an adequately sensitive method for the identification of selected aneuploidies and nonrandom CNAs in TCCs. Our results confirmed the importance of global genomic screening methods, that is array based CGH, to comprehensively determine the genomic profiles of large series of TCCs tumors. However, this technique has yet some limitations, such as not being able to detect low level mosaicism, or not detecting any change in the number of copies for a kind of compensatory effect due to the presence of high cellular heterogeneity. Thus, it is still advisable to use complementary techniques such as array-CGH and FISH, as the former is able to detect alterations at the genome level not excluding any chromosome, but the latter is able to maintain the individual data at the level of single cells, even if it focuses on few genomic regions.

  4. Gene expression profiles in paraffin-embedded core biopsy tissue predict response to chemotherapy in women with locally advanced breast cancer.

    Science.gov (United States)

    Gianni, Luca; Zambetti, Milvia; Clark, Kim; Baker, Joffre; Cronin, Maureen; Wu, Jenny; Mariani, Gabriella; Rodriguez, Jaime; Carcangiu, Marialuisa; Watson, Drew; Valagussa, Pinuccia; Rouzier, Roman; Symmans, W Fraser; Ross, Jeffrey S; Hortobagyi, Gabriel N; Pusztai, Lajos; Shak, Steven

    2005-10-10

    We sought to identify gene expression markers that predict the likelihood of chemotherapy response. We also tested whether chemotherapy response is correlated with the 21-gene Recurrence Score assay that quantifies recurrence risk. Patients with locally advanced breast cancer received neoadjuvant paclitaxel and doxorubicin. RNA was extracted from the pretreatment formalin-fixed paraffin-embedded core biopsies. The expression of 384 genes was quantified using reverse transcriptase polymerase chain reaction and correlated with pathologic complete response (pCR). The performance of genes predicting for pCR was tested in patients from an independent neoadjuvant study where gene expression was obtained using DNA microarrays. Of 89 assessable patients (mean age, 49.9 years; mean tumor size, 6.4 cm), 11 (12%) had a pCR. Eighty-six genes correlated with pCR (unadjusted P < .05); pCR was more likely with higher expression of proliferation-related genes and immune-related genes, and with lower expression of estrogen receptor (ER) -related genes. In 82 independent patients treated with neoadjuvant paclitaxel and doxorubicin, DNA microarray data were available for 79 of the 86 genes. In univariate analysis, 24 genes correlated with pCR with P < .05 (false discovery, four genes) and 32 genes showed correlation with P < .1 (false discovery, eight genes). The Recurrence Score was positively associated with the likelihood of pCR (P = .005), suggesting that the patients who are at greatest recurrence risk are more likely to have chemotherapy benefit. Quantitative expression of ER-related genes, proliferation genes, and immune-related genes are strong predictors of pCR in women with locally advanced breast cancer receiving neoadjuvant anthracyclines and paclitaxel.

  5. High Quality Genomic Copy Number Data from Archival Formalin-Fixed Paraffin-Embedded Leiomyosarcoma: Optimisation of Universal Linkage System Labelling

    Science.gov (United States)

    Salawu, Abdulazeez; Ul-Hassan, Aliya; Hammond, David; Fernando, Malee; Reed, Malcolm; Sisley, Karen

    2012-01-01

    Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment. PMID:23209738

  6. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues.

    Science.gov (United States)

    Vaca-Paniagua, Felipe; Alvarez-Gomez, Rosa María; Maldonado-Martínez, Hector Aquiles; Pérez-Plasencia, Carlos; Fragoso-Ontiveros, Veronica; Lasa-Gonsebatt, Federico; Herrera, Luis Alonso; Cantú, David; Bargallo-Rocha, Enrique; Mohar, Alejandro; Durand, Geoffroy; Forey, Nathalie; Voegele, Catherine; Vallée, Maxime; Le Calvez-Kelm, Florence; McKay, James; Ardin, Maude; Villar, Stéphanie; Zavadil, Jiri; Olivier, Magali

    2015-01-01

    Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer.

  7. Highly sensitive KRAS mutation detection from formalin-fixed paraffin-embedded biopsies and circulating tumour cells using wild-type blocking polymerase chain reaction and Sanger sequencing.

    Science.gov (United States)

    Huang, Meggie Mo Chao; Leong, Sai Mun; Chua, Hui Wen; Tucker, Steven; Cheong, Wai Chye; Chiu, Lily; Li, Mo-Huang; Koay, Evelyn Siew-Chuan

    2014-08-01

    Among patients with colorectal cancer (CRC), KRAS mutations were reported to occur in 30-51 % of all cases. CRC patients with KRAS mutations were reported to be non-responsive to anti-epidermal growth factor receptor (EGFR) monoclonal antibody (MoAb) treatment in many clinical trials. Hence, accurate detection of KRAS mutations would be critical in guiding the use of anti-EGFR MoAb therapies in CRC. In this study, we carried out a detailed investigation of the efficacy of a wild-type (WT) blocking real-time polymerase chain reaction (PCR), employing WT KRAS locked nucleic acid blockers, and Sanger sequencing, for KRAS mutation detection in rare cells. Analyses were first conducted on cell lines to optimize the assay protocol which was subsequently applied to peripheral blood and tissue samples from patients with CRC. The optimized assay provided a superior sensitivity enabling detection of as little as two cells with mutated KRAS in the background of 10(4) WT cells (0.02 %). The feasibility of this assay was further investigated to assess the KRAS status of 45 colorectal tissue samples, which had been tested previously, using a conventional PCR sequencing approach. The analysis showed a mutational discordance between these two methods in 4 of 18 WT cases. Our results present a simple, effective, and robust method for KRAS mutation detection in both paraffin embedded tissues and circulating tumour cells, at single-cell level. The method greatly enhances the detection sensitivity and alleviates the need of exhaustively removing co-enriched contaminating lymphocytes.

  8. Detection of mucormycetes and other pathogenic fungi in formalin fixed paraffin embedded and fresh tissues using the extended region of 28S rDNA.

    Science.gov (United States)

    Gade, Lalitha; Hurst, Steven; Balajee, S Arunmozhi; Lockhart, Shawn R; Litvintseva, Anastasia P

    2017-06-01

    Molecular methods of detection based on DNA-sequencing of the internal transcribed spacer 1 and 2 (ITS1 and ITS2) or 5΄ end region of 28S (D1-D2 region) of ribosomal RNA gene (rDNA) have been used extensively for molecular identification and detection of fungal infections. However, these regions are not always informative for identification of mucormycetes and other rare fungal pathogens as they often contain large introns, heterogenic regions, and/or cannot be PCR-amplified using broad range fungal PCR primers. In addition, because of the difficulties of recovering intact fungal DNA from human specimens, smaller regions of DNA are more useful for the direct detection of fungal DNA in tissues and fluids. In this study, we investigated the utility of 12F/13R PCR primers targeting a 200-230 bp region of the extended 28S region of rDNA for molecular identification of fungal DNA in formalin fixed paraffin embedded tissues and other clinical specimens. We demonstrated that this region can be successfully used for identification of all genera and some species of clinically relevant mucormycetes, as well as other medically important fungi, such as Aspergillus, Fusarium, Coccidioides, and Cryptococcus. We also demonstrated that PCR amplification and direct sequencing of the extended 28S region of rDNA was more sensitive compared to targeting the ITS2 region, as we were able to detect and identify mucormycetes and other fungal pathogens in tissues from patients with histopathological and/or culture evidence of fungal infections that were negative with PCR using ITS-specific primers. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  9. Technical reproducibility of single-nucleotide and size-based DNA biomarker assessment using DNA extracted from formalin-fixed, paraffin-embedded tissues.

    Science.gov (United States)

    Zhang, Shenli; Tan, Iain B; Sapari, Nur S; Grabsch, Heike I; Okines, Alicia; Smyth, Elizabeth C; Aoyama, Toru; Hewitt, Lindsay C; Inam, Imran; Bottomley, Dan; Nankivell, Matthew; Stenning, Sally P; Cunningham, David; Wotherspoon, Andrew; Tsuburaya, Akira; Yoshikawa, Takaki; Soong, Richie; Tan, Patrick

    2015-05-01

    DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissues has been used in the past to analyze genetic polymorphisms. We evaluated the technical reproducibility of different types of assays for gene polymorphisms using DNA extracted from FFPE material. By using the MassARRAY iPLEX system, we investigated polymorphisms in DPYD (rs1801159 and rs3918290), UMPS (rs1801019), ERCC1 (rs11615), ERCC1 (rs3212986), and ERCC2 (rs13181) in 56 FFPE DNA samples. By using PCR, followed by size-based gel electrophoresis, we also examined TYMS 5' untranslated region 2R/3R repeats and GSTT1 deletions in 50 FFPE DNA samples and 34 DNAs extracted from fresh-frozen tissues and cell lines. Each polymorphism was analyzed by two independent runs. We found that iPLEX biomarker assays measuring single-nucleotide polymorphisms provided consistent concordant results. However, by using FFPE DNA, size-based PCR biomarkers (GSTT1 and TYMS 5' untranslated region) were discrepant in 32.7% (16/49, with exact 95% CI, 19.9%-47.5%; exact binomial confidence limit test) and 4.2% (2/48, with exact 95% CI, 0.5%-14.3%) of cases, respectively, whereas no discrepancies were observed using intact genomic DNA. Our findings suggest that DNA from FFPE material can be used to reliably test single-nucleotide polymorphisms. However, results based on size-based PCR biomarkers, and particularly GSTT1 deletions, using FFPE DNA need to be interpreted with caution. Independent repeated assays should be performed on all cases to assess potential discrepancies. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  10. Gene expression patterns in formalin-fixed, paraffin-embedded core biopsies predict docetaxel chemosensitivity in breast cancer patients.

    Science.gov (United States)

    Chang, Jenny C; Makris, Andreas; Gutierrez, M Carolina; Hilsenbeck, Susan G; Hackett, James R; Jeong, Jennie; Liu, Mei-Lan; Baker, Joffre; Clark-Langone, Kim; Baehner, Frederick L; Sexton, Krsytal; Mohsin, Syed; Gray, Tara; Alvarez, Laura; Chamness, Gary C; Osborne, C Kent; Shak, Steven

    2008-03-01

    Previously, we had identified gene expression patterns that predicted response to neoadjuvant docetaxel. Other studies have validated that a high Recurrence Score (RS) by the 21-gene RT-PCR assay is predictive of worse prognosis but better response to chemotherapy. We investigated whether tumor expression of these 21 genes and other candidate genes can predict response to docetaxel. Core biopsies from 97 patients were obtained before treatment with neoadjuvant docetaxel (4 cycles, 100 mg/m2 q3 weeks). Three 10-microm FFPE sections were submitted for quantitative RT-PCR assays of 192 genes that were selected from our previous work and the literature. Of the 97 patients, 81 (84%) had sufficient invasive cancer, 80 (82%) had sufficient RNA for QRTPCR assay, and 72 (74%) had clinical response data. Mean age was 48.5 years, and the median tumor size was 6 cm. Clinical complete responses (CR) were observed in 12 (17%), partial responses in 41 (57%), stable disease in 17 (24%), and progressive disease in 2 patients (3%). A significant relationship (P<0.05) between gene expression and CR was observed for 14 genes, including CYBA. CR was associated with lower expression of the ER gene group and higher expression of the proliferation gene group from the 21 gene assay. Of note, CR was more likely with a high RS (P=0.008). We have established molecular profiles of sensitivity to docetaxel. RT-PCR technology provides a potential platform for a predictive test of docetaxel chemosensitivity using small amounts of routinely processed material.

  11. Identification of target cells by immunohistochemical detection of covalently rearranged estradiol in rehydrated paraffin sections.

    Science.gov (United States)

    Jungblut, P W; Sierralta, W D

    1998-04-01

    Estradiol is released from the binding niche of the receptor and covalently arrested in the molecular vicinity by the Mannich reaction during target fixation in acetic acid/formaldehyde. The exposed steroid is freely accessible for appropriate antibodies. It can be visualized in sections by the second antibody/enzyme technique in high resolution and without enhancements.

  12. Utilization of Cell-Transfer Technique for Molecular Testing on Hematoxylin-Eosin-Stained Sections: A Viable Option for Small Biopsies That Lack Tumor Tissues in Paraffin Block.

    Science.gov (United States)

    Wu, Howard H; Jovonovich, Stephen M; Randolph, Melissa; Post, Kristin M; Sen, Joyashree D; Curless, Kendra; Cheng, Liang

    2016-12-01

    - In some instances the standard method of doing molecular testing from formalin-fixed, paraffin-embedded block is not possible because of limited tissue. Tumor cell-enriched cell-transfer technique has been proven useful for performing immunocytochemistry and molecular testing on cytologic smears. - To establish the cell-transfer technique as a viable option for isolating tumor cells from hematoxylin-eosin (H&E)-stained slides. - Molecular testing was performed by using the cell-transfer technique on 97 archived H&E-stained slides from a variety of different tumors. Results were compared to the conventional method of molecular testing. - Polymerase chain reaction-based molecular testing via the cell-transfer technique was successfully performed on 82 of 97 samples (85%). This included 39 of 47 cases for EGFR, 10 of 11 cases for BRAF, and 33 of 39 cases for KRAS mutations. Eighty-one of 82 cell-transfer technique samples (99%) showed agreement with previous standard method results, including 4 mutations and 35 wild-type alleles for EGFR, 4 mutations and 6 wild-type alleles for BRAF, and 11 mutations and 21 wild-type alleles for KRAS. There was only 1 discrepancy: a cell-transfer technique with a false-negative >KRAS result (wild type versus G12C). - Molecular testing performed on H&E-stained sections via cell-transfer technique is useful when tissue from cell blocks and small surgical biopsy samples is exhausted and the only available material for testing is on H&E-stained slides.

  13. Usefulness of molecular biology performed with formaldehyde-fixed paraffin embedded tissue for the diagnosis of combined pulmonary invasive mucormycosis and aspergillosis in an immunocompromised patient

    Directory of Open Access Journals (Sweden)

    Vénissac Nicolas

    2010-01-01

    Full Text Available Abstract Immunocompromised patients who develop invasive filamentous mycotic infections can be efficiently treated if rapid identification of the causative fungus is obtained. We report a case of fatal necrotic pneumonia caused by combined pulmonary invasive mucormycosis and aspergillosis in a 66 year-old renal transplant recipient. Aspergillus was first identified during the course of the disease by cytological examination and culture (A. fumigatus of bronchoalveolar fluid. Hyphae of Mucorales (Rhizopus microsporus were subsequently identified by culture of a tissue specimen taken from the left inferior pulmonary lobe, which was surgically resected two days before the patient died. Histological analysis of the lung parenchyma showed the association of two different filamentous mycoses for which the morphological features were evocative of aspergillosis and mucormycosis. However, the definitive identification of the associative infection was made by polymerase chain reaction (PCR performed on deparaffinized tissue sections using specific primers for aspergillosis and mucormycosis. This case demonstrates that discrepancies between histological, cytological and mycological analyses can occur in cases of combined mycotic infection. In this regard, it shows that PCR on selected paraffin blocks is a very powerful method for making or confirming the association of different filamentous mycoses and that this method should be made available to pathology laboratories.

  14. In vitro and in vivo MMP gene expression localisation by In Situ-RT-PCR in cell culture and paraffin embedded human breast cancer cell line xenografts

    International Nuclear Information System (INIS)

    Haupt, Larisa M; Thompson, Erik W; Trezise, Ann EO; Irving, Rachel E; Irving, Michael G; Griffiths, Lyn R

    2006-01-01

    Members of the matrix metalloproteinase (MMP) family of proteases are required for the degradation of the basement membrane and extracellular matrix in both normal and pathological conditions. In vitro, MT1-MMP (MMP-14, membrane type-1-MMP) expression is higher in more invasive human breast cancer (HBC) cell lines, whilst in vivo its expression has been associated with the stroma surrounding breast tumours. MMP-1 (interstitial collagenase) has been associated with MDA-MB-231 invasion in vitro, while MMP-3 (stromelysin-1) has been localised around invasive cells of breast tumours in vivo. As MMPs are not stored intracellularly, the ability to localise their expression to their cells of origin is difficult. We utilised the unique in situ-reverse transcription-polymerase chain reaction (IS-RT-PCR) methodology to localise the in vitro and in vivo gene expression of MT1-MMP, MMP-1 and MMP-3 in human breast cancer. In vitro, MMP induction was examined in the MDA-MB-231 and MCF-7 HBC cell lines following exposure to Concanavalin A (Con A). In vivo, we examined their expression in archival paraffin embedded xenografts derived from a range of HBC cell lines of varied invasive and metastatic potential. Mouse xenografts are heterogenous, containing neoplastic human parenchyma with mouse stroma and vasculature and provide a reproducible in vivo model system correlated to the human disease state. In vitro, exposure to Con A increased MT1-MMP gene expression in MDA-MB-231 cells and decreased MT1-MMP gene expression in MCF-7 cells. MMP-1 and MMP-3 gene expression remained unchanged in both cell lines. In vivo, stromal cells recruited into each xenograft demonstrated differences in localised levels of MMP gene expression. Specifically, MDA-MB-231, MDA-MB-435 and Hs578T HBC cell lines are able to influence MMP gene expression in the surrounding stroma. We have demonstrated the applicability and sensitivity of IS-RT-PCR for the examination of MMP gene expression both in vitro and in

  15. Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study.

    Science.gov (United States)

    Iddawela, Mahesh; Rueda, Oscar; Eremin, Jenny; Eremin, Oleg; Cowley, Jed; Earl, Helena M; Caldas, Carlos

    2017-07-11

    An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks of formalin-fixed paraffin-embedded (FFPE) tissue. This study evaluated two platforms available for the analysis of DNA copy number and gene expression using FFPE samples. The cDNA-mediated annealing, selection, extension, and ligation assay (DASL™) has been developed for gene expression analysis and the Molecular Inversion Probes assay (Oncoscan™), were used for copy number analysis using FFPE tissues. Gene expression and copy number were evaluated in core-biopsy samples from patients with breast cancer undergoing neoadjuvant chemotherapy (NAC). Forty-three core-biopsies were evaluated and characteristic copy number changes in breast cancers, gains in 1q, 8q, 11q, 17q and 20q and losses in 6q, 8p, 13q and 16q, were confirmed. Regions that frequently exhibited gains in tumours showing a pathological complete response (pCR) to NAC were 1q (55%), 8q (40%) and 17q (40%), whereas 11q11 (37%) gain was the most frequent change in non-pCR tumours. Gains associated with poor survival were 11q13 (62%), 8q24 (54%) and 20q (47%). Gene expression assessed by DASL correlated with immunohistochemistry (IHC) analysis for oestrogen receptor (ER) [area under the curve (AUC) = 0.95], progesterone receptor (PR)(AUC = 0.90) and human epidermal growth factor type-2 receptor (HER-2) (AUC = 0.96). Differential expression analysis between ER+ and ER- cancers identified over-expression of TTF1, LAF-4 and C-MYB (p ≤ 0.05), and between pCR vs non-pCRs, over-expression of CXCL9, AREG, B-MYB and under-expression of ABCG2. This study was an integrative analysis of copy number and gene expression using FFPE core biopsies and showed that molecular marker data from FFPE tissues were consistent with those in previous studies using fresh-frozen samples. FFPE tissue can provide

  16. Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis.

    Science.gov (United States)

    Vukmirovic, Milica; Herazo-Maya, Jose D; Blackmon, John; Skodric-Trifunovic, Vesna; Jovanovic, Dragana; Pavlovic, Sonja; Stojsic, Jelena; Zeljkovic, Vesna; Yan, Xiting; Homer, Robert; Stefanovic, Branko; Kaminski, Naftali

    2017-01-12

    Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether genome scale transcript profiling using RNA Sequencing (RNA-Seq) could be applied to archived Formalin-Fixed Paraffin-Embedded (FFPE) IPF tissues. We isolated total RNA from 7 IPF and 5 control FFPE lung tissues and performed 50 base pair paired-end sequencing on Illumina 2000 HiSeq. TopHat2 was used to map sequencing reads to the human genome. On average ~62 million reads (53.4% of ~116 million reads) were mapped per sample. 4,131 genes were differentially expressed between IPF and controls (1,920 increased and 2,211 decreased (FDR < 0.05). We compared our results to differentially expressed genes calculated from a previously published dataset generated from FF tissues analyzed on Agilent microarrays (GSE47460). The overlap of differentially expressed genes was very high (760 increased and 1,413 decreased, FDR < 0.05). Only 92 differentially expressed genes changed in opposite directions. Pathway enrichment analysis performed using MetaCore confirmed numerous IPF relevant genes and pathways including extracellular remodeling, TGF-beta, and WNT. Gene network analysis of MMP7, a highly differentially expressed gene in both datasets, revealed the same canonical pathways and gene network candidates in RNA-Seq and microarray data. For validation by NanoString nCounter® we selected 35 genes that had a fold change of 2 in at least one dataset (10 discordant, 10 significantly differentially expressed in one dataset only and 15 concordant genes). High concordance of fold change and FDR was observed for each type of the samples (FF vs FFPE) with both microarrays (r = 0.92) and RNA-Seq (r = 0.90) and the number of discordant genes was reduced to four. Our results demonstrate that RNA sequencing of RNA

  17. Early experience with formalin-fixed paraffin-embedded (FFPE) based commercial clinical genomic profiling of gliomas-robust and informative with caveats.

    Science.gov (United States)

    Movassaghi, Masoud; Shabihkhani, Maryam; Hojat, Seyed A; Williams, Ryan R; Chung, Lawrance K; Im, Kyuseok; Lucey, Gregory M; Wei, Bowen; Mareninov, Sergey; Wang, Michael W; Ng, Denise W; Tashjian, Randy S; Magaki, Shino; Perez-Rosendahl, Mari; Yang, Isaac; Khanlou, Negar; Vinters, Harry V; Liau, Linda M; Nghiemphu, Phioanh L; Lai, Albert; Cloughesy, Timothy F; Yong, William H

    2017-08-01

    Commercial targeted genomic profiling with next generation sequencing using formalin-fixed paraffin embedded (FFPE) tissue has recently entered into clinical use for diagnosis and for the guiding of therapy. However, there is limited independent data regarding the accuracy or robustness of commercial genomic profiling in gliomas. As part of patient care, FFPE samples of gliomas from 71 patients were submitted for targeted genomic profiling to one commonly used commercial vendor, Foundation Medicine. Genomic alterations were determined for the following grades or groups of gliomas; Grade I/II, Grade III, primary glioblastomas (GBMs), recurrent primary GBMs, and secondary GBMs. In addition, FFPE samples from the same patients were independently assessed with conventional methods such as immunohistochemistry (IHC), Quantitative real-time PCR (qRT-PCR), or Fluorescence in situ hybridization (FISH) for three genetic alterations: IDH1 mutations, EGFR amplification, and EGFRvIII expression. A total of 100 altered genes were detected by the aforementioned targeted genomic profiling assay. The number of different genomic alterations was significantly different between the five groups of gliomas and consistent with the literature. CDKN2A/B, TP53, and TERT were the most common genomic alterations seen in primary GBMs, whereas IDH1, TP53, and PIK3CA were the most common in secondary GBMs. Targeted genomic profiling demonstrated 92.3%-100% concordance with conventional methods. The targeted genomic profiling report provided an average of 5.5 drugs, and listed an average of 8.4 clinical trials for the 71 glioma patients studied but only a third of the trials were appropriate for glioma patients. In this limited comparison study, this commercial next generation sequencing based-targeted genomic profiling showed a high concordance rate with conventional methods for the 3 genetic alterations and identified mutations expected for the type of glioma. While it may not be feasible to

  18. A Method to Correlate mRNA Expression Datasets Obtained from Fresh Frozen and Formalin-Fixed, Paraffin-Embedded Tissue Samples: A Matter of Thresholds.

    Directory of Open Access Journals (Sweden)

    Dana A M Mustafa

    Full Text Available Gene expression profiling of tumors is a successful tool for the discovery of new cancer biomarkers and potential targets for the development of new therapeutic strategies. Reliable profiling is preferably performed on fresh frozen (FF tissues in which the quality of nucleic acids is better preserved than in formalin-fixed paraffin-embedded (FFPE material. However, since snap-freezing of biopsy materials is often not part of daily routine in pathology laboratories, one may have to rely on archival FFPE material. Procedures to retrieve the RNAs from FFPE materials have been developed and therefore, datasets obtained from FFPE and FF materials need to be made compatible to ensure reliable comparisons are possible.To develop an efficient method to compare gene expression profiles obtained from FFPE and FF samples using the same platform.Twenty-six FFPE-FF sample pairs of the same tumors representing various cancer types, and two FFPE-FF sample pairs of breast cancer cell lines, were included. Total RNA was extracted and gene expression profiling was carried out using Illumina's Whole-Genome cDNA-mediated Annealing, Selection, extension and Ligation (WG-DASL V3 arrays, enabling the simultaneous detection of 24,526 mRNA transcripts. A sample exclusion criterion was created based on the expression of 11 stably expressed reference genes. Pearson correlation at the probe level was calculated for paired FFPE-FF, and three cut-off values were chosen. Spearman correlation coefficients between the matched FFPE and FF samples were calculated for three probe lists with varying levels of significance and compared to the correlation based on all measured probes. Unsupervised hierarchical cluster analysis was performed to verify performance of the included probe lists to compare matched FPPE-FF samples.Twenty-seven FFPE-FF pairs passed the sample exclusion criterion. From the profiles of 27 FFPE and FF matched samples, the best correlating probes were identified

  19. 21 CFR 890.5110 - Paraffin bath.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Paraffin bath. 890.5110 Section 890.5110 Food and... PHYSICAL MEDICINE DEVICES Physical Medicine Therapeutic Devices § 890.5110 Paraffin bath. (a) Identification. A paraffin bath is a device intended for medical purposes that consists of a tub to be filled...

  20. PARAFFIN SEPARATION VACUUM DISTILLATION

    Directory of Open Access Journals (Sweden)

    Zaid A. Abdulrahman

    2013-05-01

    Full Text Available Simulated column performance curves were constructed for existing paraffin separation vacuum distillation column in LAB plant (Arab Detergent Company/Baiji-Iraq. The variables considered in this study are the thermodynamic model option, top vacuum pressure, top and bottom temperatures, feed temperature, feed composition & reflux ratio. Also simulated columns profiles for the temperature, vapor & liquid flow rates composition were constructed. Four different thermodynamic model options (SRK, TSRK, PR, and ESSO were used, affecting the results within 1-25% variation for the most cases.The simulated results show that about 2% to 8 % of paraffin (C10, C11, C12, & C13 present at the bottom stream which may cause a problem in the LAB plant. The major variations were noticed for the top temperature & the  paraffin weight fractions at bottom section with top vacuum pressure. The bottom temperature above 240 oC is not recommended because the total bottom flow rate decreases sharply, where as  the weight fraction of paraffins decrease slightly. The study gives evidence about a successful simulation with CHEMCAD

  1. Specific identification of human papillomavirus type in cervical smears and paraffin sections by in situ hybridization with radioactive probes: a preliminary communication

    International Nuclear Information System (INIS)

    Gupta, J.; Gendelman, H.E.; Naghashfar, Z.; Gupta, P.; Rosenshein, N.; Sawada, E.; Woodruff, J.D.; Shah, K.

    1985-01-01

    Cervical Papanicolaou smears and paraffin sections of biopsy specimens obtained from women attending dysplasia clinics were examined for viral DNA sequences by in situ hybridization technique using 35 S-labeled cloned recombinant DNA probes of human papillomavirus (HPV) types 6, 11, and 16. These and one unrelated DNA probe complementary to measles virus RNA were labeled by nick translation using either one or two 35 S-labeled nucleotides. Paraffin sections and cervical smears were collected on pretreated slides, hybridized with the probes under stringent or nonstringent conditions for 50 h, and autoradiographed. Additional cervical specimens from the same women were examined for the presence of genus-specific papillomavirus capsid antigen by the immunoperoxidase technique. Preliminary results may be summarized as follows. The infecting virus could be identified in smears as well as in sections. Viral DNA sequences were detected only when there were condylomatous cells in the specimen and in only a proportion of the condylomatous cells. Even under stringent conditions, some specimens reacted with both HPV-6 and HPV-11. In some instances, the cells did not hybridize with any of the three probes even when duplicate specimens contained frankly condylomatous, capsid antigen-positive cells. In situ hybridization of Papanicolaou smears or of tissue sections is a practical method for diagnosis and follow-up of specific papillomavirus infection using routinely collected material

  2. Embedding, serial sectioning and staining of zebrafish embryos using JB-4 resin.

    Science.gov (United States)

    Sullivan-Brown, Jessica; Bisher, Margaret E; Burdine, Rebecca D

    2011-01-01

    Histological techniques are critical for observing tissue and cellular morphology. In this paper, we outline our protocol for embedding, serial sectioning, staining and visualizing zebrafish embryos embedded in JB-4 plastic resin-a glycol methacrylate-based medium that results in excellent preservation of tissue morphology. In addition, we describe our procedures for staining plastic sections with toluidine blue or hematoxylin and eosin, and show how to couple these stains with whole-mount RNA in situ hybridization. We also describe how to maintain and visualize immunofluorescence and EGFP signals in JB-4 resin. The protocol we outline-from embryo preparation, embedding, sectioning and staining to visualization-can be accomplished in 3 d. Overall, we reinforce that plastic embedding can provide higher resolution of cellular details and is a valuable tool for cellular and morphological studies in zebrafish.

  3. Embedding

    DEFF Research Database (Denmark)

    Høyrup, Jens

    2016-01-01

    systems, in particular place-value and quasi place-value systems. 2. The development of algebraic symbolisms. 3. The discussion whether “scientific revolutions” ever take place in mathematics, or new conceptualizations always include what preceded them. A final section investigates the relation between...

  4. Detection of MDM2/CDK4 amplification in lipomatous soft tissue tumors from formalin-fixed, paraffin-embedded tissue: comparison of multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH).

    Science.gov (United States)

    Creytens, David; van Gorp, Joost; Ferdinande, Liesbeth; Speel, Ernst-Jan; Libbrecht, Louis

    2015-02-01

    In this study, the detection of MDM2 and CDK4 amplification was evaluated in lipomatous soft tissue tumors using multiplex ligation-dependent probe amplification (MLPA), a PCR-based technique, in comparison with fluorescence in situ hybridization (FISH). These 2 techniques were evaluated in a series of 77 formalin-fixed, paraffin-embedded lipomatous tumors (27 benign adipose tumors, 28 atypical lipomatous tumors/well-differentiated liposarcomas, 18 dedifferentiated liposarcomas, and 4 pleomorphic liposarcomas). Using MLPA, with a cut-off ratio of >2, 36/71 samples (22 atypical lipomatous tumors/well-differentiated liposarcomas, and 14 dedifferentiated liposarcomas) showed MDM2 and CDK4 amplification. Using FISH as gold standard, MLPA showed a sensitivity of 90% (36/40) and a specificity of 100% (31/31) in detecting amplification of MDM2 and CDK4 in lipomatous soft tissue tumors. In case of high-level amplification (MDM2-CDK4/CEP12 ratio >5), concordance was 100%. Four cases of atypical lipomatous tumor/well-differentiated liposarcoma (4/26, 15%) with a low MDM2 and CDK4 amplification level (MDM2-CDK4/CEP12 ratio ranging between 2 and 2.5) detected by FISH showed no amplification by MLPA, although gain of MDM2 and CDK4 (ratios ranging between 1.6 and 1.9) was seen with MLPA. No amplification was detected in benign lipomatous tumors and pleomorphic liposarcomas. Furthermore, there was a very high concordance between the ratios obtained by FISH and MLPA. In conclusion, MLPA proves to be an appropriate and straightforward technique for screening MDM2/CDK4 amplification in lipomatous tumors, especially when a correct cut-off value and reference samples are chosen, and could be considered a good alternative to FISH to determine MDM2 and CDK4 amplification in liposarcomas. Moreover, because MLPA, as a multiplex technique, allows simultaneous detection of multiple chromosomal changes of interest, it could be in the future a very reliable and fast molecular analysis on

  5. 7 CFR 58.427 - Paraffin tanks.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Paraffin tanks. 58.427 Section 58.427 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards....427 Paraffin tanks. The metal tank should be adequate in size, have wood rather than metal racks to...

  6. Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.

    Science.gov (United States)

    Mohapatra, Gayatry; Engler, David A; Starbuck, Kristen D; Kim, James C; Bernay, Derek C; Scangas, George A; Rousseau, Audrey; Batchelor, Tracy T; Betensky, Rebecca A; Louis, David N

    2011-04-01

    Array comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA). Because diffuse malignant gliomas are often sampled by small biopsies, formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis; FFPE tissues are also needed to study the intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present a combination of evaluations and technical advances that provide strong support for the ready use of oligonucleotide aCGH on FFPE diffuse gliomas. We first compared aCGH using bacterial artificial chromosome (BAC) arrays in 45 paired frozen and FFPE gliomas, and demonstrate a high concordance rate between FFPE and frozen DNA in an individual clone-level analysis of sensitivity and specificity, assuring that under certain array conditions, frozen and FFPE DNA can perform nearly identically. However, because oligonucleotide arrays offer advantages to BAC arrays in genomic coverage and practical availability, we next developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. To demonstrate utility in FFPE tissues, we applied this approach to biphasic anaplastic oligoastrocytomas and demonstrate CNA differences between DNA obtained from the two components. Therefore, BAC and oligonucleotide aCGH can be sensitive and specific tools for detecting CNAs in FFPE DNA, and novel labeling techniques enable the routine use of oligonucleotide arrays for FFPE DNA. In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues.

  7. Diagnostic sensitivity and specificity of in situ hybridization and immunohistochemistry for Eastern equine encephalitis virus and West Nile virus in formalin-fixed, paraffin-embedded brain tissue of horses.

    Science.gov (United States)

    Pennick, Kate E; McKnight, Christy A; Patterson, Jon S; Latimer, Kenneth S; Maes, Roger K; Wise, Annabel G; Kiupel, Matti

    2012-03-01

    Immunohistochemistry (IHC) and in situ hybridization (ISH) can be used either to detect or to differentiate between Eastern equine encephalitis virus (EEEV) and West Nile virus (WNV) within formalin-fixed, paraffin-embedded (FFPE) brain tissue of horses. To compare the diagnostic sensitivity and specificity of ISH and IHC, FFPE brain tissue from 20 EEEV-positive horses and 16 WNV-positive horses were tested with both EEEV and WNV oligoprobes and EEEV- and WNV-specific antibodies. Reverse transcription polymerase chain reaction (RT-PCR) for detection of EEEV and WNV was used as the gold standard to confirm infection. All horses that tested positive for EEEV by RT-PCR also tested positive by IHC and ISH, except for 1 case that was false-negative by ISH. In contrast, all horses that tested positive for WNV by RT-PCR tested negative by IHC and only 2 horses tested positive by ISH. No false-positives were detected with either method for both viruses. Both IHC and ISH are highly specific and sensitive diagnostic methods to detect EEEV in equine FFPE brain tissues, although neither appear effective for the diagnosis of WNV in equine neurologic cases.

  8. Clinical Usefulness of a One-Tube Nested Reverse Transcription Quantitative Polymerase Chain Reaction Assay for Evaluating Human Epidermal Growth Factor Receptor 2 mRNA Overexpression in Formalin-Fixed and Paraffin-Embedded Breast Cancer Tissue Samples.

    Science.gov (United States)

    Wang, Hye-Young; Ahn, Sungwoo; Park, Sunyoung; Kim, SeungIl; Lee, Hyeyoung

    2017-01-01

    Currently, the two main methods used to analyze human epidermal growth factor receptor 2 (HER2) amplification or overexpression have a limited accuracy and high costs. These limitations can be overcome by the development of complementary quantitative methods. In this study, we analyzed HER2 mRNA expression in clinical formalin-fixed and paraffin-embedded (FFPE) samples using a one-tube nested reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay. We measured expression relative to 3 reference genes and compared the results to those obtained by conventional immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) assays with 226 FFPE breast cancer tissue samples. The one-tube nested RT-qPCR assay proved to be highly sensitive and specific based on comparisons with IHC (96.9 and 97.7%, respectively) and FISH (92.4 and 92.9%, respectively) obtained with the validation set. Comparisons with clinicopathological data revealed significant associations between HER2 overexpression and TNM stage (p < 0.01), histological type (p < 0.01), ER status (p < 0.001), PR status (p < 0.05), HER2 status (p < 0.001), and molecular subtypes (p < 0.001). Based on these findings, our one-tube nested RT-qPCR assay is a potentially useful and complementary screening tool for the detection of HER2 mRNA overexpression. © 2016 S. Karger AG, Basel.

  9. MicroRNAs are suitable for assessment as biomarkers from formalin-fixed paraffin-embedded tissue, and miR-24 represents an appropriate reference microRNA for diffuse large B-cell lymphoma studies.

    Science.gov (United States)

    Culpin, Rachel Emily; Sieniawski, Michal; Proctor, Stephen John; Menon, Geetha; Mainou-Fowler, Tryfonia

    2013-03-01

    Tissue biopsy specimens in the form of formalin-fixed paraffin-embedded tissue (FFPET) represent a valuable resource for biomarker identification and validation. However, to date, they remain an underused asset due to uncertainty regarding RNA extraction and the reliability of downstream techniques, including quantitative RT-PCR. Recently, much interest has emerged in the study of microRNAs; small single-stranded RNAs with a role in transcriptional regulation, that are thought to be well preserved in FFPET. In this study, we show that microRNA expression is comparable between FFPET and matched fresh-frozen samples (miR-17-5p: p=0.01, miR-92: p=0.003), and demonstrate that no significant deterioration in expression occurs over prolonged FFPET storage (p=0.06). Furthermore, microRNA expression is equivalent dependant on RNA extraction method (p<0.001) or DNAse treatment of total RNA (p<0.001). Finally, we validate miR-24 as a suitable reference microRNA for diffuse large B-cell lymphoma (DLBCL) FFPET studies.

  10. 21 CFR 172.275 - Synthetic paraffin and succinic derivatives.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Synthetic paraffin and succinic derivatives. 172... FOOD FOR HUMAN CONSUMPTION Coatings, Films and Related Substances § 172.275 Synthetic paraffin and succinic derivatives. Synthetic paraffin and succinic derivatives identified in this section may be safely...

  11. Non-hazardous organic solvents in the paraffin-embedding technique: a rational approach. Aliphatic monoesters for clearing and dewaxing: butyldecanoate

    DEFF Research Database (Denmark)

    Lyon, H; Holm, I; Prentø, P

    1995-01-01

    The aim of this study was to substitute hazardous compounds, used in tissue processing and dewaxing, with compounds having lowest possible toxicity and inflammability without impairing the morphology, staining characteristics, or diagnostic value of the tissue sections. All aromatic compounds...... and aliphatic hydrocarbons (e.g. alkanes, isoparaffins, petroleum distillates, etc.) were rejected, primarily due to their high vapour pressure. Based on a theoretical study of compounds used for clearing, a number of non-hazardous potential substitutes were chosen. The following experimental study narrowed...... the group to three unbranched, saturated, aliphatic monoesters containing 12-14 carbon atoms. On large-scale testing of these compounds, we found butyldecanoate to be the closest to an ideal substitute for aromatic and aliphatic hydrocarbons in the histology department: the section quality is at least equal...

  12. Improved method for extraction and detection of Helicobacter pylori DNA in formalin-fixed paraffin embedded gastric biopsies using laser micro-dissection

    Directory of Open Access Journals (Sweden)

    María Fernanda Loayza

    2015-01-01

    • The use of thin purification columns with 35 μL of elution buffer. The mean of DNA concentration obtained from 25 LM cut sections was 1.94± 0 .16 ng/μL, and it was efficiently amplified with qPCR in a Bio Rad iCycler instrument. The LM can improve the sample selection and DNA extraction for molecular analysis of H. pylori associated with human gastric epithelium.

  13. Retrieval of estradiol receptor in paraffin sections of resting porcine uteri by microwave treatment. Immunostaining patterns obtained with different primary antibodies.

    Science.gov (United States)

    Sierralta, W D; Thole, H H

    1996-05-01

    The unmasking of estradiol receptor in paraffin sections of Bouin's-fixed uterine tissue from ovariectomized gilts was attained with microwave treatment. Immunocytochemistry of the receptor was performed using a polyclonal or five monoclonal antibodies, two of which are commercially available, reacting with different domains of the protein and an amplified-peroxidase system for detection. With five of the antibodies, a predominance of nuclear staining was observed in cells of endometrial glands, while one monoclonal antibody (13H2), reacting with the receptor's domain E, showed a preference for the cytoplasmic receptor. In stroma, all antibodies detected more receptor in nuclei than in cytoplasm. In epithelium, the commercially available antibody H222, our monoclonals 13H2 and HT65, and the polyclonal antibody 402 demonstrated more receptor in cytoplasmic than in nuclear areas. In myometrium, the nuclei from longitudinal and ring muscles were definitely stained with the antibodies. We conclude that the accessibilities of the antibody epitopes of the receptor differ according to the functional uterine cell type.

  14. Hormone Receptor Expression Analyses in Neoplastic and Non-Neoplastic Canine Mammary Tissue by a Bead Based Multiplex Branched DNA Assay: A Gene Expression Study in Fresh Frozen and Formalin-Fixed, Paraffin-Embedded Samples.

    Directory of Open Access Journals (Sweden)

    Annika Mohr

    Full Text Available Immunohistochemistry (IHC is currently considered the method of choice for steroid hormone receptor status evaluation in human breast cancer and, therefore, it is commonly utilized for assessing canine mammary tumors. In case of low hormone receptor expression, IHC is limited and thus is complemented by molecular analyses. In the present study, a multiplex bDNA assay was evaluated as a method for hormone receptor gene expression detection in canine mammary tissues. Estrogen receptor (ESR1, progesterone receptor (PGR, prolactin receptor (PRLR and growth hormone receptor (GHR gene expressions were evaluated in neoplastic and non-neoplastic canine mammary tissues. A set of 119 fresh frozen and 180 formalin-fixed, paraffin-embedded (FFPE was comparatively analyzed and used for assay evaluation. Furthermore, a possible association between the hormone receptor expression in different histological subtypes of canine malignant mammary tumors and the castration status, breed and invasive growth of the tumor were analyzed. The multiplex bDNA assay proved to be more sensitive for fresh frozen specimens. Hormone receptor expression found was significantly decreased in malignant mammary tumors in comparison to non-neoplastic tissue and benign mammary tumors. Among the histological subtypes the lowest gene expression levels of ESR1, PGR and PRLR were found in solid, anaplastic and ductal carcinomas. In summary, the evaluation showed that the measurement of hormone receptors with the multiplex bDNA assay represents a practicable method for obtaining detailed quantitative information about gene expression in canine mammary tissue for future studies. Still, comparison with IHC or quantitative real-time PCR is needed for further validation of the present method.

  15. Chromogenic In Situ Hybridization and p16/Ki67 Dual Staining on Formalin-Fixed Paraffin-Embedded Cervical Specimens: Correlation with HPV-DNA Test, E6/E7 mRNA Test, and Potential Clinical Applications

    Directory of Open Access Journals (Sweden)

    Roberta Zappacosta

    2013-01-01

    Full Text Available Although HPV-DNA test and E6/E7 mRNA analyses remain the current standard for the confirmation of human papillomavirus (HPV infections in cytological specimens, no universally adopted techniques exist for the detection of HPV in formalin-fixed paraffin-embedded samples. Particularly, in routine laboratories, molecular assays are still time-consuming and would require a high level of expertise. In this study, we investigated the possible use of a novel HPV tyramide-based chromogenic in situ hybridization (CISH technology to locate HPV on tissue specimens. Then, we evaluate the potential usefulness of p16INK4a/Ki-67 double stain on histological samples, to identify cervical cells expressing HPV E6/E7 oncogenes. In our series, CISH showed a clear signal in 95.2% of the specimens and reached a sensitivity of 86.5%. CISH positivity always matched with HPV-DNA positivity, while 100% of cases with punctated signal joined with cervical intraepithelial neoplasia grade 2 or worse (CIN2+. p16/Ki67 immunohistochemistry gave an interpretable result in 100% of the cases. The use of dual stain significantly increased the agreement between pathologists, which reached 100%. Concordance between dual stain and E6/E7 mRNA test was 89%. In our series, both CISH and p16INK4a/Ki67 dual stain demonstrated high grade of performances. In particular, CISH would help to distinguish episomal from integrated HPV, in order to allow conclusions regarding the prognosis of the lesion, while p16INK4a/Ki67 dual stain approach would confer a high level of standardization to the diagnostic procedure.

  16. Chromogenic In Situ Hybridization and p16/Ki67 Dual Staining on Formalin-Fixed Paraffin-Embedded Cervical Specimens: Correlation with HPV-DNA Test, E6/E7 mRNA Test, and Potential Clinical Applications

    Science.gov (United States)

    Zappacosta, Roberta; Colasante, Antonella; Viola, Patrizia; D'Antuono, Tommaso; Lattanzio, Giuseppe; Capanna, Serena; Gatta, Daniela Maria Pia; Rosini, Sandra

    2013-01-01

    Although HPV-DNA test and E6/E7 mRNA analyses remain the current standard for the confirmation of human papillomavirus (HPV) infections in cytological specimens, no universally adopted techniques exist for the detection of HPV in formalin-fixed paraffin-embedded samples. Particularly, in routine laboratories, molecular assays are still time-consuming and would require a high level of expertise. In this study, we investigated the possible use of a novel HPV tyramide-based chromogenic in situ hybridization (CISH) technology to locate HPV on tissue specimens. Then, we evaluate the potential usefulness of p16INK4a/Ki-67 double stain on histological samples, to identify cervical cells expressing HPV E6/E7 oncogenes. In our series, CISH showed a clear signal in 95.2% of the specimens and reached a sensitivity of 86.5%. CISH positivity always matched with HPV-DNA positivity, while 100% of cases with punctated signal joined with cervical intraepithelial neoplasia grade 2 or worse (CIN2+). p16/Ki67 immunohistochemistry gave an interpretable result in 100% of the cases. The use of dual stain significantly increased the agreement between pathologists, which reached 100%. Concordance between dual stain and E6/E7 mRNA test was 89%. In our series, both CISH and p16INK4a/Ki67 dual stain demonstrated high grade of performances. In particular, CISH would help to distinguish episomal from integrated HPV, in order to allow conclusions regarding the prognosis of the lesion, while p16INK4a/Ki67 dual stain approach would confer a high level of standardization to the diagnostic procedure. PMID:24369532

  17. Validation of a Multiplex Allele-Specific Polymerase Chain Reaction Assay for Detection of KRAS Gene Mutations in Formalin-Fixed, Paraffin-Embedded Tissues from Colorectal Cancer Patients.

    Directory of Open Access Journals (Sweden)

    Sirirat Seekhuntod

    Full Text Available Patients with KRAS mutations do not respond to epidermal growth factor receptor (EGFR inhibitors and fail to benefit from adjuvant chemotherapy. Mutation analysis of KRAS is needed before starting treatment with monoclonal anti-EGFR antibodies in patients with metastatic colorectal cancer (mCRC. The objective of this study is to develop a multiplex allele-specific PCR (MAS-PCR assay to detect KRAS mutations.We developed a single-tube MAS-PCR assay for the detection of seven KRAS mutations (G12D, G12A, G12R, G12C, G12S, G12V, and G13D. We performed MAS-PCR assay analysis for KRAS on DNA isolated from 270 formalin-fixed paraffin-embedded (FFPE colorectal cancer tissues. Sequences of all 270 samples were determined by pyrosequencing. Seven known point-mutation DNA samples diluted with wild-type DNA were assayed to determine the limitation of detection and reproducibility of the MAS-PCR assay.Overall, the results of MAS-PCR assay were in good concordance with pyrosequencing, and only seven discordant samples were found. The MAS-PCR assay reproducibly detected 1 to 2% mutant alleles. The most common mutations were G13D in codon 13 (49.17%, G12D (25.83% and G12V (12.50% in codon 12.The MAS-PCR assay provides a rapid, cost-effective, and reliable diagnostic tool for accurate detection of KRAS mutations in routine FFPE colorectal cancer tissues.

  18. High-risk Human Papillomavirus Determination in Formalin-fixed, Paraffin-embedded Cervical Tissue Using the Roche Cobas 4800 System: A Comparative Study With Liquid-based Cytology.

    Science.gov (United States)

    Tardío, Juan C; Cambero, Olivia; Sánchez-Estévez, Carolina; Sánchez-García, Ana B; Angulo, Fernando; Moreno, Amalia

    2017-11-14

    Roche cobas 4800 human papillomavirus (HPV) test is an automated real-time polymerase chain reaction-based system that allows the simultaneous detection of 14 human papillomavirus high-risk (HR-HPV) genotypes. This test is Food and Drug Administration approved since 2011 for HPV determination in liquid-based cytologic samples, but a clinically validated technique for formalin-fixed, paraffin-embedded (FFPE) tissue specimens is presently not commercially available. In our laboratory, we have developed an HPV detection procedure in FFPE tissue by cobas 4800 HPV test. In order to validate our method, we retrospectively studied 165 FFPE cervical biopsy and conization specimens with varied diagnoses from our files. In 50 of them, we contrasted the results with those obtained from simultaneous liquid-based cytologies from the same patients. Finally, seeking the possible complementary clinical usefulness of the procedure, we compared the HPV genotypes detected in cervical intraepithelial neoplasia grade 1 (CIN1)-diagnosed biopsies from 20 patients with a subsequent high-grade CIN (CIN2+) diagnosis with those from another group of 20 patients without a posterior CIN2+ diagnosis. Eighty-seven percent of the assays provided informative results. HR-HPV was detected in 28 of 32 (88%) invasive cervical squamous carcinomas. Coincidental HR-HPV genotypes were obtained in 32 of 50 (64%) cases with simultaneous cervical biopsy and liquid-based cytologic samples. A significant higher risk of progression to CIN2+ was found when HPV16 (P=0.022) or any HR-HPV genotype (P=0.037) was detected in CIN1 biopsies. The reported procedure provides an automated, technically time-saving, easy to integrate into laboratory routine, and reliable method of HR-HPV determination in FFPE specimens.

  19. Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas

    Science.gov (United States)

    Mohapatra, Gayatry; Engler, David A.; Starbuck, Kristen D.; Kim, James C.; Bernay, Derek C.; Scangas, George A.; Rousseau, Audrey; Batchelor, Tracy T.; Betensky, Rebecca A.; Louis, David N.

    2010-01-01

    Molecular genetic analysis of cancer is rapidly evolving as a result of improvement in genomic technologies and the growing applicability of such analyses to clinical oncology. Array based comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA), particularly in solid tumors, and has been applied to the study of malignant gliomas. In the clinical setting, however, gliomas are often sampled by small biopsies and thus formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis, especially for rare types of gliomas. Moreover, the biological basis for the marked intratumoral heterogeneity in gliomas is most readily addressed in FFPE material. Therefore, for gliomas, the ability to use DNA from FFPE tissue is essential for both clinical and research applications. In this study, we have constructed a custom bacterial artificial chromosome (BAC) array and show excellent sensitivity and specificity for detecting CNAs in a panel of paired frozen and FFPE glioma samples. Our study demonstrates a high concordance rate between CNAs detected in FFPE compared to frozen DNA. We have also developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. This labeling technique was applied to a panel of biphasic anaplastic oligoastrocytomas (AOA) to identify genetic changes unique to each component. Together, results from these studies suggest that BAC and oligonucleotide aCGH are sensitive tools for detecting CNAs in FFPE DNA, and can enable genome-wide analysis of rare, small and/or histologically heterogeneous gliomas. PMID:21080181

  20. Improving the Prediction of Prostate Cancer Overall Survival by Supplementing Readily Available Clinical Data with Gene Expression Levels of IGFBP3 and F3 in Formalin-Fixed Paraffin Embedded Core Needle Biopsy Material.

    Directory of Open Access Journals (Sweden)

    Zhuochun Peng

    Full Text Available A previously reported expression signature of three genes (IGFBP3, F3 and VGLL3 was shown to have potential prognostic value in estimating overall and cancer-specific survivals at diagnosis of prostate cancer in a pilot cohort study using freshly frozen Fine Needle Aspiration (FNA samples.We carried out a new cohort study with 241 prostate cancer patients diagnosed from 2004-2007 with a follow-up exceeding 6 years in order to verify the prognostic value of gene expression signature in formalin fixed paraffin embedded (FFPE prostate core needle biopsy tissue samples. The cohort consisted of four patient groups with different survival times and death causes. A four multiplex one-step RT-qPCR test kit, designed and optimized for measuring the expression signature in FFPE core needle biopsy samples, was used. In archive FFPE biopsy samples the expression differences of two genes (IGFBP3 and F3 were measured. The survival time predictions using the current clinical parameters only, such as age at diagnosis, Gleason score, PSA value and tumor stage, and clinical parameters supplemented with the expression levels of IGFBP3 and F3, were compared.When combined with currently used clinical parameters, the gene expression levels of IGFBP3 and F3 are improving the prediction of survival time as compared to using clinical parameters alone.The assessment of IGFBP3 and F3 gene expression levels in FFPE prostate cancer tissue would provide an improved survival prediction for prostate cancer patients at the time of diagnosis.

  1. Droplet digital PCR (ddPCR) vs quantitative real-time PCR (qPCR) approach for detection and quantification of Merkel cell polyomavirus (MCPyV) DNA in formalin fixed paraffin embedded (FFPE) cutaneous biopsies.

    Science.gov (United States)

    Arvia, Rosaria; Sollai, Mauro; Pierucci, Federica; Urso, Carmelo; Massi, Daniela; Zakrzewska, Krystyna

    2017-08-01

    Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma and high viral load in the skin was proposed as a risk factor for the occurrence of this tumour. MCPyV DNA was detected, with lower frequency, in different skin cancers but since the viral load was usually low, the real prevalence of viral DNA could be underestimated. To evaluate the performance of two assays (qPCR and ddPCR) for MCPyV detection and quantification in formalin fixed paraffin embedded (FFPE) tissue samples. Both assays were designed to simultaneous detection and quantification of both MCPyV as well as house-keeping DNA in clinical samples. The performance of MCPyV quantification was investigated using serial dilutions of cloned target DNA. We also evaluated the applicability of both tests for the analysis of 76 FFPE cutaneous biopsies. The two approaches resulted equivalent with regard to the reproducibility and repeatability and showed a high degree of linearity in the dynamic range tested in the present study. Moreover, qPCR was able to quantify ≥10 5 copies per reaction, while the upper limit of ddPCR was 10 4 copies. There was not significant difference between viral load measured by the two methods The detection limit of both tests was 0,15 copies per reaction, however, the number of positive samples obtained by ddPCR was higher than that obtained by qPCR (45% and 37% respectively). The ddPCR represents a better method for detection of MCPyV in FFPE biopsies, mostly these containing low copies number of viral genome. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. The storage period of the formalin-fixed paraffin-embedded tumor blocks does not influence the concentration and purity of the isolated DNA in a series of 83 renal and thyroid carcinomas.

    Science.gov (United States)

    Nechifor-Boilă, Adela Corina; Loghin, Andrada; Vacariu, Victor; Halaţiu, Vasile Bogdan; Borda, Angela

    2015-01-01

    Optimal recovery of nucleic acids from formalin-fixed paraffin-embedded (FFPE) tissues is highly dependent on a series of pre-extraction steps, mainly related (but not limited) to fixation. The aim of our study was to investigate if the storage period of the FFPE blocks had a significant effect on the isolated DNA. We examined the quantity and purity of the isolated DNA from 83 FFPE blocks, corresponding to malignant thyroid (n=28) and renal (n=55) carcinomas that had been stored in our department for up to eight years. The DNA extraction protocol was based on a precipitation method (MasterPure™ DNA Purification Kit, Epicentre), in accordance to the manufacturer instructions, optimized in our laboratory. A spectrophotometer was used to determine the yield (A260) and purity (A260/A280 ratio) of the isolated DNA. We successfully isolated good DNA quantity and purity from all our study cases (mean concentration: 223.4 ± 104.16 ng/μL; mean A260/A280 ratio: 1.68 ± 0.09). Moreover, no statistically significant differences were observed between tumor blocks stored for 2-3 years and 7-8 years, respectively, both in terms of DNA quantity (p=0.196) and purity (p=0.663). In conclusion, we successfully validated an efficient, reproducible DNA extraction technique that provided a good range of DNA concentrations and purity, regardless the type of tissue (thyroid or kidney). Moreover, we demonstrated that the storage period of the FFPE blocks does not have a significant influence on the DNA quantity and purity.

  3. Detection of HPV-DNA by a PCR-based method in formalin-fixed, paraffin-embedded tissue from rare endocervical carcinoma types.

    Science.gov (United States)

    Nofech-Mozes, Sharon; Khalifa, Mahmoud M; Ismiil, Nadia; Dubé, Valerie; Saad, Reda S; Sun, Peizhu; Seth, Arun; Ghorab, Zeina

    2010-01-01

    High-risk human papilloma virus (HPV) seems to play a role in the pathogenesis of cervical squamous neoplasia and adenocarcinomas of the mucinous and endometrioid cell types. Cervical serous, clear cell, and small cell carcinomas differ from the conventional endocervical adenocarcinoma in their clinical characteristics. The data on the role of HPV in their pathogenesis are limited. In this study, we examined the presence of high-risk HPV-DNA in rare types of cervical carcinoma using polymerase chain reaction-based test. In-house cervical serous, clear cell, and small cell carcinoma cases accessioned between 2000 and 2008 were tested for HPV by polymerase chain reaction amplification of DNA extracted from deparaffinized sections using Roche AMPLICOR HPV Amplification Detection and Control Kits. The kit detects all 13 high-risk HPV-DNA genotypes. The positive cut-off point for AMPLICOR HPV Test was A450 = 0.2. We identified 4 serous, 3 clear cell, 1 mixed clear cell and serous, and 5 small cell carcinomas. High-risk HPV-DNA tested positive in 3 out of 4 serous carcinomas, 2 out of 3 cervical clear cell carcinomas, and all 5 cases of small cell carcinoma and the mixed cell type. Our report documents HPV status in a series of archival unusual types of adenocarcinoma of the uterine cervix. It suggests a robust association between high-risk HPV and these rare subtypes. Despite their unique clinical setting and morphologic appearance, the majority of these tumors likely share a common HPV-mediated carcinogenic pathway. Our observation is particularly significant in cervical cancer prevention as we enter the HPV vaccination era.

  4. Paraffin ingestion - the problem

    African Journals Online (AJOL)

    The incidence of paraffin ingestion is higher in the summer months. This is because ... where the average cost per patient was R348 per day. The total cost to ... petroleum companies and/or entrepreneurs and distributed ... paraffin, coal and gas. As South Africa ... and more people become involved, making control difficult.

  5. Embedded Leverage

    DEFF Research Database (Denmark)

    Frazzini, Andrea; Heje Pedersen, Lasse

    find that asset classes with embedded leverage offer low risk-adjusted returns and, in the cross-section, higher embedded leverage is associated with lower returns. A portfolio which is long low-embedded-leverage securities and short high-embedded-leverage securities earns large abnormal returns...

  6. Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM.

    Science.gov (United States)

    Kristensen, Lasse S; Wojdacz, Tomasz K; Thestrup, Britta B; Wiuf, Carsten; Hager, Henrik; Hansen, Lise Lotte

    2009-12-21

    The High Resolution Melting (HRM) technology has recently been introduced as a rapid and robust analysis tool for the detection of DNA methylation. The methylation status of multiple tumor suppressor genes may serve as biomarkers for early cancer diagnostics, for prediction of prognosis and for prediction of response to treatment. Therefore, it is important that methodologies for detection of DNA methylation continue to evolve. Sensitive Melting Analysis after Real Time - Methylation Specific PCR (SMART-MSP) and Methylation Sensitive - High Resolution Melting (MS-HRM) are two methods for single locus DNA methylation detection based on HRM. Here, we have assessed the quality of DNA extracted from up to 30 years old Formalin Fixed Paraffin Embedded (FFPE) tissue for DNA methylation analysis using SMART-MSP and MS-HRM. The quality assessment was performed on DNA extracted from 54 Non-Small Cell Lung Cancer (NSCLC) samples derived from FFPE tissue, collected over 30 years and grouped into five years intervals. For each sample, the methylation levels of the CDKN2A (p16) and RARB promoters were estimated using SMART-MSP and MS-HRM assays designed to assess the methylation status of the same CpG positions. This allowed for a direct comparison of the methylation levels estimated by the two methods for each sample. CDKN2A promoter methylation levels were successfully determined by SMART-MSP and MS-HRM in all 54 samples. Identical methylation estimates were obtained by the two methods in 46 of the samples. The methylation levels of the RARB promoter were successfully determined by SMART-MSP in all samples. When using MS-HRM to assess RARB methylation five samples failed to amplify and 15 samples showed a melting profile characteristic for heterogeneous methylation. Twenty-seven of the remaining 34 samples, for which the methylation level could be estimated, gave the same result as observed when using SMART-MSP. MS-HRM and SMART-MSP can be successfully used for single locus

  7. Analytic performance studies and clinical reproducibility of a real-time PCR assay for the detection of epidermal growth factor receptor gene mutations in formalin-fixed paraffin-embedded tissue specimens of non-small cell lung cancer

    International Nuclear Information System (INIS)

    O’Donnell, Patrick; Shieh, Felice; Wei, Wen; Lawrence, H Jeffrey; Wu, Lin; Schilling, Robert; Bloom, Kenneth; Maltzman, Warren; Anderson, Steven; Soviero, Stephen; Ferguson, Jane; Shyu, Johnny; Current, Robert; Rehage, Taraneh; Tsai, Julie; Christensen, Mari; Tran, Ha Bich; Chien, Sean Shih-Chang

    2013-01-01

    Epidermal growth factor receptor (EGFR) gene mutations identify patients with non-small cell lung cancer (NSCLC) who have a high likelihood of benefiting from treatment with anti-EGFR tyrosine kinase inhibitors. Sanger sequencing is widely used for mutation detection but can be technically challenging, resulting in longer turn-around-time, with limited sensitivity for low levels of mutations. This manuscript details the technical performance verification studies and external clinical reproducibility studies of the cobas EGFR Mutation Test, a rapid multiplex real-time PCR assay designed to detect 41 mutations in exons 18, 19, 20 and 21. The assay’s limit of detection was determined using 25 formalin-fixed paraffin-embedded tissue (FFPET)-derived and plasmid DNA blends. Assay performance for a panel of 201 specimens was compared against Sanger sequencing with resolution of discordant specimens by quantitative massively parallel pyrosequencing (MPP). Internal and external reproducibility was assessed using specimens tested in duplicate by different operators, using different reagent lots, instruments and at different sites. The effects on the performance of the cobas EGFR test of endogenous substances and nine therapeutic drugs were evaluated in ten FFPET specimens. Other tests included an evaluation of the effects of necrosis, micro-organisms and homologous DNA sequences on assay performance, and the inclusivity of the assay for less frequent mutations. A >95% hit rate was obtained in blends with >5% mutant alleles, as determined by MPP analysis, at a total DNA input of 150 ng. The overall percent agreement between Sanger sequencing and the cobas test was 96.7% (negative percent agreement 97.5%; positive percent agreement 95.8%). Assay repeatability was 98% when tested with two operators, instruments, and reagent lots. In the external reproducibility study, the agreement was > 99% across all sites, all operators and all reagent lots for 11/12 tumors tested. Test

  8. Formulation and Testing of Paraffin-Based Solid Fuels Containing Energetic Additives for Hybrid Rockets

    Science.gov (United States)

    Larson, Daniel B.; Boyer, Eric; Wachs,Trevor; Kuo, Kenneth K.; Story, George

    2012-01-01

    Many approaches have been considered in an effort to improve the regression rate of solid fuels for hybrid rocket applications. One promising method is to use a fuel with a fast burning rate such as paraffin wax; however, additional performance increases to the fuel regression rate are necessary to make the fuel a viable candidate to replace current launch propulsion systems. The addition of energetic and/or nano-sized particles is one way to increase mass-burning rates of the solid fuels and increase the overall performance of the hybrid rocket motor.1,2 Several paraffin-based fuel grains with various energetic additives (e.g., lithium aluminum hydride (LiAlH4) have been cast in an attempt to improve regression rates. There are two major advantages to introducing LiAlH4 additive into the solid fuel matrix: 1) the increased characteristic velocity, 2) decreased dependency of Isp on oxidizer-to-fuel ratio. The testing and characterization of these solid-fuel grains have shown that continued work is necessary to eliminate unburned/unreacted fuel in downstream sections of the test apparatus.3 Changes to the fuel matrix include higher melting point wax and smaller energetic additive particles. The reduction in particle size through various methods can result in more homogeneous grain structure. The higher melting point wax can serve to reduce the melt-layer thickness, allowing the LiAlH4 particles to react closer to the burning surface, thus increasing the heat feedback rate and fuel regression rate. In addition to the formulation of LiAlH4 and paraffin wax solid-fuel grains, liquid additives of triethylaluminum and diisobutylaluminum hydride will be included in this study. Another promising fuel formulation consideration is to incorporate a small percentage of RDX as an additive to paraffin. A novel casting technique will be used by dissolving RDX in a solvent to crystallize the energetic additive. After dissolving the RDX in a solvent chosen for its compatibility

  9. Microdissecção e captura a laser na investigação do gene TP53 em tecidos incluídos em parafina Laser-capture microdissection for TP53 gene analysis in paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    Shadia Muhammad Ihlaseh

    2007-02-01

    characterize its enormous potential for diagnosis and research. OBJECTIVE: This study describes the standardization of LCM and DNA extraction from formalin fixed and paraffin-embedded tissues. MATERIAL AND METHOD: The gene TP53 exon 8 and the cyclophilin gene were studied in normal and neoplastic liver and kidney samples from a chemical carcinogenesis model in rat. DNA extraction was confirmed by nested-PCR. RESULTS: Histological sections preparation for LCM and the nested-PCR procedures were standardized; 48.3% amplifications of the gene TP53 exon 8 and 51.7% of the cyclophilin gene samples were obtained. When at least one of the gene segments was considered, 79.3% samples presented amplification. DISCUSSION AND CONCLUSION: Procedures for DNA extraction from formalin fixed and paraffin-embedded tissues collected by LCM were standardized. They can be useful for DNA collection for molecular studies.

  10. Paraffin-based immunohistochemistry in the evaluation of glomerular diseases in renal biopsies

    International Nuclear Information System (INIS)

    Rathore, M.U.; Khadim, M.T.; Atique, M.

    2012-01-01

    Objective: To determine sensitivity and specificity of paraffin-based immunohistochemistry in the evaluation of glomerular diseases in renal biopsies using immunofluorescence as gold standard. Study Design: Cross-sectional analytical study. Place and Duration of Study: Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, from August 2008 to August 2009. Methodology: Seventy renal biopsy specimens fulfilling the inclusion criteria for light microscopy and immuno-fluorescence during the study period were evaluated. Antibodies to immunoglobulins (IgG, IgA, and IgM) and components of complement system (C3) were applied on 70 formalin-fixed paraffin-embedded renal biopsy specimens previously classified by means of light microscopy and immunofluorescence (IF). Staining for these antibodies was recorded as positive and negative for immunohistochemistry (IHC) and IF in paired proportions presuming IF as gold standard test. The sensitivity, specificity, positive predictive value and negative predictive value of individual antibody were calculated. Results: Of 70 patients, mean age was 33 +- 18 years ranging from 2 to 80 years. Forty five (64%) were males and 25 (36%) were females. The sensitivity, specificity and predictive values of individual antibodies to IgG, IgA, IgM and C3 were very low and generally in the range of 40 - 60%. Conclusion: The sensitivity, specificity and predictive values of immunohistochemistry on formalin-fixed paraffin-embedded renal biopsy specimens were very low and therefore, not suitable for evaluation of renal biopsies in current circumstances. (author)

  11. Quantitative aspects of enzyme histochemistry on sections of freeze-substituted glycol methacrylate-embedded rat liver

    NARCIS (Netherlands)

    Frederiks, W. M.; Bosch, K. S.

    1993-01-01

    Freeze-substituted rat liver embedded in glycol methacrylate (GMA) has been used to demonstrate the activities of several enzymes. The following enzymes could be detected in GMA-sections by the indicated histochemical procedure(s): 5'-nucleotidase (lead salt, cerium-diaminobenzidine), alkaline

  12. Integrating imaging FTIR and secondary ion mass spectrometry for the analysis of embedded paint cross-sections

    DEFF Research Database (Denmark)

    Heeren, Ron M.A.; Boon, Jaap J.; Noble, Petria

    1999-01-01

    Novel chemical imaging techniques provide new insight in the organic chemistry of embedded paint cross-sections. FTIR imaging microscopy delivers a two-dimensional image of the functional group distribution, revealing chemical aspects of the binding medium in each individual paint layer. Secondar...... and identity of various lead soaps and lead hydroxychloride in these inclusions....

  13. The Cutting of Ultrathin Sections With the Thickness Less Than 20 nm From Biological Specimens Embedded in Resin Blocks

    Czech Academy of Sciences Publication Activity Database

    Nebesářová, Jana; Hozák, Pavel; Frank, Luděk; Štěpan, P.; Vancová, Marie

    2016-01-01

    Roč. 79, č. 6 (2016), s. 512-517 ISSN 1059-910X R&D Projects: GA TA ČR(CZ) TE01020118 Institutional support: RVO:60077344 ; RVO:68378050 ; RVO:68081731 Keywords : low voltage electron microscopy * resin embedding * ultramicrotomy * ultrathin sectioning Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.147, year: 2016

  14. Plastics control paraffin buildup

    Energy Technology Data Exchange (ETDEWEB)

    1965-06-01

    Paraffin buildup in producing oil wells has been virtually eliminated by the use of plastic-coated sucker rods. The payout of the plasticing process is generally reached in less than a year, and the paraffin buildup may be inhibited for 10 yr or longer. Most of the plants applying plastic coatings to sucker rods are now fully automated, though a few still offer the hand-sprayed coating that some operators prefer. The several steps involved are described. The ideal plastic for the job is resistant to chemicals at high and low temperatures, flexible, has good adhesion, abrasion resistance, impact resistance, and a smooth glossy finish. The phenol aldehyde and epoxy resins presently offered by the industry fulfill these specifications very well; the multicoating and multibaking techniques improve their performance. Due to wide variations in the severity of the paraffin problem from one oil field to another, there is no general rule to estimate the possible savings from using plastic-coated sucker rods. The process, however, does appear to do a remarkable job in controlling paraffin buildup wherever it is a problem in producing oil by pump.

  15. Design and Testing of Digitally Manufactured Paraffin Acrylonitrile-Butadiene-Styrene Hybrid Rocket Motors

    OpenAIRE

    McCulley, Jonathan M.

    2013-01-01

    This research investigates the application of additive manufacturing techniques for fabricating hybrid rocket fuel grains composed of porous Acrylonitrile-butadiene-styrene impregnated with paraffin wax. The digitally manufactured ABS substrate provides mechanical support for the paraffin fuel material and serves as an additional fuel component. The embedded paraffin provides an enhanced fuel regression rate while having no detrimental effect on the thermodynamic burn properties of the fuel g...

  16. Detection of three common translocation breakpoints in non-Hodgkin's lymphomas by fluorescence in situ hybridization on routine paraffin-embedded tissue sections

    NARCIS (Netherlands)

    Haralambieva, E; Kleiverda, K; Mason, DY; Schuuring, E; Kluin, PM

    2002-01-01

    Non-random chromosomal translocations are specifically involved in the pathogenesis of many non-Hodgkin's lymphomas and have clinical implications as diagnostic and/or prognostic markers. Their detection is often impaired by technical problems, including the distribution of the breakpoints over

  17. Development of reliable techniques for the differential diagnosis of avian tumor viruses by immunohistochemistry and polymerase chain reaction from formalin-fixed paraffin-embedded tissue sections

    Science.gov (United States)

    In the past, several techniques have been developed as diagnostic tools for the differential diagnosis of tumours produced by Marek’s disease virus (MDV) from those induced by avian leukosis virus (ALV) and reticuloendotheliosis virus (REV). However, most current techniques are unreliable using form...

  18. Effects of tissue handling and processing steps on PCR for detection of Mycobacterium tuberculosis in formalin-fixed paraffin-embedded samples Efeitos das etapas de tratamento e processamento do tecido na PCR para detecção de Mycobacterium tuberculosis em amostras fixadas em formalina e incluídas em parafina

    Directory of Open Access Journals (Sweden)

    Denise Barcelos

    2008-12-01

    Full Text Available Development and standardization of reliable methods for detection of Mycobacterium tuberculosis in clinical samples is an important goal in laboratories throughout the world. In this work, lung and spleen fragments from a patient who died with the diagnosis of miliary tuberculosis were used to evaluate the influence of the type of fixative as well as the fixation and paraffin inclusion protocols on PCR performance in paraffin embedded specimens. Tissue fragments were fixed for four h to 48 h, using either 10% non-buffered or 10% buffered formalin, and embedded in pure paraffin or paraffin mixed with bee wax. Specimens were submitted to PCR for amplification of the human beta-actin gene and separately for amplification of the insertion sequence IS6110, specific from the M. tuberculosis complex. Amplification of the beta-actin gene was positive in all samples. No amplicons were generated by PCR-IS6110 when lung tissue fragments were fixed using 10% non-buffered formalin and were embedded in paraffin containing bee wax. In conclusion, combined inhibitory factors interfere in the detection of M. tuberculosis in stored material. It is important to control these inhibitory factors in order to implement molecular diagnosis in pathology laboratories.O desenvolvimento e a padronização de métodos confiáveis para a detecção de Mycobacterium tuberculosis em amostras clínicas é um objetivo importante nos laboratórios de todo o mundo. Neste trabalho, fragmentos de pulmão e baço de paciente que morreu com o diagnóstico de tuberculose miliar foram usados para avaliar a influência do tipo de fixador e dos protocolos de fixação e inclusão em parafina na performance da PCR. Fragmentos de tecido foram fixados por quatro h a 48 h, usando formalina não tamponada a 10% ou formalina tamponada a 10% e incluídos em parafina pura ou misturada a cera de abelha. As amostras foram submetidas a PCR para amplificação do gene da beta-actina humana e

  19. Improvised double-embedding technique of minute biopsies: a mega boon to histopathology laboratory.

    Science.gov (United States)

    Yadav, Lokendra; Thomas, Sarega; Kini, Usha

    2015-01-01

    Optimal orientation of minute mucosal biopsies is essential for a definite diagnosis in gastrointestinal pathology or to visualize neural plexuses in Hirschsprung disease. The problem of minute size of the biopsy and its orientation gets compounded when they are from neonates and mandates exhaustive strip cuts, thus delaying reporting. A modified agar-paraffin technique is aimed to make tissue embedding efficient and user-friendly by inking mapping biopsies (one or more) either fresh or fixed with surgical coloring inks followed by embedding first in agar after orientation and followed thereafter by processing, re-embedding in paraffin wax, sectioning and staining. The tissues in agar paraffin block were found to be well processed, firm, held secure and well preserved. The blocks were easy to cut, with serial sections of thickness 2-3 μ and easy to spread. The colored inks remained permanently on the tissues both in the block as well as on the sections which helped in easy identification of tissues. Agar did not interfere with any stain such as Hematoxylin and Eosin or with histochemical stains, enzyme histochemistry or immunohistochemistry. Inking biopsies and pooling them in a block when obtained from the same patient reduced the number of tissue blocks. The modified agar-paraffin embedding technique is a simple reliable user friendly method that can greatly improve the quality of diagnostic information from minute biopsies by optimal orientation, better quality of sections, faster turnaround time and cost-effectiveness by economizing on the number of paraffin blocks, manpower, chemical reagents and laboratory infrastructure.

  20. Improvised double-embedding technique of minute biopsies: A mega boon to histopathology laboratory

    Directory of Open Access Journals (Sweden)

    Lokendra Yadav

    2015-01-01

    Full Text Available Introduction: Optimal orientation of minute mucosal biopsies is essential for a definite diagnosis in gastrointestinal pathology or to visualize neural plexuses in Hirschsprung disease. The problem of minute size of the biopsy and its orientation gets compounded when they are from neonates and mandates exhaustive strip cuts, thus delaying reporting. Aim: A modified agar-paraffin technique is aimed to make tissue embedding efficient and user-friendly by inking mapping biopsies (one or more either fresh or fixed with surgical coloring inks followed by embedding first in agar after orientation and followed thereafter by processing, re-embedding in paraffin wax, sectioning and staining. Results: The tissues in agar paraffin block were found to be well processed, firm, held secure and well preserved. The blocks were easy to cut, with serial sections of thickness 2-3 μ and easy to spread. The colored inks remained permanently on the tissues both in the block as well as on the sections which helped in easy identification of tissues. Agar did not interfere with any stain such as Hematoxylin and Eosin or with histochemical stains, enzyme histochemistry or immunohistochemistry. Inking biopsies and pooling them in a block when obtained from the same patient reduced the number of tissue blocks. Conclusion: The modified agar-paraffin embedding technique is a simple reliable user friendly method that can greatly improve the quality of diagnostic information from minute biopsies by optimal orientation, better quality of sections, faster turnaround time and cost-effectiveness by economizing on the number of paraffin blocks, manpower, chemical reagents and laboratory infrastructure.

  1. EFFECT OF EMBEDDING METHODS VERSUS FIXATIVE TYPE ON KARYOMETRIC MEASURES

    NARCIS (Netherlands)

    BOON, ME; VANDERPOEL, HG; TAN, CJA; KOK, LP

    The influence of fixation and embedding methods in seven urologic tumor samples was studied karyometrically for 12 preparatory techniques. Routine histologic formalin fixation was compared with Carbowax and Kryofix fixatives. Also, histologic material was studied embedded in paraffin and plastic

  2. Preventing Paraffin-Related Injury

    Directory of Open Access Journals (Sweden)

    Dehran Swart

    2009-07-01

    Full Text Available Paraffin (called kerosene in North America and other parts of the world is the most commonly used fuel in ‎non-electrified dwellings worldwide. It is especially popular in Africa and South Asia. Although paraffin ‎offers many advantages – especially its comparatively low cost to produce – it poses two major risks of ‎injury. First, paraffin poisoning is common, either through ingestion or through inhalation of smoke and ‎fumes. Second, paraffin is highly flammable, and poses fire risk through multiple causes. This commentary ‎discusses strategies to prevent paraffin-related injury. Prevention of paraffin-related injury must be through ‎multiple strategies, and should include policy-oriented change, changes to the safety of home environments, ‎and behavioral changes targeting how individuals store and use paraffin and paraffin appliances. We review ‎successful prevention strategies in each of these domains and discuss appropriate research and community ‎initiatives that should be implemented to improve paraffin safety among at-risk populations.‎

  3. Preventing Paraffin-Related Injury

    OpenAIRE

    C. Schwebel, David; Swart, Dehran

    2009-01-01

    Paraffin (called kerosene in North America and other parts of the world) is the most commonly used fuel in ‎non-electrified dwellings worldwide. It is especially popular in Africa and South Asia. Although paraffin ‎offers many advantages – especially its comparatively low cost to produce – it poses two major risks of ‎injury. First, paraffin poisoning is common, either through ingestion or through inhalation of smoke and ‎fumes. Second, paraffin is highly flammable, and poses fire risk t...

  4. Standard Review Risk Assessment on Medium-chain and Long-chain Chlorinated paraffin PMN submissions by INEOS Chlor Americas

    Science.gov (United States)

    This assessment was conducted under EPA’s TSCA Section 5 New Chemicals Program. EPA is assessing Medium-chain Chlorinated Paraffin (MCCP) and Long-Chain Chlorinated Paraffin (LCCP) chemicals as part of its New Chemicals Review program.

  5. Standard Review Risk Assessment on Medium-chain and Long-chain Chlorinated paraffin PMN submissions by Dover Chemical

    Science.gov (United States)

    This assessment was conducted under EPA’s TSCA Section 5 New Chemicals Program. EPA is assessing Medium-chain Chlorinated Paraffin (MCCP) and Long-Chain Chlorinated Paraffin (LCCP) chemicals as part of its New Chemicals Review program.

  6. Standard Review Risk Assessment on Medium-chain and Long-chain Chlorinated paraffin PMN submissions by Qualice, LLC

    Science.gov (United States)

    This assessment was conducted under EPA’s TSCA Section 5 New Chemicals Program. EPA is assessing Medium-chain Chlorinated Paraffin (MCCP) and Long-Chain Chlorinated Paraffin (LCCP) chemicals as part of its New Chemicals Review program.

  7. Preparing paraffin wax, etc

    Energy Technology Data Exchange (ETDEWEB)

    1935-12-27

    A process is described for preparing paraffin wax by separation from substances containing bitumen, consisting of treating the raw material at an elevated temperature under such moderate conditions and by means of such organic solvents that the bitumen present in the raw material or formed in the process dissolves as well as the asphaltic and phenolic substances and the humic acids which may be said to be neither extracts nor decomposed materials, and then submitting the products and extracts to a treatment with hydrogen gas, which is effected below 300/sup 0/C, and passing the material over fixed hydrogenation catalysts above 300/sup 0/C by means of hydrogenation catalysts finely dispersed in carbonaceous materials all avoiding decomposition with the formation of volatile products.

  8. Electrochemical removal of metallic implants from Technovit 9100 New embedded hard and soft tissues prior to histological sectioning.

    Science.gov (United States)

    Willbold, Elmar; Reebmann, Mattias; Jeffries, Richard; Witte, Frank

    2013-11-01

    Solid metallic implants in soft or hard tissues are serious challenges for histological processing. However, metallic implants are more frequently used in e.g. cardiovascular or orthopaedic therapies. Before clinical use, these devices need to be tested thoroughly in a biological environment and histological analysis of their biocompatibility is a major requirement. To allow the histological analysis of metallic implants in tissues especially in calcified hard tissues, we describe a method for embedding these tissues in the resin Technovit 9100 New and removing the metallic implants by electrochemical dissolution. With the combination of these two processes, we are able to achieve 5 μm thick sections from soft or hard tissues with a superior preservation of tissue architecture and especially the implant-tissue interface. These sections can be stained by classical stainings, immunohistochemical and enzymehistochemical as well as DNA-based staining methods.

  9. Influence of Liquid Paraffin, White Soft Paraffin and Initial Hydration ...

    African Journals Online (AJOL)

    hydrated white soft paraffin on the viscosity of a cream formulated with a corticosteroid. Methods: The formulations were prepared via homogenization with variable velocity in the range 3300 - 4000 rpm. Individual series of preparations contained the ...

  10. Nitrous Paraffin Hybrid, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The Nitrous Oxide Paraffin Hybrid engine (N2OP) is a proposed technology designed to provide small launch vehicles with high specific impulse, indefinitely storable...

  11. Avaliação de dois métodos de extração de DNA de material parafinado para amplificação em PCR Evaluation of two methods of DNA extraction from paraffin-embedded material for PCR amplification

    Directory of Open Access Journals (Sweden)

    Luciana Estevam Simonato

    2007-04-01

    Full Text Available INTRODUÇÃO: Diversos métodos para extração de DNA a partir de tecidos biológicos inclusos em parafina encontram-se descritos na literatura, sendo o sucesso desse procedimento de grande importância para a realização de métodos moleculares de diagnóstico empregando a reação em cadeia da polimerase (PCR. OBJETIVO: Este estudo avaliou dois métodos de extração de DNA de material parafinado, visando à amplificação do DNA genômico pela técnica da PCR. MATERIAL E MÉTODO: Foram utilizadas 35 amostras de casos de carcinoma epidermóide de assoalho bucal diagnosticados e tratados no Centro de Oncologia Bucal da Universidade Estadual Paulista (Unesp. Os métodos de extração de DNA avaliados incluíram: 1. digestão com proteinase K seguida por purificação com Chelex 100® (BioRad; e 2. sistema QIAamp DNA minikit® (Qiagen. O DNA obtido foi quantificado por espectrofotometria e amplificado pela técnica da PCR, utilizando-se oligonucleotídeos iniciadores para betaglobina. RESULTADOS: A concentração de DNA obtido do material extraído com o primeiro método apresentou média de 120,62 ng/µl com razão entre as leituras das absorbâncias 260/280 variando de 0,8 a 1,41. Para as amostras extraídas com o segundo procedimento, o rendimento médio foi de 67,38 ng/µl, no entanto a razão 260/280 variou entre 1,11 e 2,53. O material foi submetido à PCR e, das 35 amostras extraídas com cada método, respectivamente, 29 e 30 apresentaram sinal positivo. CONCLUSÃO: Os dois métodos utilizados para obtenção de DNA de material parafinado apresentaram desempenho semelhante, revelando que ambos têm potencial para auxiliar na prática da biologia molecular diagnóstica, assim como no estudo diagnóstico retrospectivo em material parafinizado.BACKGROUND: There are several methods for DNA extraction from formalin-fixed paraffin-embedded tissues reported in the literature. High success rate on this procedure is important for the use of

  12. TULSA UNIVERSITY PARAFFIN DEPOSITION PROJECTS

    Energy Technology Data Exchange (ETDEWEB)

    Cem Sarica; Michael Volk

    2004-06-01

    As oil and gas production moves to deeper and colder water, subsea multiphase production systems become critical for economic feasibility. It will also become increasingly imperative to adequately identify the conditions for paraffin precipitation and predict paraffin deposition rates to optimize the design and operation of these multi-phase production systems. Although several oil companies have paraffin deposition predictive capabilities for single-phase oil flow, these predictive capabilities are not suitable for the multiphase flow conditions encountered in most flowlines and wellbores. For deepwater applications in the Gulf of Mexico, it is likely that multiphase production streams consisting of crude oil, produced water and gas will be transported in a single multiphase pipeline to minimize capital cost and complexity at the mudline. Existing single-phase (crude oil) paraffin deposition predictive tools are clearly inadequate to accurately design these pipelines, because they do not account for the second and third phases, namely, produced water and gas. The objective of this program is to utilize the current test facilities at The University of Tulsa, as well as member company expertise, to accomplish the following: enhance our understanding of paraffin deposition in single and two-phase (gas-oil) flows; conduct focused experiments to better understand various aspects of deposition physics; and, utilize knowledge gained from experimental modeling studies to enhance the computer programs developed in the previous JIP for predicting paraffin deposition in single and two-phase flow environments. These refined computer models will then be tested against field data from member company pipelines.

  13. Comparação de três protocolos de extração de DNA a partir de tecido fixado em formol e incluído em parafina Comparison of three DNA extraction protocols from formaldehyde-fixed and paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    José Veríssimo Fernandes

    2004-06-01

    Full Text Available OBJETIVO: Padronizar um método alternativo para extração de DNA a partir de tecido fixado em formol e conservado em arquivos de blocos de parafina, visando à realização de estudos retrospectivos. MÉTODOS: Comparou-se a eficiência de protocolos de extração de DNA a partir de tecido parafinado, para análise por reação em cadeia de polimerase (PCR, tomando-se como parâmetro um protocolo baseado em um kit comercial. Foram feitas extrações do DNA de 60 espécimes por três métodos: o protocolo A, baseado no kit GlassMAX; o B, utilizando-se o kit GFX TM; e o C, tendo como base o método de Banerjee et al.(2. A integridade e a suficiência do DNA presente na amostra foram avaliadas pela amplificação por PCR de um segmento de 110pb do gene da beta-globina humana, com visualização por meio de eletroforese em gel de poliacrilamida, corado pela prata. Resultados: Das 60 amostras analisadas, 45 apresentaram resultado positivo na PCR quando o DNA foi extraído por qualquer um dos três protocolos. Em seis amostras, a amplificação foi positiva apenas para o DNA extraído pelos protocolos A e C. Em três amostras, o resultado foi positivo apenas para o DNA extraído pelo protocolo A, e em duas, apenas para o DNA extraído pelo protocolo C. CONCLUSÕES: O protocolo C apresentou desempenho semelhante ao do protocolo A, com as vantagens de apresentar menor custo, dispensar o uso de kit comercial, além de não utilizar solventes orgânicos, revelando-se uma alternativa viável para a obtenção de DNA a partir de tecido fixado em formol e incluído em parafina.OBJECTIVE: To set up a method for DNA extraction from paraffin embedded cervical cancer specimens, previously formalin-fixed, aiming to accomplish retrospective analysis. METHODS: Sixty specimens were submitted to DNA extraction by three different methods. All of them involved digestion of the tissues by proteinase K, followed by DNA purification, based in three different approaches

  14. Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens

    International Nuclear Information System (INIS)

    Nielsen, Torsten; Storhoff, James; Wallden, Brett; Schaper, Carl; Ferree, Sean; Liu, Shuzhen; Gao, Dongxia; Barry, Garrett; Dowidar, Naeem; Maysuria, Malini

    2014-01-01

    NanoString’s Prosigna™ Breast Cancer Prognostic Gene Signature Assay is based on the PAM50 gene expression signature. The test outputs a risk of recurrence (ROR) score, risk category, and intrinsic subtype (Luminal A/B, HER2-enriched, Basal-like). The studies described here were designed to validate the analytical performance of the test on the nCounter Analysis System across multiple laboratories. Analytical precision was measured by testing five breast tumor RNA samples across 3 sites. Reproducibility was measured by testing replicate tissue sections from 43 FFPE breast tumor blocks across 3 sites following independent pathology review at each site. The RNA input range was validated by comparing assay results at the extremes of the specified range to the nominal RNA input level. Interference was evaluated by including non-tumor tissue into the test. The measured standard deviation (SD) was less than 1 ROR unit within the analytical precision study and the measured total SD was 2.9 ROR units within the reproducibility study. The ROR scores for RNA inputs at the extremes of the range were the same as those at the nominal input level. Assay results were stable in the presence of moderate amounts of surrounding non-tumor tissue (<70% by area). The analytical performance of NanoString’s Prosigna assay has been validated using FFPE breast tumor specimens across multiple clinical testing laboratories

  15. Semi-Nested Real-Time Reverse Transcription Polymerase Chain Reaction Methods for the Successful Quantitation of Cytokeratin mRNA Expression Levels for the Subtyping of Non-Small-Cell Lung Carcinoma Using Paraffin-Embedded and Microdissected Lung Biopsy Specimens

    International Nuclear Information System (INIS)

    Nakanishi, Yoko; Shimizu, Tetsuo; Tsujino, Ichiro; Obana, Yukari; Seki, Toshimi; Fuchinoue, Fumi; Ohni, Sumie; Oinuma, Toshinori; Kusumi, Yoshiaki; Yamada, Tsutomu; Takahashi, Noriaki; Hashimoto, Shu; Nemoto, Norimichi

    2013-01-01

    In patients with inoperable advanced non-small cell lung carcinomas (NSCLCs), histological subtyping using small-mount biopsy specimens was often required to decide the indications for drug treatment. The aim of this study was to assess the utility of highly sensitive mRNA quantitation for the subtyping of advanced NSCLC using small formalin fixing and paraffin embedding (FFPE) biopsy samples. Cytokeratin (CK) 6, CK7, CK14, CK18, and thyroid transcription factor (TTF)-1 mRNA expression levels were measured using semi-nested real-time quantitative (snq) reverse-transcribed polymerase chain reaction (RT-PCR) in microdissected tumor cells collected from 52 lung biopsies. Our results using the present snqRT-PCR method showed an improvement in mRNA quantitation from small FFPE samples, and the mRNA expression level using snqRT-PCR was correlated with the immunohistochemical protein expression level. CK7, CK18, and TTF-1 mRNA were expressed at significantly higher levels (P<0.05) in adenocarcinoma (AD) than in squamous cell carcinoma (SQ), while CK6 and CK14 mRNA expression was significantly higher (P<0.05) in SQ than in AD. Each histology-specific CK, particularly CK18 in AD and CK6 in SQ, were shown to be correlated with a poor prognosis (P=0.02, 0.02, respectively). Our results demonstrated that a quantitative CK subtype mRNA analysis from lung biopsy samples can be useful for predicting the histology subtype and prognosis of advanced NSCLC

  16. Human papillomavirus detection in paraffin-embedded colorectal cancer tissues.

    Science.gov (United States)

    Tanzi, Elisabetta; Bianchi, Silvia; Frati, Elena R; Amicizia, Daniela; Martinelli, Marianna; Bragazzi, Nicola L; Brisigotti, Maria Pia; Colzani, Daniela; Fasoli, Ester; Zehender, Gianguglielmo; Panatto, Donatella; Gasparini, Roberto

    2015-01-01

    Human papillomavirus (HPV) has a well-recognized aetiological role in the development of cervical cancer and other anogenital tumours. Recently, an association between colorectal cancer and HPV infection has been suggested, although this is still controversial. This study aimed at detecting and characterizing HPV infection in 57 paired biopsies from colorectal cancers and adjacent intact tissues using a degenerate PCR approach. All amplified fragments were genotyped by means of sequencing. Overall, HPV prevalence was 12.3 %. In particular, 15.8 % of tumour tissues and 8.8 % of non-cancerous tissue samples were HPV DNA-positive. Of these samples, 85.7 % were genotyped successfully, with 41.7 % of sequences identifying four genotypes of the HR (high oncogenic risk) clade Group 1; the remaining 58.3 % of HPV-genotyped specimens had an unclassified β-HPV. Examining additional cases and analysing whole genomes will help to outline the significance of these findings.

  17. Comparação de três protocolos distintos para extração de RNA de amostras fixadas em formalina e emblocadas em parafina Comparison of three different protocols for extracting RNA from formalin-fixed paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    Gisele Rodrigues Gouveia

    2011-12-01

    Full Text Available INTRODUÇÃO: Tecidos fixados em formalina e emblocados em parafina (FFEP são importantes fontes de amostras para estudos retrospectivos. Apesar de sua capacidade de preservação de proteínas e morfologia celular, a formalina interfere negativamente em testes de biologia molecular por fragmentar e modificar quimicamente os ácidos nucleicos, particularmente o ácido ribonucleico (RNA. OBJETIVO: Comparar a eficiência de três diferentes protocolos de extração de RNA para análise de expressão gênica de tecidos FFEP. MATERIAL E MÉTODOS: Amostras de linfonodo humano FEEP foram submetidas à extração de RNA utilizando-se os kits Ambion e Arcturus Bioscience e o método clássico de Trizol. Após a extração, o RNA foi quantificado e testado quanto à sua capacidade de amplificaç��o pela reação em cadeia da polimerase em tempo real (RT-PCR utilizando primers do gene endógeno gliceraldeído-3 fosfato desidrogenase (GAPDH. DISCUSSÃO/CONCLUSÃO: Todos os protocolos testados produziram quantidades adequadas e suficientes de RNA total, entretanto, somente os protocolos com uso dos kits Ambion e Arcturus produziram RNA capaz de ser amplificado pela PCR.INTRODUCTION: Formalin fixed paraffin embedded (FFPE tissues are an important sample source for retrospective studies. Despite its ability to preserve proteins and cell morphology, formalin hinders Molecular Biology tests once it fragments and chemically modifies nucleic acids, particularly RNA. OBJECTIVE: To compare the efficiency of three different RNA extraction protocols for gene expression analysis of FFEP tissues. MATERIAL AND METHODS: RNA was extracted from FFPE samples of human lymph by means of Ambion and Arcturus Bioscience kits and the classical Trizol method. After extraction, RNA was quantified and tested for amplification through real time polymerase chain reaction (RT-PCR using glyceraldehydes-3 phosphate dehydrogenase (GAPDH endogenous gene primers. DISCUSSION

  18. Detecção molecular de herpesvírus bovino 1 e 5 em amostras de encéfalo conservadas em formol e emblocadas em parafina provenientes de bovinos com doença neurológica Molecular detection of bovine herpesvirus 1 and 5 in formalin-fixed, paraffin-embedded samples from cattle with neurological disease

    Directory of Open Access Journals (Sweden)

    Laura P. Arruda

    2010-08-01

    Full Text Available A infecção por herpesvírus bovino (BoHV é uma das principais causas de doença neurológica em bovinos na região Centro-Oeste do Brasil. O uso de técnicas moleculares de diagnóstico representa uma contribuição importante para o estudo dessa doença. Este trabalho descreve o uso de uma técnica específica de PCR multiplex para identificar BoHV-5 e BoHV-1 em 76 amostras de encéfalo de bovinos fixadas em formol e incluídas em parafina. Com base nas alterações histológicas, as amostras foram separadas em 2 grupos: o Grupo 1 era composto de 40 amostras de bovinos com meningoencefalite necrosante característica da infecção por BoHV; no Grupo 2 estavam 36 amostras de casos com encefalite não-supurativa inespecífica. Identificação de BoHV-5 foi constatada em 40% das amostras do grupo 1 e em 33% das amostras do grupo 2. Não houve amplificação de DNA de BoHV-1 em nenhuma amostra.Bovine herpesvirus (BoHV is an important cause of neurological disease in cattle in the Midwest Brazil. The application of molecular diagnostic techniques represents an important contribution for the study of BoHV. This paper describes the detection of BoHV-5 and BoHV-1 by a specific multiplex PCR assay in 76 paraffin-embedded samples from central nervous system (CNS of cattle with neurological disorders. The samples were divided into 2 groups according to the histological features: Group 1 was composed of 40 cases of necrotizing meningoencephalitis (characteristic of BoHV infection, and Group 2 was composed of 36 cases of nonspecific nonsuppurative meningoencephalitis. Positive results for BoHV-5 accounted for 40% of the samples in the group 1 and 33% in the group 2. No detection of BoHV-1 was recorded.

  19. Optimization of methods to assess mitochondrial DNA in archival paraffin-embedded tissues from mammary canine tumors Otimização dos métodos para avaliar o DNA mitocondrial obtido a partir de tumores mamários caninos incluídos em parafina

    Directory of Open Access Journals (Sweden)

    Angélica C. Bertagnolli

    2008-08-01

    Full Text Available In this study we describe the alterations used to extract and amplify mitochondrial desoxyribonucleic acid (DNA from formalin-fixed paraffin-embedded samples of canine mammary tumors. The epithelial and mesenchymal components (chondromyxoid and chondroid of each tumor, as well as the normal mammary gland tissues, were manually microdissected from 19 mixed canine mammary tumors (10 benign mixed tumors and nine carcinomas arising in mixed tumors. DNA was extracted by Invisorb® Spin Tissue Mini Kit, with protocol changes proposed by the manufacturer. A 273-bp fragment was amplified by polymerase chain reaction (PCR and submitted to automatic sequence analysis. The fragment was successfully analyzed in 100% of the samples. However, an additional lysis step, the reduction of volume in buffer solutions and PCR, a higher annealing temperature and an increase in the number of PCR cycles were required. The initial PCR products were diluted and re-amplified in six samples so that they could be successfully analyzed.A presente comunicação descreve as modificações usadas para extrair e amplificar o DNA mitocondrial obtido de amostras de tumores mamários caninos fixados em formol tamponado a 10% e incluídos em parafina. Os componentes epiteliais e mesenquimais (condromixóide e condróide, bem como a mama normal adjacente, foram microdissectados manualmente de 19 tumores mamários (10 tumores mistos benignos e nove carcinomas em tumores mistos. O DNA foi extraído utilizando-se o Invisorb® Spin Tissue Mini Kit com modificações do protocolo proposto pelo fabricante. Um fragmento de 273-pb foi amplificado por reação em cadeia da polimerase (PCR e seqüenciado em seqüenciador automático. O fragmento foi analisado em 100% das amostras, entretanto modificações como lise adicional, redução do volume das soluções de extração e PCR, aumento da temperatura de anelamento e do número de ciclos de amplificação foram necessárias. Em seis

  20. Surfactants from petroleum paraffin wax

    Energy Technology Data Exchange (ETDEWEB)

    Kassem, T.M.; Hussein, M.H.; El Sayed, A.S.

    Paraffin wax from Egyptian petroleum was purified and then oxidized to fatty acids which were esterified to form their methyl esters, fractionated and then hydrolysed. The obtained fatty acids were converted into the corresponding primary amines which were converted with ethylene oxide to form nonionic surfactants. The prepared primary amines were also converted into tertiary amines and then converted into cationic surfactants through condensation with benzyl chloride or 1-chloromethylnaphthalene. Also, amine oxide surfactants were prepared by oxidation of the tertiary amines with hydrogen peroxide. The surface active properties of all the prepared surfactants were determined, and the effect of their chemical structure on the surfactant properties are discussed in this paper.

  1. Embedded Systems

    Indian Academy of Sciences (India)

    Embedded system, micro-con- troller ... Embedded systems differ from general purpose computers in many ... Low cost: As embedded systems are extensively used in con- .... operating systems for the desktop computers where scheduling.

  2. Nitrous Oxide/Paraffin Hybrid Rocket Engines

    Science.gov (United States)

    Zubrin, Robert; Snyder, Gary

    2010-01-01

    Nitrous oxide/paraffin (N2OP) hybrid rocket engines have been invented as alternatives to other rocket engines especially those that burn granular, rubbery solid fuels consisting largely of hydroxyl- terminated polybutadiene (HTPB). Originally intended for use in launching spacecraft, these engines would also be suitable for terrestrial use in rocket-assisted takeoff of small airplanes. The main novel features of these engines are (1) the use of reinforced paraffin as the fuel and (2) the use of nitrous oxide as the oxidizer. Hybrid (solid-fuel/fluid-oxidizer) rocket engines offer advantages of safety and simplicity over fluid-bipropellant (fluid-fuel/fluid-oxidizer) rocket en - gines, but the thrusts of HTPB-based hybrid rocket engines are limited by the low regression rates of the fuel grains. Paraffin used as a solid fuel has a regression rate about 4 times that of HTPB, but pure paraffin fuel grains soften when heated; hence, paraffin fuel grains can, potentially, slump during firing. In a hybrid engine of the present type, the paraffin is molded into a 3-volume-percent graphite sponge or similar carbon matrix, which supports the paraffin against slumping during firing. In addition, because the carbon matrix material burns along with the paraffin, engine performance is not appreciably degraded by use of the matrix.

  3. Technical validation of an RT-qPCR in vitro diagnostic test system for the determination of breast cancer molecular subtypes by quantification of ERBB2, ESR1, PGR and MKI67 mRNA levels from formalin-fixed paraffin-embedded breast tumor specimens.

    Science.gov (United States)

    Laible, Mark; Schlombs, Kornelia; Kaiser, Katharina; Veltrup, Elke; Herlein, Stefanie; Lakis, Sotiris; Stöhr, Robert; Eidt, Sebastian; Hartmann, Arndt; Wirtz, Ralph M; Sahin, Ugur

    2016-07-07

    MammaTyper is a novel CE-marked in vitro diagnostic RT-qPCR assay which assigns routinely processed breast cancer specimens into the molecular subtypes Luminal A-like, Luminal B-like (HER2 positive or negative), HER2 positive (non-luminal) and Triple negative (ductal) according to the mRNA expression of ERBB2, ESR1, PGR and MKI67 and the St Gallen consensus surrogate clinical definition. Until now and regarding formalin-fixed, paraffin-embedded material (FFPE), this has been a task mostly accomplished by immunohistochemistry (IHC). However the discrepancy rates of IHC for the four breast cancer biomarkers are frequently under debate, especially for Ki-67 which carries the highest degree of inter- and even intra-observer variability. Herein we describe a series of studies in FFPE specimens which aim to fully validate the analytical performance of the MammaTyper assay, including the site to site reproducibility of the individual marker measurements. Tumor RNA was extracted with the novel RNXtract RNA extraction kit. Synthetic RNA was used to assess the sensitivity of the RNXtract kit. DNA and RNA specific qPCR assays were used so as to determine analyte specificity of RNXtract. For the assessment of limit of blank, limit of detection, analytical measurement range and PCR efficiency of the MammaTyper kit serial dilutions of samples were used. Analytical precision studies of MammaTyper were built around two different real time PCR platforms and involved breast tumor samples belonging to different subtypes analyzed across multiple sites and under various stipulated conditions. The MammaTyper assay robustness was tested against RNA input variations, alternative extraction methods and tumor cell content. Individual assays were linear up to at least 32.33 and 33.56 Cqs (quantification cycles) for the two qPCR platforms tested. PCR efficiency ranged from 99 to 109 %. In qPCR platform 1, estimates for assay specific inter-site standard deviations (SD) were between 0.14 and

  4. Technical validation of an RT-qPCR in vitro diagnostic test system for the determination of breast cancer molecular subtypes by quantification of ERBB2, ESR1, PGR and MKI67 mRNA levels from formalin-fixed paraffin-embedded breast tumor specimens

    International Nuclear Information System (INIS)

    Laible, Mark; Schlombs, Kornelia; Kaiser, Katharina; Veltrup, Elke; Herlein, Stefanie; Lakis, Sotiris; Stöhr, Robert; Eidt, Sebastian; Hartmann, Arndt; Wirtz, Ralph M.; Sahin, Ugur

    2016-01-01

    MammaTyper is a novel CE-marked in vitro diagnostic RT-qPCR assay which assigns routinely processed breast cancer specimens into the molecular subtypes Luminal A-like, Luminal B-like (HER2 positive or negative), HER2 positive (non-luminal) and Triple negative (ductal) according to the mRNA expression of ERBB2, ESR1, PGR and MKI67 and the St Gallen consensus surrogate clinical definition. Until now and regarding formalin-fixed, paraffin-embedded material (FFPE), this has been a task mostly accomplished by immunohistochemistry (IHC). However the discrepancy rates of IHC for the four breast cancer biomarkers are frequently under debate, especially for Ki-67 which carries the highest degree of inter- and even intra-observer variability. Herein we describe a series of studies in FFPE specimens which aim to fully validate the analytical performance of the MammaTyper assay, including the site to site reproducibility of the individual marker measurements. Tumor RNA was extracted with the novel RNXtract RNA extraction kit. Synthetic RNA was used to assess the sensitivity of the RNXtract kit. DNA and RNA specific qPCR assays were used so as to determine analyte specificity of RNXtract. For the assessment of limit of blank, limit of detection, analytical measurement range and PCR efficiency of the MammaTyper kit serial dilutions of samples were used. Analytical precision studies of MammaTyper were built around two different real time PCR platforms and involved breast tumor samples belonging to different subtypes analyzed across multiple sites and under various stipulated conditions. The MammaTyper assay robustness was tested against RNA input variations, alternative extraction methods and tumor cell content. Individual assays were linear up to at least 32.33 and 33.56 Cqs (quantification cycles) for the two qPCR platforms tested. PCR efficiency ranged from 99 to 109 %. In qPCR platform 1, estimates for assay specific inter-site standard deviations (SD) were between 0.14 and 0

  5. Rubidium dimers in paraffin-coated cells

    International Nuclear Information System (INIS)

    Acosta, V M; Windes, D; Corsini, E; Ledbetter, M P; Karaulanov, T; Budker, D; Jarmola, A; Auzinsh, M; Rangwala, S A; Jackson Kimball, D F

    2010-01-01

    Measurements were made to determine the density of rubidium dimer vapor in paraffin-coated cells. The number density of dimers and atoms in similar paraffin-coated and uncoated cells was measured by optical spectroscopy. Due to the relatively low melting point of paraffin, a limited temperature range of 43-80 0 C was explored, with the lower end corresponding to a dimer density of less than 10 7 cm -3 . With 1 min integration time, a sensitivity to dimer number density of better than 10 6 cm -3 was achieved. No significant difference in dimer density between the cells was observed.

  6. Solubilization of paraffinic deposits for microemulsions

    Energy Technology Data Exchange (ETDEWEB)

    Gomes, Erika A.S.; Soares, Ranieri G.F.; Nascimento, Roseane E.S.; Dantas Neto, Afonso A.; Barros Neto, Eduardo L. [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil)

    2008-07-01

    The oil company has been intensifying its efforts to find more efficient solutions for the problems related to the paraffin in wells and transport lines. When applied in the flow lines, the solvents dissolve the paraffin and they must be used hot, since the temperature increases the solubility of the wax and, consequently, its removal rate. The microemulsions appear as an alternative capable of acting in the solubilization and in the inhibition of the formation of deposits due to its great interfacial area, low superficial tension and high capacity of solubilization. They present some advantages in relation to the methods of use of chemical products due to its flexibility of composition in which they can be used, presenting low toxicity and inflammability, without any loss of its capacity of solubilization. The use of oil-in-water microemulsion aims to solubilized paraffin in the disperse phase, where one can find the apolar part of the molecule of the surfactant and the also apolar chain of paraffin, occurring, therefore the 'encapsulation' of the crystal, prohibiting the growth of the chain due to the affinity of paraffin and oil. In this in case, it is possible to transport the inserted paraffin in direct micelles, reducing the precipitation and optimizing the transport. (author)

  7. In situ hybridization for the detection of infectious laryngotracheitis virus in sections of trachea from experimentally infected chickens

    DEFF Research Database (Denmark)

    Nielsen, O.L.; Handberg, Kurt; Jørgensen, Poul Henrik

    1998-01-01

    An in situ hybridization procedure for the detection of infectious laryngotracheitis virus (ILTV) in experimentally infected chickens is described. Formalin-fixed, paraffin-embedded sections of trachea, taken from chickens on days 3-10 post-inoculation (p.i.) with ILTV were hybridized with a mixt......An in situ hybridization procedure for the detection of infectious laryngotracheitis virus (ILTV) in experimentally infected chickens is described. Formalin-fixed, paraffin-embedded sections of trachea, taken from chickens on days 3-10 post-inoculation (p.i.) with ILTV were hybridized...... on day 5 p.i. No hybridization was observed in 3 out of 3 chickens examined on day 10 p.i. ILTV nucleic acid was detected in nuclei of degenerated tracheal epithelial cells and in intranuclear inclusion bodies of syncytia....

  8. Biodegradation of paraffin wax by crude Aspergillus enzyme preparations for potential use in removing paraffin deposits.

    Science.gov (United States)

    Zhang, Junhui; Xue, Quanhong; Gao, Hui; Wang, Ping

    2015-11-01

    Paraffin deposition problems have plagued the oil industry. Whist mechanical and chemical methods are problematic, microbiological method of paraffin removal is considered an alternative. However, studies have mainly investigated the use of bacteria, with little attention to the potential of fungi. The performance of six Aspergillus isolates to degrade paraffin wax was evaluated under laboratory conditions using solid enzyme preparations. The results showed that all the six enzyme preparations efficiently improved the solubility of paraffin wax in n-hexane and degraded n-alkanes in paraffin wax. The degradation process was accompanied by dynamic production of gases (CO2 and H2 ) and organic acids (oxalate and propionate). The shape of wax crystals markedly changed after enzymatic degradation, with a rough surface and a loose structure. This study indicates that extracellular enzymes from Aspergillus spp. can efficiently degrade paraffin wax. These enzyme preparations have the potential for use in oil wells with paraffin deposition problems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Recrystallization phenomena of solution grown paraffin dendrites

    NARCIS (Netherlands)

    Hollander, F.F.A.; Hollander, F.; Stasse, O.; van Suchtelen, J.; van Enckevort, W.J.P.

    2001-01-01

    Paraffin crystals were grown from decane solutions using a micro-Bridgman set up for in-situ observation of the morphology at the growth front. It is shown that for large imposed velocities, dendrites are obtained. After dendritic growth, aging or recrystallization processes set in rather quickly,

  10. Topical analgesic added to paraffin enhances paraffin bath treatment of individuals with hand osteoarthritis.

    Science.gov (United States)

    Myrer, Joseph William; Johnson, Aaron Wayne; Mitchell, Ulrike H; Measom, Gary J; Fellingham, Gilbert W

    2011-01-01

    To compare treating patients with symptomatic hand osteoarthritis (OA) with paraffin baths only (PO) (100% wax) or paraffin baths 80% wax with 20% topical analgesic (PTA). Subjects met criteria of the American College of Rheumatology for classifying symptomatic hand OA and had a Dreiser's index score >5 points. Current and average pain at rest and with movement was assessed with visual analogue scales. Hand function was assessed by the functional index for hand OA (FIHOA). Both groups had a significant reduction in their 'current' pain 15 min after the first and twelfth treatments compared to pre-treatment but there was no difference between groups (t = 0.10, p > 0.05). The PTA group had greater improvement over the 12 treatment sessions for their pain at rest (t = 2.92, p paraffin produced significantly greater pain relief at rest and during movement than paraffin baths alone after 12 treatments. Additionally, the PTA group experienced greater improved hand function.

  11. Implantation of refractive multifocal intraocular lens with a surface-embedded near section for cataract eyes complicated with a coexisting ocular pathology.

    Science.gov (United States)

    Ouchi, M; Kinoshita, S

    2015-05-01

    To evaluate the postoperative outcomes of cataract eyes complicated with coexisting ocular pathologies that underwent implantation of a refractive multifocal intraocular lens (MIOL) with a surface-embedded near section. LENTIS MPlus (Oculentis GmbH) refractive MIOLs were implanted in 15 eyes with ocular pathologies other than cataract (ie, six high-myopia eyes with an axial length longer than 28 mm, two fundus albipunctatus eyes, two branch retinal-vein occlusion eyes, four glaucoma eyes (one with high myopia), and two keratoconus eyes). Uncorrected or corrected distance and near visual acuity (VA) (UDVA, UNVA, CDVA, and CNVA), contrast sensitivity, and defocus curve were measured at 1 day and 6 months postoperatively, and each patient completed a 6-month postoperative questionnaire regarding vision quality and eyeglass use. Thirteen eyes (87%) registered 0 or better in CDVA and 12 eyes (73%) registered better than 0 in CNVA. Contrast sensitivity in the eyes of all patients was comparable to that of normal healthy subjects. No patient required eyeglasses for distance vision, but three patients (20%) required them for near vision. No patient reported poor or very poor vision quality. With careful case selection, sectorial refractive MIOL implantation is effective for treating cataract eyes complicated with ocular pathologies.

  12. A method for producing liquid paraffin

    Energy Technology Data Exchange (ETDEWEB)

    Dorodnova, V.S.; Martynenko, A.G.; Pereverzev, A.N.

    1983-01-01

    In the known method (Sp) for producing liquid paraffins (ZhP) through processing an oil fraction by crystalline carbamide in the presence of a solvent with subsequent removal of the formed complex (Km) of KA with the liquid paraffins from the deparaffinized product, staged washing and decomposition of the complex with isolation of the liquid paraffins, in order to increase the output of liquid paraffin and to improve its quality, beta,beta'-dichlorethyl ether (khloreks) in a mixture with methylethyl ketone (MEK) or methylisobutyl ketone in a ratio of 1 is used as the solvent, the processing by the crystalline carbamide is conducted with the addition of 180 to 260 percent solvent to raw material (Sr) and the washing of the composition is conducted by a solvent in the first stage and by methylethyl ketone or methylisobutyl ketone in the second stage. The crystalline carbamide for the complex formation is taken in a conversion of 60 to 70 percent for the raw material for observing the raw material to solvent ratio of from 1 to 1.8 to 2.6 to 0.6 to 0.6. The temperature in the zone of formation of the complex is maintained at 5 to 35 degrees. The presence of beta,beta'-dichlorethyl ether, which has high selectivity relative to aromatic hydrocarbons (ArU) and to resinous compounds provides for a sharp reduction in the adsorption of the undesired components on the surface of the granules of the complex and the crystalline carbamide and to a reduction in the portion of the alkylaromatic hydrocarbons (UV) extracted into the complex, which leads to a substantial improvement in the quality of the obtained liquid paraffins.

  13. Magnetization of Paraffin-Based Magnetic Nanocolloids

    Science.gov (United States)

    Dikanskii, Yu. I.; Ispiryan, A. G.; Kunikin, S. A.; Radionov, A. V.

    2018-01-01

    Using paraffin-based magnetic nanocolloids as an example, the reasons for maxima in the temperature dependence of the magnetic susceptibility of magnetic colloids have been discussed. The behavior of these dependences in a wide temperature interval has been analyzed for colloids in solid and liquid states. It has been concluded that the maximum observed at the melting point of paraffin can be attributed to freezing Brownian degrees of freedom in magnetite coarse particles, the magnetic moment of which is intimately related to the solid matrix. The second main maximum, which arises in the solid state, is explained by the superparamagnetic-magnetically hard transition of most fine particles at lower temperatures. It has been noted that the flatness of this maximum results from the polydispersity of the magnetic nanoparticle ensemble.

  14. Interaction of oil and paraffin with sodium

    Energy Technology Data Exchange (ETDEWEB)

    Kozlov, F A; Zagorulko, Yu I; Kovalev, Yu P; Lamykin, E V; Alekseev, V V; Sergeev, G P [Institute of Physics and Power Engineering, Obninsk (USSR)

    1980-05-01

    This report presents the investigation results on the kinetics of a gaseous oil pyrolysis product composition change in the presence of sodium under static conditions at 350 deg. C, 550 deg. C and 700 deg. C as well as the behaviour of oil and paraffin within the sodium circulating loops. The calculated estimations of the critical oil physical state parameters in sodium flows are given. (author)

  15. Interaction of oil and paraffin with sodium

    International Nuclear Information System (INIS)

    Kozlov, F.A.; Zagorulko, Yu.I.; Kovalev, Yu.P.; Lamykin, E.V.; Alekseev, V.V.; Sergeev, G.P.

    1980-01-01

    This report presents the investigation results on the kinetics of a gaseous oil pyrolysis product composition change in the presence of sodium under static conditions at 350 deg. C, 550 deg. C and 700 deg. C as well as the behaviour of oil and paraffin within the sodium circulating loops. The calculated estimations of the critical oil physical state parameters in sodium flows are given. (author)

  16. Embedded defects

    International Nuclear Information System (INIS)

    Barriola, M.; Vachaspati, T.; Bucher, M.

    1994-01-01

    We give a prescription for embedding classical solutions and, in particular, topological defects in field theories which are invariant under symmetry groups that are not necessarily simple. After providing examples of embedded defects in field theories based on simple groups, we consider the electroweak model and show that it contains the Z string and a one-parameter family of strings called the W(α) string. It is argued that although the members of this family are gauge equivalent when considered in isolation, each member becomes physically distinct when multistring configurations are considered. We then turn to the issue of stability of embedded defects and demonstrate the instability of a large class of such solutions in the absence of bound states or condensates. The Z string is shown to be unstable for all values of the Higgs boson mass when θ W =π/4. W strings are also shown to be unstable for a large range of parameters. Embedded monopoles suffer from the Brandt-Neri-Coleman instability. Finally, we connect the electroweak string solutions to the sphaleron

  17. Bio-paraffins: alternative products to petroleum paraffins; Bioparafinas: produtos alternativos as parafinas de petroleo

    Energy Technology Data Exchange (ETDEWEB)

    Lima, Anie Daniela Medeiros [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES). Gerencia de Hidrorrefino e Processos Especiais; Oliveira, Claudia Cristina Cardoso Calvano de; Carvalho, Ivone de Freitas; Silva, Danilo do Carmo Santos; Cruz, Valeria Senra da Silva [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES). Gerencia de Lubrificantes e Produtos Especiais]. E-mails: anie.lima, claudiacristina, ivone, danilosilva, vsenra@petrobras.com.br

    2007-04-15

    Market trends and social and environmental issues encouraged the vegetal wax presence in the world-wide paraffin market. This work presents the most commercialized vegetal waxes, soy and pal, comparing their physicochemical characteristics and their applicability with the paraffins obtained from petroleum. It also presents a characterization of the carnauba wax, produced exclusively in Brazil and a comparison with paraffins from petroleum. The carnauba wax is an alternative product, with good applicability as a substitute for waxes from petroleum or a petroleum/vegetal mixture. The characteristics of palm and soy waxes show the possible application in candles, cosmetics, foods and others industries. Brazil, having a great agricultural potential, represents a source of vegetal wax that could be use to meet the market demands. (author)

  18. Multiphoton microscopic imaging of histological sections without hematoxylin and eosin staining differentiates carcinoma in situ lesion from normal oesophagus

    Science.gov (United States)

    Chen, Jianxin; Xu, Jian; Kang, Deyong; Xu, Meifang; Zhuo, Shuangmu; Zhu, Xiaoqin; Jiang, Xingshan

    2013-10-01

    Multiphoton microscopy (MPM) has become a powerful, important tool for tissues imaging at the molecular level. In this paper, this technique was extended to histological investigations, differentiating carcinoma in situ (CIS) lesion from normal oesophagus by imaging histological sections without hematoxylin and eosin (H&E) staining. The results show that the histology procedures of dehydration, paraffin embedding, and de-paraffinizing highlighted two photon excited fluorescence of cytoplasm and nucleolus of epithelial cell and collagen in stroma. MPM has the ability to identify the characteristics of CIS lesion including changes of squamous cells and full epithelium, identification of basement membrane, especially prominent nucleolus. The studies described here show that MPM has the potential for future retrospective studies of tumor staging by employing on histological section specimens without H&E staining.

  19. Endothelial cells and hematopoiesis: a light microscopic study of fetal, normal, and pathologic human bone marrow in plastic-embedded sections.

    Science.gov (United States)

    Islam, A; Glomski, C; Henderson, E S

    1992-07-01

    The origin and morphological identity of hematopoietic progenitor cells, as well as their precursor, the pleuripotential hematopoietic stem cell (HSC), has not been established. Our studies of 2 microns sectioned undecalcified plastic-embedded bone marrow (BM) from healthy human fetuses; normal adults; patients with acute myeloblastic leukemia (AML), acute lymphoblastic leukemia (ALL), and chronic granulocytic leukemia (CGL) in various stages (chronic, accelerated, acute blastic phase, and after autografting); and patients recovering from therapy-induced marrow hypoplasia suggest that proliferative hematopoietic zones exist near the endosteum (endosteal marrow) and the vascular endothelium (capillary and sinus-lining endothelium) and a maturational zone distal to these regions. In some of these areas, morphologically recognizable hematopoietic cells were seen and interpreted as emerging and maturing in a sequential progression, suggesting an origin from the endosteal or endothelial progenitors. In other loci, early hematopoietic cells were seen in close contact with the endosteal or vascular endothelial (VE) cells. This latter relationship suggested that these areas of cellular contact were important and represented sites of cell to cell interaction that may be associated with the liberation of growth factors by endosteal and endothelial cells and their action on hematopoietic progenitor cells. Following treatment-induced hypoplasia, the endosteal and VE cells were seen to modulate, transform, and migrate into the surrounding empty and edematous marrow space as fibroblasts. Later, as hemopoietic regeneration began, clusters of regenerating hematopoietic cells were seen adjacent to bone trabecule (BT) and near the vascular endothelium. We postulate that endosteal and VE cells are the equivalent of embryonal-stage, undifferentiated mesenchyme and, under the appropriate regulatory influence, are capable of modulation and transformation (differentiation) into stromal

  20. Experimental analysis of a paraffin-based cold storage tank

    OpenAIRE

    Barbara Torregrosa-Jaime; López-Navarro, Alejandro; Corberán, José M.; Esteban-Matías, J. C.; Klinkner, L.; Payá-Herrero, Jorge

    2013-01-01

    [EN] The aim of this study is to characterize a paraffin-based cold storage tank. Novel experimental results are presented for this system which combines a significant amount of paraffin (1450 kg) immersed around 18 spiral-shaped coils disposed in counter-current flow. The paraffin has a phase-change temperature in the range 4 8 °C as measured by a 3-layer calorimeter. Different tests have been carried out with a constant mass flow rate and supply temperature. Around 31% of the paraffin has h...

  1. Development of paraffin and paraffin/bitumen composites with additions of B2O3 for thermal neutron shielding applications

    International Nuclear Information System (INIS)

    Toyen, Donruedee; Saenboonruang, Kiadtisak

    2017-01-01

    In this work, paraffin and paraffin/bitumen composites with additions of boron oxide (B 2 O 3 ) were prepared to evaluate the viscosity, flexural, and thermal neutron shielding properties for uses as thermal neutron shielding materials. The results showed that the addition of 3 wt% or 9 wt% bitumen to paraffin increased the overall flexural properties with the content of 9 wt% bitumen having the highest values. The improvement in flexural properties made the composites less brittle, stiffer, and longer-lasting. Furthermore, different contents of B 2 O 3 (0, 7, 14, 21, 28, and 35 wt%) were added to paraffin and paraffin/bitumen composites to investigate the effects of the B 2 O 3 contents. The results indicated that an increase in B 2 O 3 contents improved the shielding properties but slightly reduced the flexural properties. Specifically for 5-mm paraffin and 5-mm paraffin/bitumen samples with 35 wt% of B 2 O 3 , both samples could reduce neutron flux by more than 70%. The overall results suggested that the paraffin and paraffin/bitumen composites with additions of B 2 O 3 showed improved properties for utilization as effective thermal neutron shielding materials. (author)

  2. Embedded Hardware

    CERN Document Server

    Ganssle, Jack G; Eady, Fred; Edwards, Lewin; Katz, David J; Gentile, Rick

    2007-01-01

    The Newnes Know It All Series takes the best of what our authors have written to create hard-working desk references that will be an engineer's first port of call for key information, design techniques and rules of thumb. Guaranteed not to gather dust on a shelf!. Circuit design using microcontrollers is both a science and an art. This book covers it all. It details all of the essential theory and facts to help an engineer design a robust embedded system. Processors, memory, and the hot topic of interconnects (I/O) are completely covered. Our authors bring a wealth of experience and ideas; thi

  3. Radiometric determination of uniformity of putting paraffin on textile threads

    International Nuclear Information System (INIS)

    Ridel', Z.; Kherrmann, Eh.; Shefer, I.; Tseiner, A.

    1979-01-01

    To improve processing of the natural and synthetic fiber threads on stocking-frames, they are treated by paraffin. Paraffin is applied in the amounts nearly equal to 0.1 -1.0 g for 10 4 m of the thread's length. To determine amount of paraffin on thread and to determine uniformity if its application, a radiometric method has been developed. As a radioactive label, didocilephosphate of rare earths was used. This compound has good solubility in hydrocarbons and does not change physical properties of paraffin in the investigated field of its application as well as its concentration. It is possible to add to paraffin this radioactive label or a non-active label with subsequent its activation. Amount of paraffin, applied on a thread is determined by means of measurement of activity of thread samples of different length. Information about uniformity of paraffin application on thread have been obtained by means of autoradiography. It has been found that paraffin in mainly applied on the thread's bulges [ru

  4. Cleaning of paraffins and their microbiological transformation

    Energy Technology Data Exchange (ETDEWEB)

    Shakarashvili, T S; Bekauri, N G; Chubinidze, N G; Dididze, A V

    1982-01-01

    This paper provides a perfected technique for processing liquid C/sub 11/-C/sub 20/ alkanes extracted from Georgian oil (from the Samgori field). Utilizing this base, a biomass was derived with the aid of the Candida Guillermondy culture. The method for cleaning the paraffin complex with carbamide was simplified during the deparaffinization process of diesel fuel (fraction 200-300/sup 0/C) by application of a washing agent -petr. ether with a boiling temp. of 40-70/sup 0/C. The derived alkanes contained up to 0.2% of aromatic hydrocarbons. This eliminated the rather expensive and labor-intensive step in the dewaxing process -- adsorption chromatography. It was demonstrated that under optimal conditions the amount of cultured product was higher in n-alkanes from Samgori oil than from the petroleum utilized at the Akhmet biochemical plant.

  5. Modulated structure formation in demixing paraffin blends

    CERN Document Server

    Gilbert, E P

    2002-01-01

    Small angle scattering (SANS and SAXS) and differential scanning calorimetry have been measured from C sub 2 sub 8 :C sub 3 sub 6 normal paraffin mixtures of varying composition quenched from the melt. Satellite peaks are observed in the SAXS whose offset in Q, relative to Bragg diffraction peaks associated with the average structure, are composition dependent. The offset is close to the position of the most intense peak observed in SANS. Scattering from the quenched structures is consistent with a correlated displacement and substitutional disorder model yielding modulations that are incommensurate with the average lattice. DSC shows an additional endotherm in the mixtures that is not present in the pure components and is associated with this superstructure formation. (orig.)

  6. Modulated structure formation in demixing paraffin blends

    International Nuclear Information System (INIS)

    Gilbert, E.P.

    2002-01-01

    Small angle scattering (SANS and SAXS) and differential scanning calorimetry have been measured from C 28 :C 36 normal paraffin mixtures of varying composition quenched from the melt. Satellite peaks are observed in the SAXS whose offset in Q, relative to Bragg diffraction peaks associated with the average structure, are composition dependent. The offset is close to the position of the most intense peak observed in SANS. Scattering from the quenched structures is consistent with a correlated displacement and substitutional disorder model yielding modulations that are incommensurate with the average lattice. DSC shows an additional endotherm in the mixtures that is not present in the pure components and is associated with this superstructure formation. (orig.)

  7. Binary liquid-liquid equilibria of aniline-paraffin and furfural-paraffin systems

    Energy Technology Data Exchange (ETDEWEB)

    Sen, S.C.; Maity, S.; Ganguli, K.; Ray, P. (Calcutta Univ., (India))

    1991-12-01

    Liquid-liquid-equilibria (L-L-E) of hydrocarbon containing systems are of considerable commercial importance to refineries. But prediction of L-L-E of such systems is extremely difficult owing to the complex nature of the petroleum fluids. For treating such complex mixtures, a continuous component method is appropriate and for representing such liquids, a group contribution model like the UNIFAC is extremely convenient. It is, however, necessary to determine the appropriate group interaction parameters, and also to test the applicability of the UNIFAC method to these cases. Binary liquid-liquid-equilibria data for several aniline-paraffin and furfural-paraffin systems have been taken. These data along with data for other aniline-hydrocarbon and furfural-hydrocarbon systems from literature have been correlated using the UNIFAC model. The UNIFAC group interaction parameters have been found to have a linear temperature dependence. The CH{sub 2} groups in cyclo and non-cyclo paraffins require different interaction parameters. It was also found that a scaling of the combinatorial term is necessary for higher molecular weight hydrocarbons. 13 refs., 12 figs., 5 tabs.

  8. Modelling of an experiment INSS and paraffin moderator at JINR

    International Nuclear Information System (INIS)

    Goyal, Uttam; Kumawat, Harphool; Kumar, V.; Barashenkov, V.S.

    2002-01-01

    Intense neutron spallation source (INSS) described elsewhere is studied with paraffin moderator using the Dubna cascade code. For the present study paraffin is assumed having configuration corresponding to C 22 H 46 with density = 0.87 g/cm 3 6 cm thickness of paraffin is coated around the Pb-spallation target of size ΦxL = 8x20 cm 2 and proton beam with E lab = 1 GeV is allowed to collide at the center of the left face

  9. Photothermally Driven Refreshable Microactuators Based on Graphene Oxide Doped Paraffin.

    Science.gov (United States)

    Hou, Sichao; Wang, Miao; Guo, Shouwu; Su, Ming

    2017-08-09

    Actuators based on phase change materials (paraffin) can simultaneously produce large stroke length and large force due to thermal expansion, but the low thermal conductivity of paraffin requires high power input and long actuation time. The graphene oxide (GO) doped paraffin dynamic actuator addresses the key challenges in the design of thermal phase change actuators: Thermal conductivity and light absorbing are increased, and the response time is reduced compared to the standard phase change actuator designed with metal heating resistors. The thermal properties of GO-paraffin composites with varied loading amount are characterized to confirm the optimal loading amount of 1.0%. A multicell phase change actuator was integrated into a digital micromirror controlled optical system. A series of photothermally driven refreshable patterns were generated and confirmed with infrared imaging.

  10. Effects of short-chain chlorinated paraffins on soil organisms.

    Science.gov (United States)

    Bezchlebová, Jitka; Cernohlávková, Jitka; Kobeticová, Klára; Lána, Jan; Sochová, Ivana; Hofman, Jakub

    2007-06-01

    Despite the fact that chlorinated paraffins have been produced in relatively large amounts, and high concentrations have been found in sewage sludge applied to soils, there is little information on their concentrations in soils and the effect on soil organisms. The aim of this study was to investigate the toxicity of chlorinated paraffins in soils. The effects of short-chain chlorinated paraffins (64% chlorine content) on invertebrates (Eisenia fetida, Folsomia candida, Enchytraeus albidus, Enchytraeus crypticus, Caenorhabditis elegans) and substrate-induced respiration of indigenous microorganisms were studied. Differences were found in the sensitivity of the tested organisms to short-chain chlorinated paraffins. F. candida was identified as the most sensitive organism with LC(50) and EC(50) values of 5733 and 1230 mg/kg, respectively. Toxicity results were compared with available studies and the predicted no effect concentration (PNEC) of 5.28 mg/kg was estimated for the soil environment, based on our data.

  11. resistant containers on the incidence of paraffin (kerosene)

    African Journals Online (AJOL)

    whether its use would decrease the incidence ofparaffin ingestion. ... education to prevent paraffin poisoning. S Atr Med J 1994; 84: ... organised poster competitions, and pamphlets with ... 2-litre plastic container designed according to the.

  12. Observations of radiation damage effects in paraffin and polyethylene crystals

    International Nuclear Information System (INIS)

    Petermann, J.; Gleiter, H.; Bochum Univ.

    1973-01-01

    A report is given on electron microscopic observations on n-paraffin and polyethylene monocrystals after irradiating with electrons. The observations show that the cross-links in n-paraffin monocrystals form agglomerates which preferably occur in the neighbourhood of lattice defects. In polyethylene monocrystals, the cross-links line up in long rows parallel to the [100] or [010] direction. (orig./LH) [de

  13. Embedded Processor Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Embedded Processor Laboratory provides the means to design, develop, fabricate, and test embedded computers for missile guidance electronics systems in support...

  14. Numerical Analysis of a Paraffin/Metal Foam Composite for Thermal Storage

    Science.gov (United States)

    Di Giorgio, P.; Iasiello, M.; Viglione, A.; Mameli, M.; Filippeschi, S.; Di Marco, P.; Andreozzi, A.; Bianco, N.

    2017-01-01

    In the last decade, the use of Phase Change Materials (PCMs) as passive thermal energy storage has been widely studied both analytically and experimentally. Among the PCMs, paraffins show many advantages, such as having a high latent heat, a low vapour pressure, being chemically inert, stable and non-toxic. But, their thermal conductivity is very low with a high volume change during the melting process. An efficient way to increase their poor thermal conductivity is to couple them with open cells metallic foams. This paper deals with a theoretical analysis of paraffin melting process inside an aluminum foam. A mathematical model is developed by using the volume-averaged governing equations for the porous domain, made up by the PCM embedded into the metal foam. Non-Darcian and buoyancy effects are considered in the momentum equation, while the energy equations are modelled with the Local Thermal Non-Equilibrium (LTNE) approach. The PCM liquefaction is treated with the apparent heat capacity method and the governing equations are solved with a finite-element scheme by COMSOL Multiphysics®. A new method to calculate the coupling coefficients needed for the thermal model has been developed and the results obtained have been validated comparing them to experimental data in literature.

  15. Synthesis and application of polyaminoamide as new paraffin inhibitor from vegetable oil

    OpenAIRE

    Chen, Gang; Tang, Ying; Zhang, Jie

    2011-01-01

    Abstract In this work, a series of novel paraffin inhibitor, polyaminoamide (PAA), was designed and prepared by aminolysis and poly-condensation using soybean oil and canola oil as the raw material. The property of the PAAs as paraffin inhibitor was investigated, the results show several PAA samples are potent in paraffin inhibition, and PPC-2 is the most effective one. Besides, the paraffin crystal morphology analysis was carried out to provide the mechanism of paraffin inhibition.

  16. The relative test performance characteristics of two commercial assays for the detection of Mycobacterium tuberculosis complex in paraffin-fixed human biopsy specimens

    Directory of Open Access Journals (Sweden)

    Broukhanski George

    2008-09-01

    Full Text Available Abstract The Seeplex™ TB Detection-2 assay (Rockville, MD is a nested endpoint PCR for the Mycobacterium tuberculosis complex (MTBC targets IS6110 and MPB64 that utilizes dual priming oligonucleotide technology. When used to detect the presence of MTBC DNA in formalin-fixed paraffin-embedded tissue specimens, the sensitivity and specificity of this assay is equivalent to a labor-intensive traditional endpoint PCR assay and is more sensitive than a commercial real-time PCR assay.

  17. Methods for separating boron from borated paraffin wax and its determination by ion chromatography

    International Nuclear Information System (INIS)

    Jeyakumar, S.

    2015-01-01

    Boron compounds are found to be useful in shielding against high-energy neutrons. In radiotherapy treatments, in order to protect occupational workers and patients from the undesirable neutron and gamma doses, paraffin wax containing B 4 C/boric acid is used. Low-level borate wastes generated from the nuclear power plants have been immobilized with paraffin wax using a concentrate waste drying system (CWDS). Borated paraffin waxes are prepared by mixing calculated amounts of either boric acid or boron carbide with the molten wax. This necessitates the determination of boron at different locations in order to check the homogeneous distribution of B over the borated wax. The determination of boron in nuclear materials is inevitable due to its high neutron absorption cross section. For the determination of boron in borated waxes, not many methods have been reported. A method based on the pyrohydrolysis extraction of boron and its quantification with ion chromatography was proposed for paraffin waxes borated with H 3 BO 3 and B 4 C. The B 4 C optimum pyrohydrolysis conditions were identified. Wax samples were mixed with U 3 O 8 , which prevents the sample from flare up, and also accelerates the extraction of boron. Pyrohydrolysis was carried out with moist O 2 at 950℃ for 60 and 90 min for wax with H 3 BO 3 and wax with B 4 C, respectively. Two simple methods of separation based on alkali extraction and melting wax in alkali were also developed exclusively for wax with H 3 BO 3 . In all the separations, the recovery of B was above 98%. During IC separation, B was separated as boron-mannitol anion complex. Linear calibration was obtained between 0.1 and 50 ppm of B, and LOD was calculated as 5 ppb (S/N=3). The reproducibility was better than 5% (RSD)

  18. Proposals for best-quality immunohistochemical staining of paraffin-embedded brain tissue slides in forensics.

    Science.gov (United States)

    Trautz, Florian; Dreßler, Jan; Stassart, Ruth; Müller, Wolf; Ondruschka, Benjamin

    2018-01-03

    Immunohistochemistry (IHC) has become an integral part in forensic histopathology over the last decades. However, the underlying methods for IHC vary greatly depending on the institution, creating a lack of comparability. The aim of this study was to assess the optimal approach for different technical aspects of IHC, in order to improve and standardize this procedure. Therefore, qualitative results from manual and automatic IHC staining of brain samples were compared, as well as potential differences in suitability of common IHC glass slides. Further, possibilities of image digitalization and connected issues were investigated. In our study, automatic staining showed more consistent staining results, compared to manual staining procedures. Digitalization and digital post-processing facilitated direct analysis and analysis for reproducibility considerably. No differences were found for different commercially available microscopic glass slides regarding suitability of IHC brain researches, but a certain rate of tissue loss should be expected during the staining process.

  19. MicroRNA Expression in Formalin-fixed Paraffin-embedded Cancer Tissue

    DEFF Research Database (Denmark)

    Boisen, Mogens Karsbøl; Dehlendorff, Christian; Linnemann, Dorte

    2015-01-01

    of miRNA expression in FFPE tissue samples from patients with colorectal (CRC) and pancreatic (PC) cancer and to quantify the variability associated with sample age and fixation. METHODS: High-throughput miRNA profiling results from 203 CRC and 256 PC FFPE samples as well as from 37 paired frozen....../FFPE samples from nine other CRC tumors (methodological samples) were used. Candidate reference miRNAs were identified by their correlation with global mean expression. The stability of reference genes was analyzed according to published methods. The association between sample age and global mean mi...... to global mean expression in each cancer type. Nine of these miRNAs were present in both lists, and miR-103a-3p was the most stable reference miRNA for both CRC and PC FFPE tissue. The optimal number of reference miRNAs was 4 in CRC and 10 in PC. Sample age had a significant effect on global mi...

  20. Fluorescence in situ hybridization on formalin-fixed and paraffin-embedded tissue

    DEFF Research Database (Denmark)

    Laub Petersen, Bodil; Zeuthen, Mette Christa; Pedersen, Sanni

    2004-01-01

    Fluorescence in situ hybridization (FISH) is widely used to study numerical and structural genetic abnormalities in both metaphase and interphase cells. The technique is based on the hybridization of labeled probes to complementary sequences in the DNA or RNA of the cells. Interphase FISH is most...... in time lapse between removal of tissue and fixation, duration of fixation, enzymatic pretreatment, hybridization conditions, and posthybridization washing conditions are important factors in the hybridization. In this study, we have listed the results of a systematic approach to improve FISH on isolated...

  1. Conceptualizing Embedded Configuration

    DEFF Research Database (Denmark)

    Oddsson, Gudmundur Valur; Hvam, Lars; Lysgaard, Ole

    2006-01-01

    and services. The general idea can be named embedded configuration. In this article we intend to conceptualize embedded configuration, what it is and is not. The difference between embedded configuration, sales configuration and embedded software is explained. We will look at what is needed to make embedded...... configuration systems. That will include requirements to product modelling techniques. An example with consumer electronics will illuminate the elements of embedded configuration in settings that most can relate to. The question of where embedded configuration would be relevant is discussed, and the current...

  2. The Cellient System for Paraffin Histology Can Be Combined with HPV Testing and Morphotyping the Vaginal Microbiome Thanks to BoonFixing

    Directory of Open Access Journals (Sweden)

    Mathilde E. Boon

    2013-01-01

    Full Text Available The Cellient Automated Cell Block System (Hologic can be used to process cervical scrapes to paraffin sections. For the first study on this subject, cervical scrapes were fixed in the formalin-free fixative BoonFix. This pilot study was limited to cases classified as atypical squamous lesion of unknown significance (ASCUS and high-grade squamous lesion (HSIL as diagnosed in the ThinPrep slide. The Cellient paraffin sections were classified into negative, atypical, CIN 1, CIN 2, and CIN 3. Multiple HPV genotypes were encountered in 79% of the scrapes. This study showed that the Cellient system for paraffin sections can be combined with HPV testing thanks to the formalin-free BoonFix. In two additional studies it was shown that such samples can also be used for morphotyping the vaginal microbiome and preparing cytologic ThinPrep slides.

  3. The Cellient System for Paraffin Histology Can Be Combined with HPV Testing and Morphotyping the Vaginal Microbiome Thanks to BoonFixing.

    Science.gov (United States)

    Boon, Mathilde E

    2013-01-01

    The Cellient Automated Cell Block System (Hologic) can be used to process cervical scrapes to paraffin sections. For the first study on this subject, cervical scrapes were fixed in the formalin-free fixative BoonFix. This pilot study was limited to cases classified as atypical squamous lesion of unknown significance (ASCUS) and high-grade squamous lesion (HSIL) as diagnosed in the ThinPrep slide. The Cellient paraffin sections were classified into negative, atypical, CIN 1, CIN 2, and CIN 3. Multiple HPV genotypes were encountered in 79% of the scrapes. This study showed that the Cellient system for paraffin sections can be combined with HPV testing thanks to the formalin-free BoonFix. In two additional studies it was shown that such samples can also be used for morphotyping the vaginal microbiome and preparing cytologic ThinPrep slides.

  4. Effect of radiation on the crystals of polyethylene and paraffins

    International Nuclear Information System (INIS)

    Ungar, G.; Grubb, D.T.; Keller, A.

    1980-01-01

    Paraffins were irradiated with electrons in the electron microscope. The electron microscopic image and the electron diffraction patterns were followed as a function of dose. The objectives were: (a) to establish a connection between the 'polyethylene-type' and 'paraffin-like' behaviour and (b) to identify the phase segregation, by visual means. Increasing chain length, increasing dose rate and decreasing temperature individually and in combination, were found to favour the 'polyethylene-type' behaviour (crystal destruction through increasing lattice defects) while the reverse trend of the above three variables favoured the 'paraffin-like' behaviour (phase-segregated damaged and undamaged species). Segregated phases could in some circumstances be identified as non-diffracting 'droplets' within a crystalline matrix, with the lattice hardly affected, in the electron microscopic image. These droplets remain constant in number but increase in size as the irradiation progresses, the number of droplets depending on the chain length of the paraffin, on the irradiation temperature and on the dose rate. This behaviour, together with some further observations, reveals that the radiation-induced active species do not form crosslinks in situ but migrate over distances which can amount to μm. In contrast to the above, in the case of the lowest paraffin investigated, (C 23 H 48 ), the lattice became uniformly distorted as judged from the diffraction pattern, but the damage was observed to 'heal-out' with time. The results are discussed. (author)

  5. The effects of normal paraffins mobilizers on irradiated polypropylene

    International Nuclear Information System (INIS)

    Chen Wenxiu; Gao Ling

    1995-01-01

    The n-paraffins blended with polypropylene (PP) as mobilizer had been investigated. The effectiveness of mobilizer (n-paraffins) on irradiated polypropylene is dependent on the molecular weight of mobilizer and its content on polypropylene. The n-docosame (n-C 22 ) possesses the best effectiveness of radiation tolerance on PP among the mobilizer paraffins: n-decane (n-C 10 ), n-hexadecane (n-C 16 ), n-docosane (n-C 22 ) and n-hexatriacontane (n-C 36 ). The 2% (w/w) content of a given mobilizer is the most effective at reducing the embrittlement of irradiated PP as evidenced by the elongation at break. The physical properties of polypropylene with mobilizers such as density, Young's modulus, the Fraction of free volume and the weight swelling ratio in p-xylene at room temperature were measured. Above phenomena are related with the constructive of blended PP and demonstrated by its physical properties

  6. Reduction in spasticity in stroke patient with paraffin therapy.

    Science.gov (United States)

    Wang, Jing; Yu, Peng; Zeng, Ming; Gu, Xudong; Liu, Yan; Xiao, Mingyue

    2017-01-01

    The aim of the study was to confirm whether paraffin therapy offer clinical value in the treatment of spasticity due to stroke. Fifty-two patients with spasticity in the upper limb were included. The patients were randomized into the experimental group with paraffin therapy (n = 27) and the control group with placebo therapy (n = 25). The outcome measures besides temperature examination were undertaken at time points of 0 (T0), 2 (T1) and 4 weeks (T2) following therapy treatment. The extent of spasticity was measured using Modified Ashworth Score (MAS) during passive movement at the shoulder, elbow, wrist and finger joints. Visual analogue scale (VAS) was used to evaluate the hemiplegic upper limb pain and functional activity of the upper limb motor function was evaluated by Brunnstrom recovery stage. All adverse events were recorded. MAS decreased significantly in Exp group compared with Con group, at the time points of T1 and T2, both before and immediately after paraffin therapy. Paraffin treatment failed to show remarkable improvement in pain compared with placebo-treated patient at movement at any time point. But VAS in Exp exhibited a tendency to decrease over time in shoulder, elbow, wrist and hand. With regard to the Brunnstrom score, patients in Exp showed significant improvement at the end of trial compared to the beginning. The values of temperature showed significant increment immediately after paraffin therapy at each time point in Exp group. Paraffin therapy may be a kind of noninvasive, promising method to reduce spasticity of stroke patients.

  7. The Cellient System for Paraffin Histology Can Be Combined with HPV Testing and Morphotyping the Vaginal Microbiome Thanks to BoonFixing

    OpenAIRE

    Boon, Mathilde E.

    2013-01-01

    The Cellient Automated Cell Block System (Hologic) can be used to process cervical scrapes to paraffin sections. For the first study on this subject, cervical scrapes were fixed in the formalin-free fixative BoonFix. This pilot study was limited to cases classified as atypical squamous lesion of unknown significance (ASCUS) and high-grade squamous lesion (HSIL) as diagnosed in the ThinPrep slide. The Cellient paraffin sections were classified into negative, atypical, CIN 1, CIN 2, and CIN 3. ...

  8. Magnetic orientation of paraffin in a magnetic levitation furnace

    Science.gov (United States)

    Takahashi, K.; Umeki, C.; Mogi, I.; Koyama, K.; Awaji, S.; Motokawa, M.; Watanabe, K.

    2004-04-01

    Containerless melting of paraffin under a magnetic levitation condition has been performed by using a cryogen-free hybrid magnet and two kinds of laser furnaces. One is local irradiation of CO 2 laser light at the top of the sample. The other is homogeneous irradiation of YAG laser light with a concave ring mirror. In the latter case, reduction of the Marangoni convection on the surface of the sample and the magnetic orientation of paraffin molecules were observed. The magnetic anisotropy of the spherical sample was confirmed by the measurement of magnetization and X-ray diffraction.

  9. Magnetic orientation of paraffin in a magnetic levitation furnace

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, K.; Umeki, C.; Mogi, I.; Koyama, K.; Awaji, S.; Motokawa, M.; Watanabe, K

    2004-04-30

    Containerless melting of paraffin under a magnetic levitation condition has been performed by using a cryogen-free hybrid magnet and two kinds of laser furnaces. One is local irradiation of CO{sub 2} laser light at the top of the sample. The other is homogeneous irradiation of YAG laser light with a concave ring mirror. In the latter case, reduction of the Marangoni convection on the surface of the sample and the magnetic orientation of paraffin molecules were observed. The magnetic anisotropy of the spherical sample was confirmed by the measurement of magnetization and X-ray diffraction.

  10. Magnetic orientation of paraffin in a magnetic levitation furnace

    International Nuclear Information System (INIS)

    Takahashi, K.; Umeki, C.; Mogi, I.; Koyama, K.; Awaji, S.; Motokawa, M.; Watanabe, K.

    2004-01-01

    Containerless melting of paraffin under a magnetic levitation condition has been performed by using a cryogen-free hybrid magnet and two kinds of laser furnaces. One is local irradiation of CO 2 laser light at the top of the sample. The other is homogeneous irradiation of YAG laser light with a concave ring mirror. In the latter case, reduction of the Marangoni convection on the surface of the sample and the magnetic orientation of paraffin molecules were observed. The magnetic anisotropy of the spherical sample was confirmed by the measurement of magnetization and X-ray diffraction

  11. Spectral distribution measurements of neutrons in paraffin borax mixtures

    International Nuclear Information System (INIS)

    El-Khatib, A.M.; Gaber, M.; Abou El-Khier, M.A.

    1987-01-01

    Neutron fluxes from a compact D-T neutron source has been measured in paraffin-borax mixtures by using activation foil detectors with successive threshold energies. The absorbed doses, backscattering coefficients and build-up factors were determined as well. The contribution of thermal and intermediate neutron dose is much lower, compared to that of fast neutrons. Among the used mediums, paraffin loaded with 4% borax concentration was found to be the best absorbing medium against neutrons at near depths within the blocks, while at a depth around 12 cm the neutron absorption (or scattering) is independent on the type of the used medium. (author)

  12. Purity of paraffins used in drugs and cosmetics

    Energy Technology Data Exchange (ETDEWEB)

    Monarca, S; Fagioli, F; Morozzi, G

    1981-01-01

    A previously developed technique for the determination of polycyclic aromatic hydrocarbons (PAH's) in purified petroleum products was applied to some fully-refined paraffin samples for cosmetic and medicinal uses. The analytical procedure provided identification and quantitative assay for ng/g amounts of two well known carcinogenic PAH's, benzo-a-pyrene and benzoflouranthene. The method is compared with rapid pharmacopoeial tests based on different quality criteria. A lack of agreement between PAH content in paraffin samples and the results of the pharmacopoeial tests was noted. (1 diagram, 49 references, 5 tables)

  13. From an equilibrium based MOF adsorbent to a kinetic selective carbon molecular sieve for paraffin/iso-paraffin separation

    KAUST Repository

    Li, Baiyan

    2016-11-04

    We unveil a unique kinetic driven separation material for selectively removing linear paraffins from iso-paraffins via a molecular sieving mechanism. Subsequent carbonization and thermal treatment of CD-MOF-2, the cyclodextrin metal-organic framework, afforded a carbon molecular sieve with a uniform and reduced pore size of ca. 5.0 Å, and it exhibited highly selective kinetic separation of n-butane and n-pentane from iso-butane and iso-pentane, respectively. © The Royal Society of Chemistry.

  14. Polymorphic Embedding of DSLs

    DEFF Research Database (Denmark)

    Hofer, Christian; Ostermann, Klaus; Rendel, Tillmann

    2008-01-01

    propose polymorphic embedding of DSLs, where many different interpretations of a DSL can be provided as reusable components, and show how polymorphic embedding can be realized in the programming language Scala. With polymorphic embedding, the static type-safety, modularity, composability and rapid...

  15. Paraffin ingestion - the problem | Ellis | South African Medical Journal

    African Journals Online (AJOL)

    An effective durable, low-cost child-resistant container which is easy to pour from should be made available by petroleum companies and/or entrepreneurs and distributed through their network. This should be combined with health education on the danger of paraffin. Health care workers and administrators should be made ...

  16. Quantifying Short-Chain Chlorinated Paraffin Congener Groups

    NARCIS (Netherlands)

    Yuan, Bo; Bogdal, Christian; Berger, Urs; MacLeod, Matthew; Gebbink, Wouter A.; Alsberg, Tomas; Wit, de Cynthia A.

    2017-01-01

    Accurate quantification of short-chain chlorinated paraffins (SCCPs) poses an exceptional challenge to analytical chemists. SCCPs are complex mixtures of chlorinated alkanes with variable chain length and chlorination level; congeners with a fixed chain length (n) and number of chlorines (m) are

  17. Resettable binary latch mechanism for use with paraffin linear motors

    Science.gov (United States)

    Maus, Daryl; Tibbitts, Scott

    1991-01-01

    A new resettable Binary Latch Mechanism was developed utilizing a paraffin actuator as the motor. This linear actuator alternately latches between extended and retracted positions, maintaining either position with zero power consumption. The design evolution and kinematics of the latch mechanism are presented, as well as the development problems and lessons that were learned.

  18. The measurements of thermal neutron flux distribution in a paraffin

    Indian Academy of Sciences (India)

    The term `thermal flux' implies a Maxwellian distribution of velocity and energy corresponding to the most probable velocity of 2200 ms-1 at 293.4 K. In order to measure the thermal neutron flux density, the foil activation method was used. Thermal neutron flux determination in paraffin phantom by counting the emitted rays of ...

  19. Extracorporeal membrane oxygenation after intravenous injection of paraffin oil

    DEFF Research Database (Denmark)

    Pasgaard, Thomas; Huynh, Anh-Nhi Thi; Gjedsted, Jakob

    2016-01-01

    We present a rare cause of acute respiratory distress syndrome (ARDS) due to an accidental intravascular injection of paraffin oil. While there is no specific therapy, we decided to support the patient with veno-venous extracorporeal membrane oxygenation (V-V ECMO) to allow the ARDS to resolve. A...

  20. Bismuth toxicity in patients treated with bismuth iodoform paraffin packs.

    Science.gov (United States)

    Atwal, A; Cousin, G C S

    2016-01-01

    Bismuth is a heavy metal used in bismuth iodoform paraffin paste (BIPP) antiseptic dressings and in a number of other medical preparations. It can be absorbed systemically and cause toxicity. We report 2 cases of such neurotoxicity after it was used in operations on the jaws. Copyright © 2015. Published by Elsevier Ltd.

  1. Organic Rankine Cycle with Solar Heat Storage in Paraffin Way

    Directory of Open Access Journals (Sweden)

    Constantin LUCA

    2015-06-01

    Full Text Available The paper presents an electricity generation system based on an Organic Rankine Cycle and proposed storing the amount of the heat produced by the solar panels using large volume of paraffin wax. The proposed working fluid is R-134a refrigerant. The cycle operates at very low temperatures. A efficiency of 6,55% was obtained.

  2. Improved method of producing satisfactory sections of whole eyeball by routine histology.

    Science.gov (United States)

    Arko-Boham, Benjamin; Ahenkorah, John; Hottor, Bismarck Afedo; Dennis, Esther; Addai, Frederick Kwaku

    2014-02-01

    To overcome the loss of structural integrity when eyeball sections are prepared by wax embedding, we experimentally modified the routine histological procedure and report satisfactorily well-preserved antero-posterior sections of whole eyeballs for teaching/learning purposes. Presently histological sections of whole eyeballs are not readily available because substantial structural distortions attributable to variable consistency of tissue components (and their undesired differential shrinkage) result from routine processing. Notably, at the dehydration stage of processing, the soft, gel-like vitreous humor considerably shrinks relative to the tough fibrous sclera causing collapse of the ocular globe. Additionally, the combined effects of fixation, dehydration, and embedding at 60°C renders the eye lens too hard for microtome slicing at thicknesses suitable for light microscopy. We satisfactorily preserved intact antero-posterior sections of eyeballs via routine paraffin wax processing procedure entailing two main modifications; (i) careful needle aspiration of vitreous humor and replacement with molten wax prior to wax infiltration; (ii) softening of lens in trimmed wax block by placing a drop of concentrated liquid phenol on it for 3 h during microtomy. These variations of the routine histological method produced intact whole eyeball sections with retinal detachment as the only structural distortion. Intact sections of the eyeball obtained compares well with the laborious, expensive, and 8-week long celloidin method. Our method has wider potential usability than costly freeze drying method which requires special skills and equipment (cryotome) and does not produce whole eyeball sections. Copyright © 2013 Wiley Periodicals, Inc.

  3. Study on Thermal Degradation Characteristics and Regression Rate Measurement of Paraffin-Based Fuel

    Directory of Open Access Journals (Sweden)

    Songqi Hu

    2015-09-01

    Full Text Available Paraffin fuel has been found to have a regression rate that is higher than conventional HTPB (hydroxyl-terminated polybutadiene fuel and, thus, presents itself as an ideal energy source for a hybrid rocket engine. The energy characteristics of paraffin-based fuel and HTPB fuel have been calculated by the method of minimum free energy. The thermal degradation characteristics were measured for paraffin, pretreated paraffin, HTPB and paraffin-based fuel in different working conditions by the using differential scanning calorimetry (DSC and a thermogravimetric analyzer (TGA. The regression rates of paraffin-based fuel and HTPB fuel were tested by a rectangular solid-gas hybrid engine. The research findings showed that: the specific impulse of paraffin-based fuel is almost the same as that of HTPB fuel; the decomposition temperature of pretreated paraffin is higher than that of the unprocessed paraffin, but lower than that of HTPB; with the increase of paraffin, the initial reaction exothermic peak of paraffin-based fuel is reached in advance, and the initial reaction heat release also increases; the regression rate of paraffin-based fuel is higher than the common HTPB fuel under the same conditions; with the increase of oxidizer mass flow rate, the regression rate of solid fuel increases accordingly for the same fuel formulation.

  4. Rheology of petrolatum-paraffin oil mixtures : Applications to analogue modelling of geological processes

    NARCIS (Netherlands)

    Duarte, João C.; Schellart, Wouter P.; Cruden, Alexander R.

    2014-01-01

    Paraffins have been widely used in analogue modelling of geological processes. Petrolatum and paraffin oil are commonly used to lubricate model boundaries and to simulate weak layers. In this paper, we present rheological tests of petrolatum, paraffin oil and several homogeneous mixtures of the two.

  5. The effect of a paraffin screen on the neutron dose at the maze door of a 15 MV linear accelerator.

    Science.gov (United States)

    Krmar, M; Nikolić, D; Kuzmanović, A; Kuzmanović, Z; Ganezer, K

    2013-08-01

    The purpose of this study was to explore the effects of a paraffin screen located at various positions in the maze on the neutron dose equivalent at the maze door. The neutron dose equivalent was measured at the maze door of a room containing a 15 MV linear accelerator for x-ray therapy. Measurements were performed for several positions of the paraffin screen covering only 27.5% of the cross-sectional area of the maze. The neutron dose equivalent was also measured at all screen positions. Two simple models of the neutron source were considered in which the first assumed that the source was the cross-sectional area at the inner entrance of the maze, radiating neutrons in an isotropic manner. In the second model the reduction in the neutron dose equivalent at the maze door due to the paraffin screen was considered to be a function of the mean values of the neutron fluence and energy at the screen. The results of this study indicate that the equivalent dose at the maze door was reduced by a factor of 3 through the use of a paraffin screen that was placed inside the maze. It was also determined that the contributions to the dosage from areas that were not covered by the paraffin screen as viewed from the dosimeter, were 2.5 times higher than the contributions from the covered areas. This study also concluded that the contributions of the maze walls, ceiling, and floor to the total neutron dose equivalent were an order of magnitude lower than those from the surface at the far end of the maze. This study demonstrated that a paraffin screen could be used to reduce the neutron dose equivalent at the maze door by a factor of 3. This paper also found that the reduction of the neutron dose equivalent was a linear function of the area covered by the maze screen and that the decrease in the dose at the maze door could be modeled as an exponential function of the product φ·E at the screen.

  6. Radiotherapic Valuation of Paraffin Wax for Patients with Oral Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Na, Kyung Su; Seo, Seuk Jin; Lee, Je Hee; Yoo, Sook Heun [Dept. of Radiation Oncology, Seoul National University Hosdital, Seoul (Korea, Republic of)

    2011-03-15

    This study is designed to investigate radiotherapic valuation of Paraffin Wax, which is newly formed for this study and generally utilized in dentistry, and Mouth Piece and Putty impression, which are commonly used in radiotherapy, for oral cavity as a compensator. Each compensator was formed by 10 x 10 x 1 cm and measured radiation dose attenuation ratio with reference of water phantom which is made of tissue-equivalent materials. Two patients with oral cancer underwent DRR (Digitally Reconstructed Radiogrph) of Offline Review Program of Aria System and Portal vision for 5 times for each material to evaluate reproducibility by each filling materials. Moreover, MU (monitor unit) changes by dose absorption were considered in the case of inevitable implication of an filling materials in the range for radiotherapy. Radiation dose attenuation ratios were shown -0.7{approx}+3.7% for Mouth Piece, +0.21{approx}+0.39% for Paraffin Wax and -2.71{approx}-1.76% for Putty impression. Error ranges of reproducibility of positions were measured {+-}3 mm for Mouth Piece, {+-}2 mm for Paraffin Wax and {+-}2 mm for Putty impression. Difference of prescription MU from dose absorption with an filling material increased +7.8% (250 MU) in Putty impression and -0.9% (230 MU) in Paraffin Wax as converted into a percentage from the standard phantom, Water 232 MU. Dose reduction of boundary between cavity and tissue was observed for Mouth Piece. Mouth Piece also had low reproducibility of positions as it had no reflection of anatomy of oral cavity even though it was a proper material to separate Maxilla and Mandible during therapy. On the other hand, Putty impression was a suitable material to correctly re-position oral cavity as before. However, it risked normal tissues getting unnecessary over irradiation and it caused radiation dose decrease by -2.5% for 1cm volume in comparison of it of water phantom. Dose reduction in Paraffin Wax, Fat Tissue-Equivalent Material, was smaller than other

  7. Radiotherapic Valuation of Paraffin Wax for Patients with Oral Cancer

    International Nuclear Information System (INIS)

    Na, Kyung Su; Seo, Seuk Jin; Lee, Je Hee; Yoo, Sook Heun

    2011-01-01

    This study is designed to investigate radiotherapic valuation of Paraffin Wax, which is newly formed for this study and generally utilized in dentistry, and Mouth Piece and Putty impression, which are commonly used in radiotherapy, for oral cavity as a compensator. Each compensator was formed by 10 x 10 x 1 cm and measured radiation dose attenuation ratio with reference of water phantom which is made of tissue-equivalent materials. Two patients with oral cancer underwent DRR (Digitally Reconstructed Radiogrph) of Offline Review Program of Aria System and Portal vision for 5 times for each material to evaluate reproducibility by each filling materials. Moreover, MU (monitor unit) changes by dose absorption were considered in the case of inevitable implication of an filling materials in the range for radiotherapy. Radiation dose attenuation ratios were shown -0.7∼+3.7% for Mouth Piece, +0.21∼+0.39% for Paraffin Wax and -2.71∼-1.76% for Putty impression. Error ranges of reproducibility of positions were measured ±3 mm for Mouth Piece, ±2 mm for Paraffin Wax and ±2 mm for Putty impression. Difference of prescription MU from dose absorption with an filling material increased +7.8% (250 MU) in Putty impression and -0.9% (230 MU) in Paraffin Wax as converted into a percentage from the standard phantom, Water 232 MU. Dose reduction of boundary between cavity and tissue was observed for Mouth Piece. Mouth Piece also had low reproducibility of positions as it had no reflection of anatomy of oral cavity even though it was a proper material to separate Maxilla and Mandible during therapy. On the other hand, Putty impression was a suitable material to correctly re-position oral cavity as before. However, it risked normal tissues getting unnecessary over irradiation and it caused radiation dose decrease by -2.5% for 1cm volume in comparison of it of water phantom. Dose reduction in Paraffin Wax, Fat Tissue-Equivalent Material, was smaller than other impressions and

  8. Characterization of Fast-Scan Cyclic Voltammetric Electrodes Using Paraffin as an Effective Sealant with In Vitro and In Vivo Applications.

    Science.gov (United States)

    Ramsson, Eric S; Cholger, Daniel; Dionise, Albert; Poirier, Nicholas; Andrus, Avery; Curtiss, Randi

    2015-01-01

    Fast-scan cyclic voltammetry (FSCV) is a powerful technique for measuring sub-second changes in neurotransmitter levels. A great time-limiting factor in the use of FSCV is the production of high-quality recording electrodes; common recording electrodes consist of cylindrical carbon fiber encased in borosilicate glass. When the borosilicate is heated and pulled, the molten glass ideally forms a tight seal around the carbon fiber cylinder. It is often difficult, however, to guarantee a perfect seal between the glass and carbon. Indeed, much of the time spent creating electrodes is in an effort to find a good seal. Even though epoxy resins can be useful in this regard, they are irreversible (seals are permanent), wasteful (epoxy cannot be reused once hardener is added), hazardous (hardeners are often caustic), and require curing. Herein we characterize paraffin as an electrode sealant for FSCV microelectrodes. Paraffin boasts the advantages of near-immediate curing times, simplicity in use, long shelf-life and stable waterproof seals capable of withstanding extended cycling. Borosilicate electrode tips were left intact or broken and dipped in paraffin embedding wax. Excess wax was removed from the carbon surface with xyelenes or by repeated cycling at an extended waveform (-0.4 to 1.4V, 400 V/s, 60 Hz). Then, the waveform was switched to a standard waveform (-0.4 to 1.3V, 400 V/s, 10 Hz) and cycled until stable. Wax-sealing does not inhibit electrode sensitivity, as electrodes detected linear changes in dopamine before and after wax (then xylenes) exposure. Paraffin seals are intact after 11 days of implantation in the mouse, and still capable of measuring transient changes in in vivo dopamine. From this it is clear that paraffin wax is an effective sealant for FSCV electrodes that provides a convenient substitute to epoxy sealants.

  9. Technical advances in the sectioning of dental tissue and of on-section cross-linked collagen detection in mineralized teeth.

    Science.gov (United States)

    Singhrao, Sim K; Sloan, Alastair J; Smith, Emma L; Archer, Charles W

    2010-08-01

    Immunohistochemical detection of cross-linked fibrillar collagens in mineralized tissues is much desired for exploring the mechanisms of biomineralization in health and disease. Mineralized teeth are impossible to section when embedded in conventional media, thus limiting on-section characterization of matrix proteins by immunohistochemistry. We hypothesized that by using an especially formulated acrylic resin suitable for mineralized dental tissues, not only sectioning of teeth would be possible, but also our recently developed immunofluorescence labeling technique would be amenable to fully calcified tissues for characterization of dentinal fibrillar collagens, which remains elusive. The hypothesis was tested on fixed rodent teeth embedded in Technovit 9100 New. It was possible to cut thin (1 mum) sections of mineralized teeth, and immunofluorescence characterization of cross-linked type I fibrillar collagen was selected due to its abundance in dentine. Decalcified samples of teeth embedded in paraffin wax were also used to compare immunolabeling from either method using the same immunoreagents in equivalent concentrations. In the decalcified tissue sections, type I collagen labeling in the dentine along the tubules was "patchy" and the signal in the predentine was very weak. However, enhanced signal in mineralized samples with type I collagen was detected not only in the predentine but also at the limit between intertubular dentine, within the elements of the enamel organ and subgingival stroma. This report offers advances in sectioning mineralized dental tissues and allows the application of immunofluorescence not only for on-section protein detection but importantly for detecting cross-linked fibrous collagens in both soft and mineralized tissue sections.

  10. Neutron and gamma ray attenuation of asphalt; Comparison with paraffin and water

    International Nuclear Information System (INIS)

    Abdul-Majid, S.; Kutbi, I.I.

    1996-01-01

    Asphalt is a low cost, readily available, easy-to-cast material which is rich in hydrogen and carbon, elements most effective for fast-neutron shielding. Unlike paraffin, the material can easily be mixed with boron containing compounds, an, element of high absorption cross-section for slow neutrons. The 241 Am-Be neutron and gamma attenuation characteristic of asphalt were studied. The source is having wide applications in industry and geophysics field work. Comparisons were made with paraffin and water. The source activity was 1.11 x 1,011 Bq (3 Ci) with a neutron emission rate of 6.6 x 106 n s -1 and a tolerance of +10%. The neutron dose-equivalent rate at 1 m was 66 mSv h -1 , while the associated gamma ray exposure was ∼1.9 mC kg -1 h -1 of the bare source. A neutron remmeter was used for the neutron dose-equivalent rate measurements, which produces an energy response that approximates human body dose equivalent over a wide range of neutron energy. An air filled ionization chamber was used for the exposure rate measurements. The slow neutrons were measured by a BF 3 gas filled detector. The shielding materials were confined in an aluminum cylinder of 1 mm wall thickness where the source was kept in the middle. The neutron dose rate, the gamma ray exposure rate, and the slow neutron count rate were measured at different shield radii and at different distances from its outer surface. The neutron doses of asphalt at the surface of cylindrical shields of 8, 12, 16, 20, and 24 cm radii in mSv h -1 were 0.85, 0.4, 0.25, 0.13, and 0.06, respectively, while the gamma ray exposure mC kg -1 h -1 were 7, 4.4 2.5, 1.3, and 0.88, respectively. The neutron dose rate attenuation of asphalt was very close to that of water, but slightly lower than that of paraffin, while the gamma ray attenuation was close to that of water but higher than that of paraffin

  11. Preparation and Characterization of Modified Montmorillonite/Paraffin Phase Change Microcapsules for Energy Storage

    Directory of Open Access Journals (Sweden)

    LIN Sen

    2017-03-01

    Full Text Available The phase change microcapsules of modified montmorillonite/paraffin were prepared by Pickering emulsion method. Analytic techniques of optical microscopy, scanning electron microscopy(SEM, infrared spectroscopy(FTIR, differential scanning calorimetry(DSC and thermogravimetry(TG were utilized for characterizing chemical structure, morphology and thermal properties. Results show that modified montmorillonite as a new type wall material has excellent performance for protecting core material of paraffin. FTIR spectra of phase change of modified montmorillonite/paraffin microcapsules shows that their characteristic peaks match with corresponding peaks of pure paraffin and modified montmorillonite. DSC results indicate that modified montmorillonite/paraffin microcapsules have similar solid-liquid phase change temperature with pure paraffin. The phase transition enthalpy values of microcapsules with paraffin contents varying from 55% to 80% are 110.5-147.2J/g, indicating that microcapsules have excellent thermal storage performance and the phase change properties can be adjusted by changing contents of paraffin. TG results confirm that modified montmorillonite/paraffin microcapsules have outstanding thermal stability. The presented study indicates that modified montmorillonite is a suitable wall material for preparing paraffin microcapsule. Modified montmorillonite/paraffin microcapsules have advantages of low cost and high performance with a great application potential in the field of thermal storage.

  12. Preparation and thermal energy storage properties of paraffin/expanded graphite composite phase change material

    International Nuclear Information System (INIS)

    Zhang, Zhengguo; Zhang, Ni; Peng, Jing; Fang, Xiaoming; Gao, Xuenong; Fang, Yutang

    2012-01-01

    Highlights: ► EG was obtained by microwave irradiation to prepare the paraffin/EG composite PCM. ► Composite PCM was characterized by XRD to investigate the chemical compatibility. ► Temperature profiles of the composite PCM were obtained during thermal energy storage. -- Abstract: The paraffin/expanded graphite (EG) composite phase change material (PCM) was prepared by absorbing liquid paraffin into EG, in which paraffin was chosen as the PCM. EG was produced by microwave irradiation performed at room temperature. It was found that the EG prepared at 800 W irradiation power for 10 s exhibited the maximum sorption capacity of 92 wt% for paraffin. Scanning electron microscopy images showed that paraffin was uniformly dispersed in the pores of EG. Differential scanning calorimeter analysis indicated that the melting temperature of the composite PCM was close to that of paraffin, and its latent heat was equivalent to the calculated value based on the mass fraction of paraffin in the composite. X-ray diffraction analysis showed that the composite PCM was just a combination of paraffin with EG, and no new substance was produced. Thermal energy storage performance of the composite PCM was tested in a latent thermal energy storage (LTES) system. Transients of axial and radial temperature profiles were obtained in the LTES for the composite PCM and paraffin. The thermal energy storage charging duration for the composite PCM was reduced obviously compared to paraffin.

  13. Embedding beyond electrostatics

    DEFF Research Database (Denmark)

    Nåbo, Lina J.; Olsen, Jógvan Magnus Haugaard; Holmgaard List, Nanna

    2016-01-01

    We study excited states of cholesterol in solution and show that, in this specific case, solute wave-function confinement is the main effect of the solvent. This is rationalized on the basis of the polarizable density embedding scheme, which in addition to polarizable embedding includes non-electrostatic...... repulsion that effectively confines the solute wave function to its cavity. We illustrate how the inclusion of non-electrostatic repulsion results in a successful identification of the intense π → π∗ transition, which was not possible using an embedding method that only includes electrostatics....... This underlines the importance of non-electrostatic repulsion in quantum-mechanical embedding-based methods....

  14. Embedded systems handbook

    CERN Document Server

    Zurawski, Richard

    2005-01-01

    Embedded systems are nearly ubiquitous, and books on individual topics or components of embedded systems are equally abundant. Unfortunately, for those designers who thirst for knowledge of the big picture of embedded systems there is not a drop to drink. Until now. The Embedded Systems Handbook is an oasis of information, offering a mix of basic and advanced topics, new solutions and technologies arising from the most recent research efforts, and emerging trends to help you stay current in this ever-changing field.With preeminent contributors from leading industrial and academic institutions

  15. Web Server Embedded System

    Directory of Open Access Journals (Sweden)

    Adharul Muttaqin

    2014-07-01

    Full Text Available Abstrak Embedded sistem saat ini menjadi perhatian khusus pada teknologi komputer, beberapa sistem operasi linux dan web server yang beraneka ragam juga sudah dipersiapkan untuk mendukung sistem embedded, salah satu aplikasi yang dapat digunakan dalam operasi pada sistem embedded adalah web server. Pemilihan web server pada lingkungan embedded saat ini masih jarang dilakukan, oleh karena itu penelitian ini dilakukan dengan menitik beratkan pada dua buah aplikasi web server yang tergolong memiliki fitur utama yang menawarkan “keringanan” pada konsumsi CPU maupun memori seperti Light HTTPD dan Tiny HTTPD. Dengan menggunakan parameter thread (users, ramp-up periods, dan loop count pada stress test embedded system, penelitian ini menawarkan solusi web server manakah diantara Light HTTPD dan Tiny HTTPD yang memiliki kecocokan fitur dalam penggunaan embedded sistem menggunakan beagleboard ditinjau dari konsumsi CPU dan memori. Hasil penelitian menunjukkan bahwa dalam hal konsumsi CPU pada beagleboard embedded system lebih disarankan penggunaan Light HTTPD dibandingkan dengan tiny HTTPD dikarenakan terdapat perbedaan CPU load yang sangat signifikan antar kedua layanan web tersebut Kata kunci: embedded system, web server Abstract Embedded systems are currently of particular concern in computer technology, some of the linux operating system and web server variegated also prepared to support the embedded system, one of the applications that can be used in embedded systems are operating on the web server. Selection of embedded web server on the environment is still rarely done, therefore this study was conducted with a focus on two web application servers belonging to the main features that offer a "lightness" to the CPU and memory consumption as Light HTTPD and Tiny HTTPD. By using the parameters of the thread (users, ramp-up periods, and loop count on a stress test embedded systems, this study offers a solution of web server which between the Light

  16. Embedded systems handbook networked embedded systems

    CERN Document Server

    Zurawski, Richard

    2009-01-01

    Considered a standard industry resource, the Embedded Systems Handbook provided researchers and technicians with the authoritative information needed to launch a wealth of diverse applications, including those in automotive electronics, industrial automated systems, and building automation and control. Now a new resource is required to report on current developments and provide a technical reference for those looking to move the field forward yet again. Divided into two volumes to accommodate this growth, the Embedded Systems Handbook, Second Edition presents a comprehensive view on this area

  17. Use of surfactants in cleaning paraffin from oil wells

    Energy Technology Data Exchange (ETDEWEB)

    Liebold, G; Rehberg, W

    1969-05-01

    The use of surfactants is described especially oxethylated alkylphenols, in the cleaning of oil wells from paraffin. Aqueous 1 or 10% solutions of the surfactant were injected into the well through the annulus, partially in combination with demulsifiers (for example Separol-brands of BASF). Injection was accomplished continuously or in intervals; in the beginning of 50 ppm surfactant, afterward 15 to 30 ppm as related to the wet crude was necessary. Efficiency of the treatment could be proved by the decrease of pressure in the pipes, the loosening of paraffin shells, and considerably prolonged operation periods in wells which otherwise would have come to a standstill. In quite a number of wells, treatment with hot oil and electric heating could be completely replaced by injection of surfactants. (11 refs.)

  18. Gas condensate--raw material for producing liquid paraffin hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Aliyeva, R.B.; Alikishi-Zade, G.Yu.; Kuliyev, A.M.; Leonidov, A.N.; Pereverzev, A.N.

    1980-01-01

    The problem of efficient utilization of gas condensates as raw material for removal of a valuable product, liquid paraffins, is examined. A classification of gas condensates is given which is used as raw material for removing these hydrocarbons: gas condensate with high content of n-alkanes (25-40 mass percent), with average content (18-25 mass percent), with low content (12-18 mass percent), light weight fractions compositions, which do not contain fractions up to 200/sup 0/, and also, content ofless than 12% n-alkanes. Gas condensate I-III groups are 30% of the total reserve of gas condensate. Liquid paraffins hydrocarbons, produced from fractions of diesel fuel, which has been removed from Shatlyk gas condensate under conditions which simulate virtual processes of caramide deparaffinization meet all requirements without additional refining.

  19. Oils; lubricants; paraffin-wax compositions; hydrocarbon condensation products

    Energy Technology Data Exchange (ETDEWEB)

    1934-04-04

    Petroleum hydrocarbons such as gasoline, kerosene, Diesel fuel oil, lubricating-oil, and paraffin wax, and like hydrocarbons such as are obtainable from shale oil and by the hydrogenation of carbonaceous materials, are improved by addition of products obtained by condensing a cyclic hydrocarbon with a saturated dihalogen derivative of an aliphatic hydrocarbon containing less than five carbon atoms. The addition of the condensation products increases the viscosity of the hydrocarbon oils specified, and is particularly useful in the case of lubricating-oils; addition of the condensation products to paraffin wax increases the transparency and adherent properties of the wax, and is useful in the manufacture of moulded articles such as candles; the products may also be used in solid lubricating-compositions.

  20. Romanian plant produces protein concentrate from paraffin-nourished yeasts

    Energy Technology Data Exchange (ETDEWEB)

    1985-01-01

    One of the world's few factories in which proteins are produced by continuous biotechnology is located in Romania. Here, at the bioproteins plant, microorganisms are converted into a flour which contains a protein concentrate that is so essential to the fattening of swine, cattle, sheep, fowl, and fish. These microorganisms are Candida type yeasts. The culture medium in which they are grown contains sulfates and phosphates. Paraffin, a petroleum product, supplies the carbon that is essential to the microorganisms viability.

  1. Paraffin scintillator for radioassay of solid support samples

    International Nuclear Information System (INIS)

    Fujii, Haruo; Takiue, Makoto

    1989-01-01

    A new paraffin scintillator used for solid support sample counting has been proposed, and its composition and various characteristics are described. The solid support sample treated with this scintillator can be easily handled because of rigid sample conditions. This technique provides great advantages such as the elimination of a large volume of scintillator and little radioactive waste material by using an economical polyethylene bag instead of the conventional counting vial. (author)

  2. Household and caregiver characteristics and behaviours as predictors of unsafe exposure of children to paraffin appliances.

    Science.gov (United States)

    Van Niekerk, A; Govender, R; Hornsby, N; Swart, L

    2017-06-01

    This study examines adult safety knowledge and practices regarding the use of paraffin cooking appliances. The use of these is common in South Africa with injury risks that are poorly understood. This cross-sectional study was in an informal settlement in Johannesburg, South Africa, where children were reportedly at high risk for burns. This study sought to clarify relationships between key risks and developed individual and composite variables from theoretical constructs and operational definitions of risks for burns. Risks included Child Use of Paraffin Appliances, Child Proximity to Cooking, Risky Stove Use, Caregiver's Burn Treatment Knowledge, Children Locked in House, Children Alone in House. Number of children remains as in proof as this was not a composite scale. Child Proximity to Cooking was associated with more children in the home. Households where children were in greater proximity to cooking were 6 times more likely to be left alone at home, with caregivers with no education over 100 times more likely to lock their children at home. Children locked in were often from homes where caregivers used appliances unsafely. In settings with hazardous energy use, compressed household configurations, and families with multiple children, Risky Stove Use and the practice of locking children in the home may be catastrophic. Copyright © 2016 Elsevier Ltd and ISBI. All rights reserved.

  3. Process for paraffin isomerization of a distillate range hydrocarbon feedstock

    Energy Technology Data Exchange (ETDEWEB)

    Chen, N.Y.; Garwood, W.E.; McCullen, S.B.

    1993-01-19

    Various catalytic processes have been proposed to isomerize n-paraffins so as to lower the pour point of distillate range hydrocarbon feedstocks. However, many available feedstocks contain nitrogen impurities which tend to poison conventional paraffin isomerization catalysts. A process has been developed to obviate or alleviate this problem. According to the invention, the paraffin-containing feedstock is contacted with a crystalline aluminosilicate zeolite catalyst having pore openings defined by a ratio of sorption of n-hexane to o-xylene of over 3 vol % and the ability to crack 3-methylpentane in preference to 2,3 dimethylbutane under defined conditions. The zeolite catalyst includes a Group VIII metal and has a zeolite SiO[sub 2]/Al[sub 2]O[sub 3] ratio of at least 20:1. The contacting is carried out at 199-454 C and a pressure of 100-1,000 psig, preferably 250-600 psig. The group of medium pore zeolites which can be used in the process of the invention includes ZSM-22, ZSM-23, and ZSM-35. The Group VIII metals used in the catalyst are preferably selected from Pt, Pd, Ir, Os, Rh, and Ru and the metal is preferably incorporated into the zeolite by ion exchange up to a metal content of preferably 0.1-3 wt %. Experiments are described to illustrate the invention. 1 tab.

  4. Automatic Measuring System for Oil Stream Paraffin Deposits Parameters

    Science.gov (United States)

    Kopteva, A. V.; Koptev, V. Yu

    2018-03-01

    This paper describes a new method for monitoring oil pipelines, as well as a highly efficient and automated paraffin deposit monitoring method. When operating oil pipelines, there is an issue of paraffin, resin and salt deposits on the pipeline walls that come with the oil stream. It ultimately results in frequent transportation suspension to clean or even replace pipes and other equipment, thus shortening operation periods between repairs, creating emergency situations and increasing production expenses, badly affecting environment, damaging ecology and spoil underground water, killing animals, birds etc. Oil spills contaminate rivers, lakes, and ground waters. Oil transportation monitoring issues are still subject for further studying. Thus, there is the need to invent a radically new automated process control and management system, together with measurement means intellectualization. The measurement principle is based on the Lambert-Beer law that describes the dependence between the gamma-radiation frequency and the density together with the linear attenuation coefficient for a substance. Using the measuring system with high accuracy (± 0,2%), one can measure the thickness of paraffin deposits with an absolute accuracy of ± 5 mm, which is sufficient to ensure reliable operation of the pipeline system. Safety is a key advantage, when using the proposed control system.

  5. Evaluation of performance loss of paraffin oil loaded filtering facepieces.

    Science.gov (United States)

    Tombolini, Francesca; Listrani, Stefano; Campopiano, Antonella; Plebani, Carmela

    2016-01-01

    Penetration measurements through commercially available filtering facepieces were performed with monodisperse DEHS aerosols ranging from 0.03 μm to 0.40 μm (either singly charged or neutralized), before and after 500 mg of paraffin oil loading. The distinct behavior of Coulomb and polarization capture efficiency is studied: as in the case of non loading also in the case of loading 500 mg of paraffin oil, the electrostatic capture mechanisms are mainly due to the Coulomb contribution up to aerosol particle diameter of about 0.10 μm, just when the polarization contribution becomes substantial. Both Coulomb and polarization capture mechanisms are influenced by the presence of 500 mg of paraffin oil, resulting less effective than the oil unloaded case of about 12% and 11%, respectively. By the occupational hygiene point of view, there is a degradation in the filter performance due to oil loading that the user does not realize because there is no remarkable variation in the breathing resistance.

  6. The data embedding method

    Energy Technology Data Exchange (ETDEWEB)

    Sandford, M.T. II; Bradley, J.N.; Handel, T.G.

    1996-06-01

    Data embedding is a new steganographic method for combining digital information sets. This paper describes the data embedding method and gives examples of its application using software written in the C-programming language. Sandford and Handel produced a computer program (BMPEMBED, Ver. 1.51 written for IBM PC/AT or compatible, MS/DOS Ver. 3.3 or later) that implements data embedding in an application for digital imagery. Information is embedded into, and extracted from, Truecolor or color-pallet images in Microsoft{reg_sign} bitmap (.BMP) format. Hiding data in the noise component of a host, by means of an algorithm that modifies or replaces the noise bits, is termed {open_quote}steganography.{close_quote} Data embedding differs markedly from conventional steganography, because it uses the noise component of the host to insert information with few or no modifications to the host data values or their statistical properties. Consequently, the entropy of the host data is affected little by using data embedding to add information. The data embedding method applies to host data compressed with transform, or {open_quote}lossy{close_quote} compression algorithms, as for example ones based on discrete cosine transform and wavelet functions. Analysis of the host noise generates a key required for embedding and extracting the auxiliary data from the combined data. The key is stored easily in the combined data. Images without the key cannot be processed to extract the embedded information. To provide security for the embedded data, one can remove the key from the combined data and manage it separately. The image key can be encrypted and stored in the combined data or transmitted separately as a ciphertext much smaller in size than the embedded data. The key size is typically ten to one-hundred bytes, and it is in data an analysis algorithm.

  7. Smart Multicore Embedded Systems

    DEFF Research Database (Denmark)

    This book provides a single-source reference to the state-of-the-art of high-level programming models and compilation tool-chains for embedded system platforms. The authors address challenges faced by programmers developing software to implement parallel applications in embedded systems, where ve...

  8. Embedded engineering education

    CERN Document Server

    Kaštelan, Ivan; Temerinac, Miodrag; Barak, Moshe; Sruk, Vlado

    2016-01-01

    This book focuses on the outcome of the European research project “FP7-ICT-2011-8 / 317882: Embedded Engineering Learning Platform” E2LP. Additionally, some experiences and researches outside this project have been included. This book provides information about the achieved results of the E2LP project as well as some broader views about the embedded engineering education. It captures project results and applications, methodologies, and evaluations. It leads to the history of computer architectures, brings a touch of the future in education tools and provides a valuable resource for anyone interested in embedded engineering education concepts, experiences and material. The book contents 12 original contributions and will open a broader discussion about the necessary knowledge and appropriate learning methods for the new profile of embedded engineers. As a result, the proposed Embedded Computer Engineering Learning Platform will help to educate a sufficient number of future engineers in Europe, capable of d...

  9. Study on paraffin/expanded graphite composite phase change thermal energy storage material

    International Nuclear Information System (INIS)

    Zhang Zhengguo; Fang Xiaoming

    2006-01-01

    A paraffin/expanded graphite composite phase change thermal energy storage material was prepared by absorbing the paraffin into an expanded graphite that has an excellent absorbability. In such a composite, the paraffin serves as a latent heat storage material and the expanded graphite acts as the supporting material, which prevents leakage of the melted paraffin from its porous structure due to the capillary and surface tension forces. The inherent structure of the expanded graphite did not change in the composite material. The solid-liquid phase change temperature of the composite PCM was the same as that of the paraffin, and the latent heat of the paraffin/expanded graphite composite material was equivalent to the calculated value based on the mass ratio of the paraffin in the composite. The heat transfer rate of the paraffin/expanded graphite composite was obviously higher than that of the paraffin due to the combination with the expanded graphite that had a high thermal conductivity. The prepared paraffin/expanded graphite composite phase change material had a large thermal storage capacity and improved thermal conductivity and did not experience liquid leakage during its solid-liquid phase change

  10. Embedded Linux in het onderwijs

    NARCIS (Netherlands)

    Dr Ruud Ermers

    2008-01-01

    Embedded Linux wordt bij steeds meer grote bedrijven ingevoerd als embedded operating system. Binnen de opleiding Technische Informatica van Fontys Hogeschool ICT is Embedded Linux geïntroduceerd in samenwerking met het lectoraat Architectuur van Embedded Systemen. Embedded Linux is als vakgebied

  11. Brauer type embedding problems

    CERN Document Server

    Ledet, Arne

    2005-01-01

    This monograph is concerned with Galois theoretical embedding problems of so-called Brauer type with a focus on 2-groups and on finding explicit criteria for solvability and explicit constructions of the solutions. The advantage of considering Brauer type embedding problems is their comparatively simple condition for solvability in the form of an obstruction in the Brauer group of the ground field. This book presupposes knowledge of classical Galois theory and the attendant algebra. Before considering questions of reducing the embedding problems and reformulating the solvability criteria, the

  12. Time-dependent embedding

    OpenAIRE

    Inglesfield, J. E.

    2007-01-01

    A method of solving the time-dependent Schr\\"odinger equation is presented, in which a finite region of space is treated explicitly, with the boundary conditions for matching the wave-functions on to the rest of the system replaced by an embedding term added on to the Hamiltonian. This time-dependent embedding term is derived from the Fourier transform of the energy-dependent embedding potential, which embeds the time-independent Schr\\"odinger equation. Results are presented for a one-dimensi...

  13. Thermophysical properties estimation of paraffin/graphite composite phase change material using an inverse method

    International Nuclear Information System (INIS)

    Lachheb, Mohamed; Karkri, Mustapha; Albouchi, Fethi; Mzali, Foued; Nasrallah, Sassi Ben

    2014-01-01

    Highlights: • Preparation of paraffin/graphite composites by uni-axial compression technique. • Measurement of thermophysical properties of paraffin/graphite using the periodic method. • Measurement of the experimental densities of paraffin/graphite composites. • Prediction of the effective thermal conductivity using analytical models. - Abstract: In this paper, two types of graphite were combined with paraffin in an attempt to improve thermal conductivity of paraffin phase change material (PCM): Synthetic graphite (Timrex SFG75) and graphite waste obtained from damaged Tubular graphite Heat Exchangers. These paraffin/graphite phase change material (PCM) composites are prepared by the cold uniaxial compression technique and the thermophysical properties were estimated using a periodic temperature method and an inverse technique. Results showed that the thermal conductivity and thermal diffusivity are greatly influenced by the graphite addition

  14. Liquid-Embedded Elastomer Electronics

    Science.gov (United States)

    Kramer, Rebecca; Majidi, Carmel; Park, Yong-Lae; Paik, Jamie; Wood, Robert

    2012-02-01

    Hyperelastic sensors are fabricated by embedding a silicone rubber film with microchannels of conductive liquid. In the case of soft tactile sensors, pressing the surface of the elastomer will deform the cross-section of underlying channels and change their electrical resistance. Soft pressure sensors may be employed in a variety of applications. For example, a network of pressure sensors can serve as artificial skin by yielding detailed information about contact pressures. This concept was demonstrated in a hyperelastic keypad, where perpendicular conductive channels form a quasi-planar network within an elastomeric matrix that registers the location, intensity and duration of applied pressure. In a second demonstration, soft curvature sensors were used for joint angle proprioception. Because the sensors are soft and stretchable, they conform to the host without interfering with the natural mechanics of motion. This marked the first use of liquid-embedded elastomer electronics to monitor human or robotic motion. Finally, liquid-embedded elastomers may be implemented as conductors in applications that call for flexible or stretchable circuitry, such as robotic origami.

  15. Electronics for embedded systems

    CERN Document Server

    Bindal, Ahmet

    2017-01-01

    This book provides semester-length coverage of electronics for embedded systems, covering most common analog and digital circuit-related issues encountered while designing embedded system hardware. It is written for students and young professionals who have basic circuit theory background and want to learn more about passive circuits, diode and bipolar transistor circuits, the state-of-the-art CMOS logic family and its interface with older logic families such as TTL, sensors and sensor physics, operational amplifier circuits to condition sensor signals, data converters and various circuits used in electro-mechanical device control in embedded systems. The book also provides numerous hardware design examples by integrating the topics learned in earlier chapters. The last chapter extensively reviews the combinational and sequential logic design principles to be able to design the digital part of embedded system hardware.

  16. Embedded Fragments Registry (EFR)

    Data.gov (United States)

    Department of Veterans Affairs — In 2009, the Department of Defense estimated that approximately 40,000 service members who served in OEF/OIF may have embedded fragment wounds as the result of small...

  17. Smart Multicore Embedded Systems

    DEFF Research Database (Denmark)

    This book provides a single-source reference to the state-of-the-art of high-level programming models and compilation tool-chains for embedded system platforms. The authors address challenges faced by programmers developing software to implement parallel applications in embedded systems, where very...... specificities of various embedded systems from different industries. Parallel programming tool-chains are described that take as input parameters both the application and the platform model, then determine relevant transformations and mapping decisions on the concrete platform, minimizing user intervention...... and hiding the difficulties related to the correct and efficient use of memory hierarchy and low level code generation. Describes tools and programming models for multicore embedded systems Emphasizes throughout performance per watt scalability Discusses realistic limits of software parallelization Enables...

  18. The use of naturally occurring selectively isolated bacteria for inhibiting paraffin deposition

    Energy Technology Data Exchange (ETDEWEB)

    Lazar, I.; Voicu, A.; Dobrota, S.; Petrisor, I.G.; Stefanescu, M.; Sandulescu, L. [Institute of Biology of the Romanian Academy, Spl. Independentei 296, Bucharest (Romania); Nicolescu, C.; Mucenica, D. [PETROSTAR Ploiesti, Bdul Bucuresti 35, Ploiesti (Romania)

    1999-01-01

    One of the most severe problems at any oil fields producing paraffinic oils is that of paraffin depositions. Romania which has a long experience in oil production is also faced with this problem in many oil fields. The microbial treatment, based on the activity of naturally occurring, selectively isolated bacteria, is already proved as an effective alternative to conventional methods to prevent and remove paraffin damage. Using such kind of bacterial products, exciting results for inhibiting paraffin depositions have been obtained. In this paper results concerning the naturally occurring bacteria selectively isolated from hydrocarbon polluted sites as well as from paraffinic oils, semi-solid and solid paraffin depositions are presented. After a laboratory screening, 15 bacterial strains (BS 1-15), three bacterial consortia (BC 1-3) and a Special Bacterial Consortium (SBC1) were selected. For the selection of bacterial consortia, the classical enrichment culture method has been used. The Special Bacterial Consortium resulted from a mixture of BS 1-15 and BC 1-3 following the steps of the classical enrichment culture method. The BS 1-15, BC 1-3 and SBC1 have been tested for their performances in producing biosurfactants and biosolvents as well as for hydrocarbon utilisation. The SBC1 has been tested for its ability in degradation of hydrocarbons contained in several types of paraffinic or non-paraffinic oils, and then for inhibiting paraffin deposition on a `flow equipment` using two types of paraffinic oils. The SBC1 has been also tested for degradation of hydrocarbons contained in semi-solid and solid paraffin depositions. The results obtained could support further applications to prevent and control paraffin depositions

  19. The use of naturally occurring selectively isolated bacteria for inhibiting paraffin deposition

    International Nuclear Information System (INIS)

    Lazar, I.; Voicu, A.; Dobrota, S.; Petrisor, I.G.; Stefanescu, M.; Sandulescu, L.; Nicolescu, C.; Mucenica, D.

    1999-01-01

    One of the most severe problems at any oil fields producing paraffinic oils is that of paraffin depositions. Romania which has a long experience in oil production is also faced with this problem in many oil fields. The microbial treatment, based on the activity of naturally occurring, selectively isolated bacteria, is already proved as an effective alternative to conventional methods to prevent and remove paraffin damage. Using such kind of bacterial products, exciting results for inhibiting paraffin depositions have been obtained. In this paper results concerning the naturally occurring bacteria selectively isolated from hydrocarbon polluted sites as well as from paraffinic oils, semi-solid and solid paraffin depositions are presented. After a laboratory screening, 15 bacterial strains (BS 1-15), three bacterial consortia (BC 1-3) and a Special Bacterial Consortium (SBC1) were selected. For the selection of bacterial consortia, the classical enrichment culture method has been used. The Special Bacterial Consortium resulted from a mixture of BS 1-15 and BC 1-3 following the steps of the classical enrichment culture method. The BS 1-15, BC 1-3 and SBC1 have been tested for their performances in producing biosurfactants and biosolvents as well as for hydrocarbon utilisation. The SBC1 has been tested for its ability in degradation of hydrocarbons contained in several types of paraffinic or non-paraffinic oils, and then for inhibiting paraffin deposition on a 'flow equipment' using two types of paraffinic oils. The SBC1 has been also tested for degradation of hydrocarbons contained in semi-solid and solid paraffin depositions. The results obtained could support further applications to prevent and control paraffin depositions

  20. Determining the color of solid paraffines in a KNS-2 colorimeter

    Energy Technology Data Exchange (ETDEWEB)

    Rozova, L P; Gladyshev, V P; Ivanov, V S; Men' kov, P A

    1980-01-01

    A new method is presented for determining the color of solid paraffines in a recently developed KNS-2 colorimeter. The essence of this particular method lies in a comparison of the intensity of the color of a melted paraffin sample with a set of standard light filters. The color of the paraffin is expressed in conditional brands. The method is simple, reliable and has good result convergence.

  1. Integration of catalyst design and reactor engineering in paraffins dehydrogenation

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, D.; Miracca, I. [Snamprogetti S.p.A., S. Donato Milanese (Italy)

    2005-07-01

    Unfortunately, olefins are not a natural fossil resource. Their production requires sophisticated and costly technologies, highly demanding in terms of investments and energy. Dehydrogenations are applied industrially to light alkanes (propane to propylene for polymers and isobutane to iso-butylene for gasoline and polymers) as well as long linear ones (C{sub 10}-C{sub 14} to linear-alkyl-benzenes) and for the production of styrene from ethylbenzene. The light paraffins dehydrogenation sustains a network of technologies allowing an integrated approach to create value from Natural Gas. (orig.)

  2. A Local Composition Model for Paraffinic Solid Solutions

    DEFF Research Database (Denmark)

    Coutinho, A.P. João; Knudsen, Kim; Andersen, Simon Ivar

    1996-01-01

    The description of the solid-phase non-ideality remains the main obstacle in modelling the solid-liquid equilibrium of hydrocarbons. A theoretical model, based on the local composition concept, is developed for the orthorhombic phase of n-alkanes and tested against experimental data for binary sy...... systems. It is shown that it can adequately predict the experimental phase behaviour of paraffinic mixtures. This work extends the applicability of local composition models to the solid phase. Copyright (C) 1996 Elsevier Science Ltd....

  3. The influence of expanded graphite on thermal properties for paraffin/high density polyethylene/chlorinated paraffin/antimony trioxide as a flame retardant phase change material

    International Nuclear Information System (INIS)

    Zhang Ping; Song Lei; Lu Hongdian; Wang Jian; Hu Yuan

    2010-01-01

    The influences of expanded graphite (EG) on the thermal properties of chlorinated paraffin (CP) and antimony trioxide (AT) on phase change material which bases on paraffin/high density polyethylene (HDPE) are studied. Differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), thermogravimetric analysis-Fourier transform infrared spectrometry (TGA-FTIR), microscale combustion calorimeter (MCC) and cone calorimeter (CONE) were used to evaluate the influence of EG on paraffin/HDPE/CP/AT system. The DSC results indicated that the latent heat value of PCM could be increased when the mass fraction of HDPE was decreased in the PCM, and EG could confine the molecular heat movement of paraffin. EG could improve the thermal stability and increase the char residue at high temperature for paraffin/HDPE/CP/AT hybrid. The volatilized products formed on thermal degradation of paraffin/HDPE/CP/AT with EG showed the release of CO 2 gas was hastened and increased, and the amount of combustible gases were decreased by TGA-FTIR analysis. The MCC and CONE results presented that the flame retardant efficiency of CP/AT could be improved by adding EG in paraffin/HDPE/CP/AT system.

  4. Professional Windows Embedded Compact 7

    CERN Document Server

    Phung, Samuel; Joubert, Thierry; Hall, Mike

    2011-01-01

    Learn to program an array of customized devices and solutions As a compact, highly efficient, scalable operating system, Windows Embedded Compact 7 (WEC7) is one of the best options for developing a new generation of network-enabled, media-rich, and service-oriented devices. This in-depth resource takes you through the benefits and capabilities of WEC7 so that you can start using this performance development platform today. Divided into several major sections, the book begins with an introduction and then moves on to coverage of OS design, application development, advanced application developm

  5. Improved resolution by mounting of tissue sections for laser microdissection.

    Science.gov (United States)

    van Dijk, M C R F; Rombout, P D M; Dijkman, H B P M; Ruiter, D J; Bernsen, M R

    2003-08-01

    Laser microbeam microdissection has greatly facilitated the procurement of specific cell populations from tissue sections. However, the fact that a coverslip is not used means that the morphology of the tissue sections is often poor. To develop a mounting method that greatly improves the morphological quality of tissue sections for laser microbeam microdissection purposes so that the identification of target cells can be facilitated. Fresh frozen tissue and formalin fixed, paraffin wax embedded tissue specimens were used to test the morphological quality of mounted and unmounted tissue. The mounting solution consisted of an adhesive gum and blue ink diluted in water. Interference of the mounting solution with DNA quality was analysed by the polymerase chain reaction using 10-2000 cells isolated by microdissection from mounted and unmounted tissue. The mounting solution greatly improved the morphology of tissue sections for laser microdissection purposes and had no detrimental effects on the isolation and efficiency of amplification of DNA. One disadvantage was that the mounting solution reduced the cutting efficiency of the ultraviolet laser. To minimise this effect, the mounting solution should be diluted as much as possible. Furthermore, the addition of blue ink to the mounting medium restores the cutting efficiency of the laser. The mounting solution is easy to prepare and apply and can be combined with various staining methods without compromising the quality of the DNA extracted.

  6. Method of removing paraffin from mineral oils, shale oils, tar oils, and their fractions or residues

    Energy Technology Data Exchange (ETDEWEB)

    Palmquist, F T.E.

    1949-09-08

    A method is described for removing paraffin from mineral oils, shale oils, tar oils, and their fractions or residues by centrifuging in the presence of oil-dissolving and paraffin-precipitating solvents, by which the precipitated paraffin is made to pass through an indifferent auxiliary liquid, in which a removal of oil takes place, characterized in that as auxiliary liquid is used a liquid or mixture of liquids whose surface tension against the oil solution is sufficiently low for the paraffin to pass the layer of auxiliary liquid in the form of separate crystals.

  7. Images of paraffin monolayer crystals with perfect contrast: Minimization of beam-induced specimen motion

    International Nuclear Information System (INIS)

    Glaeser, R.M.; McMullan, G.; Faruqi, A.R.; Henderson, R.

    2011-01-01

    Quantitative analysis of electron microscope images of organic and biological two-dimensional crystals has previously shown that the absolute contrast reached only a fraction of that expected theoretically from the electron diffraction amplitudes. The accepted explanation for this is that irradiation of the specimen causes beam-induced charging or movement, which in turn causes blurring of the image due to image or specimen movement. In this paper, we used three different approaches to try to overcome this image-blurring problem in monolayer crystals of paraffin. Our first approach was to use an extreme form of spotscan imaging, in which a single image was assembled on film by the successive illumination of up to 50,000 spots, each of a diameter of around 7 nm. The second approach was to use the Medipix II detector with its zero-noise readout to assemble a time-sliced series of images of the same area in which each frame from a movie with up to 400 frames had an exposure of only 500 electrons. In the third approach, we simply used a much thicker carbon support film to increase the physical strength and conductivity of the support. Surprisingly, the first two methods involving dose fractionation in space or time produced only partial improvements in contrast whereas the third approach produced many virtually perfect images, where the absolute contrast predicted from the electron diffraction amplitudes was observed in the images. We conclude that it is possible to obtain consistently almost perfect images of beam-sensitive specimens if they are attached to an appropriately strong and conductive support; however great care is needed in practice and the problem remains of how to best image ice-embedded biological structures in the absence of a strong, conductive support film. -- Research Highlights: →Three ideas were tested to improve the contrast of images of an organic specimen. →High-resolution images of paraffin on thick carbon films can have perfect contrast

  8. Images of paraffin monolayer crystals with perfect contrast: Minimization of beam-induced specimen motion

    Energy Technology Data Exchange (ETDEWEB)

    Glaeser, R.M. [Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720 (United States); McMullan, G.; Faruqi, A.R. [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom); Henderson, R., E-mail: rh15@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom)

    2011-01-15

    Quantitative analysis of electron microscope images of organic and biological two-dimensional crystals has previously shown that the absolute contrast reached only a fraction of that expected theoretically from the electron diffraction amplitudes. The accepted explanation for this is that irradiation of the specimen causes beam-induced charging or movement, which in turn causes blurring of the image due to image or specimen movement. In this paper, we used three different approaches to try to overcome this image-blurring problem in monolayer crystals of paraffin. Our first approach was to use an extreme form of spotscan imaging, in which a single image was assembled on film by the successive illumination of up to 50,000 spots, each of a diameter of around 7 nm. The second approach was to use the Medipix II detector with its zero-noise readout to assemble a time-sliced series of images of the same area in which each frame from a movie with up to 400 frames had an exposure of only 500 electrons. In the third approach, we simply used a much thicker carbon support film to increase the physical strength and conductivity of the support. Surprisingly, the first two methods involving dose fractionation in space or time produced only partial improvements in contrast whereas the third approach produced many virtually perfect images, where the absolute contrast predicted from the electron diffraction amplitudes was observed in the images. We conclude that it is possible to obtain consistently almost perfect images of beam-sensitive specimens if they are attached to an appropriately strong and conductive support; however great care is needed in practice and the problem remains of how to best image ice-embedded biological structures in the absence of a strong, conductive support film. -- Research Highlights: {yields}Three ideas were tested to improve the contrast of images of an organic specimen. {yields}High-resolution images of paraffin on thick carbon films can have perfect

  9. Problems in waterflooding fields containing paraffinic crude oils

    Energy Technology Data Exchange (ETDEWEB)

    Kovalev, A G; Lyutin, L V; Perevalov, V G

    1968-11-01

    When Caspian seawater is injected into the Uzen field reservoir, the temperature of the reservoir oil can be lowered 10/sup 0/ to 20/sup 0/C below initial reservoir temperature. Because Uzen crude oil is saturated with paraffin, the cold injection water can deposit paraffin in the formation and reduce oil recovery. In a related study, it was shown that the lower temperature should not adversely affect capillary and wettability behavior of the crude oil in the reservoir. Oil recovery was found to be essentially independent of water composition. However, fresh water is easier to handle in injection systems than brines. Several studies have shown that oil recovery from Uzen field should be increased by use of hot injection water. Various methods of heating the water are discussed. To reduce corrosivity and scaling of hot brine, sodium hexametaphosphate is added in concentrations of 2 to 15 mg/liter. It is concluded that it would be practical to use hot injection water in this field.

  10. Embedded Systems Design: Optimization Challenges

    DEFF Research Database (Denmark)

    Pop, Paul

    2005-01-01

    Summary form only given. Embedded systems are everywhere: from alarm clocks to PDAs, from mobile phones to cars, almost all the devices we use are controlled by embedded systems. Over 99% of the microprocessors produced today are used in embedded systems, and recently the number of embedded systems...

  11. Polymerase chain reaction-based method for the identification of Leishmania (Viannia) braziliensis and Leishmania (Viannia) guyanensis in mucosal tissues conserved in paraffin.

    Science.gov (United States)

    Prestes, Suzane Ribeiro; Guerra, Jorge Augusto de Oliveira; Romero, Gustavo Adolfo Sierra; Magalhaes, Laylah Kelre Costa; Santana, Rosa Amelia Gonçalves; Maciel, Marcel Gonçalves; Custódio, Ana; Barbosa, Maria das Graças Vale; Silveira, Henrique

    2015-01-01

    In the Americas, mucosal leishmaniasis is primarily associated with infection by Leishmania (Viannia) braziliensis. However, Leishmania (Viannia) guyanensis is another important cause of this disease in the Brazilian Amazon. In this study, we aimed at detecting Leishmaniadeoxyribonucleic acid (DNA) within paraffin-embedded fragments of mucosal tissues, and characterizing the infecting parasite species. We evaluated samples collected from 114 patients treated at a reference center in the Brazilian Amazon by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analyses. Direct examination of biopsy imprints detected parasites in 10 of the 114 samples, while evaluation of hematoxylin and eosin-stained slides detected amastigotes in an additional 17 samples. Meanwhile, 31/114 samples (27.2%) were positive for Leishmania spp. kinetoplast deoxyribonucleic acid (kDNA) by PCR analysis. Of these, 17 (54.8%) yielded amplification of the mini-exon PCR target, thereby allowing for PCR-RFLP-based identification. Six of the samples were identified as L. (V.) braziliensis, while the remaining 11 were identified as L. (V.) guyanensis. The results of this study demonstrate the feasibility of applying molecular techniques for the diagnosis of human parasites within paraffin-embedded tissues. Moreover, our findings confirm that L. (V.) guyanensisis a relevant causative agent of mucosal leishmaniasis in the Brazilian Amazon.

  12. Smart multicore embedded systems

    CERN Document Server

    Bertels, Koen; Karlsson, Sven; Pacull, François

    2014-01-01

    This book provides a single-source reference to the state-of-the-art of high-level programming models and compilation tool-chains for embedded system platforms. The authors address challenges faced by programmers developing software to implement parallel applications in embedded systems, where very often they are forced to rewrite sequential programs into parallel software, taking into account all the low level features and peculiarities of the underlying platforms. Readers will benefit from these authors’ approach, which takes into account both the application requirements and the platform specificities of various embedded systems from different industries. Parallel programming tool-chains are described that take as input parameters both the application and the platform model, then determine relevant transformations and mapping decisions on the concrete platform, minimizing user intervention and hiding the difficulties related to the correct and efficient use of memory hierarchy and low level code generati...

  13. Paraffin molecule mobility in channel clathrates of urea on spectroscopic NMR relaxation data

    CERN Document Server

    Kriger, Y G; Chekhova, G N

    2001-01-01

    The temperature dependences of the protons spin-lattice relaxation time (T sub I) in the channel clathrates of urea with paraffins are measured. The data on the T sub I are interpreted within the frames of the model of the paraffins molecules and their fragments orientation in the clathrate channels. The dynamics peculiarities are connected with the disproportion effects of these compounds

  14. Enhanced thermal properties with graphene oxide in the urea-formaldehyde microcapsules containing paraffin PCMs.

    Science.gov (United States)

    Qiao, Zhen; Mao, Jian

    2017-02-01

    In this study, compact urea-formaldehyde microcapsules containing paraffin (UFP) phase change materials (PCMs) were prepared via in situ polymerisation. The thermal conductivity of the PCMs was enhanced without influencing their enthalpy by adding graphene oxide (GO). Two modification methods were investigated: One in which GO is added to the inside of microcapsules, defined as "paraffin/GO@UF composite"; and another in which GO is coated onto the surface of shell, defined as "paraffin@UF/GO composite". The GO sheets were visible in scanning electron microscope (SEM) images of paraffin@UF/GO composite. The thermal conductivity was 0.2236 ± 0.0003 W/(m·K) for UFP particles, was 0.2517 ± 0.0003 W/(m·K) for the paraffin/GO@UF composite (10 wt%), and was 1.0670 ± 0.0020 W/(m·K) for paraffin@UF/GO composite (10 wt%), respectively. The encapsulation efficiency of all samples exceeded 80% (w/w) and all samples exhibited favourable thermal stability and reliability. The IR emissivity of paraffin@UF/GO was lower than that of paraffin/GO@UF when the same GO amount was added to the composite.

  15. High paraffin Kumkol petroleum processing under fuel and lubricant petroleum scheme

    International Nuclear Information System (INIS)

    Nadirov, N.K.; Konaev, Eh.N.

    1997-01-01

    Technological opportunity of high paraffin Kumkol petroleum processing under the fuel and lubricant scheme with production of lubricant materials in short supply, combustible materials and technical paraffin is shown. Mini petroleum block putting into operation on Kumkol deposit is reasonable economically and raises profitableness of hydrocarbon raw material production. (author)

  16. Sealing-free fast-response paraffin/nanoporous gold hybrid actuator

    Science.gov (United States)

    Ye, Xing-Long; Jin, Hai-Jun

    2017-09-01

    Paraffin-based actuators can deliver large actuation strokes and high actuation stress, but often suffer from a low response rate and leaking problems. Here, we report a new paraffin/metal hybrid actuator, which was fabricated by infiltrating nanoporous gold with paraffin. It exhibits a fast actuation rate owing to the high thermal conductivity of the inter-connected metal phase, and requires no external sealing because liquid paraffin can be well confined in nanoscale channels, due to the large capillarity. We found that in this hybrid actuator, the stress generated by actuation is negligibly small when the characteristic size of the nanoporous gold (L) is above ˜70 nm, and increases dramatically with a decreasing size when L paraffin wax—the paraffin in smaller pores can sustain larger tensile stress, and thus the contraction of paraffin during cooling can be translated into larger compression stress and strain energy in a metal framework, leading to a larger actuation stress and energy. We also demonstrate that complex actuation motions can be achieved by incorporating hierarchical-structured nanoporous metal with paraffin.

  17. Corrugated paraffin nanocomposite films as large stroke thermal actuators and self-activating thermal interfaces.

    Science.gov (United States)

    Copic, Davor; Hart, A John

    2015-04-22

    High performance active materials are of rapidly growing interest for applications including soft robotics, microfluidic systems, and morphing composites. In particular, paraffin wax has been used to actuate miniature pumps, solenoid valves, and composite fibers, yet its deployment is typically limited by the need for external volume constraint. We demonstrate that compact, high-performance paraffin actuators can be made by confining paraffin within vertically aligned carbon nanotube (CNT) films. This large-stroke vertical actuation is enabled by strong capillary interaction between paraffin and CNTs and by engineering the CNT morphology by mechanical compression before capillary-driven infiltration of the molten paraffin. The maximum actuation strain of the corrugated CNT-paraffin films (∼0.02-0.2) is comparable to natural muscle, yet the maximum stress is limited to ∼10 kPa by collapse of the CNT network. We also show how a CNT-paraffin film can serve as a self-activating thermal interface that closes a gap when it is heated. These new CNT-paraffin film actuators could be produced by large-area CNT growth, infiltration, and lamination methods, and are attractive for use in miniature systems due to their self-contained design.

  18. Polarizable Density Embedding

    DEFF Research Database (Denmark)

    Olsen, Jógvan Magnus Haugaard; Steinmann, Casper; Ruud, Kenneth

    2015-01-01

    We present a new QM/QM/MM-based model for calculating molecular properties and excited states of solute-solvent systems. We denote this new approach the polarizable density embedding (PDE) model and it represents an extension of our previously developed polarizable embedding (PE) strategy. The PDE...... model is a focused computational approach in which a core region of the system studied is represented by a quantum-chemical method, whereas the environment is divided into two other regions: an inner and an outer region. Molecules belonging to the inner region are described by their exact densities...

  19. Preparation and thermal properties of form stable paraffin phase change material encapsulation

    International Nuclear Information System (INIS)

    Liu Xing; Liu Hongyan; Wang Shujun; Zhang Lu; Cheng Hua

    2006-01-01

    Paraffin waxes are cheap and have moderate thermal energy storage density but low thermal conductivity and, hence, require large surface area to be used in energy storage. Form stable paraffin phase change materials (PCM) in which paraffin serves as a latent heat storage material and polyolefins act as a supporting material, because of paraffin leakage, are required to be improved. The form stable paraffin PCM in the present paper was encapsulated in an inorganic silica gel polymer successfully by in situ polymerization. The differential scanning calorimeter (DSC) was used to measure its thermal properties. At the same time, the Washburn equation, which measures the wetting properties of powder materials, was used to test the hydrophilic-lipophilic properties of the PCMs. The result indicated that the enthalpy of the microencapsulated PCMs was reduced little, while their hydrophilic properties were enhanced largely

  20. Experimental study on heat capacity of paraffin/water phase change emulsion

    International Nuclear Information System (INIS)

    Huang, L.; Noeres, P.; Petermann, M.; Doetsch, C.

    2010-01-01

    A paraffin/water phase change emulsion is a multifunctional fluid in which fine paraffin droplets are dispersed in water by a surfactant. This paper presents an experimental study on the heat capacity of an emulsion containing 30 wt.% paraffin in a test rig. The results show that the heat capacity of the emulsion consists of the sensible heat capacity of water and that of the paraffin as well as the latent heat capacity of the paraffin during the phase transition solid-liquid. The emulsion is an attractive alternative to chilled water for comfort cooling applications, because it has a heat capacity of 50 kJ/kg from 5 to 11 deg. C, which is two times as high as that of water in the same temperature range.

  1. Carbon nanotube/paraffin/montmorillonite composite phase change material for thermal energy storage.

    Science.gov (United States)

    Li, Min; Guo, Qiangang; Nutt, Steven

    2017-04-01

    A composite phase change material (PCM) comprised of organic montmorillonite (OMMT)/paraffin/grafted multi-walled nanotube (MWNT) is synthesized via ultrasonic dispersion and liquid intercalation. The microstructure of the composite PCM has been characterized to determine the phase distribution, and thermal properties (latent heat and thermal conductivity) have been measured by differential scanning calorimetry (DSC) and a thermal constant analyzer. The results show that paraffin molecules are intercalated in the montmorillonite layers and the grafted MWNTs are dispersed in the montmorillonite layers. The latent heat is 47.1 J/g, and the thermal conductivity of the OMMT/paraffin/grafted MWNT composites is 34% higher than that of the OMMT/paraffin composites and 65% higher than that of paraffin.

  2. Exogenous lipoid pneumonia caused by paraffin in an amateur fire breather.

    Science.gov (United States)

    Weinberg, I; Fridlender, Z G

    2010-05-01

    Paraffin has characteristics that make it popular among fire breathers. To describe a case of paraffin-induced lipoid pneumonia in a fire breather. The patient was evaluated clinically in relation to his occupational history. A 32-year-old man presented with dyspnoea, tachypnoea and non-productive cough of 2 h duration that started immediately following an attempt to blow fire using paraffin as the volatile substance. He was discharged from the emergency ward but returned the next day presenting again with dyspnoea accompanied by mid-sternal pain, fever (38.1 degrees C) and leucocytosis. Chest radiography showed perihilar punctuate infiltrations. A diagnosis of exogenous lipoid pneumonia caused by paraffin was made, and the patient was treated, with full recovery within a week. Fire breathers must be viewed as a population at risk of paraffin-induced lipoid pneumonia.

  3. Paraffin as oxygen vector modulates tyrosine phenol lyase production by Citrobacter freundii MTCC 2424.

    Science.gov (United States)

    Azmi, Wamik; Kumar, Ajay; Dev, Varun

    2013-06-01

    The efficiency of three oxygen-vectors liquid paraffin, silicone oil and n-dodecane in the production of tyrosine phenol lyase (TPL) by Citrobacter freundii MTCC 2424 was evaluated at 4% (v/v) concentration. The liquid paraffin as oxygenvectors was found to exhibit a stimulatory effect on TPL synthesis. The liquid paraffin at 6% (v/v) resulted in 34% increase in the TPL synthesis accompanied by a 13% increase in the production of cell mass at a 10 L scale. This improvement in TPL and cell mass production in the presence of liquid paraffin can be related to the fact that liquid paraffin was capable of maintaining dissolved O2 concentration above 28% throughout the course of the fermentation. Maintenance of the dissolved O2 concentration above 28% could be viewed in terms of an adequate oxygen supply to the rapidly dividing cells of the bacterium, which in turn resulted in enhanced synthesis of TPL and cell mass.

  4. Ionic liquids for separation of olefin-paraffin mixtures

    Science.gov (United States)

    Dai, Sheng; Luo, Huimin; Huang, Jing-Fang

    2013-09-17

    The invention is directed to an ionic liquid comprising (i) a cationic portion containing a complex of a silver (I) ion and one or more neutral ligands selected from organoamides, organoamines, olefins, and organonitriles, and (ii) an anionic portion having the chemical formula ##STR00001## wherein m and n are independently 0 or an integer of 1 or above, and p is 0 or 1, provided that when p is 0, the group --N--SO.sub.2--(CF.sub.2).sub.nCF.sub.3 subtended by p is replaced with an oxide atom connected to the shown sulfur atom. The invention is also directed to a method for separating an olefin from an olefin-paraffin mixture by passing the mixture through a layer of the ionic liquid described above.

  5. Round-Robin Test of Paraffin Phase-Change Material

    Science.gov (United States)

    Vidi, S.; Mehling, H.; Hemberger, F.; Haussmann, Th.; Laube, A.

    2015-11-01

    A round-robin test between three institutes was performed on a paraffin phase-change material (PCM) in the context of the German quality association for phase-change materials. The aim of the quality association is to define quality and test specifications for PCMs and to award certificates for successfully tested materials. To ensure the reproducibility and comparability of the measurements performed at different institutes using different measuring methods, a round-robin test was performed. The sample was unknown. The four methods used by the three participating institutes in the round-robin test were differential scanning calorimetry, Calvet calorimetry and three-layer calorimetry. Additionally, T-history measurements were made. The aim of the measurements was the determination of the enthalpy as a function of temperature. The results achieved following defined test specifications are in excellent agreement.

  6. Controlled release of insect sex pheromones from paraffin wax and emulsions.

    Science.gov (United States)

    Atterholt, C A; Delwiche, M J; Rice, R E; Krochta, J M

    1999-02-22

    Paraffin wax and aqueous paraffin emulsions can be used as controlled release carriers for insect sex pheromones for mating disruption of orchard pests. Paraffin can be applied at ambient temperature as an aqueous emulsion, adheres to tree bark or foliage, releases pheromone for an extended period of time, and will slowly erode from bark and biodegrade in soil. Pheromone emulsions can be applied with simple spray equipment. Pheromone release-rates from paraffin were measured in laboratory flow-cell experiments. Pheromone was trapped from an air stream with an adsorbent, eluted periodically, and quantified by gas chromatography. Pheromone release from paraffin was partition-controlled, providing a constant (zero-order) release rate. A typical paraffin emulsion consisted of 30% paraffin, 4% pheromone, 4% soy oil, 1% vitamin E, 2% emulsifier, and the balance water. Soy oil and vitamin E acted as volatility suppressants. A constant release of oriental fruit moth pheromone from paraffin emulsions was observed in the laboratory for more than 100 days at 27 degreesC, with release-rates ranging from 0.4 to 2 mg/day, depending on the concentration and surface area of the dried emulsion. The use of paraffin emulsions is a viable method for direct application of insect pheromones for mating disruption. Sprayable formulations can be designed to release insect pheromones to the environment at a rate necessary for insect control by mating disruption. At temperatures below 38 degreesC, zero-order release was observed. At 38 degreesC and higher, pheromone oxidation occurred. A partition-controlled release mechanism was supported by a zero-order pheromone release-rate, low air/wax partition coefficients, and pheromone solubility in paraffin.

  7. Embedding JIT into MRP

    NARCIS (Netherlands)

    Flapper, S.D.P.; Miltenburg, G.J.; Wijngaard, J.

    1991-01-01

    Today many companies who are using MRP production control systems are investigating how they can produce some or all of their products using just-in time (JIT) principles. They wonder to what extent MRP can provide support for JIT production. This paper describes how JIT can be embedded into MRP. A

  8. Embedded Multimaterial Extrusion Bioprinting

    NARCIS (Netherlands)

    Rocca, Marco; Fragasso, Alessio; Liu, Wanjun; Heinrich, Marcel A.; Zhang, Yu Shrike

    Embedded extrusion bioprinting allows for the generation of complex structures that otherwise cannot be achieved with conventional layer-by-layer deposition from the bottom, by overcoming the limits imposed by gravitational force. By taking advantage of a hydrogel bath, serving as a sacrificial

  9. Embedded data representations

    DEFF Research Database (Denmark)

    Willett, Wesley; Jansen, Yvonne; Dragicevic, Pierre

    2017-01-01

    We introduce embedded data representations, the use of visual and physical representations of data that are deeply integrated with the physical spaces, objects, and entities to which the data refers. Technologies like lightweight wireless displays, mixed reality hardware, and autonomous vehicles...

  10. Polarizable Density Embedding

    DEFF Research Database (Denmark)

    Reinholdt, Peter; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard

    2017-01-01

    We analyze the performance of the polarizable density embedding (PDE) model-a new multiscale computational approach designed for prediction and rationalization of general molecular properties of large and complex systems. We showcase how the PDE model very effectively handles the use of large...

  11. Embedded enzymes catalyse capture

    Science.gov (United States)

    Kentish, Sandra

    2018-05-01

    Membrane technologies for carbon capture can offer economic and environmental advantages over conventional amine-based absorption, but can suffer from limited gas flux and selectivity to CO2. Now, a membrane based on enzymes embedded in hydrophilic pores is shown to exhibit combined flux and selectivity that challenges the state of the art.

  12. The Resin-Embedded Cornea Prepared Via Rapid Processing Protocol : A Good Histomorphometric Target for Clinical Investigation in Ophthalmology and Optometry

    Science.gov (United States)

    Cheah, Pike See; Mohidin, Norhani; Mohd Ali, Bariah; Maung, Myint; Latif, Azian Abdul

    2008-01-01

    This study illustrates and quantifies the changes on corneal tissue between the paraffin-embedded and resin-embedded blocks and thus, selects a better target in investigational ophthalmology and optometry via light microscopy. Corneas of two cynomolgus monkeys (Macaca fascicularis) were used in this study. The formalin-fixed cornea was prepared in paraffin block via the conventional tissue processing protocol (4-day protocol) and stained with haematoxylin and eosin. The glutaraldehyde-fixed cornea was prepared in resin block via the rapid and modified tissue processing procedure (1.2-day protocol) and stained with toluidine blue. The paraffin-embedded sample exhibits various undesired tissue damage and artifact such as thinner epithelium (due to the substantial volumic extraction from the tissue), thicker stroma layer (due to the separation of lamellae and the presence of voids) and the distorted endothelium. In contrast, the resin-embedded corneal tissue has demonstrated satisfactory corneal ultrastructural preservation. The rapid and modified tissue processing method for preparing the resin-embedded is particularly beneficial to accelerate the microscopic evaluation in ophthalmology and optometry. PMID:22570589

  13. Interaction study of polyisobutylene with paraffins by NMR using the evaluation of spin-lattice relaxation times for hydrogen nuclei

    International Nuclear Information System (INIS)

    Marques, Rosana G.G.; Tavares, Maria I.B.

    2001-01-01

    The evaluation of spin-lattice relaxation times of 1 H for polyisobutylene/paraffin systems, were obtained using the classic inversion recovery technique, and also through Cross Polarization Magic Angle Spinning (CP/MAS) techniques varying the contact time and also by the delayed contact time pulse sequence. NMR results showed that the polyisobutylene/paraffin systems in which high molecular weight paraffins were used, is heterogeneous. However, for paraffins with low molecular weight, the system presents good homogeneity. (author)

  14. Images of paraffin monolayer crystals with perfect contrast: minimization of beam-induced specimen motion

    Science.gov (United States)

    Glaeser, R.M.; McMullan, G.; Faruqi, A.R.; Henderson, R.

    2013-01-01

    Quantitative analysis of electron microscope images of organic and biological two-dimensional crystals has previously shown that the absolute contrast reached only a fraction of that expected theoretically from the electron diffraction amplitudes. The accepted explanation for this is that irradiation of the specimen causes beam-induced charging or movement, which in turn causes blurring of the image due to image or specimen movement. In this paper, we used three different approaches to try to overcome this image-blurring problem for monolayer crystals of paraffin. Our first approach was to use an extreme form of spotscan imaging, in which a single image was assembled on film by the successive illumination of up to 50,000 spots each of diameter around 7nm. The second approach was to use the Medipix II detector with its zero-noise readout to assemble a time-sliced series of images of the same area in which each frame from a movie with up to 400 frames had an exposure of only 500 electrons. In the third approach, we simply used a much thicker carbon support film to increase the physical strength and conductivity of the support. Surprisingly, the first two methods involving dose fractionation respectively in space or time produced only partial improvements in contrast whereas the third approach produced many virtually perfect images, in which the absolute contrast predicted from the electron diffraction amplitudes was observed in the images. We conclude that it is possible to obtain consistently almost perfect images of beam-sensitive specimens if they are attached to an appropriately strong and conductive support, but great care is needed in practice and the problem of how best to image ice-embedded biological structures in the absence of a strong, conductive support film requires more work. PMID:21185452

  15. Drilling azimuth gamma embedded design

    Directory of Open Access Journals (Sweden)

    Zhou Yi Ren

    2016-01-01

    Full Text Available Embedded drilling azimuth gamma design, the use of radioactive measuring principle embedded gamma measurement while drilling a short section analysis. Monte Carlo method, in response to the density of horizontal well logging numerical simulation of 16 orientation, the orientation of horizontal well analysed, calliper, bed boundary location, space, different formation density, formation thickness, and other factors inclined strata dip the impact by simulating 137Cs sources under different formation conditions of the gamma distribution, to determine the orientation of drilling density tool can detect window size and space, draw depth of the logging methods. The data 360° azimuth imaging, image processing method to obtain graph, display density of the formation, dip and strata thickness and other parameters, the logging methods obtain real-time geo-steering. To establish a theoretical basis for the orientation density logging while drilling method implementation and application of numerical simulation in-depth study of the MWD azimuth and density log response factors of horizontal wells.

  16. The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when?

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Haselkorn, Tamara; Bunce, Michael

    2007-01-01

    . Cross-linking not only complicates isolation of nucleic acid but also introduces polymerase "blocks" during PCR. A wide variety of methods exists for the recovery of DNA and RNA from archival tissues, and although a number of previous studies have qualitatively compared the relative merits....... These include methods of pre-treating the samples prior to extraction, extraction and nucleic acid purification methods themselves, and a post-extraction enzymatic repair technique. We find that although many of the published methods have distinct positive effects on some characteristics of the nucleic acids...

  17. RNA Sequencing of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining

    Directory of Open Access Journals (Sweden)

    Yan Guo

    2016-01-01

    Full Text Available Background. Proper rRNA depletion is crucial for the successful utilization of FFPE specimens when studying gene expression. We performed a study to evaluate two major rRNA depletion methods: Ribo-Zero and RNase H. RNAs extracted from 4 samples were treated with the two rRNA depletion methods in duplicate and sequenced (N=16. We evaluated their reducibility, ability to detect RNA, and ability to molecularly subtype these triple negative breast cancer specimens. Results. Both rRNA depletion methods produced consistent data between the technical replicates. We found that the RNase H method produced higher quality RNAseq data as compared to the Ribo-Zero method. In addition, we evaluated the RNAseq data generated from the FFPE tissue samples for noncoding RNA, including lncRNA, enhancer/super enhancer RNA, and single nucleotide variation (SNV. We found that the RNase H is more suitable for detecting high-quality, noncoding RNAs as compared to the Ribo-Zero and provided more consistent molecular subtype identification between replicates. Unfortunately, neither method produced reliable SNV data. Conclusions. In conclusion, for FFPE specimens, the RNase H rRNA depletion method performed better than the Ribo-Zero. Neither method generates data sufficient for SNV detection.

  18. Investigation of Epstein-Barr virus DNA in formalin-fixed and paraffin- embedded breast cancer tissues.

    Science.gov (United States)

    Kalkan, Ahmet; Ozdarendeli, Aykut; Bulut, Yasemin; Yekeler, Hayrettin; Cobanoglu, Bengu; Doymaz, Mehmet Z

    2005-01-01

    To investigate etiological role of Epstein-Barr virus (EBV) DNA in breast cancer. The presence of EBV DNA in 57 breast cancer tissues was investigated with a sensitive PCR assay. The breast cancer tissues were from invasive ductular (n=28), lobular (n=20) and other miscellaneous carcinomas (n=9). Tissues from normal breasts and patients with various benign breast diseases (n=55): fibrocystic disease (n=34), fibroadenoma (n=16), hyperplasia, and granulomatous mastitis (n=5), were used as control samples. EBV DNA was detected in 13 (23%) cancerous tissues (7 ductular, 4 lobular, 2 other carcinoma) and 19 (35%) in the control tissues. The difference between EBV presence in malignant and benign tissues was not statistically significant (p>0.05). The presence of EBV DNA was detected almost equally in both breast cancer and normal tissues, which indicates no etiological role for EBV in breast cancer. We suggest further etiological studies. Copyright (c) 2005 S. Karger AG, Basel.

  19. Embedding in thermosetting resins

    International Nuclear Information System (INIS)

    Buzonniere, A. de

    1985-01-01

    Medium activity waste coming either from nuclear power plants in operation such as evaporator concentrates, spent resins, filter cartridges or the dismantling of installations are embedded in order to obtain a product suitable for long term disposal. Embedding in thermosetting resins (polyester or epoxy) is one among currently used techniques; it is being developed by the CEA (Commissariat a l'Energie Atomique) and Technicatome (subsidiary of CEA and EDF). The process is easy to operate and yields excellent results particularly as far as volume reduction and radioelement containment (cesium particularly) are concerned. The process has already been in operation in four stationary plants for several years. Extension of the process to mobile units has been completed by Technicatome in collaboration with the CEA [fr

  20. Retrofit with membrane the Paraffin/Olefin separation

    Energy Technology Data Exchange (ETDEWEB)

    Motelica, A.; Bruinsma, O.S.L.; Kreiter, R.; Den Exter, M.J.; Vente, J.F. [ECN Biomass and Energy Efficiency, Petten (Netherlands)

    2012-10-15

    Olefins, such as ethylene, propylene, and butadiene, are among the most produced intermediates in petrochemical industry. They are produced from a wide range of hydrocarbon feedstocks (ethane, propane, butane, naphtha, gas oil) via a cracking process. The last step in this process is the separation of olefins from other hydrocarbons, which is traditionally performed with distillation. As the physicochemical properties, such as volatility and boiling point, of the compounds are very similar, the purification becomes capital and energy intensive. For example, the top of an ethylene/ethane distillation column needs to be chilled to -30C and this requires large amount of electric energy consumption. The separation of butadiene from the C4-fraction is performed with the aid of an additional solvent. This solvent has to be regenerated at the cost of additional high temperature steam. To overcome these separation disadvantages of olefin/paraffin separation, different separation methods have been investigated and proposed in recent years. Suggested options are based on better heat integration of the overall process, or on novel separation systems such as Heat Integrated Distillation Columns, membrane separation, adsorption-desorption systems or on hybrid separation methods, for example, distillation combined with membrane separation.

  1. Chlorinated paraffins wrapping of carbon nanotubes: A theoretical investigation

    Science.gov (United States)

    Ding, Qiuyue; Ding, Ning; Chen, Xiangfeng; Wu, Chi-Man Lawrence

    2018-04-01

    How nanomaterials interact with pollutants is the central for understanding their environmental behavior and practical application. In this work, molecular dynamics (MD) and density functional theoretical (DFT) methods were used to investigated the influence of carbon chain length, degree of chlorination, chain configuration, and chirality of chlorinated paraffin (CP) and diameter of single-walled carbon nanotubes (SWNTs) on the interaction between CPs and SWNTs. The simulation results demonstrated that CP chain length and chlorination degree played considerably important roles in determining interaction strength between SWNTs and CPs. The interaction energies increased with increasing chain length and chlorination degree. The chirality of SWNT exerted negligible influence on the interaction energy between SWNTs and CPs. On the contrary, interaction energy increased with increasing radius of SWNTs due to the surface curvatures. This result was rationalized by considering the decrease in SWNT curvature with increasing radius, which resulted in plane-like CNT wall. The negligible influence of CP chain configurations was attributed to relative flexibility of CP carbon chains, which can wrap on tubes through conformational changes with low-energy barriers. MD results indicated that CPs could adsorb on SWNT surface rapidly in aqueous environment. Charge transfer and electronic density results indicated that the interaction between CPs and SWNTs was physisorption in nature. This work provides fundamental information regarding SWNTs as sorbents for CPs extraction and adsorptive removal from environmental water system.

  2. Efficient filtration system for paraffin-catalyst slurry separation

    Directory of Open Access Journals (Sweden)

    Khodagholi Mohammad Ali

    2013-01-01

    Full Text Available The filtration efficiency for separating liquid paraffin (or water from a slurry consisting of 25 weight% spherical alumina in a Slurry Bubble Column Reactor (SBCR comprised of a cylindrical tube of 10 cm diameter and 150 cm length was studied. Various differential pressures (ΔP were applied to two separate tubular sintered metal stainless steel filter elements with nominal pore size of 4 and 16μm. The experimental results disclosed that the rate of filtrations increased on applying higher differential pressure to the filter element. Albeit this phenomenon is limited to moderate ΔPs and for ΔP more than 1 bar is neither harmful nor helpful. The highest filtration rates at ΔPs higher than 1 bar were 170 and 248 ml/minute for 4 and 16μm respectively. Using water as the liquid in slurry the rate of filtration enhanced to 4 folds, and this issue reveals impact of viscosity on filtration efficiency clearly. In all situations, the total amount of particles present in the filtrate part never exceeded a few parts per million (ppm. The statistical analysis of the SEM image of the filtrate indicated that by applying higher pressure difference to the filter element the frequency percent of larger particle size increases. The operation of filter cake removing was performed with back flashing of 300 ml of clean liquid with pressures of 3-5 bar of N2 gas.

  3. Quantifying Short-Chain Chlorinated Paraffin Congener Groups.

    Science.gov (United States)

    Yuan, Bo; Bogdal, Christian; Berger, Urs; MacLeod, Matthew; Gebbink, Wouter A; Alsberg, Tomas; de Wit, Cynthia A

    2017-09-19

    Accurate quantification of short-chain chlorinated paraffins (SCCPs) poses an exceptional challenge to analytical chemists. SCCPs are complex mixtures of chlorinated alkanes with variable chain length and chlorination level; congeners with a fixed chain length (n) and number of chlorines (m) are referred to as a "congener group" C n Cl m . Recently, we resolved individual C n Cl m by mathematically deconvolving soft ionization high-resolution mass spectra of SCCP mixtures. Here we extend the method to quantifying C n Cl m by introducing C n Cl m specific response factors (RFs) that are calculated from 17 SCCP chain-length standards with a single carbon chain length and variable chlorination level. The signal pattern of each standard is measured on APCI-QTOF-MS. RFs of each C n Cl m are obtained by pairwise optimization of the normal distribution's fit to the signal patterns of the 17 chain-length standards. The method was verified by quantifying SCCP technical mixtures and spiked environmental samples with accuracies of 82-123% and 76-109%, respectively. The absolute differences between calculated and manufacturer-reported chlorination degrees were -0.9 to 1.0%Cl for SCCP mixtures of 49-71%Cl. The quantification method has been replicated with ECNI magnetic sector MS and ECNI-Q-Orbitrap-MS. C n Cl m concentrations determined with the three instruments were highly correlated (R 2 > 0.90) with each other.

  4. Embedded software verification and debugging

    CERN Document Server

    Winterholer, Markus

    2017-01-01

    This book provides comprehensive coverage of verification and debugging techniques for embedded software, which is frequently used in safety critical applications (e.g., automotive), where failures are unacceptable. Since the verification of complex systems needs to encompass the verification of both hardware and embedded software modules, this book focuses on verification and debugging approaches for embedded software with hardware dependencies. Coverage includes the entire flow of design, verification and debugging of embedded software and all key approaches to debugging, dynamic, static, and hybrid verification. This book discusses the current, industrial embedded software verification flow, as well as emerging trends with focus on formal and hybrid verification and debugging approaches. Includes in a single source the entire flow of design, verification and debugging of embedded software; Addresses the main techniques that are currently being used in the industry for assuring the quality of embedded softw...

  5. Preparation and Properties of Paraffin/TiO2/Active-carbon Composite Phase Change Materials

    Directory of Open Access Journals (Sweden)

    HAO Yong-gan

    2016-11-01

    Full Text Available A novel composite phase change materials (PCMs of paraffin/TiO2/active-carbon was prepared by a microemulsion method, where paraffin acted as a PCM and titanium dioxide (TiO2 as matrix material, and a small amount of active carbon was added to improve the thermal conductivity. The compositions, morphology and thermal properties of the paraffin/TiO2/active-carbon composite PCMs were characterized by XRD, SEM, TGA and DSC respectively. The shape stability during phase change process of this composite was also tested. The results show that paraffin is well encapsulated by TiO2 matrix, and thus exhibiting excellent shape-stabilized phase change feature. Besides, this composite PCM also presents superhydrophobic property. Therefore, these multifunctional features will endow PCMs with important application potential in energy efficient buildings.

  6. Recent developments in capabilities for analysing chlorinated paraffins in environmental matrices: A review

    NARCIS (Netherlands)

    van Mourik, L.M.; Leonards, P.E.G.; Gaus, C.; de Boer, J.

    2015-01-01

    Concerns about the high production volumes, persistency, bioaccumulation potential and toxicity of chlorinated paraffin (CP) mixtures, especially short-chain CPs (SCCPs), are rising. However, information on their levels and fate in the environment is still insufficient, impeding international

  7. Quantum-chemical study of hydride transfer in catalytic transformation of paraffins on zeolites

    NARCIS (Netherlands)

    Kazansky, V.B.; Frash, M.V.; Santen, van R.A.; Chon, H.; Ihm, S.-K.; Uh, Y.S.

    1997-01-01

    Ab initio quantum-chemical cluster calculations demonstrate that the activated complexes of hydride transfer reaction in catalytic transformation of paraffins on zeolites very much resembles adsorbed nonclassical carbonium ions. The calculated activation energies for reactions involving propane and

  8. Effect of paraffin saturation in a crude oil on operation of a field

    Energy Technology Data Exchange (ETDEWEB)

    Trebin, G F; Kapyrin, Yu V

    1968-11-01

    Both theoretical and practical studies in recent years have shown that in planning operational procedures for an oil field, the paraffin saturation of the crude oil must be considered. If the crude oil is essentially saturated with paraffin at reservoir condition, then paraffin deposition can occur around the well and in the well. Temperature in the reservoir can be lowered by 2 mechanisms: (1) by injection of water below reservoir temperature, and (2) by expansion of produced gas and consequent cooling of the produced oil. Possible application of these principles to several Soviet oil fields is discussed. In the Uzen field, a preliminary investigation is under way to test the feasibility of heating the injection water to prevent paraffin deposition in the reservoir.

  9. Flow restrictor silicon membrane microvalve actuated by optically controlled paraffin phase transition

    International Nuclear Information System (INIS)

    Kolari, K; Havia, T; Stuns, I; Hjort, K

    2014-01-01

    Restrictor valves allow proportional control of fluid flow but are rarely integrated in microfluidic systems. In this study, an optically actuated silicon membrane restrictor microvalve is demonstrated. Its actuation is based on the phase transition of paraffin, using a paraffin wax mixed with a suitable concentration of optically absorbing nanographite particles. Backing up the membrane with oil (the melted paraffin) allows for a compliant yet strong contact to the valve seat, which enables handling of high pressures. At flow rates up to 30 µL min −1 and at a pressure of 2 bars, the valve can successfully be closed and control the flow level by restriction. The use of this paraffin composite as an adhesive layer sandwiched between the silicon valve and glass eases fabrication. This type of restrictor valve is best suited for high pressure, low volume flow silicon-based nanofluidic systems. (paper)

  10. Unsteady Flame Embedding

    KAUST Repository

    El-Asrag, Hossam A.

    2011-01-01

    Direct simulation of all the length and time scales relevant to practical combustion processes is computationally prohibitive. When combustion processes are driven by reaction and transport phenomena occurring at the unresolved scales of a numerical simulation, one must introduce a dynamic subgrid model that accounts for the multiscale nature of the problem using information available on a resolvable grid. Here, we discuss a model that captures unsteady flow-flame interactions- including extinction, re-ignition, and history effects-via embedded simulations at the subgrid level. The model efficiently accounts for subgrid flame structure and incorporates detailed chemistry and transport, allowing more accurate prediction of the stretch effect and the heat release. In this chapter we first review the work done in the past thirty years to develop the flame embedding concept. Next we present a formulation for the same concept that is compatible with Large Eddy Simulation in the flamelet regimes. The unsteady flame embedding approach (UFE) treats the flame as an ensemble of locally one-dimensional flames, similar to the flamelet approach. However, a set of elemental one-dimensional flames is used to describe the turbulent flame structure directly at the subgrid level. The calculations employ a one-dimensional unsteady flame model that incorporates unsteady strain rate, curvature, and mixture boundary conditions imposed by the resolved scales. The model is used for closure of the subgrid terms in the context of large eddy simulation. Direct numerical simulation (DNS) data from a flame-vortex interaction problem is used for comparison. © Springer Science+Business Media B.V. 2011.

  11. Embedded microcontroller interfacing

    CERN Document Server

    Gupta, Gourab Sen

    2010-01-01

    Mixed-Signal Embedded Microcontrollers are commonly used in integrating analog components needed to control non-digital electronic systems. They are used in automatically controlled devices and products, such as automobile engine control systems, wireless remote controllers, office machines, home appliances, power tools, and toys. Microcontrollers make it economical to digitally control even more devices and processes by reducing the size and cost, compared to a design that uses a separate microprocessor, memory, and input/output devices. In many undergraduate and post-graduate courses, teachi

  12. Impact of 50% Synthesized Iso-Paraffins (SIP) on F-76 Fuel Coalescence

    Science.gov (United States)

    2013-12-16

    petroleum JP-5 and Synthesized Iso-Paraffins (SIP). SIP fuels are made from direct fermentation of sugar into olefinic hydrocarbons. The olefinic...manufactured scaled down filter/coalescer and separator to simulate the performance of a full-scale filter separator system. This test is designed to predict...5 and Synthesized Iso-Paraffins (SIP). SIP fuels are made from direct fermentation of sugar into olefinic hydrocarbons. The olefinic hydrocarbons

  13. Impact of 50% Synthesized Iso-Paraffins (SIP) on Middle Distillate Fuel Filtration and Coalescence

    Science.gov (United States)

    2014-10-30

    Paraffins DEFINITIONS Coalescence - the ability to shed water Conventional Material Source - crude oil , natural gas liquid condensates...Impact of 50% Synthesized Iso-Paraffins (SIP) on Middle Distillate Fuel Filtration and Coalescence NF&LCFT REPORT 441/15-003 30 October 2014...heavy oil , shale oil , and oil sands Effluent - stream leaving a system Influent - stream entering a system Turnover - time required to flow the

  14. Experimental preliminary exploration on determining grease thickness simulated by paraffin in petroleum pipelines

    International Nuclear Information System (INIS)

    Zhao Nongxiao; Arkin, Abulim; Yang Kunjie; Wang Shiheng; Shi Feiyue

    2009-01-01

    1.25 MeV γ-ray of 60 Co Compton scattering coefficient in the simple of paraffin,are measured by γ-ray energy spectrum analysis in two determining means. At the same experimental condition, we have used this scattering coefficient to determining grease thickness simulated by paraffin. The result show the average relative difference is about 1.29% for the best group. (authors)

  15. Paraffin Granuloma Associated with Buried Glans Penis-Induced Sexual and Voiding Dysfunction

    OpenAIRE

    Chon, Wonhee; Koo, Ja Yun; Park, Min Jung; Choi, Kyung-Un; Park, Hyun Jun; Park, Nam Cheol

    2017-01-01

    A paraffinoma is a type of inflammatory lipogranuloma that develops after the injection of an artificial mineral oil, such as paraffin or silicon, into the foreskin or the subcutaneous tissue of the penis for the purpose of penis enlargement, cosmetics, or prosthesis. The authors experienced a case of macro-paraffinoma associated with sexual dysfunction, voiding dysfunction, and pain caused by a buried glans penis after a paraffin injection for penis enlargement that had been perform...

  16. Feasibility study on embedded transport core calculations

    International Nuclear Information System (INIS)

    Ivanov, B.; Zikatanov, L.; Ivanov, K.

    2007-01-01

    The main objective of this study is to develop an advanced core calculation methodology based on embedded diffusion and transport calculations. The scheme proposed in this work is based on embedded diffusion or SP 3 pin-by-pin local fuel assembly calculation within the framework of the Nodal Expansion Method (NEM) diffusion core calculation. The SP 3 method has gained popularity in the last 10 years as an advanced method for neutronics calculation. NEM is a multi-group nodal diffusion code developed, maintained and continuously improved at the Pennsylvania State University. The developed calculation scheme is a non-linear iteration process, which involves cross-section homogenization, on-line discontinuity factors generation, and boundary conditions evaluation by the global solution passed to the local calculation. In order to accomplish the local calculation, a new code has been developed based on the Finite Elements Method (FEM), which is capable of performing both diffusion and SP 3 calculations. The new code will be used in the framework of the NEM code in order to perform embedded pin-by-pin diffusion and SP 3 calculations on fuel assembly basis. The development of the diffusion and SP 3 FEM code is presented first following by its application to several problems. Description of the proposed embedded scheme is provided next as well as the obtained preliminary results of the C3 MOX benchmark. The results from the embedded calculations are compared with direct pin-by-pin whole core calculations in terms of accuracy and efficiency followed by conclusions made about the feasibility of the proposed embedded approach. (authors)

  17. The use of paraffin wax in a new solar cooker with inner and outer reflectors

    Directory of Open Access Journals (Sweden)

    Arabacigil Bihter

    2015-01-01

    Full Text Available In this paper, the potential use and effectiveness of paraffin wax in a new solar cooker was experimentally investigated during daylight and late evening hours. For these experiments, a cooker having an inner reflecting surface was designed, constructed by filling paraffin wax and metal shavings. The side- and sub-surface temperatures of the paraffin wax in the cooker are measured in the summer months of June and July. The thermal efficiency of the cooker was tested on different conditions. The results show that the optimum angle of the outer reflector is 30°. Here, the peak temperature of the paraffin wax in the solar cooker was 83.4 °C. The average solar radiation reflected makes a contribution of 9.26% to the temperature of paraffin wax with the outer reflector. The solar cooker with the outer reflector angle of 30° receives also reflected radiation from the inner reflectors. Besides, the heating time is decreased to approximately 1 hour. The designed solar cooker can be effectively used with 30.3% daily thermal efficiency and paraffin wax due to the amount of energy stored.

  18. Enhanced Thermo-Optical Switching of Paraffin-Wax Composite Spots under Laser Heating.

    Science.gov (United States)

    Said, Asmaa; Salah, Abeer; Fattah, Gamal Abdel

    2017-05-12

    Thermo-optical switches are of particular significance in communications networks where increasingly high switching speeds are required. Phase change materials (PCMs), in particular those based on paraffin wax, provide wealth of exciting applications with unusual thermally-induced switching properties, only limited by paraffin's rather low thermal conductivity. In this paper, the use of different carbon fillers as thermal conductivity enhancers for paraffin has been investigated, and a novel structure based on spot of paraffin wax as a thermo-optic switch is presented. Thermo-optical switching parameters are enhanced with the addition of graphite and graphene, due to the extreme thermal conductivity of the carbon fillers. Differential Scanning Calorimetry (DSC) and Scanning electron microscope (SEM) are performed on paraffin wax composites, and specific heat capacities are calculated based on DSC measurements. Thermo-optical switching based on transmission is measured as a function of the host concentration under conventional electric heating and laser heating of paraffin-carbon fillers composites. Further enhancements in thermo-optical switching parameters are studied under Nd:YAG laser heating. This novel structure can be used in future networks with huge bandwidth requirements and electric noise free remote aerial laser switching applications.

  19. Thermal conductivity enhancement of paraffin by adding boron nitride nanostructures: A molecular dynamics study

    International Nuclear Information System (INIS)

    Lin, Changpeng; Rao, Zhonghao

    2017-01-01

    Highlights: • Different contributions to thermal conductivity are obtained. • Thermal conductivity of paraffin could be improved by boron nitride. • Crystallization effect from boron nitride was the key factor. • Paraffin nanocomposite is the desirable candidate for thermal energy storage. - Abstract: While paraffin is widely used in thermal energy storage today, its low thermal conductivity has become a bottleneck for the further applications. Here, we construct two kinds of paraffin-based phase change material nanocomposites through introducing boron nitride (BN) nanostructures into n-eicosane to enhance the thermal conductivity. Molecular dynamics (MD) simulation was adopted to estimate their thermal conductivities and related thermal properties. The results indicate that, after adding BN nanostructures, the latent heat of composites is reduced compared with the pure paraffin and they both show a glass-like thermal conductivity which increases as the temperature rises. This happens because the increasing temperature leads to gradually smaller inconsistency in vibrational density of state along three directions and increasingly significant overlaps among them. Furthermore, by decomposing the thermal conductivity, it is found that the major contribution to the overall thermal conductivity comes from BN nanostructures, while the contribution of n-eicosane is insignificant. Though the thermal conductivity from n-eicosane term is small, it has been improved greatly compared with amorphous state of n-eicosane, mainly due to the crystallization effects from BN nanostructures. This work will provide microscopic views and insights into the thermal mechanism of paraffin and offer effective guidances to enhance the thermal conductivity.

  20. Electrically conductive carbon nanofiber/paraffin wax composites for electric thermal storage

    International Nuclear Information System (INIS)

    Zhang Kun; Han Baoguo; Yu Xun

    2012-01-01

    Highlights: ► Carbon nanofiber (CNF)/paraffin wax composite is found to be a promising electric thermal storage material. ► The thermal storage capacity of CNF/paraffin wax composite is five times of traditional electric thermal storage material. ► CNF is shown to be an effective conductive filler for the composite. - Abstract: The research of electric thermal storage (ETS) has attracted a lot of attention recently, which converts off-peak electrical energy into thermal energy and release it later at peak hours. In this study, new electric thermal storage composites are developed by employing paraffin wax as thermal storage media and carbon nanofiber (CNF) as conductive fillers. Electric heating and thermal energy release performances of the CNF/paraffin wax composites are experimentally investigated. Experimental results show that, when the composites are heated to about 70 °C, the developed electrically conductive CNF/paraffin wax composites present a thermal storage capacity of about 280 kJ/kg, which is five times of that of traditional thermal storage medium such as ceramic bricks (54 kJ/kg). The CNF/paraffin wax composites can also effectively store the thermal energy and release the thermal energy in later hours.

  1. Chemical changes in the chloroform-paraffin system irradiated by 60Co gamma-rays, 1

    International Nuclear Information System (INIS)

    Yoshino, Tomio; Sakaue, Muneko; Shimizu, Yasuko; Kawamura, Fumio.

    1979-01-01

    It has been reported that the chloroform-paraffin-dye system have excellent sensitivity for radiation as a solid chemical dosimeter or a phantom. However, the chemical changes in the irradiated system are not examined in detail. In the present study, the effect of paraffin on changes in the above system of a liquid state irradiated by 60 Co γ-rays was examined by using various normal paraffin, and the other variable factors on the changes were done. When the chloroform solution and the solution containing 25 per cent of paraffin by volume with 5.0 x 15 -5 mol/liter of Methyl Yellow as a dye were irradiated by 2000 R, G values for the formation of hydrogen chloride in the both solutions were 8.4 and 10.8, respectively, and were little affected by the kind of those, from C 6 (hexane) to C 36 (hexatria-contane). These results suggest that chlorine radical formed by radiolysis of chloroform may react with hydrogen atom from paraffin, thereby increasing the amount of hydrogen chloride. Presence of oxygen increased G value of the chloroform solution from 7.6 to 8.4, but did little that of the solution containing paraffin. (author)

  2. Investigation of rare chronic lipoid pneumonia associated with occupational exposure to paraffin aerosol.

    Science.gov (United States)

    Han, Chenghong; Liu, Lihai; Du, Shiping; Mei, Jianhua; Huang, Ling; Chen, Min; Lei, Yongliang; Qian, Junwen; Luo, Jianyong; Zhang, Meibian

    2016-09-30

    Occupational exposure to paraffin is an infrequent cause of lipoid pneumonia (LP) and related data are scare. We investigated the possible relationship between three rare cases of chronic LP and occupational exposure to paraffin aerosol in an iron foundry. The three cases of LP and their workplaces were investigated using data from field investigations, air monitoring, pulmonary radiological examinations, cell staining, and lung biopsies. The patients had long-term occupational exposure to paraffin. X-ray diffraction testing revealed that the raw material from the workshop was paraffin crystal. The air concentrations of paraffin aerosol in workplaces were significantly higher than outdoor background levels. Small diffuse and miliary shadows with unclear edges were observed throughout the whole lungs via radiography. Computed tomography revealed diffuse punctate nodules and a high density of stripe-like shadows in both lungs (ground-glass opacity in a lower lobe, and a mass-like lesion and high translucent area near the bottom of the lung). Lipid-laden macrophages were found in the sputum and bronchial lavage. A broadened alveolar septum and local focal fibrosis were also discovered via lung biopsy. The inflammatory reaction in the lung tissues appeared to resolve over time. These three rare cases of chronic LP in workers during molding and repair processes were associated with occupational paraffin aerosol exposure. Therefore, primary prevention is essential for molding or repairing workers in the iron foundry, and a differential diagnosis of occupational chronic LP (vs. pneumoconiosis) should be considered when treating these workers.

  3. Embedded Multimaterial Extrusion Bioprinting.

    Science.gov (United States)

    Rocca, Marco; Fragasso, Alessio; Liu, Wanjun; Heinrich, Marcel A; Zhang, Yu Shrike

    2018-04-01

    Embedded extrusion bioprinting allows for the generation of complex structures that otherwise cannot be achieved with conventional layer-by-layer deposition from the bottom, by overcoming the limits imposed by gravitational force. By taking advantage of a hydrogel bath, serving as a sacrificial printing environment, it is feasible to extrude a bioink in freeform until the entire structure is deposited and crosslinked. The bioprinted structure can be subsequently released from the supporting hydrogel and used for further applications. Combining this advanced three-dimensional (3D) bioprinting technique with a multimaterial extrusion printhead setup enables the fabrication of complex volumetric structures built from multiple bioinks. The work described in this paper focuses on the optimization of the experimental setup and proposes a workflow to automate the bioprinting process, resulting in a fast and efficient conversion of a virtual 3D model into a physical, extruded structure in freeform using the multimaterial embedded bioprinting system. It is anticipated that further development of this technology will likely lead to widespread applications in areas such as tissue engineering, pharmaceutical testing, and organs-on-chips.

  4. Learning optimal embedded cascades.

    Science.gov (United States)

    Saberian, Mohammad Javad; Vasconcelos, Nuno

    2012-10-01

    The problem of automatic and optimal design of embedded object detector cascades is considered. Two main challenges are identified: optimization of the cascade configuration and optimization of individual cascade stages, so as to achieve the best tradeoff between classification accuracy and speed, under a detection rate constraint. Two novel boosting algorithms are proposed to address these problems. The first, RCBoost, formulates boosting as a constrained optimization problem which is solved with a barrier penalty method. The constraint is the target detection rate, which is met at all iterations of the boosting process. This enables the design of embedded cascades of known configuration without extensive cross validation or heuristics. The second, ECBoost, searches over cascade configurations to achieve the optimal tradeoff between classification risk and speed. The two algorithms are combined into an overall boosting procedure, RCECBoost, which optimizes both the cascade configuration and its stages under a detection rate constraint, in a fully automated manner. Extensive experiments in face, car, pedestrian, and panda detection show that the resulting detectors achieve an accuracy versus speed tradeoff superior to those of previous methods.

  5. Adsorption of polyvinylalcohol on paraffin-water interfaces and the properties of paraffin-in-water emulsions stabilized by polyvinylalcohol : an experimental study

    NARCIS (Netherlands)

    Lankveld, J.M.G.

    1970-01-01

    The adsorption of polyvinylalcohol (PVA) on the paraffin-water interface has been studied by interfacial tension measurements and by direct measurement of the adsorption with emulsions. The aim of the study was to provide more insight into the factors which influence the adsorption of polymers

  6. Spatially Embedded Inequality

    DEFF Research Database (Denmark)

    Holck, Lotte

    2016-01-01

    /methodology/approach: – The (re)production of inequality is explored by linking research on organizational space with HRM diversity management. Data from an ethnographic study undertaken in a Danish municipal center illustrates how a substructure of inequality is spatially upheld alongside a formal diversity policy. Archer...... and ethnification of job categories. However, the same spatial structures allows for a variety of opposition and conciliation strategies among minority employees, even though the latter tend to prevail in a reproduction rather than a transformation of the organizational opportunity structures. Research limitations...... the more subtle, spatially embedded forms of inequality. Originality/value: – Theoretical and empirical connections between research on organizational space and HRM diversity management have thus far not been systematically studied. This combination might advance knowledge on the persistence of micro...

  7. Embedded sensor systems

    CERN Document Server

    Agrawal, Dharma Prakash

    2017-01-01

    This inspiring textbook provides an introduction to wireless technologies for sensors, explores potential use of sensors for numerous applications, and utilizes probability theory and mathematical methods as a means of embedding sensors in system design. It discusses the need for synchronization and underlying limitations, inter-relation between given coverage and connectivity to number of sensors needed, and the use of geometrical distance to determine location of the base station for data collection and explore use of anchor nodes for relative position determination of sensors. The book explores energy conservation, communication using TCP, the need for clustering and data aggregation, and residual energy determination and energy harvesting. It covers key topics of sensor communication like mobile base stations and relay nodes, delay-tolerant sensor networks, and remote sensing and possible applications. The book defines routing methods and do performance evaluation for random and regular sensor topology an...

  8. Communicating embedded systems networks applications

    CERN Document Server

    Krief, Francine

    2013-01-01

    Embedded systems become more and more complex and require having some knowledge in various disciplines such as electronics, data processing, telecommunications and networks. Without detailing all the aspects related to the design of embedded systems, this book, which was written by specialists in electronics, data processing and telecommunications and networks, gives an interesting point of view of communication techniques and problems in embedded systems. This choice is easily justified by the fact that embedded systems are today massively communicating and that telecommunications and network

  9. Advances in embedded computer vision

    CERN Document Server

    Kisacanin, Branislav

    2014-01-01

    This illuminating collection offers a fresh look at the very latest advances in the field of embedded computer vision. Emerging areas covered by this comprehensive text/reference include the embedded realization of 3D vision technologies for a variety of applications, such as stereo cameras on mobile devices. Recent trends towards the development of small unmanned aerial vehicles (UAVs) with embedded image and video processing algorithms are also examined. The authoritative insights range from historical perspectives to future developments, reviewing embedded implementation, tools, technolog

  10. Embedded Systems Design with FPGAs

    CERN Document Server

    Pnevmatikatos, Dionisios; Sklavos, Nicolas

    2013-01-01

    This book presents methodologies for modern applications of embedded systems design, using field programmable gate array (FPGA) devices.  Coverage includes state-of-the-art research from academia and industry on a wide range of topics, including advanced electronic design automation (EDA), novel system architectures, embedded processors, arithmetic, dynamic reconfiguration and applications. Describes a variety of methodologies for modern embedded systems design;  Implements methodologies presented on FPGAs; Covers a wide variety of applications for reconfigurable embedded systems, including Bioinformatics, Communications and networking, Application acceleration, Medical solutions, Experiments for high energy physics, Astronomy, Aerospace, Biologically inspired systems and Computational fluid dynamics (CFD).

  11. Embedding Complementarity in HCI Methods

    DEFF Research Database (Denmark)

    Nielsen, Janni; Yssing, Carsten; Tweddell Levinsen, Karin

    2007-01-01

    Differences in cultural contexts constitute differences in cognition, and research has shown that different cultures may use different cognitive tools for perception and reasoning. The cultural embeddings are significant in relation to HCI, because the cultural context is also embedded in the tec......Differences in cultural contexts constitute differences in cognition, and research has shown that different cultures may use different cognitive tools for perception and reasoning. The cultural embeddings are significant in relation to HCI, because the cultural context is also embedded...

  12. Embedding potentials for excited states of embedded species

    International Nuclear Information System (INIS)

    Wesolowski, Tomasz A.

    2014-01-01

    Frozen-Density-Embedding Theory (FDET) is a formalism to obtain the upper bound of the ground-state energy of the total system and the corresponding embedded wavefunction by means of Euler-Lagrange equations [T. A. Wesolowski, Phys. Rev. A 77(1), 012504 (2008)]. FDET provides the expression for the embedding potential as a functional of the electron density of the embedded species, electron density of the environment, and the field generated by other charges in the environment. Under certain conditions, FDET leads to the exact ground-state energy and density of the whole system. Following Perdew-Levy theorem on stationary states of the ground-state energy functional, the other-than-ground-state stationary states of the FDET energy functional correspond to excited states. In the present work, we analyze such use of other-than-ground-state embedded wavefunctions obtained in practical calculations, i.e., when the FDET embedding potential is approximated. Three computational approaches based on FDET, that assure self-consistent excitation energy and embedded wavefunction dealing with the issue of orthogonality of embedded wavefunctions for different states in a different manner, are proposed and discussed

  13. Thermal characterizations of the paraffin wax/low density polyethylene blends as a solid fuel

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Soojong; Moon, Heejang; Kim, Jinkon, E-mail: jkkim@kau.ac.kr

    2015-08-10

    Highlights: • Regression rate of blends fuel is higher than polymer fuel. • LDPE is an effective mixing ingredient for the combustion efficiency. • Blends fuel is a uniform mixture with two degradation steps. • LDPE plays a positive role for the low sensitivity to the thermal deformation • Blends with low LDPE content can be an effective fuel for hybrid rocket application. - Abstract: Thermal characterizations of a novel solid fuel for hybrid rocket application, based on the paraffin wax blends with low density polyethylene (LDPE) concentration of 5% (SF-5) and 10% (SF-10) were conducted. Both the increased regression rate in comparison with the polymeric fuel, and the improved combustion efficiency in comparison with the pure paraffin fuel reveal that the blend fuels achieve higher combustion performance. The morphology of the shape stabilized paraffin wax/LDPE blends was characterized by the scanning electron microscopy (SEM). Although the SEM observation indicated the blends have uniform mixtures, they showed two degradation steps confirming the immiscibility of components in the crystalline phase from thermogravimetric analysis (TGA). The differential scanning calorimeter (DSC) results showed that the melting temperature of LDPE in the blends decreased with an increase of paraffin wax content. The decreasing total specific melting enthalpy of blended fuels with decreasing paraffin wax content is in fairly good agreement with the additive rule. In thermomechanical analysis (TMA), the linear coefficient of thermal expansion (LCTE) seems to decrease with an increase of LDPE loading, however, the loaded LDPE do merely affect the LCTE in case of the blends with low LDPE concentration. It was found that a blend of low concentration of LDPE with a relatively high concentration of paraffin wax can lead to a potential novel fuel for rocket application, a contrary case with respect to the field of phase change materials (PCM) where a blend of high concentration

  14. The role of paraffin oil on the interaction between denitrifying anaerobic methane oxidation and Anammox processes.

    Science.gov (United States)

    Fu, Liang; Ding, Zhao-Wei; Ding, Jing; Zhang, Fang; Zeng, Raymond J

    2015-10-01

    Methane is sparingly soluble in water, resulting in a slow reaction rate in the denitrifying anaerobic methane oxidation (DAMO) process. The slow rate limits the feasibility of research to examine the interaction between the DAMO and the anaerobic ammonium oxidation (Anammox) process. In this study, optimized 5 % (v/v) paraffin oil was added as a second liquid phase to improve methane solubility in a reactor containing DAMO and Anammox microbes. After just addition, methane solubility was found to increase by 25 % and DAMO activity was enhanced. After a 100-day cultivation, the paraffin reactor showed almost two times higher consumption rates of NO3 (-) (0.2268 mmol/day) and NH4 (+) (0.1403 mmol/day), compared to the control reactor without paraffin oil. The microbes tended to distribute in the oil-water interface. The quantitative (q) PCR result showed the abundance of gene copies of DAMO archaea, DAMO bacteria, and Anammox bacteria in the paraffin reactor were higher than those in the control reactor after 1 month. Fluorescence in situ hybridization revealed that the percentages of the three microbes were 55.5 and 77.6 % in the control and paraffin reactors after 100 days, respectively. A simple model of mass balance was developed to describe the interactions between DAMO and Anammox microbes and validate the activity results. A mechanism was proposed to describe the possible way that paraffin oil enhanced DAMO activity. It is quite clear that paraffin oil enhances not only DAMO activity but also Anammox activity via the interaction between them; both NO3 (-) and NH4 (+) consumption rates were about two times those of the control.

  15. Mechanisms of radiation - chemical conversion of high-paraffinic crude oil

    International Nuclear Information System (INIS)

    Zaikin, Yu.A.; Zaikina, R.F.; Silverman, J.

    2002-01-01

    Complete text of publication follows. Regularities of radiation-thermal cracking (RTC) are studied in high-paraffinic oil. Irradiation of oil samples by 2 MeV electrons was performed using a special facility assembled at the electron accelerator ELU-4. The following characteristic RTC features were observed in oil with high contents of heavy paraffins: low level of isomerization in light RTC fractions; very high polymerization rate and low olefin contents in RTC products; relatively low yields of light fractions at low irradiation dose rates; increase in the molecular weight of the gasoline fraction as the irradiation dose rate grows. Similar intense polymerization of RTC products was observed in our experiments with such wastes of oil extraction as asphalt-pitch-paraffin sediments (APPS). Theoretically this feedstock contains great reserves of hydrogen, and, therefore, has high potential yields of light fractions. However, in this case RTC was accompanied by intense reactions of polymerization and chemical adsorption that limited the maximum yields of light RTC products to 40% in our experiments. A specific feature of APPS radiation-induced destruction is formation of the big amount of a reactive paraffinic residue. As a result of interaction with the polymerizing residue the light liquid fractions were completely absorbed and the heavy residue got denser and solidified after several days of exposure at room temperature. RTC regularities in heavy paraffinic oil differ from those observed both in highly viscous petroleum feedstock and light paraffin oils. We attribute these observations to the behavior of heavy alkyl radicals that initiate polymerization and isomerization in heavy paraffin fractions

  16. Thermal characterizations of the paraffin wax/low density polyethylene blends as a solid fuel

    International Nuclear Information System (INIS)

    Kim, Soojong; Moon, Heejang; Kim, Jinkon

    2015-01-01

    Highlights: • Regression rate of blends fuel is higher than polymer fuel. • LDPE is an effective mixing ingredient for the combustion efficiency. • Blends fuel is a uniform mixture with two degradation steps. • LDPE plays a positive role for the low sensitivity to the thermal deformation • Blends with low LDPE content can be an effective fuel for hybrid rocket application. - Abstract: Thermal characterizations of a novel solid fuel for hybrid rocket application, based on the paraffin wax blends with low density polyethylene (LDPE) concentration of 5% (SF-5) and 10% (SF-10) were conducted. Both the increased regression rate in comparison with the polymeric fuel, and the improved combustion efficiency in comparison with the pure paraffin fuel reveal that the blend fuels achieve higher combustion performance. The morphology of the shape stabilized paraffin wax/LDPE blends was characterized by the scanning electron microscopy (SEM). Although the SEM observation indicated the blends have uniform mixtures, they showed two degradation steps confirming the immiscibility of components in the crystalline phase from thermogravimetric analysis (TGA). The differential scanning calorimeter (DSC) results showed that the melting temperature of LDPE in the blends decreased with an increase of paraffin wax content. The decreasing total specific melting enthalpy of blended fuels with decreasing paraffin wax content is in fairly good agreement with the additive rule. In thermomechanical analysis (TMA), the linear coefficient of thermal expansion (LCTE) seems to decrease with an increase of LDPE loading, however, the loaded LDPE do merely affect the LCTE in case of the blends with low LDPE concentration. It was found that a blend of low concentration of LDPE with a relatively high concentration of paraffin wax can lead to a potential novel fuel for rocket application, a contrary case with respect to the field of phase change materials (PCM) where a blend of high concentration

  17. A review of the performance and structural considerations of paraffin wax hybrid rocket fuels with additives

    Science.gov (United States)

    Veale, Kirsty; Adali, Sarp; Pitot, Jean; Brooks, Michael

    2017-12-01

    Paraffin wax as a hybrid rocket fuel has not been comprehensively characterised, especially regarding the structural feasibility of the material in launch applications. Preliminary structural testing has shown paraffin wax to be a brittle, low strength material, and at risk of failure under launch loading conditions. Structural enhancing additives have been identified, but their effect on motor performance has not always been considered, nor has any standard method of testing been identified between research institutes. A review of existing regression rate measurement techniques on paraffin wax based fuels and the results obtained with various additives are collated and discussed in this paper. The review includes 2D slab motors that enable visualisation of liquefying fuel droplet entrainment and the effect of an increased viscosity on the droplet entrainment mechanism, which can occur with the addition of structural enhancing polymers. An increased viscosity has been shown to reduce the regression rate of liquefying fuels. Viscosity increasing additives that have been tested include EVA and LDPE. Both these additives increase the structural properties of paraffin wax, where the elongation and UTS are improved. Other additives, such as metal hydrides, aluminium and boron generally offer improvements on the regression rate. However, very little consideration has been given to the structural effects these additives have on the wax grain. A 40% aluminised grain, for example, offers a slight increase in the UTS but reduces the elongation of paraffin wax. Geometrically accurate lab-scale motors have also been used to determine the regression rate properties of various additives in paraffin wax. A concise review of all available regression rate testing techniques and results on paraffin wax based hybrid propellants, as well as existing structural testing data, is presented in this paper.

  18. Numerical performance study of paraffin wax dispersed with alumina in a concentric pipe latent heat storage system

    Directory of Open Access Journals (Sweden)

    Valan Arasu Amirtham

    2013-01-01

    Full Text Available Latent heat energy storage systems using paraffin wax could have lower heat transfer rates during melting/freezing processes due to its inherent low thermal conductivity. The thermal conductivity of paraffin wax can be enhanced by employing high conductivity materials such as alumina (Al2O3. A numerical analysis has been carried out to study the performance enhancement of paraffin wax with nanoalumina (Al2O3 particles in comparison with simple paraffin wax in a concentric double pipe heat exchanger. Numerical analysis indicates that the charge-discharge rates of thermal energy can be greatly enhanced using paraffin wax with alumina as compared with a simple paraffin wax as PCM.

  19. Formulation, Casting, and Evaluation of Paraffin-Based Solid Fuels Containing Energetic and Novel Additives for Hybrid Rockets

    Science.gov (United States)

    Larson, Daniel B.; Desain, John D.; Boyer, Eric; Wachs, Trevor; Kuo, Kenneth K.; Borduin, Russell; Koo, Joseph H.; Brady, Brian B.; Curtiss, Thomas J.; Story, George

    2012-01-01

    This investigation studied the inclusion of various additives to paraffin wax for use in a hybrid rocket motor. Some of the paraffin-based fuels were doped with various percentages of LiAlH4 (up to 10%). Addition of LiAlH4 at 10% was found to increase regression rates between 7 - 10% over baseline paraffin through tests in a gaseous oxygen hybrid rocket motor. Mass burn rates for paraffin grains with 10% LiAlH4 were also higher than those of the baseline paraffin. RDX was also cast into a paraffin sample via a novel casting process which involved dissolving RDX into dimethylformamide (DMF) solvent and then drawing a vacuum on the mixture of paraffin and RDX/DMF in order to evaporate out the DMF. It was found that although all DMF was removed, the process was not conducive to generating small RDX particles. The slow boiling generated an inhomogeneous mixture of paraffin and RDX. It is likely that superheating the DMF to cause rapid boiling would likely reduce RDX particle sizes. In addition to paraffin/LiAlH4 grains, multi-walled carbon nanotubes (MWNT) were cast in paraffin for testing in a hybrid rocket motor, and assorted samples containing a range of MWNT percentages in paraffin were imaged using SEM. The fuel samples showed good distribution of MWNT in the paraffin matrix, but the MWNT were often agglomerated, indicating that a change to the sonication and mixing processes were required to achieve better uniformity and debundled MWNT. Fuel grains with MWNT fuel grains had slightly lower regression rate, likely due to the increased thermal conductivity to the fuel subsurface, reducing the burning surface temperature.

  20. Bioaccumulation and biomagnification of short and medium chain polychlorinated paraffins in different species of fish from Liaodong Bay, North China

    OpenAIRE

    Huang, Huiting; Gao, Lirong; Xia, Dan; Qiao, Lin

    2017-01-01

    Chlorinated paraffins (CPs) are highly complex technical mixtures, and the short chain chlorinated paraffins (SCCPs) are classed as persistent and have been included in the Stockholm Convention. However, there have been few studies of SCCPs and medium chain chlorinated paraffins (MCCPs) and their bioaccumulation and biomagnification in different species of fish. The present study investigated the levels, congener group profiles, bioaccumulation, and biomagnification of SCCPs and MCCPs in diff...

  1. Modeling of Embedded Human Systems

    Science.gov (United States)

    2013-07-01

    ISAT study [7] for DARPA in 20051 concretized the notion of an embedded human, who is a necessary component of the system. The proposed work integrates...Technology, IEEE Transactions on, vol. 16, no. 2, pp. 229–244, March 2008. [7] C. J. Tomlin and S. S. Sastry, “Embedded humans,” tech. rep., DARPA ISAT

  2. Paraffin oil as a "methane vector" for rapid and high cell density cultivation of Methylosinus trichosporium OB3b.

    Science.gov (United States)

    Han, Bing; Su, Tao; Wu, Hao; Gou, Zhongxuan; Xing, Xin-Hui; Jiang, Hao; Chen, Yin; Li, Xin; Murrell, J Colin

    2009-06-01

    Slow growth and relatively low cell densities of methanotrophs have limited their uses in industrial applications. In this study, a novel method for rapid cultivation of Methylosinus trichosporium OB3b was studied by adding a water-immiscible organic solvent in the medium. Paraffin oil was the most effective at enhancing cell growth and final cell density. This is at least partially due to the increase of methane gas transfer between gas and medium phases since methane solubility is higher in paraffin than in water/nitrate minimal salt medium. During cultivation with paraffin oil at 5% (v/v) in the medium, M. trichosporium OB3b cells also showed higher concentrations of the intermediary metabolites, such as formic acid and pyruvic acid, and consumed more methane compared with the control. Paraffin as methane vector to improve methanotroph growth was further studied in a 5-L fermentor at three concentrations (i.e., 2.5%, 5%, and 10%). Cell density reached about 14 g dry weight per liter with 5% paraffin, around seven times higher than that of the control (without paraffin). Cells cultivated with paraffin tended to accumulate around the interface between oil droplets and the water phase and could exist in oil phase in the case of 10% (v/v) paraffin. These results indicated that paraffin could enhance methanotroph growth, which is potentially useful in cultivation of methanotrophs in large scale in industry.

  3. Zeolitic imidazolate frameworks with optimized pore structure for olefin/paraffin-separation

    Energy Technology Data Exchange (ETDEWEB)

    Paula, C.; Boehme, U.; Hartmann, M. [Erlangen-Nuernberg Univ. (Germany). Erlangen Catalysis Resource Center

    2013-11-01

    In the chemical industry, the largest part of energy is spent on separation processes such as the separation of olefin/paraffin mixtures from steam cracker effluents by low-temperature rectification. A suitable alternative to this energy and cost intensive process is separation by selective adsorption with suitable microporous adsorbent. In this work, different ZIFs (Zeolitic Imidazolate Frameworks) have been explored with respect to their separation of olefins and paraffins. The studied materials (e.g. ZIF-8 (SOD-Topology), ZIF-71 (RHO-Topology)) were selected because of their low diameter of the largest pore entrance (0.29 to 4.2 nm) which is close to the kinetic diameter of the C{sub 2} to C{sub 4} olefins and paraffins under study. In contrast to other MOF- or zeolite-based adsorbents, in ZIF-8 and ZIF-71, the paraffin is preferentially adsorbed, which is evident from the single-component adsorption isotherms at different temperature. In the corresponding mixture breakthrough curves, the olefin breaks through first and the alkane even displaces the olefin from the pores. Thus, ZIF-8 and ZIF-71 are interesting candidates for the envisaged paraffin/olefin separation. Whether the observed separation behavior is due to the structural properties of the studied ZIFs or a consequence of peculiar chemical properties is subject to further studies. (orig.) (Published in summary form only)

  4. Diluent paraffin nature and plutonium(IV) organic solution lamination: new results and new approach

    International Nuclear Information System (INIS)

    Renard, E.V.; Ivanchenko, V.A.; Chizhov, A.A.; Neumojev, N.V.

    1994-01-01

    The knowledge of the relation between the diluent composition and structure and the critical (maximum achievable) concentration (CC(Me)) of metals, including plutonium(IV), in the organic phase is an actual goal of a radiochemical extraction technology (PUREX process). Using γ-spectrometry analysis with high accuracy, the parameter CC(Pu) has been determined in application to Pu(IV) nitrate solution in 30% (vol.) TBP diluent solutions. n-Paraffins C 10 C 16 , iso-paraffins (mono- and dimethylderivatives), iso-paraffins with C-quaternare atoms (hydrogenated mixtures of tetra- and pentapropylene isomers) have been used as diluents. Regular correlations between CC(Pu) parameters and some individual (and mixture) diluent structure characteristics, including practically linear inversely proportional decrease of CC(Pu) with C-atom number increase (in molecules of n-C n H 2n+2 ), symbatically development of this relation to both the paraffin types (n- and iso-) have been found. The general straight proportional relation between CC(Pu)-parameter and fluidity (F=1/η, where η-dynamic viscosity at given temperature) has been discovered for all paraffins investigated - both individual and mixtures - at different temperatures. ((orig.))

  5. A nano-graphite/paraffin phase change material with high thermal conductivity

    International Nuclear Information System (INIS)

    Li, Min

    2013-01-01

    Highlights: ► Paraffin and NG formed a nanoscale compound. ► The thermal conductivity increased gradually with the content of NG. ► The thermal conductivity of the material containing 10% NG were 0.9362 W/m K. - Abstract: Nano-graphite (NG)/paraffin composites were prepared as composite phase change materials. NG has the function of improving the thermal conductivity of the composite. The microstructure and thermal properties of the materials were examined with environmental scanning electron microscopy and differential scanning calorimetry. The results indicated that the NG layers were randomly dispersed in the paraffin, and the thermal conductivity increased gradually with the content of NG. Thermal conductivity of the material containing 10% NG were 0.9362 W/m K

  6. Microwave reflection properties of planar anisotropy Fe50Ni50 powder/paraffin composites

    International Nuclear Information System (INIS)

    Wei Jian-Qiang; Zhang Zhao-Qi; Han Rui; Wang Tao; Li Fa-Shen

    2012-01-01

    The reflection properties of planar anisotropy Fe 50 Ni 50 powder/paraffin composites have been studied in the microwave frequency range. The permeability of Fe 50 Ni 50 powder/paraffin composites is greatly enhanced by introducing the planar anisotropy, and can be further enhanced by using a rotational orientation method. The complex permeability can be considered as the superposition of two types of magnetic resonance. The resonance peak at high frequency is attributed to the natural resonance, while the peak at low frequency is attributed to the domain-wall resonance. The simulated results of the microwave reflectivity show that the matching thickness, peak frequency, permeability, and permittivity are closely related to the quarter wavelength matching condition. The Fe 50 Ni 50 powder/paraffin composites can be attractive candidates for thinner microwave absorbers in the L-band (1–2 GHz). (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  7. Murine immune response induced by Leishmania major during the implantation of paraffin tablets.

    Science.gov (United States)

    Reis, Maria Letícia Costa; Ferreira, Vanessa Martins; Zhang, Xia; Gonçalves, Ricardo; Vieira, Leda Quércia; Tafuri, Washington Luiz; Mosser, David M; Tafuri, Wagner Luiz

    2010-11-01

    We carried out a model of chronic inflammation using a subcutaneous paraffin tablet in mice experimentally infected with Leishmania major. It was previously reported that the parasite load following paraffin implantation occurred at a peak of 21 days in both BALB/c and C57BL/6 mice. At the present study, we have investigated what cytokines and chemokines are directly related to the parasite load in C57BL/6 mice. All mice were divided in four groups: mice implanted with paraffin tablets; mice experimentally infected with L. major; mice implanted with paraffin tablets and experimentally infected with L. major; and mice submitted only to the surgery were used for the Real-Time Polymerase Chain Reaction (RT-PCR) controls. Fragments of skin tissue and the tissue surrounding the paraffin tablets (inflammatory capsule) were collected for histopathology and RT-PCR studies. By 21 days, a diffuse chronic inflammatory reaction was mainly observed in the deep dermis where macrophages parasitized with Leishmania amastigotes were also found. RT-PCR analysis has shown that BALB/c mice showed strong IL-4 and IL-10 mRNA expression than controls with very little expression of IFN-γ. In contrast, both IFN-γ and IL-10 mRNA was found in higher levels in C57BL/6 animals. Moreover, in C57BL/6 mice the expression of chemokines mRNA of CCL3/MIP-1α was more highly expressed than CCL2/MCP-1. We conclude that the Th1 immune response C57BL/6 did not change to a Th2 response, even though C57BL/6 animals presented higher parasitism than BALB/c mice 21 days after infection and paraffin implantation.

  8. Determination Of Adsorption And Paraffin Characterization Of Treatment To Adsorb Vegetable Oil

    International Nuclear Information System (INIS)

    Aminah, Neneng Siti; Mulijani, Sri; Sudirman; Ridwan

    2004-01-01

    Using vegetable oil repeatedly, beside affect on quality decline of food and the oil itself, it is harmful to human health. Some poisoning and carcinogenic symptom were founded with experiment using animals. According to that fact, the aim of the research is using paraffin and candle to adsorb used vegetable oil and to convert into solid sample, so it can be easily wasted. At first, 2 g of sample was poured into the heated oil, with gently stirrer until it turned cold and harden. Each sample and standard before and after treatment was characterized with Ftir, XRD, and DSc. The result shows that paraffins adsorbs 40 ml used vegetable oil with 2 g sample in proportion. That proportion is lower than the standard which can adsorb 66.67 ml vegetable oil in the same weight sample. The difference of paraffin and standard is caused by physical properties within that two materials, and it can be explained by Ftir, X-Ray Diffraction (XRD) and differential scanning calorimetry (DSc). Based on result of Ftir analysis, standard consented of saturated hydrocarbon compound (alkanes) whereas paraffin consisted of unsaturated hydrocarbon compound (alkenes). Infrared spectrum after treatment showed the changes of compound, O-H and esters group were formed and it shows characterised the adsorption process. The result of DSc analysis showed that crystalline the melting point of standard is 75,3 o C and paraffin is 54,17 o C. The result of analysis XRD, described that standard and paraffin before treatment are crystalline whereas after treatment are am orf

  9. Modification in the assembly technique of histological sections for analysis of spatial distribution of boron by autoradiography

    International Nuclear Information System (INIS)

    Portu, A; Carpano, M; Dagrosa, A; Pozzi, E; Thorp, S; Curotto, P; Cabrini, R L; Saint Martin, G

    2012-01-01

    . It is necessary to find out other techniques to preserve necrotic areas for quantification. The preparation of tissue sections embedded in paraffin is widely used in pathology laboratories technique. To achieve these cuts, the samples must be processed previously. The aim of this study was to evaluate the feasibility of using tissue sections embedded in paraffin as alternative arrangement, in order to preserve the structures that are damaged in frozen sections (author)

  10. Simulation and sensitivity analysis for heavy linear paraffins production in LAB production Plant

    Directory of Open Access Journals (Sweden)

    Karimi Hajir

    2014-12-01

    Full Text Available Linear alkyl benzene (LAB is vastly utilized for the production of biodegradable detergents and emulsifiers. Predistillation unit is a part of LAB production plant in which that produced heavy linear paraffins (nC10-nC13. In this study, a mathematical model has been developed for heavy linear paraffins production in distillation columns, which has been solved using a commercial code. The models have been validated by the actual data. The effects of process parameters such as reflux rate, and reflux temperature using Gradient Search technique has been investigated. The sensitivity analysis shows that optimum reflux in columns are achieved.

  11. A method for removing sulfur bearing compounds from paraffinous hydrocarbons or a directly distilled benzine fraction

    Energy Technology Data Exchange (ETDEWEB)

    Konyukhova, T.P.; Bolotskaya, I.A.; Mikhaylova, L.A.; Sadykov, A.N.; Shitovkin, N.T.; Vlasov, V.V.

    1983-01-01

    In the known method for removing sulfurorganic compounds from paraffinous hydrocarbons or a directly distilled gasoline fraction through their adsorption using natural zeolite, in order to increase the degree of purification, clinoptilolite (Kp), which contains SiO2 and A12O3 in a molar ratio of 10.6 to 16.7 is used as the natural zeolite. The purification of the paraffinous hydrocarbons through clinoptilolite adsorption as compared with mordenite adsorption makes it possible to increase the degree of their purification of ethylmercaptane and dimethylsulfide. The effectiveness of clinoptilolite is also confirmed in removing mercaptanes and sulfides from directly distilled gasoline fractions.

  12. Sampling and transport of paraffin waste form from CWDS of nuclear power plant

    International Nuclear Information System (INIS)

    Lee, J. M.; Hwang, J. H.; Kim, C. R.; Park, J. W.

    2000-01-01

    Sampling and transport of paraffin waste form from concentrated waste drying system (CWDS) of domestic nuclear power plant were performed to collect the leaching characteristic data for the disposal of radioactive waste. Transport was performed according to the national regulations and the internal rules of the nuclear power plant. The sample of paraffin waste form was classified as L type package according to the regulation and radiation exposure of operator was measured in the range of 6 to 12 mrem that was less than the estimated amount

  13. Paraffin Granuloma Associated with Buried Glans Penis-Induced Sexual and Voiding Dysfunction

    Directory of Open Access Journals (Sweden)

    Wonhee Chon

    2017-08-01

    Full Text Available A paraffinoma is a type of inflammatory lipogranuloma that develops after the injection of an artificial mineral oil, such as paraffin or silicon, into the foreskin or the subcutaneous tissue of the penis for the purpose of penis enlargement, cosmetics, or prosthesis. The authors experienced a case of macro-paraffinoma associated with sexual dysfunction, voiding dysfunction, and pain caused by a buried glans penis after a paraffin injection for penis enlargement that had been performed 35 years previously. Herein, this case is presented with a literature review.

  14. Paraffin Granuloma Associated with Buried Glans Penis-Induced Sexual and Voiding Dysfunction.

    Science.gov (United States)

    Chon, Wonhee; Koo, Ja Yun; Park, Min Jung; Choi, Kyung Un; Park, Hyun Jun; Park, Nam Cheol

    2017-08-01

    A paraffinoma is a type of inflammatory lipogranuloma that develops after the injection of an artificial mineral oil, such as paraffin or silicon, into the foreskin or the subcutaneous tissue of the penis for the purpose of penis enlargement, cosmetics, or prosthesis. The authors experienced a case of macro-paraffinoma associated with sexual dysfunction, voiding dysfunction, and pain caused by a buried glans penis after a paraffin injection for penis enlargement that had been performed 35 years previously. Herein, this case is presented with a literature review. Copyright © 2017 Korean Society for Sexual Medicine and Andrology.

  15. Phylogenetic trees and Euclidean embeddings.

    Science.gov (United States)

    Layer, Mark; Rhodes, John A

    2017-01-01

    It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.

  16. Tensor Train Neighborhood Preserving Embedding

    Science.gov (United States)

    Wang, Wenqi; Aggarwal, Vaneet; Aeron, Shuchin

    2018-05-01

    In this paper, we propose a Tensor Train Neighborhood Preserving Embedding (TTNPE) to embed multi-dimensional tensor data into low dimensional tensor subspace. Novel approaches to solve the optimization problem in TTNPE are proposed. For this embedding, we evaluate novel trade-off gain among classification, computation, and dimensionality reduction (storage) for supervised learning. It is shown that compared to the state-of-the-arts tensor embedding methods, TTNPE achieves superior trade-off in classification, computation, and dimensionality reduction in MNIST handwritten digits and Weizmann face datasets.

  17. Determination of paraffins in food simulants and packaging materials by liquid chromatography with evaporative mass detection and identification of paraffin type by liquid chromatography/gas chromatography and fourier transform infrared spectroscopy

    NARCIS (Netherlands)

    Simal-Gándara, J.; Sarria-Vidal, M.; Rijk, M.A.H.

    2000-01-01

    A liquid chromatographic method with evaporative mass detection (EMD) is described for the determination of paraffins in food contact materials that do not contain polyolefin oligomers, or paraffins migrating from these materials into fatty food simulants or certain simple foods. A normal-phase

  18. Parametric embedding for class visualization.

    Science.gov (United States)

    Iwata, Tomoharu; Saito, Kazumi; Ueda, Naonori; Stromsten, Sean; Griffiths, Thomas L; Tenenbaum, Joshua B

    2007-09-01

    We propose a new method, parametric embedding (PE), that embeds objects with the class structure into a low-dimensional visualization space. PE takes as input a set of class conditional probabilities for given data points and tries to preserve the structure in an embedding space by minimizing a sum of Kullback-Leibler divergences, under the assumption that samples are generated by a gaussian mixture with equal covariances in the embedding space. PE has many potential uses depending on the source of the input data, providing insight into the classifier's behavior in supervised, semisupervised, and unsupervised settings. The PE algorithm has a computational advantage over conventional embedding methods based on pairwise object relations since its complexity scales with the product of the number of objects and the number of classes. We demonstrate PE by visualizing supervised categorization of Web pages, semisupervised categorization of digits, and the relations of words and latent topics found by an unsupervised algorithm, latent Dirichlet allocation.

  19. Embedded System for Biometric Identification

    OpenAIRE

    Rosli, Ahmad Nasir Che

    2010-01-01

    This chapter describes the design and implementation of an Embedded System for Biometric Identification from hardware and software perspectives. The first part of the chapter describes the idea of biometric identification. This includes the definition of

  20. Hardware Support for Embedded Java

    DEFF Research Database (Denmark)

    Schoeberl, Martin

    2012-01-01

    The general Java runtime environment is resource hungry and unfriendly for real-time systems. To reduce the resource consumption of Java in embedded systems, direct hardware support of the language is a valuable option. Furthermore, an implementation of the Java virtual machine in hardware enables...... worst-case execution time analysis of Java programs. This chapter gives an overview of current approaches to hardware support for embedded and real-time Java....

  1. Molecular Properties through Polarizable Embedding

    DEFF Research Database (Denmark)

    Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

    2011-01-01

    We review the theory related to the calculation of electric and magnetic molecular properties through polarizable embedding. In particular, we derive the expressions for the response functions up to the level of cubic response within the density functional theory-based polarizable embedding (PE......-DFT) formalism. In addition, we discuss some illustrative applications related to the calculation of nuclear magnetic resonance parameters, nonlinear optical properties, and electronic excited states in solution....

  2. A Foundation for Embedded Languages

    DEFF Research Database (Denmark)

    Rhiger, Morten

    2003-01-01

    Recent work on embedding object languages into Haskell use "phantom types" (i.e., parameterized types whose parameter does not occur on the right-hand side of the type definition) to ensure that the embedded object-language terms are simply typed. But is it a safe assumption that only simply...... be answered affirmatively for an idealized Haskell-like language and discuss to which extent Haskell can be used as a meta-language....

  3. Unsupervised Document Embedding With CNNs

    OpenAIRE

    Liu, Chundi; Zhao, Shunan; Volkovs, Maksims

    2017-01-01

    We propose a new model for unsupervised document embedding. Leading existing approaches either require complex inference or use recurrent neural networks (RNN) that are difficult to parallelize. We take a different route and develop a convolutional neural network (CNN) embedding model. Our CNN architecture is fully parallelizable resulting in over 10x speedup in inference time over RNN models. Parallelizable architecture enables to train deeper models where each successive layer has increasin...

  4. Preparation and characterization of form-stable paraffin/polycaprolactone composites as phase change materials for thermal energy storage

    Directory of Open Access Journals (Sweden)

    Aludin M.S.

    2017-01-01

    Full Text Available Paraffin is Phase Change Materials (PCM that possesses desirable properties such as high thermal energy storage and thermal stability to make it suitable for thermal energy storage applications. However, paraffin has been reported to leak out during the melting process. In this study, composites were prepared by dissolving paraffin and polycaprolactone (PCL at varied mass percent compositions in chloroform and then purified through precipitation techniques. The leakage test was conducted by placing the composite samples on a set of four-layer filter papers and left in a furnace at 90°C for 1 hour. By incorporating PCL into paraffin phase, the leakage mass percentage was drastically reduced. The PCL polymer matrix in the composites may have trapped the paraffin molecules during melting process thus prevent it from leaking.

  5. Screening of short- and medium-chain chlorinated paraffins in selected riverine sediments and sludge from the Czech Republic.

    Science.gov (United States)

    Pribylová, Petra; Klánová, Jana; Holoubek, Ivan

    2006-11-01

    Wide distribution of chlorinated paraffins in the environment has already been demonstrated in several studies; however, information about their levels in the Central Europe is still very limited. First study focused on the SCCP contamination of the Czech aquatic environment have been performed recently, and its results motivated the authors to analyze sediments from a wide set of the Czech rivers in order to obtain more detailed information. Thirty-six sediment samples from eleven rivers and five drainage vents neighboring the chemical factories were analyzed; special attention was paid to the industrial areas. For the first time in the Czech Republic, medium-chain in addition to short-chain chlorinated paraffins were analyzed using GC-ECNI-MS. Chlorinated paraffins were detected in sediment samples on the concentration levels up to 347 ngg(-1) for short-chain chlorinated paraffins, and 5575 ngg(-1) for medium-chain chlorinated paraffins. Average chlorination degree of SCCPs was 65%.

  6. Preparation of Paraffin@Poly(styrene-co-acrylic acid) Phase Change Nanocapsules via Combined Miniemulsion/Emulsion Polymerization.

    Science.gov (United States)

    Zhang, Feng; Liu, Tian-Yu; Hou, Gui-Hua; Guan, Rong-Feng; Zhang, Jun-Hao

    2018-06-01

    The fast development of solid-liquid phase change materials calls for nanomaterials with large specific surface area for rapid heat transfer and encapsulation of phase change materials to prevent potential leakage. Here we report a combined miniemulsion/emulsion polymerization method to prepare poly(styrene-co-acrylic acid)-encapsulated paraffin (paraffin@P(St-co-AA)) nanocapsules. The method could suppress the shortcomings of common miniemulsion polymerization (such as evaporation of monomer and decomposition of initiator during ultrasonication). The paraffin@P(St-co-AA) nanocapsules are uniform in size and the polymer shell can be controlled by the weight ratio of St to paraffin. The phase change behavior of the nanocapsules is similar to that of pure paraffin. We believe our method can also be utilized to synthesize other core-shell phase change materials.

  7. Preparation and thermal energy storage properties of paraffin/calcined diatomite composites as form-stable phase change materials

    International Nuclear Information System (INIS)

    Sun, Zhiming; Zhang, Yuzhong; Zheng, Shuilin; Park, Yuri; Frost, Ray L.

    2013-01-01

    Highlights: ► Composite phase change material (PCM) was prepared by blending composite paraffin and calcined diatomite. ► The optimum mixed proportion was obtained through differential scanning calorimetry. ► Thermal energy storage properties of the composite PCMs were determined by DSC. ► Thermal cycling test showed that the prepared PCMs are thermally reliable and chemically stable. - Abstract: A composite paraffin-based phase change material (PCM) was prepared by blending composite paraffin and calcined diatomite through the fusion adsorption method. In this study, raw diatomite was purified by thermal treatment in order to improve the adsorption capacity of diatomite, which acted as a carrier material to prepare shape-stabilized PCMs. Two forms of paraffin (paraffin waxes and liquid paraffin) with different melting points were blended together by the fusion method, and the optimum mixed proportion with a suitable phase-transition temperature was obtained through differential scanning calorimetry (DSC) analysis. Then the prepared composite paraffin was adsorbed in calcined diatomite. The prepared paraffin/calcined diatomite composites were characterized by the scanning electron microscope (SEM) and Fourier transformation infrared (FT-IR) analysis techniques. Thermal energy storage properties of the composite PCMs were determined by DSC method. DSC results showed that there was an optimum adsorption ratio between composite paraffin and calcined diatomite and the phase-transition temperature and the latent heat of the composite PCMs were 33.04 °C and 89.54 J/g, respectively. Thermal cycling test of composite PCMs showed that the prepared material is thermally reliable and chemically stable. The obtained paraffin/calcined diatomite composites have proper latent heat and melting temperatures, and show practical significance and good potential application value

  8. Preparation and thermal energy storage properties of paraffin/calcined diatomite composites as form-stable phase change materials

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Zhiming [School of Chemical and Environmental Engineering, China University of Mining and Technology, Beijing 100083 (China); Chemistry Discipline, Faculty of Science and Technology, Queensland University of Technology, 2 George Street, GPO Box 2434, Brisbane, Queensland 4001 (Australia); Zhang, Yuzhong [School of Chemical and Environmental Engineering, China University of Mining and Technology, Beijing 100083 (China); Zheng, Shuilin, E-mail: shuilinzh@yahoo.com.cn [School of Chemical and Environmental Engineering, China University of Mining and Technology, Beijing 100083 (China); Park, Yuri [Chemistry Discipline, Faculty of Science and Technology, Queensland University of Technology, 2 George Street, GPO Box 2434, Brisbane, Queensland 4001 (Australia); Frost, Ray L., E-mail: r.frost@qut.edu.au [Chemistry Discipline, Faculty of Science and Technology, Queensland University of Technology, 2 George Street, GPO Box 2434, Brisbane, Queensland 4001 (Australia)

    2013-04-20

    Highlights: ► Composite phase change material (PCM) was prepared by blending composite paraffin and calcined diatomite. ► The optimum mixed proportion was obtained through differential scanning calorimetry. ► Thermal energy storage properties of the composite PCMs were determined by DSC. ► Thermal cycling test showed that the prepared PCMs are thermally reliable and chemically stable. - Abstract: A composite paraffin-based phase change material (PCM) was prepared by blending composite paraffin and calcined diatomite through the fusion adsorption method. In this study, raw diatomite was purified by thermal treatment in order to improve the adsorption capacity of diatomite, which acted as a carrier material to prepare shape-stabilized PCMs. Two forms of paraffin (paraffin waxes and liquid paraffin) with different melting points were blended together by the fusion method, and the optimum mixed proportion with a suitable phase-transition temperature was obtained through differential scanning calorimetry (DSC) analysis. Then the prepared composite paraffin was adsorbed in calcined diatomite. The prepared paraffin/calcined diatomite composites were characterized by the scanning electron microscope (SEM) and Fourier transformation infrared (FT-IR) analysis techniques. Thermal energy storage properties of the composite PCMs were determined by DSC method. DSC results showed that there was an optimum adsorption ratio between composite paraffin and calcined diatomite and the phase-transition temperature and the latent heat of the composite PCMs were 33.04 °C and 89.54 J/g, respectively. Thermal cycling test of composite PCMs showed that the prepared material is thermally reliable and chemically stable. The obtained paraffin/calcined diatomite composites have proper latent heat and melting temperatures, and show practical significance and good potential application value.

  9. Methanogenic biodegradation of paraffinic solvent hydrocarbons in two different oil sands tailings.

    Science.gov (United States)

    Mohamad Shahimin, Mohd Faidz; Siddique, Tariq

    2017-04-01

    Microbial communities drive many biogeochemical processes in oil sands tailings and cause greenhouse gas emissions from tailings ponds. Paraffinic solvent (primarily C 5 -C 6 ; n- and iso-alkanes) is used by some oil sands companies to aid bitumen extraction from oil sands ores. Residues of unrecovered solvent escape to tailings ponds during tailings deposition and sustain microbial metabolism. To investigate biodegradation of hydrocarbons in paraffinic solvent, mature fine tailings (MFT) collected from Albian and CNRL ponds were amended with paraffinic solvent at ~0.1wt% (final concentration: ~1000mgL -1 ) and incubated under methanogenic conditions for ~1600d. Albian and CNRL MFTs exhibited ~400 and ~800d lag phases, respectively after which n-alkanes (n-pentane and n-hexane) in the solvent were preferentially metabolized to methane over iso-alkanes in both MFTs. Among iso-alkanes, only 2-methylpentane was completely biodegraded whereas 2-methylbutane and 3-methylpentane were partially biodegraded probably through cometabolism. 16S rRNA gene pyrosequencing showed dominance of Anaerolineaceae and Methanosaetaceae in Albian MFT and Peptococcaceae and co-domination of "Candidatus Methanoregula" and Methanosaetaceae in CNRL MFT bacterial and archaeal communities, respectively, during active biodegradation of paraffinic solvent. The results are important for developing future strategies for tailings reclamation and management of greenhouse gas emissions. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Application of magnetic tools designed by Ecopetrol to inhibit paraffin in the production systems

    International Nuclear Information System (INIS)

    Medina Z, Carlos; Pelaez U, Carlos; Buendia I, Hernando; Pena C, Alvaro

    1995-01-01

    The present article narrates the experiences and the results obtained with these tools in 3 representative historical cases of a group of 16, using a technique of magnetic inhibition of paraffin which has been proven with great success in diverse parts of the world, making of this a non expensive inhibition method and of continuous treatment

  11. Developments and interlaboratory study of the analysis of short-chain chlorinated paraffins

    NARCIS (Netherlands)

    van Mourik, L. M.; van der Veen, I.; Crum, S.; de Boer, J.

    To survey the conformity and quality of the results between laboratories for short-chain chlorinated paraffins (SCCPs) determination, we reviewed current and novel analytical methods and organized four worldwide laboratory exercises between 2011 and 2017. Participants were requested to analyse test

  12. Developments and interlaboratory study of the analysis of short-chain chlorinated paraffins

    NARCIS (Netherlands)

    Mourik, van L.M.; Veen, van der I.; Crum, S.; Boer, de J.

    2018-01-01

    To survey the conformity and quality of the results between laboratories for short-chain chlorinated paraffins (SCCPs) determination, we reviewed current and novel analytical methods and organized four worldwide laboratory exercises between 2011 and 2017. Participants were requested to analyse test

  13. Analysis of Steam Heating of a Two-Layer TBP/N-Paraffin/Nitric Acid Mixtures

    International Nuclear Information System (INIS)

    Laurinat, J.E.; Hassan, N.M.; Rudisill, T.S.; Askew, N.M.

    1998-01-01

    This report presents an analysis of steam heating of a two-layer tri-n-butyl phosphate (TBP)/n-paraffin-nitric acid mixture.The purpose of this study is to determine if the degree of mixing provided by the steam jet or by bubbles generated by the TBP/nitric acid reaction is sufficient to prevent a runaway reaction

  14. Thermal characterization of polymer matrix composites containing microencapsulated paraffin in solid or liquid state

    International Nuclear Information System (INIS)

    Sari-Bey, Sana; Fois, Magali; Krupa, Igor; Ibos, Laurent; Benyoucef, Boumédiène

    2014-01-01

    Highlights: • Thermal characterization of PCL/Micronal composites. • Melting enthalpy and heat capacity measured by DSC. • Interest: have measured thermal properties at different temperatures. • Thermophysical properties measurement temperatures chosen outside phase changes. • Characteristics useful to model composites heat transfer for LHTES applications. - Abstract: This work focuses on the study of heat transfer mechanisms in composites materials which may be used for Latent Heat Thermal Energy Storage applications. These composites contain phase change material (PCM) which can absorb and release energy during thermal cycling. PCM’s used here are paraffins microencapsulated in poly(methylmethacrylate); microencapsulation avoids the flow of paraffin when it is in the liquid state. Samples with different paraffin weight fractions and particles shape and distribution were studied in this work. Scanning Electron Microscopy and Differential Scanning Calorimetry were used to determine morphology and perform measurements of phase changes temperatures, enthalpies and heat capacity respectively. Further, a periodic method (DICO) allowed measuring thermal conductivity (λ) and diffusivity (a) of the composites at temperatures below and above of the paraffin phase change from crystalline solid to isotropic liquid

  15. Paraffin Nanocomposites for Heat Management of Lithium-Ion Batteries: A Computational Investigation

    Directory of Open Access Journals (Sweden)

    A. H. N. Shirazi

    2016-01-01

    Full Text Available Lithium-ion (Li-ion batteries are currently considered as vital components for advances in mobile technologies such as those in communications and transport. Nonetheless, Li-ion batteries suffer from temperature rises which sometimes lead to operational damages or may even cause fire. An appropriate solution to control the temperature changes during the operation of Li-ion batteries is to embed batteries inside a paraffin matrix to absorb and dissipate heat. In the present work, we aimed to investigate the possibility of making paraffin nanocomposites for better heat management of a Li-ion battery pack. To fulfill this aim, heat generation during a battery charging/discharging cycles was simulated using Newman’s well established electrochemical pseudo-2D model. We couple this model to a 3D heat transfer model to predict the temperature evolution during the battery operation. In the later model, we considered different paraffin nanocomposites structures made by the addition of graphene, carbon nanotubes, and fullerene by assuming the same thermal conductivity for all fillers. This way, our results mainly correlate with the geometry of the fillers. Our results assess the degree of enhancement in heat dissipation of Li-ion batteries through the use of paraffin nanocomposites. Our results may be used as a guide for experimental set-ups to improve the heat management of Li-ion batteries.

  16. Drug release from non-aqueous suspensions. II. The release of methylxanthines from paraffin suspensions

    NARCIS (Netherlands)

    Blaey, C.J. de; Fokkens, J.G.

    1984-01-01

    The release of 3 methylxanthines, i.e. caffeine, theobromine and theophylline, from suspensions in liquid paraffin to an aqueous phase was determined in an in vitro apparatus. The release rates were determined as a function of the pH of the aqueous phase. It was proved that the release process was

  17. The impact of child-resistant containers on the incidence of paraffin ...

    African Journals Online (AJOL)

    The commonest cause of accidental poisoning in the South African black paediatric population is paraffin ingestion. In this intervention study a specifically designed child-resistant container (CRG) was introduced to evaluate whether its use would decrease the incidence ofparaffin ingestion. CRCs were distributed to 20 000 ...

  18. Thermal properties and crystallization behaviour of solid N-paraffin components derived from Mukta crude oil

    Czech Academy of Sciences Publication Activity Database

    Khan, H. U.; Nautiyal, S. P.; Agrawal, K. M.; Sharma, R. L.; Sikora, Antonín

    2001-01-01

    Roč. 43, č. 1 (2001), s. 13-16 ISSN 1335-3055 R&D Projects: GA AV ČR KSK4050111 Institutional research plan: CEZ:AV0Z4050913 Keywords : paraffin s * crude oil * urea adductables Subject RIV: CD - Macromolecular Chemistry

  19. Technical and Economic Analysis of Injecting Enhancers into High-Paraffin Oil Heaters

    Science.gov (United States)

    Konakhina, I. A.; Khamidullina, G. R.; Khusnutdinova, E. M.

    2017-09-01

    This paper covers an algorithm of how to optimize the selection of preferred solutions to upgrade heat-exchange equipment. The algorithm is discussed in terms of high-paraffin oil heaters as compared with other heat-exchange surface features.

  20. Antibacterial and antifungal effect of high pH and paraffin wax ...

    African Journals Online (AJOL)

    The antibacterial and antifungal effects of high pH (9, 10) and paraffin wax were determined. Determination of antibacterial and antifungal activity of the combined treatments was achieved by aerobic mesophilic count of bacteria and fungi on the surface of the tomatoes, peppers and oranges using serial dilution and pour ...

  1. Effect of functional groups on thermal conductivity of graphene/paraffin nanocomposite

    Energy Technology Data Exchange (ETDEWEB)

    Zabihi, Zabiholah; Araghi, Houshang, E-mail: araghi@aut.ac.ir

    2016-11-25

    In this paper, thermal conductivity of graphene/paraffin nanocomposite using micromechanical model has been studied. The behavior of thermal conductivity of nanocomposite as a function of volume fraction of graphene is studied. Then is shown that as the interfacial thermal resistance at the graphene–paraffin interface decreases, the thermal conductivity of nanocomposite increases. In order to reduce the interfacial thermal resistance, functional groups in the interface between graphene and paraffin are used. It can be observed that using functional groups of hydrogen, methyl and phenyl in the interface of nanocomposite, contributes to the improvement of the thermal conductivity. Moreover, as the rate of coverage of the surface of graphene with functional groups of H, CH{sub 3} and C{sub 6}H{sub 5} increases, the thermal conductivity of nanocomposite improves. - Highlights: • Thermal conductivity nanocomposite exhibit nonlinear behavior with volume faction. • Phenyl is better to form the thermal conductivity network in paraffin. • The thickness of interfacial layer can be obtained 12.75 nm.

  2. Effect of microbial treatment on the prevention and removal of paraffin deposits on stainless steel surfaces.

    Science.gov (United States)

    Xiao, Meng; Li, Wen-Hong; Lu, Mang; Zhang, Zhong-Zhi; Luo, Yi-Jing; Qiao, Wei; Sun, Shan-Shan; Zhong, Wei-Zhang; Zhang, Min

    2012-11-01

    In this study, biosurfactant-producing strain N2 and non-biosurfactant producing stain KB18 were used to investigate the effects of microbial treatment on the prevention and removal of paraffin deposits on stainless steel surfaces. Strain N2, with a biosurfactant production capacity, reduced the contact angle of stainless steel to 40.04°, and the corresponding adhesion work of aqueous phase was decreased by 26.5 mJ/m(2). By contrast, KB18 could only reduce the contact angle to 50.83°, with a corresponding 7.6 mJ/m(2) decrease in the aqueous phase work adhesion. The paraffin removal test showed that the paraffin removal efficiencies of strain N2 and KB18 were 79.0% and 61.2%, respectively. Interestingly, the N2 cells could attach on the surface of the oil droplets to inhibit droplets coalescence. These results indicate that biosurfactant-producing strains can alter the wettability of stainless steel and thus eliminate paraffin deposition. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Hydrogen peroxide modified Mg-Al-O oxides supported Pt-Sn catalysts for paraffin dehydrogenation

    NARCIS (Netherlands)

    Lai, Y.; He, Songbo; Luo, S.; Bi, W.; Li, XianRu; Sun, Chenglin; Seshan, Kulathuiyer

    2015-01-01

    In this work, a new method to prepare Mg–Al–O oxide by co-precipitation method with addition of H2O2 was developed. The application of Mg–Al–O as a support of Pt–Sn catalysts for paraffin dehydrogenation was investigated. Characterization results indicated that modification of H2O2 (i) enlarged the

  4. A new insert sample approach to paper spray mass spectrometry: a paper substrate with paraffin barriers.

    Science.gov (United States)

    Colletes, T C; Garcia, P T; Campanha, R B; Abdelnur, P V; Romão, W; Coltro, W K T; Vaz, B G

    2016-03-07

    The analytical performance for paper spray (PS) using a new insert sample approach based on paper with paraffin barriers (PS-PB) is presented. The paraffin barrier is made using a simple, fast and cheap method based on the stamping of paraffin onto a paper surface. Typical operation conditions of paper spray such as the solvent volume applied on the paper surface, and the paper substrate type are evaluated. A paper substrate with paraffin barriers shows better performance on analysis of a range of typical analytes when compared to the conventional PS-MS using normal paper (PS-NP) and PS-MS using paper with two rounded corners (PS-RC). PS-PB was applied to detect sugars and their inhibitors in sugarcane bagasse liquors from a second generation ethanol process. Moreover, the PS-PB proved to be excellent, showing results for the quantification of glucose in hydrolysis liquors with excellent linearity (R(2) = 0.99), limits of detection (2.77 mmol L(-1)) and quantification (9.27 mmol L(-1)). The results are better than for PS-NP and PS-RC. The PS-PB was also excellent in performance when compared with the HPLC-UV method for glucose quantification on hydrolysis of liquor samples.

  5. High-throughput sequencing and copy number variation detection using formalin fixed embedded tissue in metastatic gastric cancer.

    Directory of Open Access Journals (Sweden)

    Seokhwi Kim

    Full Text Available In the era of targeted therapy, mutation profiling of cancer is a crucial aspect of making therapeutic decisions. To characterize cancer at a molecular level, the use of formalin-fixed paraffin-embedded tissue is important. We tested the Ion AmpliSeq Cancer Hotspot Panel v2 and nCounter Copy Number Variation Assay in 89 formalin-fixed paraffin-embedded gastric cancer samples to determine whether they are applicable in archival clinical samples for personalized targeted therapies. We validated the results with Sanger sequencing, real-time quantitative PCR, fluorescence in situ hybridization and immunohistochemistry. Frequently detected somatic mutations included TP53 (28.17%, APC (10.1%, PIK3CA (5.6%, KRAS (4.5%, SMO (3.4%, STK11 (3.4%, CDKN2A (3.4% and SMAD4 (3.4%. Amplifications of HER2, CCNE1, MYC, KRAS and EGFR genes were observed in 8 (8.9%, 4 (4.5%, 2 (2.2%, 1 (1.1% and 1 (1.1% cases, respectively. In the cases with amplification, fluorescence in situ hybridization for HER2 verified gene amplification and immunohistochemistry for HER2, EGFR and CCNE1 verified the overexpression of proteins in tumor cells. In conclusion, we successfully performed semiconductor-based sequencing and nCounter copy number variation analyses in formalin-fixed paraffin-embedded gastric cancer samples. High-throughput screening in archival clinical samples enables faster, more accurate and cost-effective detection of hotspot mutations or amplification in genes.

  6. Diagnosis of filamentous fungi on tissue sections by immunohistochemistry using anti-aspergillus antibody.

    Science.gov (United States)

    Challa, Sundaram; Uppin, Shantveer G; Uppin, Megha S; Pamidimukkala, Umabala; Vemu, Lakshmi

    2015-06-01

    Identification based on histology alone has limitations as Aspergillus species share morphology with other filamentous fungi. Differentiation of Aspergillus species from hyalohyphomycetes and dematiaceous fungi is important as the antifungal susceptibility varies among different species and genera. Given these problems, ancillary techniques are needed to increase specificity. Our aim was to study the utility of immunohistochemistry (IHC) with anti-Aspergillus antibody in the identification of Aspergillus species and to differentiate them from other filamentous fungi. Fifty formalin fixed, paraffin embedded tissue sections including 47 from cases of culture proven filamentous fungi, 3 from colonies of cultures of hyalohyphomycetes, and 11 smears from cultures were subjected to IHC studies using polyclonal rabbit anti-Aspergillus antibody (Abcam, UK) after antigen retrieval. The IHC on tissue sections was positive in 88% cases involving culture proven Aspergillus species. There was no cross reactivity with Mucorales species, Candida species, dematiaceous fungi and hyalohyphomycetes. Hence immunohistochemistry can be used as an ancillary technique for the diagnosis of Aspergillus species. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Variation in penetration of submicrometric particles through electrostatic filtering facepieces during exposure to paraffin oil aerosol.

    Science.gov (United States)

    Plebani, Carmela; Listrani, Stefano; Tranfo, Giovanna; Tombolini, Francesca

    2012-01-01

    Several studies show the increase of penetration through electrostatic filters during exposure to an aerosol flow, because of particle deposition on filter fibers. We studied the effect of increasing loads of paraffin oil aerosol on the penetration of selected particle sizes through an electrostatic filtering facepiece. FFP2 facepieces were exposed for 8 hr to a flow rate of 95.0 ± 0.5 L/min of polydisperse paraffin aerosol at 20.0 ± 0.5 mg/m(3). The penetration of bis(2-ethylhexyl)sebacate (DEHS) monodisperse neutralized aerosols, with selected particle size in the 0.03-0.40 μm range, was measured immediately prior to the start of the paraffin aerosol loading and at 1, 4, and 8 hr after the start of paraffin aerosol loading. Penetration through isopropanol-treated facepieces not oil paraffin loaded was also measured to evaluate facepiece behavior when electrostatic capture mechanisms are practically absent. During exposure to paraffin aerosol, DEHS penetration gradually increased for all aerosol sizes, and the most penetrating particle size (0.05 μm at the beginning of exposure) shifted slightly to larger diameters. After the isopropanol treatment, the higher penetration value was 0.30 μm. In addition to an increased penetration during paraffin loading at a given particle size, the relative degree of increase was greater as the particle size increased. Penetration value measured after 8 hr for 0.03-μm particles was on average 1.6 times the initial value, whereas it was about 8 times for 0.40-μm particles. This behavior, as well evidenced in the measurements of isopropanol-treated facepieces, can be attributed to the increasing action in particle capture of the electrostatic forces (Coulomb and polarization), which depend strictly on the diameter and electrical charge of neutralized aerosol particles. With reference to electrostatic filtering facepieces as personal protective equipment, results suggest the importance of complying with the manufacturer

  8. Embedded Linux projects using Yocto project cookbook

    CERN Document Server

    González, Alex

    2015-01-01

    If you are an embedded developer learning about embedded Linux with some experience with the Yocto project, this book is the ideal way to become proficient and broaden your knowledge with examples that are immediately applicable to your embedded developments. Experienced embedded Yocto developers will find new insight into working methodologies and ARM specific development competence.

  9. Trusted computing for embedded systems

    CERN Document Server

    Soudris, Dimitrios; Anagnostopoulos, Iraklis

    2015-01-01

    This book describes the state-of-the-art in trusted computing for embedded systems. It shows how a variety of security and trusted computing problems are addressed currently and what solutions are expected to emerge in the coming years. The discussion focuses on attacks aimed at hardware and software for embedded systems, and the authors describe specific solutions to create security features. Case studies are used to present new techniques designed as industrial security solutions. Coverage includes development of tamper resistant hardware and firmware mechanisms for lightweight embedded devices, as well as those serving as security anchors for embedded platforms required by applications such as smart power grids, smart networked and home appliances, environmental and infrastructure sensor networks, etc. ·         Enables readers to address a variety of security threats to embedded hardware and software; ·         Describes design of secure wireless sensor networks, to address secure authen...

  10. Comparison of SVM, RF and ELM on an Electronic Nose for the Intelligent Evaluation of Paraffin Samples

    Directory of Open Access Journals (Sweden)

    Hong Men

    2018-01-01

    Full Text Available Paraffin odor intensity is an important quality indicator when a paraffin inspection is performed. Currently, paraffin odor level assessment is mainly dependent on an artificial sensory evaluation. In this paper, we developed a paraffin odor analysis system to classify and grade four kinds of paraffin samples. The original feature set was optimized using Principal Component Analysis (PCA and Partial Least Squares (PLS. Support Vector Machine (SVM, Random Forest (RF, and Extreme Learning Machine (ELM were applied to three different feature data sets for classification and level assessment of paraffin. For classification, the model based on SVM, with an accuracy rate of 100%, was superior to that based on RF, with an accuracy rate of 98.33–100%, and ELM, with an accuracy rate of 98.01–100%. For level assessment, the R2 related to the training set was above 0.97 and the R2 related to the test set was above 0.87. Through comprehensive comparison, the generalization of the model based on ELM was superior to those based on SVM and RF. The scoring errors for the three models were 0.0016–0.3494, lower than the error of 0.5–1.0 measured by industry standard experts, meaning these methods have a higher prediction accuracy for scoring paraffin level.

  11. Design Methodologies for Secure Embedded Systems

    CERN Document Server

    Biedermann, Alexander

    2011-01-01

    Embedded systems have been almost invisibly pervading our daily lives for several decades. They facilitate smooth operations in avionics, automotive electronics, or telecommunication. New problems arise by the increasing employment, interconnection, and communication of embedded systems in heterogeneous environments: How secure are these embedded systems against attacks or breakdowns? Therefore, how can embedded systems be designed to be more secure? And how can embedded systems autonomically react to threats? Facing these questions, Sorin A. Huss is significantly involved in the exploration o

  12. A RANDOMISED TRIAL OF LIQUID PARAFFIN VERSUS LACTULOSE IN THE TREATMENT OF CHRONIC FUNCTIONAL CONSTIPATION IN CHILDREN

    Directory of Open Access Journals (Sweden)

    F. Farahmand

    2007-07-01

    Full Text Available "nLiquid paraffin has been suggested as a good laxative comparing to lactulose as a treatment option in pediatric constipation. This study was performed to compare liquid paraffin with lactulose in pediatric constipation. A total of 247 patients (127 males and 120 females aged 2-12 years (mean 4.1 ± 2.7 years with chronic functional constipation were included in an 8 week, randomized, controlled trial. After faecal disimpaction, patients received oral liquid paraffin (1-2 cc/kg/day or lactulose (1-2 cc/kg/day. Primary outcome measures were: defecation and encopresis frequency per week and successful treatment after 8 weeks. Success was defined as a defecation frequency ≥ 3 per week and encopresis ≤ 1 every two weeks. Secondary outcome measures were side effects during 8 weeks of treatment. A significant increase in defecation frequency, liquid paraffin group, 3 pre, versus, 12 post treatment per week and lactulose group: 3 pre, versus 8 post, per week was found. A significant decrease in encopresis frequency, liquid paraffin: 10 pre, versus 1 post per week; lactulose: 9 pre, versus 3 post per week, was found in both groups. However success was significantly higher in the liquid paraffin group (85% compared with the lactulose group (29%. Liquid paraffin patients reported less abdominal pain, straining and pain at defecation than children using lactulose. Liquid paraffin is more effective than lactulose in the treatment of chronic functional constipation of childhood. It provided a higher success rate with fewer side effects. Liquid paraffin should be the laxative of first choice in childhood functional constipation.

  13. Insight into the influence of liquid paraffin for methanol synthesis on Cu(110) surface using continuum and atomistic models

    Energy Technology Data Exchange (ETDEWEB)

    Jiao, Wei-Hong [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Liu, Shi-Zhong [Department of Chemistry, Stony Brook University, Stony Brook, NY 11794 (United States); Zuo, Zhi-Jun, E-mail: zuozhijun@tyut.edu.cn [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Ren, Rui-Peng; Gao, Zhi-Hua [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Huang, Wei, E-mail: huangwei@tyut.edu.cn [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China)

    2016-11-30

    Highlights: • The influence of liquid paraffin is studied using continuum and atomistic models. • Liquid paraffin does not alter the reaction pathways of CO hydrogenation and WGS. • Liquid paraffin alters the reaction pathways of CO{sub 2} hydrogenation. - Abstract: Methanol synthesis from CO/CO{sub 2} hydrogenation and water-gas shift (WGS) reaction on Cu(110) in liquid paraffin and vacuum have been systematically researched with density functional theory calculation (DFT). For methanol synthesis from CO hydrogenation, the reaction pathways in liquid paraffin and vacuum are CO + H → HCO → H{sub 2}CO → H{sub 3}CO → H{sub 3}COH; in the case of WGS, the reaction pathways in liquid paraffin and vacuum are CO + 2H{sub 2}O → CO + 2OH + 2H → CO + H{sub 2}O + O + H{sub 2} → CO{sub 2} + H{sub 2}O + H{sub 2}; the reaction pathways of methanol synthesis from CO{sub 2} hydrogenation in liquid paraffin and vacuum are CO{sub 2} + H → HCOO → H{sub 2}COO → H{sub 2}CO → H{sub 3}CO → H{sub 3}COH and CO{sub 2} + H → HCOO → HCOOH → H{sub 2}COOH → H{sub 3}CO → H{sub 3}COH, respectively. The result shows that liquid paraffin does not affect the reaction mechanisms of methanol synthesis from CO and WGS, but it changes the reaction mechanisms of methanol synthesis from CO{sub 2} hydrogenation. Hirshfeld charge and the d-band centers indicate that the catalytic activity of Cu(110) in liquid paraffin is smaller than that in vacuum. Our results also show that it is necessary to consider both continuum and atomistic models in the slurry bed.

  14. Certifiable Java for Embedded Systems

    DEFF Research Database (Denmark)

    Schoeberl, Martin; Dalsgaard, Andreas Engelbredt; Hansen, Rene Rydhof

    2014-01-01

    The Certifiable Java for Embedded Systems (CJ4ES) project aimed to develop a prototype development environment and platform for safety-critical software for embedded applications. There are three core constituents: A profile of the Java programming language that is tailored for safety......-critical applications, a predictable Java processor built with FPGA technology, and an Eclipse based application development environment that binds the profile and the platform together and provides analyses that help to provide evidence that can be used as part of a safety case. This paper summarizes key contributions...

  15. Morphware - Fremtidens Embedded System Platform

    DEFF Research Database (Denmark)

    Madsen, Jan

    2006-01-01

    FPGA'er bliver i stigende grad brugt som komponenter i embedded systemer. Faldende priser, større kapacitet og en større felksibilitet har gjort FPGA'en til en attraktiv og konkurrencedygtig teknologi der tillader en stadig stigende grad af system integration, hvor traditionel hardware og software...... kombineres og rekonfigureres. Muligheden for at rekonfigurere systemet, og specielt rekonfigurerer det medens det kører, giver nogle helt nye muligheder for at designe og programmere embedded systemer. Dette foredrag vil give et indblik i disse nye og fremtidige muligheder....

  16. Implementation of an embedded computer

    OpenAIRE

    Pikl, Bojan

    2011-01-01

    The goal of this thesis is to describe a production of an embedded computer. The thesis describes development and production of an embedded computer for the medical diode laser DL30 that is being developed in Robomed d.o.o.. The first part of the thesis describes the choice of hardware devices. I mostly describe the technologies that one can buy on the market. Moreover for every part of the computer installed and developed there is an argument why we selected that exact part. The second part ...

  17. Homogeneous Spaces and Equivariant Embeddings

    CERN Document Server

    Timashev, DA

    2011-01-01

    Homogeneous spaces of linear algebraic groups lie at the crossroads of algebraic geometry, theory of algebraic groups, classical projective and enumerative geometry, harmonic analysis, and representation theory. By standard reasons of algebraic geometry, in order to solve various problems on a homogeneous space it is natural and helpful to compactify it keeping track of the group action, i.e. to consider equivariant completions or, more generally, open embeddings of a given homogeneous space. Such equivariant embeddings are the subject of this book. We focus on classification of equivariant em

  18. A Foundation for Embedded Languages

    DEFF Research Database (Denmark)

    Rhiger, Morten

    2003-01-01

    Recent work on embedding object languages into Haskell use "phantom types" (i.e., parameterized types whose parameter does not occur on the right-hand side of the type definition) to ensure that the embedded object-language terms are simply typed. But is it a safe assumption that only simply......-typed terms can be represented in Haskell using phantom types? And conversely, can all simply-typed terms be represented in Haskell under the restrictions imposed by phantom types? In this article we investigate the conditions under which these assumptions are true: We show that these questions can...

  19. A Foundation for Embedded Languages

    DEFF Research Database (Denmark)

    Rhiger, Morten

    2002-01-01

    Recent work on embedding object languages into Haskell use "phantom types" (i.e., parameterized types whose parameter does not occur on the right-hand side of the type definition) to ensure that the embedded object-language terms are simply typed. But is it a safe assumption that only simply......-typed terms can be represented in Haskell using phantom types? And conversely, can all simply-typed terms be represented in Haskell under the restrictions imposed by phantom types? In this article we investigate the conditions under which these assumptions are true: We show that these questions can...

  20. Secret data embedding scheme modifying the frequency of ...

    Indian Academy of Sciences (India)

    such as banking, e-commerce, e-signature, distance learning, e-government ... received a growing attention in conjunction with the new tools and methods ... Essential points of the image processing and data embedding are clarified in the next section. ..... The proposed scheme's numerical performance is shown in table 6.