SITES OF LIPOPROTEIN LIPASE ACTIVITY IN ADIPOSE TISSUE PERFUSED WITH CHYLOMICRONS

PubMed Central

Blanchette-Mackie, E. Joan; Scow, Robert O.

1971-01-01

Lipoprotein lipase activity was studied in rat parametrial adipose tissue perfused with chylomicrons and in gelatin blocks containing postheparin plasma and chylomicrons. The tissues and blocks were fixed in glutaraldehyde and incubated in 0.035 M CaCl2-0.1 M Tris medium (pH 8.3) at 38°C. The doubly labeled chylomicron triglycerides (glycerol-3H and palmitate-14C) in the tissues and blocks were hydrolyzed during incubation to free fatty acids (FFA) and the FFA remained in the specimens; hydrolysis was inhibited by 0.004 M diethyl paranitrophenyl phosphate (E-600). Incubated blocks and tissue were treated with 0.05 M Pb(NO3)2, postfixed in OsO4, dehydrated with acetone, embedded in Epon, and examined by electron microscopy. The incubated blocks contained electronlucent areas and granular and laminar precipitates at sites of hydrolysis. Similar precipitates were found in incubated tissue, within vacuoles and microvesicles of capillary endothelium, and in the subendothelial space (between the endothelium and pericytes), but not in the capillary lumen or in or near fat cells. The cytochemical reaction was greatly reduced, in blocks and tissues incubated with E-600. It is concluded that plasma glycerides are hydrolyzed by lipoprotein lipase in capillary endothelial cells and in the subendothelial space of adipose tissue and that glycerides across the endothelial cells within a membrane-bounded system. PMID:4329521

Fully automated three-dimensional microscopy system

NASA Astrophysics Data System (ADS)

Kerschmann, Russell L.

2000-04-01

Tissue-scale structures such as vessel networks are imaged at micron resolution with the Virtual Tissue System (VT System). VT System imaging of cubic millimeters of tissue and other material extends the capabilities of conventional volumetric techniques such as confocal microscopy, and allows for the first time the integrated 2D and 3D analysis of important tissue structural relationships. The VT System eliminates the need for glass slide-mounted tissue sections and instead captures images directly from the surface of a block containing a sample. Tissues are en bloc stained with fluorochrome compounds, embedded in an optically conditioned polymer that suppresses image signals form dep within the block , and serially sectioned for imaging. Thousands of fully registered 2D images are automatically captured digitally to completely convert tissue samples into blocks of high-resolution information. The resulting multi gigabyte data sets constitute the raw material for precision visualization and analysis. Cellular function may be seen in a larger anatomical context. VT System technology makes tissue metrics, accurate cell enumeration and cell cycle analyses possible while preserving full histologic setting.

Immunohistochemistry for the detection of neural and inflammatory cells in equine brain tissue

PubMed Central

Liu, Junjie; Herrington, Jenna M.; Vallario, Kelsey

2016-01-01

Phenotypic characterization of cellular responses in equine infectious encephalitides has had limited description of both peripheral and resident cell populations in central nervous system (CNS) tissues due to limited species-specific reagents that react with formalin-fixed, paraffin embedded tissue (FFPE). This study identified a set of antibodies for investigating the immunopathology of infectious CNS diseases in horses. Multiple commercially available staining reagents and antibodies derived from antigens of various species for manual immunohistochemistry (IHC) were screened. Several techniques and reagents for heat-induced antigen retrieval, non-specific protein blocking, endogenous peroxidase blocking, and visualization-detection systems were tested during IHC protocol development. Boiling of slides in a low pH, citrate-based buffer solution in a double-boiler system was most consistent for epitope retrieval. Pressure-cooking, microwaving, high pH buffers, and proteinase K solutions often resulted in tissue disruption or no reactivity. Optimal blocking reagents and concentrations of each working antibody were determined. Ultimately, a set of monoclonal (mAb) and polyclonal antibodies (pAb) were identified for CD3+ (pAb A0452, Dako) T-lymphocytes, CD79αcy+ B-lymphocytes (mAb HM57, Dako), macrophages (mAb MAC387, Leica), NF-H+ neurons (mAb NAP4, EnCor Biotechnology), microglia/macrophage (pAb Iba-1, Wako), and GFAP+ astrocytes (mAb 5C10, EnCor Biotechnology). In paraffin embedded tissues, mAbs and pAbs derived from human and swine antigens were very successful at binding equine tissue targets. Individual, optimized protocols are provided for each positively reactive antibody for analyzing equine neuroinflammatory disease histopathology. PMID:26855862

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

PubMed

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 < 0.001). Overall, remaining proportion of 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.

High-quality cell block preparation from scraping of conventional cytology slide: a technical report on a modified cytoscrape cell block technique.

PubMed

Choi, Y I; Jakhongir, M; Choi, S J; Kim, L; Park, I S; Han, J Y; Kim, J M; Chu, Y C

2016-12-01

Immunocytochemistry (ICC) on formalin-fixed paraffin embedded cell blocks is an ancillary tool commonly recruited for differential diagnoses of fine needle aspiration cytology (FNAC) samples. However, the quality of conventional cell blocks in terms of adequate cellularity and evenness of distribution of cytologic material is not always satisfactory for ICC. We introduce a modified agarose-based cytoscrape cell block (CCB) technique that can be effectively used for the preparation of cell blocks from scrapings of conventional FNAC slides. A decoverslipped FNAC slide was mounted with a small amount of water. The cytological material was scraped off the slide into a tissue mold by scraping with a cell scraper. The cytoscrape material was pelleted by centrifugation and pre-embedded in ultra-low gelling temperature agarose and then re-embedded in conventional agarose. The final agarose gel disk was processed and embedded in paraffin. The quality of the ICC on the CCB sections was identical to that of the immunohistochemical stains on histological sections. By scrapping and harvesting the entirety of the cytological material off the cytology slide into a compact agarose cell button, we could avoid the risk of losing diagnostic material during the CCB preparation. This modified CCB technique enables concentration and focusing of minute material while maintaining the entire amount of the cytoscrape material on the viewing spot of the CCB sections. We believe this technique can be effectively used to improve the level of confidence in diagnosis of FNAC especially when the FNAC slides are the only sample available.

Beam deceleration for block-face scanning electron microscopy of embedded biological tissue.

PubMed

Ohta, Keisuke; Sadayama, Shoji; Togo, Akinobu; Higashi, Ryuhei; Tanoue, Ryuichiro; Nakamura, Kei-ichiro

2012-04-01

The beam deceleration (BD) method for scanning electron microscopes (SEM) also referred to as "retarding" was applied to back-scattered electron (BSE) imaging of the flat block face of a resin embedded biological specimen under low accelerating voltage and low beam current conditions. BSE imaging was performed with 0-4 kV of BD on en bloc stained rat hepatocyte. BD drastically enhanced the compositional contrast of the specimen and also improved the resolution at low landing energy levels (1.5-3 keV) and a low beam current (10 pA). These effects also functioned in long working distance observation, however, stage tilting caused uncorrectable astigmatism in BD observation. Stage tilting is mechanically required for a FIB/SEM, so we designed a novel specimen holder to minimize the unfavorable tilting effect. The FIB/SEM 3D reconstruction using the new holder showed a reasonable contrast and resolution high enough to analyze individual cell organelles and also the mitochondrial cristae structures (~5 nm) of the hepatocyte. These results indicate the advantages of BD for block face imaging of biological materials such as cells and tissues under low-voltage and low beam current conditions. Copyright © 2011 Elsevier Ltd. All rights reserved.

Mechanical signaling coordinates the embryonic heart

NASA Astrophysics Data System (ADS)

Chiou, Kevin; Rocks, Jason; Prosser, Benjamin; Discher, Dennis; Liu, Andrea

The heart is an active material which relies on robust signaling mechanisms between cells in order to produce well-timed, coordinated beats. Heart tissue is composed primarily of active heart muscle cells (cardiomyocytes) embedded in a passive extracellular matrix. During a heartbeat, cardiomyocyte contractions are coordinated across the heart to form a wavefront that propagates through the tissue to pump blood. In the adult heart, this contractile wave is coordinated via intercellular electrical signaling.Here we present theoretical and experimental evidence for mechanical coordination of embryonic heartbeats. We model cardiomyocytes as mechanically excitable Eshelby inclusions embedded in an overdamped elastic-fluid biphasic medium. For physiological parameters, this model replicates recent experimental measurements of the contractile wavefront which are not captured by electrical signaling models. We additionally challenge our model by pharmacologically blocking gap junctions, inhibiting electrical signaling between myocytes. We find that while adult hearts stop beating almost immediately after gap junctions are blocked, embryonic hearts continue beating even at significantly higher concentrations, providing strong support for a mechanical signaling mechanism.

Correlative Imaging of Fluorescent Proteins in Resin-Embedded Plant Material1

PubMed Central

Bell, Karen; Mitchell, Steve; Paultre, Danae; Posch, Markus; Oparka, Karl

2013-01-01

Fluorescent proteins (FPs) were developed for live-cell imaging and have revolutionized cell biology. However, not all plant tissues are accessible to live imaging using confocal microscopy, necessitating alternative approaches for protein localization. An example is the phloem, a tissue embedded deep within plant organs and sensitive to damage. To facilitate accurate localization of FPs within recalcitrant tissues, we developed a simple method for retaining FPs after resin embedding. This method is based on low-temperature fixation and dehydration, followed by embedding in London Resin White, and avoids the need for cryosections. We show that a palette of FPs can be localized in plant tissues while retaining good structural cell preservation, and that the polymerized block face can be counterstained with cell wall probes. Using this method we have been able to image green fluorescent protein-labeled plasmodesmata to a depth of more than 40 μm beneath the resin surface. Using correlative light and electron microscopy of the phloem, we were able to locate the same FP-labeled sieve elements in semithin and ultrathin sections. Sections were amenable to antibody labeling, and allowed a combination of confocal and superresolution imaging (three-dimensional-structured illumination microscopy) on the same cells. These correlative imaging methods should find several uses in plant cell biology. PMID:23457228

Overview on Techniques to Construct Tissue Arrays with Special Emphasis on Tissue Microarrays

PubMed Central

Vogel, Ulrich

2014-01-01

With the advent of new histopathological staining techniques (histochemistry, immunohistochemistry, in situ hybridization) and the discovery of thousands of new genes, mRNA, and proteins by molecular biology, the need grew for a technique to compare many different cells or tissues on one slide in a cost effective manner and with the possibility to easily track the identity of each specimen: the tissue array (TA). Basically, a TA consists of at least two different specimens per slide. TAs differ in the kind of specimens, the number of specimens installed, the dimension of the specimens, the arrangement of the specimens, the embedding medium, the technique to prepare the specimens to be installed, and the technique to construct the TA itself. A TA can be constructed by arranging the tissue specimens in a mold and subsequently pouring the mold with the embedding medium of choice. In contrast, preformed so-called recipient blocks consisting of the embedding medium of choice have punched, drilled, or poured holes of different diameters and distances in which the cells or tissue biopsies will be deployed manually, semi-automatically, or automatically. The costs of constructing a TA differ from a few to thousands of Euros depending on the technique/equipment used. Remarkably high quality TAs can be also achieved by low cost techniques. PMID:27600339

Proteomic analysis of formalin-fixed paraffin embedded tissue by MALDI imaging mass spectrometry

PubMed Central

Casadonte, Rita; Caprioli, Richard M

2012-01-01

Archived formalin-fixed paraffin-embedded (FFPE) tissue collections represent a valuable informational resource for proteomic studies. Multiple FFPE core biopsies can be assembled in a single block to form tissue microarrays (TMAs). We describe a protocol for analyzing protein in FFPE -TMAs using matrix-assisted laser desorption/ionization (MAL DI) imaging mass spectrometry (IMS). The workflow incorporates an antigen retrieval step following deparaffinization, in situ trypsin digestion, matrix application and then mass spectrometry signal acquisition. The direct analysis of FFPE -TMA tissue using IMS allows direct analysis of multiple tissue samples in a single experiment without extraction and purification of proteins. The advantages of high speed and throughput, easy sample handling and excellent reproducibility make this technology a favorable approach for the proteomic analysis of clinical research cohorts with large sample numbers. For example, TMA analysis of 300 FFPE cores would typically require 6 h of total time through data acquisition, not including data analysis. PMID:22011652

Specimen block counter-staining for localization of GUS expression in transgenic arabidopsis and tobacco

NASA Technical Reports Server (NTRS)

Kim, M. K.; Choi, J-W; Jeon, J-H; Franceschi, V. R.; Davin, L. B.; Lewis, N. G.

2002-01-01

A simple counter-staining procedure has been developed for comparative beta-glucuronidase (GUS) expression and anatomical localization in transgenic herbaceous arabidopsis and tobacco. This protocol provides good anatomical visualization for monitoring chimeric gene expression at both the organ and tissue levels. It can be used with different histochemical stains and can be extended to the study of woody species. The specimens are paraffin-embedded, the block is trimmed to reveal internal structure, safranin-O staining solution is briefly applied to the surface of the block, then washed off and, after drying, a drop of immersion oil is placed on the stained surface for subsequent photographic work. This gives tissue counter-staining with good structural preservation without loss of GUS staining product; moreover, sample observation is rapid and efficient compared to existing procedures.

Standoff Acoustic Shear Wave Imaging Using LFM Chirps

DTIC Science & Technology

2011-03-21

is typically ignored due to the large wavelengths in biological tissue. For the test material presented in this paper ( expanded polystyrene foam...inhomogeneous sound speed, 1( )c x , for a 2.5×5×7 cm steel parallelepiped embedded in a 15×23×23 cm block of expanded polystyrene foam, which

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction.

PubMed

Patel, Palak G; Selvarajah, Shamini; Boursalie, Suzanne; How, Nathan E; Ejdelman, Joshua; Guerard, Karl-Philippe; Bartlett, John M; Lapointe, Jacques; Park, Paul C; Okello, John B A; Berman, David M

2016-08-21

Formalin-fixed paraffin embedded tissue (FFPET) represents a valuable, well-annotated substrate for molecular investigations. The utility of FFPET in molecular analysis is complicated both by heterogeneous tissue composition and low yields when extracting nucleic acids. A literature search revealed a paucity of protocols addressing these issues, and none that showed a validated method for simultaneous extraction of RNA and DNA from regions of interest in FFPET. This method addresses both issues. Tissue specificity was achieved by mapping cancer areas of interest on microscope slides and transferring annotations onto FFPET blocks. Tissue cores were harvested from areas of interest using 0.6 mm microarray punches. Nucleic acid extraction was performed using a commercial FFPET extraction system, with modifications to homogenization, deparaffinization, and Proteinase K digestion steps to improve tissue digestion and increase nucleic acid yields. The modified protocol yields sufficient quantity and quality of nucleic acids for use in a number of downstream analyses, including a multi-analyte gene expression platform, as well as reverse transcriptase coupled real time PCR analysis of mRNA expression, and methylation-specific PCR (MSP) analysis of DNA methylation.

Cold-Temperature Plastic Resin Embedding of Liver for DNA- and RNA-Based Genotyping

PubMed Central

Finkelstein, Sydney D.; Dhir, Rajiv; Rabinovitz, Mordechai; Bischeglia, Michelle; Swalsky, Patricia A.; DeFlavia, Petrina; Woods, Jeffrey; Bakker, Anke; Becich, Michael

1999-01-01

The standard practice of tissue fixation in 10% formalin followed by embedding in paraffin wax preserves cellular morphology at the expense of availability and quality of DNA and RNA. The negative effect on cellular constituents results from a combination of extensive cross-linking and strand scission of DNA, RNA, and proteins induced by formaldehyde as well as RNA loss secondary to ubiquitous RNase activity and negative effects of high temperature exposure during paraffin melting, microscopic section collection, and tissue adherence to glass slides. An effective strategy to correlate cellular phenotype with molecular genotype involves microdissection of tissue sections based on specific histopathological features followed by genotyping of minute representative samples for specific underlying molecular alterations. Currently, this approach is limited to short-length polymerase chain reaction amplification (<250 bp) of DNA, due to the negative effects of standard tissue fixation and processing. To overcome this obstacle and permit both cellular morphology and nucleic acid content to be preserved to the fullest extent, we instituted a system of cold-temperature plastic resin embedding based on the use of the water-miscible methyl methacrylate polymer known as Immunobed (Polysciences, Warminster, PA). The system is simple, easy to adapt to clinical practice, and cost-effective. Immunobed tissue sections demonstrate a cellular appearance equivalent or even superior to that of standard tissue sections. Moreover, thin sectioning (0.5–1.0 μm thickness) renders ultrastructural evaluation feasible on plastic-embedded blocks. Tissue microdissection is readily performed, yielding high levels of long DNA and RNA for genomic and transcription-based correlative molecular analysis. We recommend the use of Immunobed or similar products for use in molecular anatomical pathology. PMID:11272904

Comparison of Two Methods of RNA Extraction from Formalin-Fixed Paraffin-Embedded Tissue Specimens

PubMed Central

Gouveia, Gisele Rodrigues; Ferreira, Suzete Cleusa; Ferreira, Jerenice Esdras; Siqueira, Sheila Aparecida Coelho; Pereira, Juliana

2014-01-01

The present study aimed to compare two different methods of extracting RNA from formalin-fixed paraffin-embedded (FFPE) specimens of diffuse large B-cell lymphoma (DLBCL). We further aimed to identify possible influences of variables—such as tissue size, duration of paraffin block storage, fixative type, primers used for cDNA synthesis, and endogenous genes tested—on the success of amplification from the samples. Both tested protocols used the same commercial kit for RNA extraction (the RecoverAll Total Nucleic Acid Isolation Optimized for FFPE Samples from Ambion). However, the second protocol included an additional step of washing with saline buffer just after sample rehydration. Following each protocol, we compared the RNA amount and purity and the amplification success as evaluated by standard PCR and real-time PCR. The results revealed that the extra washing step added to the RNA extraction process resulted in significantly improved RNA quantity and quality and improved success of amplification from paraffin-embedded specimens. PMID:25105117

Pathological α-synuclein in gastrointestinal tissues from prodromal Parkinson disease patients.

PubMed

Stokholm, Morten Gersel; Danielsen, Erik Hvid; Hamilton-Dutoit, Stephen Jacques; Borghammer, Per

2016-06-01

It has been hypothesized that Lewy pathology initiates in the enteric nervous system years prior to debut of clinical motor symptoms in Parkinson disease patients. This study investigates whether Lewy pathology is present in various gastrointestinal tract tissues from Parkinson disease patients in the prodromal phase. We used the Danish National Pathology Registry to identify archived paraffin-embedded tissue blocks from 57 Parkinson disease patients (98 blocks) and 90 control subjects (98 blocks). We employed 2 different immunohistochemistry techniques visualizing aggregated α-synuclein and phosphorylated α-synuclein. Thirty-nine Parkinson disease patients contributed tissues obtained in the prodromal disease phase, whereas 18 Parkinson disease patients contributed tissues obtained solely after Parkinson diagnosis. Prodromal tissues were obtained on average 7.0 years prior to diagnosis (range = 20 years to 4 months), and postdiagnosis tissue on average 2.8 years after diagnosis (range = 2 days to 18 years). Phosphorylated α-synuclein positivity was seen in 22 of 39 (56%) prodromal Parkinson disease subjects and 30 of 67 (45%) prodromal tissue blocks. These fractions were significantly higher compared to control subjects (p = 0.0001 and p = 0.0032, respectively). In contrast, no significant difference was seen in the positivity rate between prodromal Parkinson disease patients and controls when using the aggregated α-synuclein immunohistochemistry technique. We detected Lewy pathology in the gastrointestinal tract of patients up to 20 years prior to their Parkinson disease diagnosis. These findings are in accordance with a hypothesized prodromal disease phase spanning 10 to 20 years. Ann Neurol 2016;79:940-949. © 2016 American Neurological Association.

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

PubMed

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.

Determination of the methylation status of MGMT in different regions within glioblastoma multiforme.

PubMed

Hamilton, Mark G; Roldán, Gloria; Magliocco, Anthony; McIntyre, John B; Parney, Ian; Easaw, Jacob C

2011-04-01

Epigenetic silencing of the MGMT gene through promoter methylation correlates with improved survival in Glioblastoma Multiforme (GBM) patients receiving concurrent chemoradiotherapy. Although the clinical benefit is primarily seen in patients with methylated MGMT promoter, some unmethylated patients also respond to Temozolomide. One possible explanation may be intratumoral heterogeneity. This study was designed to assess the methylation status of the MGMT promoter in different areas of GBM and determine if methylation status varied depending on the fixation technique (paraffin-embedding versus fresh frozen) used to store tissue. Using intraoperative navigation, biopsies were obtained from three distinct regions: the enhancing outer area, the non-enhancing inner core, and an area immediately outside the enhancing region. Only patients with GBM were included for evaluation and analysis. Samples taken from each area were divided with half stored by flash freezing and the other half stored using paraffin fixation. Methylation Specific-PCR (MS-PCR) was used for analysis of MGMT promoter methylation. Thirteen patients were included. Ten were male with a median age of 62 years. In each patient, samples were taken from the enhancing rim and the necrotic centre. However, it was not considered safe or feasible to obtain samples from the area immediately adjacent to the enhancing tumor rim in one case. All patients were homogeneous for methylation status throughout their tumor and tissue taken adjacent to it when frozen tissue was used. However, four patients had discrepancies in the MGMT promoter status between the frozen and paraffin-embedded blocks and one patient was not homogeneous within the tumor when paraffin-embedded tissue was used. MGMT promoter methylation status was homogeneous in all GBM tumors. Our observation that methylation status varied depending if the DNA was extracted from paraffin-embedded versus frozen tissue is concerning. Although the reason for this is unclear, we postulate that the timing from resection to fixation or the process of fixation itself may potentially alter methylation status in paraffin-embedded tumors.

Structurally Caused Freezing Point Depression of Biological Tissues

PubMed Central

Bloch, Rene; Walters, D. H.; Kuhn, Werner

1963-01-01

When investigating the freezing behaviour (by thermal analysis) of the glycerol-extracted adductor muscle of Mytilus edulis it was observed that the temperature of ice formation in the muscular tissue was up to 1.5°C lower than the freezing point of the embedding liquid, a 0.25 N KCl solution with pH = 4.9 with which the tissue had been equilibrated prior to the freezing experiment. A smaller freezing point depression was observed if the pH values of the embedding 0.25 N KCl solution were above or below pH = 4.9. Reasoning from results obtained previously in analogous experiments with artificial gels, the anomalous freezing depression is explained by the impossibility of growing at the normal freezing temperature regular macroscopic crystals inside the gel, due to the presence of the gel network. The freezing temperature is here determined by the size of the microprisms penetrating the meshes of the network at the lowered freezing temperature. This process leads finally to an ice block of more or less regular structure in which the filaments are embedded. Prerequisite for this hindrance of ideal ice growth is a sufficient tensile strength of the filamental network. The existence of structurally caused freezing point depression in biological tissue is likely to invalidate many conclusions reported in the literature, in which hypertonicity was deduced from cryoscopic data. PMID:13971682

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

PubMed

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.

Determination of ABO genotypes with DNA extracted from formalin-fixed, paraffin-embedded tissues.

PubMed

Yamada, M; Yamamoto, Y; Tanegashima, A; Kane, M; Ikehara, Y; Fukunaga, T; Nishi, K

1994-01-01

The gene encoding the specific glycosyltransferases which catalyze the conversion of the H antigen to A or B antigens shows a slight but distinct variation in its allelic nucleotide sequence and can be divided into 6 genotypes when digested with specific restriction enzymes. We extracted DNA from formalin-fixed, paraffin-embedded tissues using SDS/proteinase K treatment followed by phenol/chloroform extraction. The sequence of nucleotides for the A, B and O genes was amplified by the polymerase chain reaction (PCR). DNA fragments of 128 bp and 200 bp could be amplified in the second round of PCR, using an aliquot of the first round PCR product as template. Degraded DNA from paraffin blocks stored for up to 10.7 years could be successfully typed. The ABO genotype was deduced from the digestion patterns with an appropriate combination of restriction enzymes and was compatible with the phenotype obtained from the blood sample.

One-Step Preservation of Phosphoproteins and Tissue Morphology at Room Temperature for Diagnostic and Research Specimens

PubMed Central

Mueller, Claudius; Edmiston, Kirsten H.; Carpenter, Calvin; Gaffney, Eoin; Ryan, Ciara; Ward, Ronan; White, Susan; Memeo, Lorenzo; Colarossi, Cristina; Petricoin, Emanuel F.; Liotta, Lance A.; Espina, Virginia

2011-01-01

Background There is an urgent need to measure phosphorylated cell signaling proteins in cancer tissue for the individualization of molecular targeted kinase inhibitor therapy. However, phosphoproteins fluctuate rapidly following tissue procurement. Snap-freezing preserves phosphoproteins, but is unavailable in most clinics and compromises diagnostic morphology. Formalin fixation preserves tissue histomorphology, but penetrates tissue slowly, and is unsuitable for stabilizing phosphoproteins. We originated and evaluated a novel one-step biomarker and histology preservative (BHP) chemistry that stabilizes signaling protein phosphorylation and retains formalin-like tissue histomorphology with equivalent immunohistochemistry in a single paraffin block. Results Total protein yield extracted from BHP-fixed, routine paraffin-embedded mouse liver was 100% compared to snap-frozen tissue. The abundance of 14 phosphorylated proteins was found to be stable over extended fixation times in BHP fixed paraffin embedded human colon mucosa. Compared to matched snap-frozen tissue, 8 phosphoproteins were equally preserved in mouse liver, while AMPKβ1 Ser108 was slightly elevated after BHP fixation. More than 25 tissues from mouse, cat and human specimens were evaluated for preservation of histomorphology. Selected tissues were evaluated in a multi-site, independent pathology review. Tissue fixed with BHP showed equivalent preservation of cytoplasmic and membrane cytomorphology, with significantly better nuclear chromatin preservation by BHP compared to formalin. Immunohistochemical staining of 13 non-phosphorylated proteins, including estrogen receptor alpha, progesterone receptor, Ki-67 and Her2, was equal to or stronger in BHP compared to formalin. BHP demonstrated significantly improved immunohistochemical detection of phosphorylated proteins ERK Thr202/Tyr204, GSK3-α/β Ser21/Ser9, p38-MAPK Thr180/Tyr182, eIF4G Ser1108 and Acetyl-CoA Carboxylase Ser79. Conclusion In a single paraffin block BHP preserved the phosphorylation state of several signaling proteins at a level comparable to snap-freezing, while maintaining the full diagnostic immunohistochemical and histomorphologic detail of formalin fixation. This new tissue fixative has the potential to greatly facilitate personalized medicine, biobanking, and phospho-proteomic research. PMID:21858221

ultraLM and miniLM: Locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy.

PubMed

Brama, Elisabeth; Peddie, Christopher J; Wilkes, Gary; Gu, Yan; Collinson, Lucy M; Jones, Martin L

2016-12-13

In-resin fluorescence (IRF) protocols preserve fluorescent proteins in resin-embedded cells and tissues for correlative light and electron microscopy, aiding interpretation of macromolecular function within the complex cellular landscape. Dual-contrast IRF samples can be imaged in separate fluorescence and electron microscopes, or in dual-modality integrated microscopes for high resolution correlation of fluorophore to organelle. IRF samples also offer a unique opportunity to automate correlative imaging workflows. Here we present two new locator tools for finding and following fluorescent cells in IRF blocks, enabling future automation of correlative imaging. The ultraLM is a fluorescence microscope that integrates with an ultramicrotome, which enables 'smart collection' of ultrathin sections containing fluorescent cells or tissues for subsequent transmission electron microscopy or array tomography. The miniLM is a fluorescence microscope that integrates with serial block face scanning electron microscopes, which enables 'smart tracking' of fluorescent structures during automated serial electron image acquisition from large cell and tissue volumes.

Multimodal Hierarchical Imaging of Serial Sections for Finding Specific Cellular Targets within Large Volumes

PubMed Central

Wacker, Irene U.; Veith, Lisa; Spomer, Waldemar; Hofmann, Andreas; Thaler, Marlene; Hillmer, Stefan; Gengenbach, Ulrich; Schröder, Rasmus R.

2018-01-01

Targeting specific cells at ultrastructural resolution within a mixed cell population or a tissue can be achieved by hierarchical imaging using a combination of light and electron microscopy. Samples embedded in resin are sectioned into arrays consisting of ribbons of hundreds of ultrathin sections and deposited on pieces of silicon wafer or conductively coated coverslips. Arrays are imaged at low resolution using a digital consumer like smartphone camera or light microscope (LM) for a rapid large area overview, or a wide field fluorescence microscope (fluorescence light microscopy (FLM)) after labeling with fluorophores. After post-staining with heavy metals, arrays are imaged in a scanning electron microscope (SEM). Selection of targets is possible from 3D reconstructions generated by FLM or from 3D reconstructions made from the SEM image stacks at intermediate resolution if no fluorescent markers are available. For ultrastructural analysis, selected targets are finally recorded in the SEM at high-resolution (a few nanometer image pixels). A ribbon-handling tool that can be retrofitted to any ultramicrotome is demonstrated. It helps with array production and substrate removal from the sectioning knife boat. A software platform that allows automated imaging of arrays in the SEM is discussed. Compared to other methods generating large volume EM data, such as serial block-face SEM (SBF-SEM) or focused ion beam SEM (FIB-SEM), this approach has two major advantages: (1) The resin-embedded sample is conserved, albeit in a sliced-up version. It can be stained in different ways and imaged with different resolutions. (2) As the sections can be post-stained, it is not necessary to use samples strongly block-stained with heavy metals to introduce contrast for SEM imaging or render the tissue blocks conductive. This makes the method applicable to a wide variety of materials and biological questions. Particularly prefixed materials e.g., from biopsy banks and pathology labs, can directly be embedded and reconstructed in 3D. PMID:29630046

Effect of using different cover image quality to obtain robust selective embedding in steganography

NASA Astrophysics Data System (ADS)

Abdullah, Karwan Asaad; Al-Jawad, Naseer; Abdulla, Alan Anwer

2014-05-01

One of the common types of steganography is to conceal an image as a secret message in another image which normally called a cover image; the resulting image is called a stego image. The aim of this paper is to investigate the effect of using different cover image quality, and also analyse the use of different bit-plane in term of robustness against well-known active attacks such as gamma, statistical filters, and linear spatial filters. The secret messages are embedded in higher bit-plane, i.e. in other than Least Significant Bit (LSB), in order to resist active attacks. The embedding process is performed in three major steps: First, the embedding algorithm is selectively identifying useful areas (blocks) for embedding based on its lighting condition. Second, is to nominate the most useful blocks for embedding based on their entropy and average. Third, is to select the right bit-plane for embedding. This kind of block selection made the embedding process scatters the secret message(s) randomly around the cover image. Different tests have been performed for selecting a proper block size and this is related to the nature of the used cover image. Our proposed method suggests a suitable embedding bit-plane as well as the right blocks for the embedding. Experimental results demonstrate that different image quality used for the cover images will have an effect when the stego image is attacked by different active attacks. Although the secret messages are embedded in higher bit-plane, but they cannot be recognised visually within the stegos image.

An artificial test substrate for evaluating electron microscopic immunocytochemical labeling reactions.

PubMed

Gagne, G D; Miller, M F

1987-08-01

We describe an artificial substrate system for optimization of labeling parameters in electron microscope immunocytochemical studies. The system involves use of blocks of glutaraldehyde-polymerized BSA into which a desired antigen is incorporated by a simple soaking procedure. The resulting antigen-impregnated artificial substrate can then be fixed and embedded identically to a piece of tissue. The BSA substrate can also be dried and then sectioned for immunolabeling with or without chemical fixation and without exposing the antigen to dehydrating agents and embedding resins. The effects of various fixation and embedding procedures can thus be evaluated separately. Other parameters affecting immunocytochemical labeling, such as antibody and conjugate concentration, can also be evaluated. We used this system, along with immunogold labeling, to determine quantitatively the optimal fixation and embedding conditions for labeling of hepatitis B surface antigen (HbsAg), human IgG, and horseradish peroxidase. Using unfixed and unembedded HBsAg, we were able to detect antigen concentrations below 20 micrograms/ml. We have shown that it is not possible to label HBsAg within resin-embedded cells using conventional aldehyde fixation protocols and polyclonal antibodies.

Let Archived Paraffin Blocks Be Utilized for Research with Waiver of Informed Consent.

PubMed

Kim, Yong-Jin; Park, Jeong Sik; Ko, Karam; Jeong, Chang Rok

2018-05-01

Advances in biomedical and genetic research have contributed to more effective public health improvement via bench-to-bed research and the emergence of personalized medicine. This has certainly showcased the importance of archived human tissues, especially paraffin-embedded blocks in pathology. Currently in Korea, undue legislative regulations of the Bioethics and Safety Act suspend and at times discourage studies from taking place. In this paper, the authors underline the value of paraffin blocks in the era of personalized and translational medicine. We discuss detailed clauses regarding the applicability of paraffin blocks from a legal perspective and compare Korea's regulations with those of other countries. The necessity for allowing waived consent and Institutional Review Board (IRB) approval will be argued throughout. The authors suggest that researchers declare the following to obtain IRB approval and waiver of informed consents: research could not be practically carried out without a waiver of consent; the proposed research presents no more than minimal risk of harm to subjects, and the waiver of consent will not adversely affect the rights and welfare of subjects; and research will not utilize a tissue block if only 1 is available for each subject, to allow future clinical use such as re-evaluation or further studies.

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

PubMed

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.

Quality Control of RNA Preservation and Extraction from Paraffin-Embedded Tissue: Implications for RT-PCR and Microarray Analysis

PubMed Central

Pichler, Martin; Zatloukal, Kurt

2013-01-01

Analysis of RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathological diagnostics. We have performed a comprehensive and systematic investigation of the impact of factors in the pre-analytical workflow, such as different fixatives, fixation time, RNA extraction method and storage of tissues in paraffin blocks, on several downstream reactions including complementary DNA (cDNA) synthesis, quantitative reverse transcription polymerase chain reaction (qRT-PCR) and microarray hybridization. We compared the effects of routine formalin fixation with the non-crosslinking, alcohol-based Tissue Tek Xpress Molecular Fixative (TTXMF, Sakura Finetek), and cryopreservation as gold standard for molecular analyses. Formalin fixation introduced major changes into microarray gene expression data and led to marked gene-to-gene variations in delta-ct values of qRT-PCR. We found that qRT-PCR efficiency and gene-to-gene variations were mainly attributed to differences in the efficiency of cDNA synthesis as the most sensitive step. These differences could not be reliably detected by quality assessment of total RNA isolated from formalin-fixed tissues by electrophoresis or spectrophotometry. Although RNA from TTXMF fixed samples was as fragmented as RNA from formalin fixed samples, much higher cDNA yield and lower ct-values were obtained in qRT-PCR underlining the negative impact of crosslinking by formalin. In order to better estimate the impact of pre-analytical procedures such as fixation on the reliability of downstream analysis, we applied a qRT-PCR-based assay using amplicons of different length and an assay measuring the efficiency of cDNA generation. Together these two assays allowed better quality assessment of RNA extracted from fixed and paraffin-embedded tissues and should be used to supplement quality scores derived from automated electrophoresis. A better standardization of the pre-analytical workflow, application of additional quality controls and detailed sample information would markedly improve the comparability and reliability of molecular studies based on formalin-fixed and paraffin-embedded tissue samples. PMID:23936242

A simple method for the construction of small format tissue arrays

PubMed Central

Hidalgo, A; Piña, P; Guerrero, G; Lazos, M; Salcedo, M

2003-01-01

Tissue arrays can evaluate molecular targets in high numbers of samples in parallel. Array construction presents technical difficulties and tissue arrayers are expensive, particularly for small and medium sized laboratories. This report describes a method for the construction of 36 sample arrays using widely available materials. A blunted 16 gauge needle for bone marrow aspiration was used to extract paraffin wax cylinders and manually define a 6 × 6 matrix on a blank paraffin wax block. Tissue cores from 36 paraffin wax embedded premalignant lesions and invasive cervical carcinomas were injected into the matrix using a 14 gauge needle. This tissue array was sectioned using a standard microtome and used for the immunodetection of CD44 variant 9 and interleukin 18 with satisfactory results. This method can be applied in any laboratory, without the need of specialised equipment, offering a good alternative for the wider application of tissue arrays. PMID:12560397

Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks

PubMed Central

Simmons, Alan J.; Scurrah, Cherie’ R.; McKinley, Eliot T.; Herring, Charles A.; Irish, Jonathan M.; Washington, Mary K.; Coffey, Robert J.; Lau, Ken S.

2016-01-01

Cellular heterogeneity poses a significant challenge to understanding tissue level phenotypes and confounds conventional bulk analyses. To facilitate the analysis of signaling at the single-cell level in human tissues, we applied mass cytometry using CyTOF (Cytometry Time-of-Flight) to formalin-fixed paraffin-embedded (FFPE) normal and diseased intestinal specimens. We developed and validated a technique called FFPE-DISSECT (Disaggregation for Intracellular Signaling in Single Epithelial Cells from Tissue), a single-cell approach for characterizing native signaling states from embedded solid tissue samples. We applied FFPE-DISSECT coupled to mass cytometry and found differential signaling by tumor necrosis factor α (TNF-α) in intestinal enterocytes, goblet cells and enteroendocrine cells, implicating the role of the downstream RAS-RAF-MEK-ERK signaling pathway in dictating goblet cell identity. In addition, application of FFPE-DISSECT, mass cytometry, and data-driven computational analyses to human colon specimens confirmed reduced differentiation in colorectal cancer (CRC) compared to normal colon, and revealed quantitative increases in inter- and intra-tissue heterogeneity in CRC with regards to the modular regulation of signaling pathways. Specifically, modular co-regulation of the kinases P38 and ERK, the translation regulator 4EBP1, and the transcription factor CREB in the proliferative compartment of the normal colon was loss in CRC, as evidenced by their impaired coordination over samplings of single cells in tissue. Our data suggest that this single-cell approach, applied in conjunction with genomic annotation, such as microsatellite instability and mutations in KRAS and BRAF, allows rapid and detailed characterization of cellular heterogeneity from clinical repositories of embedded human tissues. FFPE-DISSECT coupled of mass cytometry can be used for deriving cellular landscapes from archived patient samples, beyond CRC, and as a high resolution tool for disease characterization and subtyping. PMID:27729552

Effect of Cell-seeded Hydroxyapatite Scaffolds on Rabbit Radius Bone Regeneration

DTIC Science & Technology

2013-06-22

OK) for 14 d via a tissue processer (Leica TP1020 system; Bannockburn, IL). Samples were then embedded in photocuring resin (Technovit 7200 VLC ...Kulzer, Germany) and polymerized under blue light for 24 h. Block samples were adhered to a parallel plexiglass slide using the Exakt 7210 VLC system...induction, choice of evaluation time point, and use of a nonhealing defect. For example, a more challenging radial defect (1.5 cm) in rabbits and the

Automatic segementation of histological structures in normal and neoplastic mammary gland tissue sections

NASA Astrophysics Data System (ADS)

Fernandez-Gonzalez, Rodrigo; Deschamps, Thomas; Idica, Adam; Malladi, Ravikanth; Ortiz de Solorzano, Carlos

2003-07-01

In this paper we present a scheme for real time segmentation of histological structures in microscopic images of normal and neoplastic mammary gland sections. Paraffin embedded or frozen tissue blocks are sliced, and sections are stained with hematoxylin and eosin (H&E). The sections are then imaged using conventional bright field microscopy. The background of the images is corrected by arithmetic manipulation using a "phantom." Then we use the fast marching method with a speed function that depends on the brightness gradient of the image to obtain a preliminary approximation to the boundaries of the structures of interest within a region of interest (ROI) of the entire section manually selected by the user. We use the result of the fast marching method as the initial condition for the level set motion equation. We run this last method for a few steps and obtain the final result of the segmentation. These results can be connected from section to section to build a three-dimensional reconstruction of the entire tissue block that we are studying.

A new technique for the rapid screening and selection of large pieces of tissue for ultrastructural evaluation.

PubMed

Dalley, B K; Seliger, W G

1980-05-01

A simple and rapid technique is described for the screening of Epon embedded organ slices for the location, isolation, and removal of small specific sites for ultrastructural study with the transmission electron microscope. This procedure consists of perfusion fixation followed by making 1 to 21/2 mm thick slices of relatively large pieces of the organs, control of the degree and evenness of the osmium staining by addition of 3% sodium iodate, and infiltration with a fluorescent dye prior to embedment in Epon. Tissue slices are embedded in wafer-shaped blocks, generally with several slices in one "wafer", and are examined in a controlled manner using a rapid form of serial surface polishing. Each level of the polished wafer is examined using an epi-illuminated fluorescence microscope, and selected sites are chosen at each level for ultrastructural study. Methods are also described for marking each selected site using a conventional slide marker, and for the removal of the selected site in the form of a small disc of Epon, after which the Epon wafer can be further serially polished and the examination continued. Areas to be thin-sectioned are removed using a core drill mounted on a model-maker's drill press. The technique is simple, does not require the destruction of remaining tissues to evaluate more critically a single small site, allows for the easy maintenance of tissue orientation, and the most time-consuming portions of the technique can be quickly taught to a person with no previous histological training.

Optimization of a Histopathological Biomarker for Sphingomyelin Accumulation in Acid Sphingomyelinase Deficiency

PubMed Central

Johnson, Jennifer; Maloney, Colleen L.; Yandl, Emily; Griffiths, Denise; Thurberg, Beth L.; Ryan, Susan

2012-01-01

Niemann-Pick disease (types A and B), or acid sphingomyelinase deficiency, is an inherited deficiency of acid sphingomyelinase, resulting in intralysosomal accumulation of sphingomyelin in cells throughout the body, particularly within those of the reticuloendothelial system. These cellular changes result in hepatosplenomegaly and pulmonary infiltrates in humans. A knockout mouse model mimics many elements of human ASMD and is useful for studying disease histopathology. However, traditional formalin-fixation and paraffin embedding of ASMD tissues dissolves sphingomyelin, resulting in tissues with a foamy cell appearance, making quantitative analysis of the substrate difficult. To optimize substrate fixation and staining, a modified osmium tetroxide and potassium dichromate postfixation method was developed to preserve sphingomyelin in epon-araldite embedded tissue and pulmonary cytology specimens. After processing, semi-thin sections were incubated with tannic acid solution followed by staining with toluidine blue/borax. This modified method provides excellent preservation and staining contrast of sphingomyelin with other cell structures. The resulting high-resolution light microscopy sections permit digital quantification of sphingomyelin in light microscopic fields. A lysenin affinity stain for sphingomyelin was also developed for use on these semi-thin epon sections. Finally, ultrathin serial sections can be cut from these same tissue blocks and stained for ultrastructural examination by electron microscopy. PMID:22614361

Topochemistry of trace metals in nasal mucosa. Potentialities of some histochemical methods and energy dispersive X-ray microanalysis.

PubMed

Torjussen, W; Haug, F M; Olsen, A; Andersen, I

1978-01-01

Histochemical methods and energy dispersive X-ray micro-analysis (EDX-analysis) were evaluated in model experiments and on tissue sections for their usefulness in detecting traces of metals in biological tissue. The goal for this study was to establish a method for localization of nickel deposits in the nasal mucosa, where it has been found in concentrations between 1 and 40 microgram/g in nickel exposed individuals. The histochemical methods tested were staining with dimethylglyoxime, rubeanic acid and dithizone, the Turnbull and Prussian blue methods and TIMM'S sulphide silver procedure. In model experiments nickel-, cobalt-, copper-, zinc- and ironsalts were applied to thin-layer chromatography sheets (TLC-sheets) and stained by the histochemical methods. Spots containing 500 and 50 ng of these metals represented the smallest amounts that could consistently be detected in these experiments, except for the sulphide silver method which seemed a little more sensitive. With the latter method, moreover, zinc was detected in 40 micrometer thick cryostat sections of gelatine made up with 1 microgram/g of the metal. For nickel the corresponding figure was 10 to 50 microgram/g. On specimens of nasal mucosa from nickel-exposed workers, a faint colour was obtained in 40 micron thick cryostat sections from specimens that had been immersed in dithizone, but the colour was too weak for histological analysis. None of the other coloured chelating agents caused noticeable staining when applied to blocks or to cryostat sections. TIMM'S sulphide silver method caused strong staining of the basal layers of the surface epithelium and of fibroblast-like cells in the underlying connective tissue. This staining pattern is described in more detail in a separate report. Rat liver tissue was analyzed by atomic absorption before and after araldite embedding. Blocks of gelatine made up with nickel, copper, zinc and iron were embedded in epoxy resin and analyzed by atomic absorption. Large changes in the metal concentrations, usually an increase, were found after embedding. Ultrathin sections from this material were used to test the sensitivity of the EDX-equipment. Referring to the concentrations determined by atomic absorption in the embedded material, iron was detected at 1215 microgram/g and 362 microgram/g (gelatine standards) but not at 167 microgram/g (rat liver). Similar values could not be determined for nickel, copper or zinc, because of background radiation resulting from the presence of these metals in the instrument. We did not succeed in establishing a procedure for detecting nickel deposits in nasal mucosa with any of the methods which were tested. The most sensitive but least specific of the tested methods for visualizing heavy metals in the nasal mucosa, was TIMM'S sulphide silver procedure. The preparation of tissue for this method is discussed.

Analysis of p53 gene mutations in human gliomas by polymerase chain reaction-based single-strand conformation polymorphism and DNA sequencing.

PubMed

Sarkar, F H; Kupsky, W J; Li, Y W; Sreepathi, P

1994-03-01

Mutations in the p53 gene have been recognized in brain tumors, and clonal expansion of p53 mutant cells has been shown to be associated with glioma progression. However, studies on the p53 gene have been limited by the need for frozen tissues. We have developed a method utilizing polymerase chain reaction (PCR) for the direct analysis of p53 mutation by single-strand conformation polymorphism (SSCP) and by direct DNA sequencing of the p53 gene using a single 10-microns paraffin-embedded tissue section. We applied this method to screen for p53 gene mutations in exons 5-8 in human gliomas utilizing paraffin-embedded tissues. Twenty paraffin blocks containing tumor were selected from surgical specimens from 17 different adult patients. Tumors included six anaplastic astrocytomas (AAs), nine glioblastomas (GBs), and two mixed malignant gliomas (MMGs). The tissue section on the stained glass slide was used to guide microdissection of an unstained adjacent tissue section to ensure > 90% of the tumor cell population for p53 mutational analysis. Simultaneously, microdissection of the tissue was also carried out to obtain normal tissue from adjacent areas as a control. Mutations in the p53 gene were identified in 3 of 17 (18%) patients by PCR-SSCP analysis and subsequently confirmed by PCR-based DNA sequencing. Mutations in exon 5 resulting in amino acid substitution were found in one thalamic AA (codon 158, CGC > CTT: Arg > Leu) and one cerebral hemispheric GB (codon 151, CCG > CTG: Pro > Leu).(ABSTRACT TRUNCATED AT 250 WORDS)

in Paraffin- Embedded Laryngeal Carcinoma Tissue

PubMed

Hosseini, Seyed Zinab; Makvandi, Manoochehr; Samarbafzade, Alireza; Timori, Ali; Ranjbar, Nastaran; Saki, Nader; Nisi, Nilofar; Shahani, Toran; Varnaseri, Mehran; Angali Ahmadi, Kambiz

2017-04-01

Background and Objective: Human papilloma virus (HPV) 16 and HPV18 have been detected in head and neck squamous cell carcinomas (HNSCC) and there is evidence that detection of HPVs would have better prognostic value than patients with HNSCC negative for HPVs. Thus, this study was conducted to evaluate frequency of HPV 16 and HPV 18 genotypes in patients with laryngeal carcinoma. Materials and methods: Fifty formalin-fixed, paraffin-embedded (FFPE) tissue blocks of laryngeal cancers were collected. Sections were prepared at 5 μm and DNA was extracted from each sample and subjected to the polymerase chain reaction (PCR) to detect HPV-16/18 DNA s. Results: All samples were squamous cell carcinomas (SCCs). Overall 14/50 (28%) were positive for HPVs, 8 (18%) with HPV-16 and 6 (12%) with HPV-18. Additionally, 2 (4%) mixed infections of HPV 16 and 18 genotypes were observed among these cases. Conclusions: Overall, 28% of HNSCC samples proved positive for HPV16 and HPV18 genotypes, two high-risk HPV types. It is important to further assess whether such viral infection, could be a risk factor in HNSCC progression. Creative Commons Attribution License

Development and validation of a protocol for optimizing the use of paraffin blocks in molecular epidemiological studies: The example from the HPV-AHEAD study.

PubMed

Mena, Marisa; Lloveras, Belen; Tous, Sara; Bogers, Johannes; Maffini, Fausto; Gangane, Nitin; Kumar, Rekha Vijay; Somanathan, Thara; Lucas, Eric; Anantharaman, Devasena; Gheit, Tarik; Castellsagué, Xavier; Pawlita, Michael; de Sanjosé, Silvia; Alemany, Laia; Tommasino, Massimo

2017-01-01

Worldwide use of formalin-fixed paraffin-embedded blocks (FFPE) is extensive in diagnosis and research. Yet, there is a lack of optimized/standardized protocols to process the blocks and verify the quality and presence of the targeted tissue. In the context of an international study on head and neck cancer (HNC)-HPV-AHEAD, a standardized protocol for optimizing the use of FFPEs in molecular epidemiology was developed and validated. First, a protocol for sectioning the FFPE was developed to prevent cross-contamination and distributed between participating centers. Before processing blocks, all sectioning centers underwent a quality control to guarantee a satisfactory training process. The first and last sections of the FFPEs were used for histopathological assessment. A consensus histopathology evaluation form was developed by an international panel of pathologists and evaluated for four indicators in a pilot analysis in order to validate it: 1) presence/type of tumor tissue, 2) identification of other tissue components that could affect the molecular diagnosis and 3) quality of the tissue. No HPV DNA was found in sections from empty FFPE generated in any histology laboratories of HPV-AHEAD consortium and all centers passed quality assurance for processing after quality control. The pilot analysis to validate the histopathology form included 355 HNC cases. The form was filled by six pathologists and each case was randomly assigned to two of them. Most samples (86%) were considered satisfactory. Presence of >50% of invasive carcinoma was observed in all sections of 66% of cases. Substantial necrosis (>50%) was present in <2% of samples. The concordance for the indicators targeted to validate the histopathology form was very high (kappa > 0.85) between first and last sections and fair to high between pathologists (kappa/pabak 0.21-0.72). The protocol allowed to correctly process without signs of contamination all FFPE of the study. The histopathology evaluation of the cases assured the presence of the targeted tissue, identified the presence of other tissues that could disturb the molecular diagnosis and allowed the assessment of tissue quality.

Visualisation of Collagen in fixed skeletal muscle tissue using fluorescently tagged Collagen binding protein CNA35.

PubMed

Mohammadkhah, Melika; Simms, Ciaran K; Murphy, Paula

2017-02-01

Detection and visualisation of Collagen structure are important to understand the relationship between mechanical behaviour and microstructure in skeletal muscle since Collagen is the main structural protein in animal connective tissues, and is primarily responsible for their passive load-bearing properties. In the current study, the direct detection and visualization of Collagen using fluorescently tagged CNA35 binding protein (fused to EGFP or tdTomato) is reported for the first time on fixed skeletal muscle tissue. This Technical Note also establishes a working protocol by examining tissue preparation, dilution factor, exposure time etc. for sensitivity and specificity. Penetration of the binding protein into intact mature skeletal muscle was found to be very limited, but detection works well on tissue sections with higher sensitivity on wax embedded sections compared to frozen sections. CNA35 fused to tdTomato has a higher sensitivity than CNA35 fused to EGFP but both show specific detection. Best results were obtained with 15μm wax embedded sections, with blocking of non-specific binding in 1% BSA and antigen retrieval in Sodium Citrate. There was a play-off between dilution of the binding protein and time of incubation but both CNA35-tdTomato and CNA35-EGFP worked well with approximately 100μg/ml of purified protein with overnight incubation, while CNA35-tdTomato could be utilized at 5 fold less concentration. This approach can be applied to study the relationship between skeletal muscle micro-structure and to observe mechanical response to applied deformation. It can be used more broadly to detect Collagen in a variety of fixed tissues, useful for structure-functions studies, constitutive modelling, tissue engineering and assessment of muscle tissue pathologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Application of RT-PCR in formalin-fixed and paraffin-embedded lung cancer tissues.

PubMed

Zhang, Fan; Wang, Zhuo-min; Liu, Hong-yu; Bai, Yun; Wei, Sen; Li, Ying; Wang, Min; Chen, Jun; Zhou, Qing-hua

2010-01-01

To analyze gene expression in formalin-fixed, paraffin-embedded lung cancer tissues using modified method. Total RNA from frozen tissues was extracted using TRIZOL reagent. RNA was extracted from formalin-fixed, paraffin-embedded tissues by digestion with proteinase K before the acid-phenol:chloroform extraction and carrier precipitation. We modified this method by using a higher concentration of proteinase K and a longer digestion time, optimized to 16 hours. RT-PCR and real-time RT-PCR were used to check reproducibility and the concordance between frozen and paraffin-embedded samples. The results showed that the RNA extracted from the paraffin-embedded lung tissues had high quality with the most fragment length between 28S and 18S bands (about 1000 to 2000 bases). The housekeeping gene GUSB exhibited low variation of expression in frozen and paraffin-embedded lung tissues, whereas PGK1 had the lowest variation in lymphoma tissues. Furthermore, real-time PCR analysis of the expression of known prognostic genes in non-small cell lung carcinoma (NSCLC) demonstrated an extremely high correlation (r>0.880) between the paired frozen and formalin-fixed, paraffin-embedded specimens. This improved method of RNA extraction is suitable for real-time quantitative RT-PCR, and may be used for global gene expression profiling of paraffin-embedded tissues.

Self-recovery reversible image watermarking algorithm

PubMed Central

Sun, He; Gao, Shangbing; Jin, Shenghua

2018-01-01

The integrity of image content is essential, although most watermarking algorithms can achieve image authentication but not automatically repair damaged areas or restore the original image. In this paper, a self-recovery reversible image watermarking algorithm is proposed to recover the tampered areas effectively. First of all, the original image is divided into homogeneous blocks and non-homogeneous blocks through multi-scale decomposition, and the feature information of each block is calculated as the recovery watermark. Then, the original image is divided into 4×4 non-overlapping blocks classified into smooth blocks and texture blocks according to image textures. Finally, the recovery watermark generated by homogeneous blocks and error-correcting codes is embedded into the corresponding smooth block by mapping; watermark information generated by non-homogeneous blocks and error-correcting codes is embedded into the corresponding non-embedded smooth block and the texture block via mapping. The correlation attack is detected by invariant moments when the watermarked image is attacked. To determine whether a sub-block has been tampered with, its feature is calculated and the recovery watermark is extracted from the corresponding block. If the image has been tampered with, it can be recovered. The experimental results show that the proposed algorithm can effectively recover the tampered areas with high accuracy and high quality. The algorithm is characterized by sound visual quality and excellent image restoration. PMID:29920528

Vascularization after treatment of gingival recession defects with platelet-rich fibrin or connective tissue graft.

PubMed

Eren, Gülnihal; Kantarcı, Alpdoğan; Sculean, Anton; Atilla, Gül

2016-11-01

The aim of this study was to evaluate histologically the following treatment of bilateral localized gingival recessions with coronally advanced flap (CAF) combined with platelet-rich fibrin (PRF) or subepithelial connective tissue graft (SCTG). Tissue samples were harvested from 14 subjects either 1 or 6 months after the surgeries. The 2-mm punch biopsies were obtained from the mid-portion of the grafted sites. Neutral buffered formalin fixed, paraffin-embedded 5-μm thick tissue sections were stained with hematoxylin eosin and Masson's trichrome in order to analyze the collagen framework, epithelium thickness and rete-peg length. Multiple sequential sections were cut from paraffin-embedded blocks of tissue and immunohistochemically prepared for detection of vascular endothelial growth factor, CD31 and CD34, for the assessment of vascularization. Rete peg formation was significantly increased in the sites treated with PRF compared to the SCTG group after 6 months (p < 0.05). On the contrary, the number of vessels was increased in the SCTG group compared to the PRF group after 6 months (p < 0.05). No statistically significant differences were observed in the collagen density. Staining intensity of CD31 increased in submucosal area of PRF group than SCTG group after 1 month. Higher staining intensity of CD34 was observed in the submucosal area of PRF group compared with SCTG group after 6 months. The results of the present study suggest that in histological evaluation because of its biological compounds, PRF results earlier vessel formation and tissue maturation compared to connective tissue graft. PRF regulated the vascular response associated with an earlier wound healing.

Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues.

PubMed

Sengüven, Burcu; Baris, Emre; Oygur, Tulin; Berktas, Mehmet

2014-01-01

Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.

An interventional multispectral photoacoustic imaging platform for the guidance of minimally invasive procedures

NASA Astrophysics Data System (ADS)

Xia, Wenfeng; Nikitichev, Daniil I.; Mari, Jean Martial; West, Simeon J.; Ourselin, Sebastien; Beard, Paul C.; Desjardins, Adrien E.

2015-07-01

Precise and efficient guidance of medical devices is of paramount importance for many minimally invasive procedures. These procedures include fetal interventions, tumor biopsies and treatments, central venous catheterisations and peripheral nerve blocks. Ultrasound imaging is commonly used for guidance, but it often provides insufficient contrast with which to identify soft tissue structures such as vessels, tumors, and nerves. In this study, a hybrid interventional imaging system that combines ultrasound imaging and multispectral photoacoustic imaging for guiding minimally invasive procedures was developed and characterized. The system provides both structural information from ultrasound imaging and molecular information from multispectral photoacoustic imaging. It uses a commercial linear-array ultrasound imaging probe as the ultrasound receiver, with a multimode optical fiber embedded in a needle to deliver pulsed excitation light to tissue. Co-registration of ultrasound and photoacoustic images is achieved with the use of the same ultrasound receiver for both modalities. Using tissue ex vivo, the system successfully discriminated deep-located fat tissue from the surrounding muscle tissue. The measured photoacoustic spectrum of the fat tissue had good agreement with the lipid spectrum in literature.

Addition of phosphotungstic acid to ethanol for dehydration improves both the ultrastructure and antigenicity of pituitary tissue embedded in LR White acrylic resin.

PubMed

Sakai, Yuko; Hosaka, Masahiro; Hira, Yoshiki; Watanabe, Tsuyoshi

2005-12-01

Although hydrophilic acrylic resins including LR White have been widely utilized as embedding media for immunocytochemical use, the constituents of tissues are often extracted by the resin monomer during the infiltration process of the embedment, resulting in a discernible impairment of the ultrastructure when the tissue is weakly fixed only with aldehydes. To minimize the extraction by the resin monomer, the embedding procedure with LR White resin was reexamined in the present study. Among the treatments tested, a partial dehydration with 70% ethanol containing 2% phosphotungstic acid (PTA) well preserved the ultrastructure of the pituitary tissue without spoiling the antigenicity of LHbeta and other representative markers for the Golgi apparatus. In addition, treatment with 1% tannic acid (TA) prior to the dehydration described above synergistically improved both the ultrastructure and antigenicity of the tissue so that the orientation of the Golgi apparatus could be determined by double immunogold labeling with commercially available anti-GM130 and anti-TGN38 antibodies. The ultrathin sections from the LR White-embedded tissue treated with TA and dehydrated in 70% ethanol containing 2% PTA also enhanced contrast without conventional heavy-metal staining with uranyl acetate and lead citrate. Our findings further suggest that the precipitation of TA and PTA protected the tissue from being extracted during the embedment, probably because an insoluble complex was transiently formed with the constituents of the tissue. This simple modification of the LR White embedment can extend the application of post-embedding immunocytochemistry as an alternative to pre-embedding immunolabeling with frozen ultrathin sections.

Using IFN-γ antibodies to identify the pathogens of fungal rhinosinusitis: A novel immunohistochemical approach

PubMed Central

Yan, Yuyan; Zhao, Zuotao; Dong, Gehong; Han, Yiding; Yang, Dongmei; Yin, Hongyan; Piao, Yingshi; He, Chunyan; Tian, Cheng; Wan, Hongfei; Li, Xue; Jin, Yulan; Fang, Jugao; Liu, Honggang

2018-01-01

Fungal rhinosinusitis (FRS) is commonly caused by various Aspergillus species (spp) and Mucorales fungi, and the treatment and prognosis of cases differ depending on the causative fungus. The present study describes a novel immunohistochemical method that has high sensitivity and specificity for distinguishing between these two types of fungi in patients with FRS. Three groups were included in the study. Group A included formalin-fixed paraffin-embedded blocks of 51 nasal tissue specimens of patients with FRS (27 Aspergillus spp and 24 Mucorales) that were continuously obtained from the Department of Pathology of Tongren Hospital in Beijing as the experimental group and 34 cultures (26 Aspergillus spp and 8 Mucorales) of FRS that were randomly selected from the bacterial laboratory of Tongren Hospital in Beijing to verify the staining results of the paraffin-embedded blocks. Formalin-fixed paraffin-embedded blocks of 10 esophageal cancer specimens were included in Group B as the positive control group. All specimens in Groups A and B were stained with interferon-γ (IFN-γ) antibody. Group C consisted of the same specimens as described in Group A, however, when performing the immunohistochemical assay, IFN-γ antibody was replaced by PBS and this served as the negative control group. The differences in IFN-γ immunohistochemical staining between Aspergillus spp and Mucorales were analyzed. Staining of IFN-γ in paraffin-embedded samples was positive in 92.6% (25/27) of specimens in which Aspergillus spp were the causative pathogen, which was significantly higher compared with specimens in which Mucorales was causative (P<0.001), with only 4.2% (1/24) of specimens staining positive for IFN-γ. Immunohistochemical staining of cell cultures was 100% positive for Aspergillus spp, whereas all Mucorales were negative. Thus, the results of the current study indicated that IFN-γ antibody immunohistochemical staining may be used as a novel diagnostic tool to distinguish between Aspergillus spp and Mucorales when identifying the causative agent in FRS, providing a useful supplementary test to the current immunohistochemical methods in the clinical diagnosis of FRS. PMID:29286163

The prognostic implication of the expression of EGFR, p53, cyclin D1, Bcl-2 and p16 in primary locally advanced oral squamous cell carcinoma cases: a tissue microarray study.

PubMed

Solomon, Monica Charlotte; Vidyasagar, M S; Fernandes, Donald; Guddattu, Vasudev; Mathew, Mary; Shergill, Ankur Kaur; Carnelio, Sunitha; Chandrashekar, Chetana

2016-12-01

Oral squamous cell carcinomas comprise a heterogeneous tumor cell population with varied molecular characteristics, which makes prognostication of these tumors a complex and challenging issue. Thus, molecular profiling of these tumors is advantageous for an accurate prognostication and treatment planning. This is a retrospective study on a cohort of primary locally advanced oral squamous cell carcinomas (n = 178) of an Indian rural population. The expression of EGFR, p53, cyclin D1, Bcl-2 and p16 in a cohort of primary locally advanced oral squamous cell carcinomas was evaluated. A potential biomarker that can predict the tumor response to treatment was identified. Formalin-fixed paraffin-embedded tumor blocks of (n = 178) of histopathologically diagnosed cases of locally advanced oral squamous cell carcinomas were selected. Tissue microarray blocks were constructed with 2 cores of 2 mm diameter from each tumor block. Four-micron-thick sections were cut from these tissue microarray blocks. These tissue microarray sections were immunohistochemically stained for EGFR, p53, Bcl-2, cyclin D1 and p16. In this cohort, EGFR was the most frequently expressed 150/178 (84%) biomarker of the cases. Kaplan-Meier analysis showed a significant association (p = 0.038) between expression of p53 and a poor prognosis. A Poisson regression analysis showed that tumors that expressed p53 had a two times greater chance of recurrence (unadjusted IRR-95% CI 2.08 (1.03, 4.5), adjusted IRR-2.29 (1.08, 4.8) compared with the tumors that did not express this biomarker. Molecular profiling of oral squamous cell carcinomas will enable us to categorize our patients into more realistic risk groups. With biologically guided tumor characterization, personalized treatment protocols can be designed for individual patients, which will improve the quality of life of these patients.

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.

PubMed

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.

Utility of bronchial lavage fluids for epithelial growth factor receptor mutation assay in lung cancer patients: Comparison between cell pellets, cell blocks and matching tissue specimens

PubMed Central

Asaka, Shiho; Yoshizawa, Akihiko; Nakata, Rie; Negishi, Tatsuya; Yamamoto, Hiroshi; Shiina, Takayuki; Shigeto, Shohei; Matsuda, Kazuyuki; Kobayashi, Yukihiro; Honda, Takayuki

2018-01-01

The detection of epidermal growth factor receptor (EGFR) mutations is necessary for the selection of suitable patients with non-small cell lung cancer (NSCLC) for treatment with EGFR tyrosine kinase inhibitors. Cytology specimens are known to be suitable for EGFR mutation detection, although tissue specimens should be prioritized; however, there are limited studies that examine the utility of bronchial lavage fluid (BLF) in mutation detection. The purpose of the present study was to investigate the utility of BLF specimens for the detection of EGFR mutations using a conventional quantitative EGFR polymerase chain reaction (PCR) assay. Initially, quantification cycle (Cq) values of cell pellets, cell-free supernatants and cell blocks obtained from three series of 1% EGFR mutation-positive lung cancer cell line samples were compared for mutation detection. In addition, PCR analysis of BLF specimens obtained from 77 consecutive NSCLC patients, detecting EGFR mutations was validated, and these results were compared with those for the corresponding formalin-fixed paraffin-embedded (FFPE) tissue specimens obtained by surgical resection or biopsy of 49 of these patients. The Cq values for mutation detection were significantly lower in the cell pellet group (average, 29.58) compared with the other groups, followed by those in cell-free supernatants (average, 34.15) and in cell blocks (average, 37.12) for all three series (P<0.05). Mutational status was successfully analyzed in 77 BLF specimens, and the results obtained were concordant with those of the 49 matching FFPE tissue specimens. Notably, EGFR mutations were even detected in 10 cytological specimens that contained insufficient tumor cells. EGFR mutation testing with BLF specimens is therefore a useful and reliable method, particularly when sufficient cancer cells are not obtained. PMID:29399190

Evaluation of collagen in connective tissue walls of odontogenic cysts--a histochemical study.

PubMed

Vij, Ruchieka; Vij, Hitesh; Rao, Nirmala N

2011-03-01

The purpose of this study was to evaluate the nature of collagen in the connective tissue walls of odontogenic cysts, like the odontogenic keratocyst (OKC), dentigerous cyst and radicular cyst using picrosirius red stained sections. Furthermore, it was intended to assess if the capsular connective tissue can affect the nature of overlying epithelium, thus emphasizing the role of epithelial-mesenchymal interactions in biological behaviour of the cysts. The material for the study included 51 formalin-fixed paraffin-embedded tissue blocks (15 odontogenic keratocyst, 15 dentigerous cysts, 15 radicular cysts and four normal mucosa and two dental follicular tissue as controls), retrieved from the Department of Oral Pathology and Microbiology, MCODS, Manipal. Tissue blocks were sectioned at 5-μm thickness, stained with picrosirius red stain and observed with polarization and light microscopy. Few sections of OKC and dentigerous cyst exhibited greenish-yellow birefringence in sub-epithelial region, whereas others showed a yellowish-orange birefringence under polarization microscopy. Most radicular cysts had yellowish-orange to orange birefringence. Shift in colour in case OKC and dentigerous cyst was attributed to the presence of inflammation in those sections. These regions also exhibited either a change in phenotype or thickness of overlying epithelium. This technique can be used to study the nature of collagen fibres in odontogenic cyst walls. Further studies with an increased sample size and using various epithelial and mesenchymal markers and ssDNA antibodies should be carried out to confirm the effect of epithelial-mesenchymal interactions on the nature of epithelium of odontogenic cysts. © 2010 John Wiley & Sons A/S.

Validation of a standardized extraction method for formalin-fixed paraffin-embedded tissue samples.

PubMed

Lagheden, Camilla; Eklund, Carina; Kleppe, Sara Nordqvist; Unger, Elizabeth R; Dillner, Joakim; Sundström, Karin

2016-07-01

Formalin-fixed paraffin-embedded (FFPE) samples can be DNA-extracted and used for human papillomavirus (HPV) genotyping. The xylene-based gold standard for extracting FFPE samples is laborious, suboptimal and involves health hazards for the personnel involved. To compare extraction with the standard xylene method to a xylene-free method used in an HPV LabNet Global Reference Laboratory at the Centers for Disease Control (CDC); based on a commercial method with an extra heating step. Fifty FFPE samples were randomly selected from a national audit of all cervical cancer cases diagnosed in Sweden during 10 years. For each case-block, a blank-block was sectioned, as a control for contamination. For xylene extraction, the standard WHO Laboratory Manual protocol was used. For the CDC method, the manufacturers' protocol was followed except for an extra heating step, 120°C for 20min. Samples were extracted and tested in parallel with β-globin real-time PCR, HPV16 real-time PCR and HPV typing using modified general primers (MGP)-PCR and Luminex assays. For a valid result the blank-block had to be betaglobin-negative in all tests and the case-block positive for beta-globin. Overall, detection was improved with the heating method and the amount of HPV-positive samples increased from 70% to 86% (p=0.039). For all samples where HPV type concordance could be evaluated, there was 100% type concordance. A xylene-free and robust extraction method for HPV-DNA typing in FFPE material is currently in great demand. Our proposed standardized protocol appears to be generally useful. Copyright © 2016. Published by Elsevier B.V.

Independent prognostic value of eosinophil and mast cell infiltration in colorectal cancer tissue.

PubMed

Nielsen, H J; Hansen, U; Christensen, I J; Reimert, C M; Brünner, N; Moesgaard, F

1999-12-01

Overall peritumoural inflammatory cell infiltration is a prognostic variable in solid tumours, but the survival-related impact of the individual cell types within the infiltrate has still not been fully evaluated and compared with the conventional disease classification. In the present study, the prognostic value of individual white cell counts in the peritumoural inflammatory infiltrate in colorectal cancer was assessed. Intra-operative tumour tissue samples from 584 patients undergoing elective surgery for colorectal cancer were included. None of the patients received pre- or post-operative adjuvant chemotherapy. Tissue blocks were cut from the periphery of the tumours and embedded in paraffin. All blocks included both tumour tissue and normal bowel tissue. Serial sections of 4 microm were analysed for tumour tissue inflammatory cell infiltration using a computer- and video-assisted microscope, which allowed semi-automated quantification of cells within a fixed area. Total white cells and individual counts of eosinophils, neutrophils, mast cells, lymphocytes, and plasma cells were evaluated in every tumour specimen. Stratification into four groups with similar numbers of events was used to dichotomize the cell counts with respect to survival. The median observation period was 61 (49-75) months. In a multivariate analysis including Dukes' stage, gender, age, peri-operative blood transfusion, tumour location, and counts of specific inflammatory cells, only advanced Dukes' stage ( p< 0.0001), high age ( p=0.0003), and tumour location in the rectum predicted poor survival, while high counts of eosinophils ( p=0.006) and mast cells ( p=0.02) predicted good survival. Tumour-associated eosinophilia and mastocytosis appear to be independent prognostic variables in colorectal cancer. Future studies should investigate the potential biological role of tumour tissue eosinophils and mast cells in the modulation of tumour growth. Copyright 1999 John Wiley & Sons, Ltd.

Background staining of visualization systems in immunohistochemistry: comparison of the Avidin-Biotin Complex system and the EnVision+ system.

PubMed

Vosse, Bettine A H; Seelentag, Walter; Bachmann, Astrid; Bosman, Fred T; Yan, Pu

2007-03-01

The aim of this study was to evaluate specific immunostaining and background staining in formalin-fixed, paraffin-embedded human tissues with the 2 most frequently used immunohistochemical detection systems, Avidin-Biotin-Peroxidase (ABC) and EnVision+. A series of fixed tissues, including breast, colon, kidney, larynx, liver, lung, ovary, pancreas, prostate, stomach, and tonsil, was used in the study. Three monoclonal antibodies, 1 against a nuclear antigen (Ki-67), 1 against a cytoplasmic antigen (cytokeratin), and 1 against a cytoplasmic and membrane-associated antigen and a polyclonal antibody against a nuclear and cytoplasmic antigen (S-100) were selected for these studies. When the ABC system was applied, immunostaining was performed with and without blocking of endogenous avidin-binding activity. The intensity of specific immunostaining and the percentage of stained cells were comparable for the 2 detection systems. The use of ABC caused widespread cytoplasmic and rare nuclear background staining in a variety of normal and tumor cells. A very strong background staining was observed in colon, gastric mucosa, liver, and kidney. Blocking avidin-binding capacity reduced background staining, but complete blocking was difficult to attain. With the EnVision+ system no background staining occurred. Given the efficiency of the detection, equal for both systems or higher with EnVision+, and the significant background problem with ABC, we advocate the routine use of the EnVision+ system.

Anatomical variation in a patient with lateral femoral cutaneous nerve entrapment neuropathy.

PubMed

Kokubo, Rinko; Kim, Kyongsong; Morimoto, Daijiro; Isu, Toyohiko; Iwamoto, Naotaka; Kitamura, Takao; Morita, Akio

2018-05-02

This 53-year-old man had a 10-year history of paresthesia and pain in the right antero-lateral thigh exacerbated by prolonged standing and walking. His symptoms improved completely but transiently by lateral femoral cutaneous nerve (LFCN) block. The diagnosis was LFCN entrapment (LFCN-EN). As additional treatment with drugs and repeat LFCN block was ineffective, we performed surgical decompression under local anesthesia. A nerve stimulator located the LFCN 4.5 cm medial to the anterior superior iliac spine, it formed a sharp curve and was embedded in connective tissue. Proximal dissection showed it to run parallel to the femoral nerve at the level of the inguinal ligament. The inguinal ligament was partially released to complete dissection/release. Postoperatively, his symptoms improved and the numeric rating scale fell from 8 to 1. Copyright © 2018. Published by Elsevier Inc.

Banking for the future: an Australian experience in brain banking.

PubMed

Sarris, M; Garrick, T M; Sheedy, D; Harper, C G

2002-06-01

The New South Wales (NSW) Tissue Resource Centre (TRC) has been set up to provide Australian and international researchers with fixed and frozen brain tissue from cases that are well characterised, both clinically and pathologically, for projects related to neuropsychiatric and alcohol-related disorders. A daily review of the Department of Forensic Medicine provides initial information regarding a potential collection. If the case adheres to the strict inclusion criteria, the pathologist performing the postmortem examination is approached regarding retention of the brain tissue. The next of kin of the deceased is then contacted requesting permission to retain the brain for medical research. Cases are also obtained through donor programmes, where donors are assessed and consent to donate their brain during life. Once the brain is removed at autopsy, the brain is photographed, weighed and the volume determined, the brainstem and cerebellum are removed. The two hemispheres are divided, one hemisphere is fresh frozen and one fixed (randomised). Prior to freezing, the hemisphere is sliced into 1-cm coronal slices and a set of critical area blocks is taken. All frozen tissues are kept bagged at -80 degrees C. The other hemisphere is fixed in 15% buffered formalin for 2 weeks, embedded in agar and sliced at 3-mm intervals in the coronal plane. Tissue blocks from these slices are used for neuropathological analysis to exclude any other pathology. The TRC currently has 230 cases of both fixed and frozen material that has proven useful in a range of techniques in many research projects. These techniques include quantitative analyses of brain regions using neuropathological, neurochemical, neuropharmacological and gene expression assays.

Conductive resins improve charging and resolution of acquired images in electron microscopic volume imaging

PubMed Central

Nguyen, Huy Bang; Thai, Truc Quynh; Saitoh, Sei; Wu, Bao; Saitoh, Yurika; Shimo, Satoshi; Fujitani, Hiroshi; Otobe, Hirohide; Ohno, Nobuhiko

2016-01-01

Recent advances in serial block-face imaging using scanning electron microscopy (SEM) have enabled the rapid and efficient acquisition of 3-dimensional (3D) ultrastructural information from a large volume of biological specimens including brain tissues. However, volume imaging under SEM is often hampered by sample charging, and typically requires specific sample preparation to reduce charging and increase image contrast. In the present study, we introduced carbon-based conductive resins for 3D analyses of subcellular ultrastructures, using serial block-face SEM (SBF-SEM) to image samples. Conductive resins were produced by adding the carbon black filler, Ketjen black, to resins commonly used for electron microscopic observations of biological specimens. Carbon black mostly localized around tissues and did not penetrate cells, whereas the conductive resins significantly reduced the charging of samples during SBF-SEM imaging. When serial images were acquired, embedding into the conductive resins improved the resolution of images by facilitating the successful cutting of samples in SBF-SEM. These results suggest that improving the conductivities of resins with a carbon black filler is a simple and useful option for reducing charging and enhancing the resolution of images obtained for volume imaging with SEM. PMID:27020327

Lectin-binding histochemistry of non-decalcified growth plate cartilage: a postembedment method for light microscopy of epon-embedded tissue.

PubMed

Farnum, C E; Wilsman, N J

1984-06-01

A postembedment method for the localization of lectin-binding glycoconjugates was developed using Epon-embedded growth plate cartilage from Yucatan miniature swine. By testing a variety of etching, blocking, and incubation procedures, a standard protocol was developed for 1 micron thick sections that allowed visualization of both intracellular and extracellular glycoconjugates with affinity for wheat germ agglutinin and concanavalin A. Both fluorescent and peroxidase techniques were used, and comparisons were made between direct methods and indirect methods using the biotin-avidin bridging system. Differential extracellular lectin binding allowed visualization of interterritorial , territorial, and pericellular matrices. Double labeling experiments showed the precision with which intracellular binding could be localized to specific cytoplasmic compartments, with resolution of binding to the Golgi apparatus, endoplasmic reticulum, and nuclear membrane at the light microscopic level. This method allows the localization of both intracellular and extracellular lectin-binding glycoconjugates using fixation and embedment procedures that are compatible with simultaneous ultrastructural analysis. As such it should have applicability both to the morphological analysis of growth plate organization during normal endochondral ossification, as well as to the diagnostic pathology of matrix abnormalities in disease states of growing cartilage.

Comparison of Methods for the Extraction of DNA from Formalin-Fixed, Paraffin-Embedded Archival Tissues

PubMed Central

Sengüven, Burcu; Baris, Emre; Oygur, Tulin; Berktas, Mehmet

2014-01-01

Aim: Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. Methods: DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. Results: The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Conclusion: Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE. PMID:24688314

Validation of the Complexity INdex in SARComas prognostic signature on formalin-fixed, paraffin-embedded, soft tissue sarcomas.

PubMed

Le Guellec, S; Lesluyes, T; Sarot, E; Valle, C; Filleron, T; Rochaix, P; Valentin, T; Pérot, G; Coindre, J-M; Chibon, F

2018-05-31

Prediction of metastatic outcome in sarcomas is challenging for clinical management since they are aggressive and carry a high metastatic risk. A 67-gene expression signature, the Complexity INdex in SARComas (CINSARC), has been identified as a better prognostic factor than the reference pathological grade. Since it cannot be applied easily in standard laboratory practice, we assessed its prognostic value using nanoString on formalin-fixed, paraffin-embedded (FFPE) blocks to evaluate its potential in clinical routine practice and guided therapeutic management. A code set consisting of 67 probes derived from the 67 genes of the CINSARC signature was built and named NanoCind®. To compare the performance of RNA-seq and nanoString (NanoCind®), we used expressions of various sarcomas (n=124, frozen samples) using both techniques and compared predictive values based on CINSARC risk groups and clinical annotations. We also used nanoString on FFPE blocks (n=67) and matching frozen and FFPE samples (n=45) to compare their level of agreement. Metastasis-free survival and agreement values in classification groups were evaluated. CINSARC strongly predicted metastatic outcome using nanoString on frozen samples (HR = 2.9, 95% CI 1.23-6.82) with similar risk-group classifications (86%). While more than 50% of FFPE blocks were not analyzable by RNA-seq owing to poor RNA quality, all samples were analyzable with nanoString. When similar (risk-group) classifications were measured with frozen tumors (RNA-seq) compared to FFPE blocks (84% agreement), the CINSARC signature was still a predictive factor of metastatic outcome with nanoString on FFPE samples (HR = 4.43, 95% CI 1.25-15.72). CINSARC is a material-independent prognostic signature for metastatic outcome in sarcomas and outperforms histological grade. Unlike RNA-seq, nanoString is not influenced by the poor quality of RNA extracted from FFPE blocks. The CINSARC signature can potentially be used in combination with nanoString (NanoCind®) in routine clinical practice on FFPE blocks to predict metastatic outcome.

An RGB colour image steganography scheme using overlapping block-based pixel-value differencing

PubMed Central

Pal, Arup Kumar

2017-01-01

This paper presents a steganographic scheme based on the RGB colour cover image. The secret message bits are embedded into each colour pixel sequentially by the pixel-value differencing (PVD) technique. PVD basically works on two consecutive non-overlapping components; as a result, the straightforward conventional PVD technique is not applicable to embed the secret message bits into a colour pixel, since a colour pixel consists of three colour components, i.e. red, green and blue. Hence, in the proposed scheme, initially the three colour components are represented into two overlapping blocks like the combination of red and green colour components, while another one is the combination of green and blue colour components, respectively. Later, the PVD technique is employed on each block independently to embed the secret data. The two overlapping blocks are readjusted to attain the modified three colour components. The notion of overlapping blocks has improved the embedding capacity of the cover image. The scheme has been tested on a set of colour images and satisfactory results have been achieved in terms of embedding capacity and upholding the acceptable visual quality of the stego-image. PMID:28484623

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

EPA Science Inventory

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...

Teaching Embedded System Concepts for Technological Literacy

ERIC Educational Resources Information Center

Winzker, M.; Schwandt, A.

2011-01-01

A basic understanding of technology is recognized as important knowledge even for students not connected with engineering and computer science. This paper shows that embedded system concepts can be taught in a technological literacy course. An embedded system teaching block that has been used in an electronics module for non-engineers is…

Micro-precise spatiotemporal delivery system embedded in 3D printing for complex tissue regeneration.

PubMed

Tarafder, Solaiman; Koch, Alia; Jun, Yena; Chou, Conrad; Awadallah, Mary R; Lee, Chang H

2016-04-25

Three dimensional (3D) printing has emerged as an efficient tool for tissue engineering and regenerative medicine, given its advantages for constructing custom-designed scaffolds with tunable microstructure/physical properties. Here we developed a micro-precise spatiotemporal delivery system embedded in 3D printed scaffolds. PLGA microspheres (μS) were encapsulated with growth factors (GFs) and then embedded inside PCL microfibers that constitute custom-designed 3D scaffolds. Given the substantial difference in the melting points between PLGA and PCL and their low heat conductivity, μS were able to maintain its original structure while protecting GF's bioactivities. Micro-precise spatial control of multiple GFs was achieved by interchanging dispensing cartridges during a single printing process. Spatially controlled delivery of GFs, with a prolonged release, guided formation of multi-tissue interfaces from bone marrow derived mesenchymal stem/progenitor cells (MSCs). To investigate efficacy of the micro-precise delivery system embedded in 3D printed scaffold, temporomandibular joint (TMJ) disc scaffolds were fabricated with micro-precise spatiotemporal delivery of CTGF and TGFβ3, mimicking native-like multiphase fibrocartilage. In vitro, TMJ disc scaffolds spatially embedded with CTGF/TGFβ3-μS resulted in formation of multiphase fibrocartilaginous tissues from MSCs. In vivo, TMJ disc perforation was performed in rabbits, followed by implantation of CTGF/TGFβ3-μS-embedded scaffolds. After 4 wks, CTGF/TGFβ3-μS embedded scaffolds significantly improved healing of the perforated TMJ disc as compared to the degenerated TMJ disc in the control group with scaffold embedded with empty μS. In addition, CTGF/TGFβ3-μS embedded scaffolds significantly prevented arthritic changes on TMJ condyles. In conclusion, our micro-precise spatiotemporal delivery system embedded in 3D printing may serve as an efficient tool to regenerate complex and inhomogeneous tissues.

CUBIC pathology: three-dimensional imaging for pathological diagnosis.

PubMed

Nojima, Satoshi; Susaki, Etsuo A; Yoshida, Kyotaro; Takemoto, Hiroyoshi; Tsujimura, Naoto; Iijima, Shohei; Takachi, Ko; Nakahara, Yujiro; Tahara, Shinichiro; Ohshima, Kenji; Kurashige, Masako; Hori, Yumiko; Wada, Naoki; Ikeda, Jun-Ichiro; Kumanogoh, Atsushi; Morii, Eiichi; Ueda, Hiroki R

2017-08-24

The examination of hematoxylin and eosin (H&E)-stained tissues on glass slides by conventional light microscopy is the foundation for histopathological diagnosis. However, this conventional method has some limitations in x-y axes due to its relatively narrow range of observation area and in z-axis due to its two-dimensionality. In this study, we applied a CUBIC pipeline, which is the most powerful tissue-clearing and three-dimensional (3D)-imaging technique, to clinical pathology. CUBIC was applicable to 3D imaging of both normal and abnormal patient-derived, human lung and lymph node tissues. Notably, the combination of deparaffinization and CUBIC enabled 3D imaging of specimens derived from paraffin-embedded tissue blocks, allowing quantitative evaluation of nuclear and structural atypia of an archival malignant lymphoma tissue. Furthermore, to examine whether CUBIC can be applied to practical use in pathological diagnosis, we performed a histopathological screening of a lymph node metastasis based on CUBIC, which successfully improved the sensitivity in detecting minor metastatic carcinoma nodules in lymph nodes. Collectively, our results indicate that CUBIC significantly contributes to retrospective and prospective clinicopathological diagnosis, which might lead to the establishment of a novel field of medical science based on 3D histopathology.

Fabrication of 3D Reconstituted Organoid Arrays by DNA-programmed Assembly of Cells (DPAC)

PubMed Central

Todhunter, Michael E; Weber, Robert J; Farlow, Justin; Jee, Noel Y; Cerchiari, Alec E; Gartner, Zev J

2016-01-01

Tissues are the organizational units of function in metazoan organisms. Tissues comprise an assortment of cellular building blocks, soluble factors, and extracellular matrix (ECM) that are composed into specific three dimensional (3D) structures. The capacity to reconstitute tissues in vitro with the structural complexity observed in vivo is key to understanding processes such as morphogenesis, homeostasis, and disease. In this unit, we describe DNA-programmed Assembly of Cells (DPAC), a method to fabricate viable, functional arrays of organoid-like tissues within 3D ECM gels. In DPAC, dissociated cells are chemically functionalized with degradable oligonucleotide “velcro,” allowing rapid, specific, and reversible cell adhesion to a two-dimensional (2D) template patterned with complementary DNA. An iterative assembly process builds up organoids, layer-by-layer, from this initial 2D template and into the third dimension. Cleavage of the DNA releases the completed array of tissues that are captured and fully embedded in ECM gels for culture and observation. DPAC controls the size, shape, composition, and spatial heterogeneity of organoids, and permits positioning constituent cells with single-cell resolution even within cultures several centimeters long. PMID:27622567

Histological Assessment of PAXgene Tissue Fixation and Stabilization Reagents

PubMed Central

Kap, Marcel; Smedts, Frank; Oosterhuis, Wolter; Winther, Rosa; Christensen, Nanna; Reischauer, Bilge; Viertler, Christian; Groelz, Daniel; Becker, Karl-Friedrich; Zatloukal, Kurt; Langer, Rupert; Slotta-Huspenina, Julia; Bodo, Koppany; de Jong, Bas; Oelmuller, Uwe; Riegman, Peter

2011-01-01

Within SPIDIA, an EC FP7 project aimed to improve pre analytic procedures, the PAXgene Tissue System (PAXgene), was designed to improve tissue quality for parallel molecular and morphological analysis. Within the SPIDIA project promising results were found in both genomic and proteomic experiments with PAXgene-fixed and paraffin embedded tissue derived biomolecules. But, for this technology to be accepted for use in both clinical and basic research, it is essential that its adequacy for preserving morphology and antigenicity is validated relative to formalin fixation. It is our aim to assess the suitability of PAXgene tissue fixation for (immuno)histological methods. Normal human tissue specimens (n = 70) were collected and divided into equal parts for fixation either with formalin or PAXgene. Sections of the obtained paraffin-embedded tissue were cut and stained. Morphological aspects of PAXgene-fixed tissue were described and also scored relative to formalin-fixed tissue. Performance of PAXgene-fixed tissue in immunohistochemical and in situ hybridization assays was also assessed relative to the corresponding formalin-fixed tissues. Morphology of PAXgene-fixed paraffin embedded tissue was well preserved and deemed adequate for diagnostics in most cases. Some antigens in PAXgene-fixed and paraffin embedded sections were detectable without the need for antigen retrieval, while others were detected using standard, formalin fixation based, immunohistochemistry protocols. Comparable results were obtained with in situ hybridization and histochemical stains. Basically all assessed histological techniques were found to be applicable to PAXgene-fixed and paraffin embedded tissue. In general results obtained with PAXgene-fixed tissue are comparable to those of formalin-fixed tissue. Compromises made in morphology can be called minor compared to the advantages in the molecular pathology possibilities. PMID:22110732

Larger core size has superior technical and analytical accuracy in bladder tissue microarray.

PubMed

Eskaros, Adel Rh; Egloff, Shanna A Arnold; Boyd, Kelli L; Richardson, Joyce E; Hyndman, M Eric; Zijlstra, Andries

2017-03-01

The construction of tissue microarrays (TMAs) with cores from a large number of paraffin-embedded tissues (donors) into a single paraffin block (recipient) is an effective method of analyzing samples from many patient specimens simultaneously. For the TMA to be successful, the cores within it must capture the correct histologic areas from the donor blocks (technical accuracy) and maintain concordance with the tissue of origin (analytical accuracy). This can be particularly challenging for tissues with small histological features such as small islands of carcinoma in situ (CIS), thin layers of normal urothelial lining of the bladder, or cancers that exhibit intratumor heterogeneity. In an effort to create a comprehensive TMA of a bladder cancer patient cohort that accurately represents the tumor heterogeneity and captures the small features of normal and CIS, we determined how core size (0.6 vs 1.0 mm) impacted the technical and analytical accuracy of the TMA. The larger 1.0 mm core exhibited better technical accuracy for all tissue types at 80.9% (normal), 94.2% (tumor), and 71.4% (CIS) compared with 58.6%, 85.9%, and 63.8% for 0.6 mm cores. Although the 1.0 mm core provided better tissue capture, increasing the number of replicates from two to three allowed with the 0.6 mm core compensated for this reduced technical accuracy. However, quantitative image analysis of proliferation using both Ki67+ immunofluorescence counts and manual mitotic counts demonstrated that the 1.0 mm core size also exhibited significantly greater analytical accuracy (P=0.004 and 0.035, respectively, r 2 =0.979 and 0.669, respectively). Ultimately, our findings demonstrate that capturing two or more 1.0 mm cores for TMA construction provides superior technical and analytical accuracy over the smaller 0.6 mm cores, especially for tissues harboring small histological features or substantial heterogeneity.

Protocol for HER2 FISH determination on PAXgene-fixed and paraffin-embedded tissue in breast cancer.

PubMed

Oberauner-Wappis, Lisa; Loibner, Martina; Viertler, Christian; Groelz, Daniel; Wyrich, Ralf; Zatloukal, Kurt

2016-04-01

Molecular diagnostics in personalized medicine increasingly relies on the combination of a variety of analytical technologies to characterize individual diseases and to select patients for targeted therapies. The gold standard for tissue-based diagnostics is fixation in formalin and embedding in paraffin, which results in excellent preservation of morphology but negatively impacts on a variety of molecular assays. The formalin-free, non-cross-linking PAXgene tissue system preserves morphology in a similar way to formalin, but also preserves biomolecules essentially in a similar way to cryopreservation, which markedly widens the spectrum, sensitivity and accuracy of molecular analytics. In this study, we have developed and tested a protocol for PAXgene-fixed and paraffin-embedded tissues for fluorescent in situ hybridization (FISH). The implementation of a 24-h formalin postfixation step of slides from PAXgene-fixed and paraffin-embedded tissues allowed us to use the assays approved for formalin-fixed and paraffin-embedded tissues. The equivalence of the methodologies was demonstrated by FISH analysis of HER2 amplification in breast cancer cases. The 24-h postfixation step of the slides used for FISH can be well integrated in the routine diagnostic workflow and allows the remaining PAXgene-fixed and paraffin-embedded tissue to be used for further molecular testing. © 2016 The Authors. International Journal of Experimental Pathology published by John Wiley & Sons Ltd on behalf of Company of the International Journal of Experimental Pathology (CIJEP).

Development of a neutral embedding resin for optical imaging of fluorescently labeled biological tissue

NASA Astrophysics Data System (ADS)

Zhou, Hongfu; Gang, Yadong; Chen, Shenghua; Wang, Yu; Xiong, Yumiao; Li, Longhui; Yin, Fangfang; Liu, Yue; Liu, Xiuli; Zeng, Shaoqun

2017-10-01

Plastic embedding is widely applied in light microscopy analyses. Previous studies have shown that embedding agents and related techniques can greatly affect the quality of biological tissue embedding and fluorescent imaging. Specifically, it is difficult to preserve endogenous fluorescence using currently available acidic commercial embedding resins and related embedding techniques directly. Here, we developed a neutral embedding resin that improved the green fluorescent protein (GFP), yellow fluorescent protein (YFP), and DsRed fluorescent intensity without adjusting the pH value of monomers or reactivating fluorescence in lye. The embedding resin had a high degree of polymerization, and its fluorescence preservation ratios for GFP, YFP, and DsRed were 126.5%, 155.8%, and 218.4%, respectively.

Prostate cancer outcome and tissue levels of metal ions

USGS Publications Warehouse

Sarafanov, A.G.; Todorov, T.I.; Centeno, J.A.; MacIas, V.; Gao, W.; Liang, W.-M.; Beam, C.; Gray, Marion A.; Kajdacsy-Balla, A.

2011-01-01

BACKGROUNDThere are several studies examining prostate cancer and exposure to cadmium, iron, selenium, and zinc. Less data are available on the possible influence of these metal ions on prostate cancer outcome. This study measured levels of these ions in prostatectomy samples in order to examine possible associations between metal concentrations and disease outcome.METHODSWe obtained formalin fixed paraffin embedded tissue blocks of prostatectomy samples of 40 patients with PSA recurrence, matched 1:1 (for year of surgery, race, age, Gleason grading, and pathology TNM classification) with tissue blocks from 40 patients without recurrence (n = 80). Case–control pairs were compared for the levels of metals in areas adjacent to tumors. Inductively coupled plasma-mass spectrometry (ICP-MS) was used for quantification of Cd, Fe, Zn, and Se.RESULTSPatients with biochemical (PSA) recurrence of disease had 12% lower median iron (95 µg/g vs. 111 µg/g; P = 0.04) and 21% lower zinc (279 µg/g vs. 346 µg/g; P = 0.04) concentrations in the normal-appearing tissue immediately adjacent to cancer areas. Differences in cadmium (0.489 µg/g vs. 0.439 µg/g; 4% higher) and selenium (1.68 µg/g vs. 1.58 µg/g; 5% higher) levels were not statistically significant in recurrence cases, when compared to non-recurrences (P = 0.40 and 0.21, respectively).CONCLUSIONSThere is an association between low zinc and low iron prostate tissue levels and biochemical recurrence in prostate cancer. Whether these novel findings are a cause or effect of more aggressive tumors, or whether low zinc and iron prostatic levels raise implications for therapy, remains to be investigated. 

The fabrication of nanopatterns with Au nanoparticles-embedded micelles via nanoimprint lithography.

PubMed

Lee, Jung-Pil; Kim, Eun-Uk; Koh, Haeng-Deog; Kang, Nam-Goo; Jung, Gun-Young; Lee, Jae-Suk

2009-09-09

We fabricated nanopatterns with Au nanoparticles-embedded micelles (Au-micelles) by self-assembly of block copolymers via nanoimprint lithography. The micelle structure prepared by self-assembled block copolymers was used as a template for the synthesis of Au nanoparticles (Au NPs). Au NPs were synthesized in situ inside the micelles of polystyrene-block-poly(2-vinylpyridine) (PS- b-P2VP). Au-micelles were arranged on the trenches of the polymer template, which was imprinted by nanoimprint lithography. The fabrication of line-type and dot-type nanopatterns was carried out by the combined method. In addition, multilayer nanopatterns of the Au-micelles were also proposed.

Embedding and Chemical Reactivation of Green Fluorescent Protein in the Whole Mouse Brain for Optical Micro-Imaging

PubMed Central

Gang, Yadong; Zhou, Hongfu; Jia, Yao; Liu, Ling; Liu, Xiuli; Rao, Gong; Li, Longhui; Wang, Xiaojun; Lv, Xiaohua; Xiong, Hanqing; Yang, Zhongqin; Luo, Qingming; Gong, Hui; Zeng, Shaoqun

2017-01-01

Resin embedding has been widely applied to fixing biological tissues for sectioning and imaging, but has long been regarded as incompatible with green fluorescent protein (GFP) labeled sample because it reduces fluorescence. Recently, it has been reported that resin-embedded GFP-labeled brain tissue can be imaged with high resolution. In this protocol, we describe an optimized protocol for resin embedding and chemical reactivation of fluorescent protein labeled mouse brain, we have used mice as experiment model, but the protocol should be applied to other species. This method involves whole brain embedding and chemical reactivation of the fluorescent signal in resin-embedded tissue. The whole brain embedding process takes a total of 7 days. The duration of chemical reactivation is ~2 min for penetrating 4 μm below the surface in the resin-embedded brain. This protocol provides an efficient way to prepare fluorescent protein labeled sample for high-resolution optical imaging. This kind of sample was demonstrated to be imaged by various optical micro-imaging methods. Fine structures labeled with GFP across a whole brain can be detected. PMID:28352214

A review on "A Novel Technique for Image Steganography Based on Block-DCT and Huffman Encoding"

NASA Astrophysics Data System (ADS)

Das, Rig; Tuithung, Themrichon

2013-03-01

This paper reviews the embedding and extraction algorithm proposed by "A. Nag, S. Biswas, D. Sarkar and P. P. Sarkar" on "A Novel Technique for Image Steganography based on Block-DCT and Huffman Encoding" in "International Journal of Computer Science and Information Technology, Volume 2, Number 3, June 2010" [3] and shows that the Extraction of Secret Image is Not Possible for the algorithm proposed in [3]. 8 bit Cover Image of size is divided into non joint blocks and a two dimensional Discrete Cosine Transformation (2-D DCT) is performed on each of the blocks. Huffman Encoding is performed on an 8 bit Secret Image of size and each bit of the Huffman Encoded Bit Stream is embedded in the frequency domain by altering the LSB of the DCT coefficients of Cover Image blocks. The Huffman Encoded Bit Stream and Huffman Table

Imaging cellular and subcellular structure of human brain tissue using micro computed tomography

NASA Astrophysics Data System (ADS)

Khimchenko, Anna; Bikis, Christos; Schweighauser, Gabriel; Hench, Jürgen; Joita-Pacureanu, Alexandra-Teodora; Thalmann, Peter; Deyhle, Hans; Osmani, Bekim; Chicherova, Natalia; Hieber, Simone E.; Cloetens, Peter; Müller-Gerbl, Magdalena; Schulz, Georg; Müller, Bert

2017-09-01

Brain tissues have been an attractive subject for investigations in neuropathology, neuroscience, and neurobiol- ogy. Nevertheless, existing imaging methodologies have intrinsic limitations in three-dimensional (3D) label-free visualisation of extended tissue samples down to (sub)cellular level. For a long time, these morphological features were visualised by electron or light microscopies. In addition to being time-consuming, microscopic investigation includes specimen fixation, embedding, sectioning, staining, and imaging with the associated artefacts. More- over, optical microscopy remains hampered by a fundamental limit in the spatial resolution that is imposed by the diffraction of visible light wavefront. In contrast, various tomography approaches do not require a complex specimen preparation and can now reach a true (sub)cellular resolution. Even laboratory-based micro computed tomography in the absorption-contrast mode of formalin-fixed paraffin-embedded (FFPE) human cerebellum yields an image contrast comparable to conventional histological sections. Data of a superior image quality was obtained by means of synchrotron radiation-based single-distance X-ray phase-contrast tomography enabling the visualisation of non-stained Purkinje cells down to the subcellular level and automated cell counting. The question arises, whether the data quality of the hard X-ray tomography can be superior to optical microscopy. Herein, we discuss the label-free investigation of the human brain ultramorphology be means of synchrotron radiation-based hard X-ray magnified phase-contrast in-line tomography at the nano-imaging beamline ID16A (ESRF, Grenoble, France). As an example, we present images of FFPE human cerebellum block. Hard X-ray tomography can provide detailed information on human tissues in health and disease with a spatial resolution below the optical limit, improving understanding of the neuro-degenerative diseases.

A Project-Based Laboratory for Learning Embedded System Design with Industry Support

ERIC Educational Resources Information Center

Lee, Chyi-Shyong; Su, Juing-Huei; Lin, Kuo-En; Chang, Jia-Hao; Lin, Gu-Hong

2010-01-01

A project-based laboratory for learning embedded system design with support from industry is presented in this paper. The aim of this laboratory is to motivate students to learn the building blocks of embedded systems and practical control algorithms by constructing a line-following robot using the quadratic interpolation technique to predict the…

Bacterial filamentation accelerates colonization of adhesive spots embedded in biopassive surfaces

NASA Astrophysics Data System (ADS)

Möller, Jens; Emge, Philippe; Avalos Vizcarra, Ima; Kollmannsberger, Philip; Vogel, Viola

2013-12-01

Sessile bacteria adhere to engineered surfaces and host tissues and pose a substantial clinical and economical risk when growing into biofilms. Most engineered and biological interfaces are of chemically heterogeneous nature and provide adhesive islands for bacterial attachment and growth. To mimic either defects in a surface coating of biomedical implants or heterogeneities within mucosal layers (Peyer's patches), we embedded micrometre-sized adhesive islands in a poly(ethylene glycol) biopassive background. We show experimentally and computationally that filamentation of Escherichia coli can significantly accelerate the bacterial surface colonization under physiological flow conditions. Filamentation can thus provide an advantage to a bacterial population to bridge non-adhesive distances exceeding 5 μm. Bacterial filamentation, caused by blocking of bacterial division, is common among bacterial species and can be triggered by environmental conditions or antibiotic treatment. While great awareness exists that the build-up of antibiotic resistance serves as intrinsic survival strategy, we show here that antibiotic treatment can actually promote surface colonization by triggering filamentation, which in turn prevents daughter cells from being washed away. Our combined microfabrication and computational approaches provide quantitative insights into mechanisms that enable biofouling of biopassive surfaces with embedded adhesive spots, even for spot distances that are multiples of the bacterial length.

Subsurface thermal behaviour of tissue mimics embedded with large blood vessels during plasmonic photo-thermal therapy.

PubMed

Paul, Anup; Narasimhan, Arunn; Das, Sarit K; Sengupta, Soujit; Pradeep, Thalappil

2016-11-01

The purpose of this study was to understand the subsurface thermal behaviour of a tissue phantom embedded with large blood vessels (LBVs) when exposed to near-infrared (NIR) radiation. The effect of the addition of nanoparticles to irradiated tissue on the thermal sink behaviour of LBVs was also studied. Experiments were performed on a tissue phantom embedded with a simulated blood vessel of 2.2 mm outer diameter (OD)/1.6 mm inner diameter (ID) with a blood flow rate of 10 mL/min. Type I collagen from bovine tendon and agar gel were used as tissue. Two different nanoparticles, gold mesoflowers (AuMS) and graphene nanostructures, were synthesised and characterised. Energy equations incorporating a laser source term based on multiple scattering theories were solved using finite element-based commercial software. The rise in temperature upon NIR irradiation was seen to vary according to the position of the blood vessel and presence of nanoparticles. While the maximum rise in temperature was about 10 °C for bare tissue, it was 19 °C for tissue embedded with gold nanostructures and 38 °C for graphene-embedded tissues. The axial temperature distribution predicted by computational simulation matched the experimental observations. A different subsurface temperature distribution has been obtained for different tissue vascular network models. The position of LBVs must be known in order to achieve optimal tissue necrosis. The simulation described here helps in predicting subsurface temperature distributions within tissues during plasmonic photo-thermal therapy so that the risks of damage and complications associated with in vivo experiments and therapy may be avoided.

Quality control in diagnostic immunohistochemistry: integrated on-slide positive controls.

PubMed

Bragoni, A; Gambella, A; Pigozzi, S; Grigolini, M; Fiocca, R; Mastracci, L; Grillo, F

2017-11-01

Standardization in immunohistochemistry is a priority in modern pathology and requires strict quality control. Cost containment has also become fundamental and auditing of all procedures must take into account both these principles. Positive controls must be routinely performed so that their positivity guarantees the appropriateness of the immunohistochemical procedure. The aim of this study is to develop a low cost (utilizing a punch biopsy-PB-tool) procedure to construct positive controls which can be integrated in the patient's tissue slide. Sixteen frequently used control blocks were selected and multiple cylindrical samples were obtained using a 5-mm diameter punch biopsy tool, separately re-embedding them in single blocks. For each diagnostic immunoreaction requiring a positive control, an integrated PB-control section (cut from the appropriate PB-control block) was added to the top right corner of the diagnostic slide before immunostaining. This integrated control technique permitted a saving of 4.75% in total direct lab costs and proved to be technically feasible and reliable. Our proposal is easy to perform and within the reach of all pathology labs, requires easily available tools, its application costs is less than using external paired controls and ensures that a specific control for each slide is always available.

Inspection of a large concrete block containing embedded defects using ground penetrating radar

NASA Astrophysics Data System (ADS)

Eisenmann, David; Margetan, Frank J.; Koester, Lucas; Clayton, Dwight

2016-02-01

Ground penetrating radar (GPR), also known as impulse response radar, was used to examine a thick concrete block containing reinforcing steel bars (rebar) and embedded defects. The block was located at the University of Minnesota, measured approximately 7 feet tall by 7 feet wide by 40 inches deep, and was intended to simulate certain aspects of a concrete containment wall at a nuclear power plant. This paper describes the measurements that were made and various analyses of the data. We begin with a description of the block itself and the GPR equipment and methods used in our inspections. The methods include the application of synthetic aperture focusing techniques (SAFT). We then present and discuss GPR images of the block's interior made using 1600-MHz, 900-MHz, and 400-MHz antennas operating in pulse/echo mode. A number of the embedded defects can be seen, and we discuss how their relative detectability can be quantified by comparison to the response from nearby rebar. We next discuss through-transmission measurements made using pairs of 1600-MHz and 900-MHz antennas, and the analysis of that data to deduce the average electromagnetic (EM) wave speed and attenuation of the concrete. Through the 40-inch thickness, attenuation rises approximately linearly with frequency at a rate near 0.7 dB/inch/GHz. However, there is evidence that EM properties vary with depth in the block. We conclude with a brief summary and a discussion of possible future work.

Affective context interferes with cognitive control in unipolar depression: An fMRI investigation

PubMed Central

Dichter, Gabriel S.; Felder, Jennifer N.; Smoski, Moria J.

2009-01-01

Background Unipolar major depressive disorder (MDD) is characterized by aberrant amygdala responses to sad stimuli and poor cognitive control, but the interactive effects of these impairments are poorly understood. Aim To evaluate brain activation in MDD in response to cognitive control stimuli embedded within sad and neutral contexts. Method Fourteen adults with MDD and fifteen matched controls participated in a mixed block/event-related functional magnetic resonance imaging (fMRI) task that presented oddball target stimuli embedded within blocks of sad or neutral images. Results Target events activated similar prefrontal brain regions in both groups. However, responses to target events embedded within blocks of emotional images revealed a clear group dissociation. During neutral blocks, the control group demonstrated greater activation to targets in the midfrontal gyrus and anterior cingulate relative to the MDD group, replicating previous findings of prefrontal hypo-activation in MDD samples to cognitive control stimuli. However, during sad blocks, the MDD group demonstrated greater activation in a number of prefrontal regions, including the mid-, inferior, and orbito-frontal gyri and the anterior cingulate, suggesting that relatively more prefrontal brain activation was required to disengage from the sad images to respond to the target events. Limitations A larger sample size would have provided greater statistical power, and more standardized stimuli would have increased external validity. Conclusions This double dissociation of prefrontal responses to target events embedded within neutral and sad context suggests that MDD impacts not only responses to affective events, but extends to other cognitive processes carried out in the context of affective engagement. This implies that emotional reactivity to sad events in MDD may impact functioning more broadly than previously understood. PMID:18706701

Comparison of fixation and processing methods for hairless guinea pig skin following sulfur mustard exposure. (Reannouncement with new availability information)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bryant, M.A.; Braue Jr, E.H.

1992-12-31

Ten anesthetized hairless guinea pigs Crl:IAF(HA)BR were exposed to 10 pi of neat sulfur mustard (HD) in a vapor cup on their skin for 7 min. At 24 h postexposure, the guinea pigs were euthanatized and skin sections taken for histologic evaluation. The skin was fixed using either 10% neutral buffered formalin (NBF), McDowell Trump fixative (4CF-IG), Zenker`s formol-saline (Helly`s fluid), or Zenker`s fluid. Fixed skin sections were cut in half: one half was embedded in paraffin and the other half in plastic (glycol methacrylate). Paraffin-embedded tissue was stained with hematoxylin and eosin; plastic-embedded tissue was stained with Lee`s methylenemore » blue basic fuchsin. Skin was also frozen unfixed, sectioned by cryostat, and stained with pinacyanole. HD-exposed skin was evaluated histologically for the presence of epidermal and follicular necrosis, microblister formation, epidermitis, and intracellular edema to determine the optimal fixation and embedding method for lesion preservation. The percentage of histologic sections with lesions varied little between fixatives and was similar for both paraffin and plastic embedding material. Plastic-embedded sections were thinner, allowing better histologic evaluation, but were more difficult to stain. Plastic embedding material did not infiltrate tissue fixed in Zenker`s fluid or Zenker`s formol-saline. Frozen tissue sections were prepared in the least processing time and lesion preservation was comparable to fixed tissue. It was concluded that standard histologic processing using formalin fixation and paraffin embedding is adequate for routine histopathological evaluation of HD skin lesions in the hairless guinea pig.... Sulfur mustard, Vesicating agents, Pathology, Hairless guinea pig model, Fixation.« less

Self-assembly of silk-elastinlike protein polymers into three-dimensional scaffolds for biomedical applications

NASA Astrophysics Data System (ADS)

Zeng, Like

Production of brand new protein-based materials with precise control over the amino acid sequences at single residue level has been made possible by genetic engineering, through which artificial genes can be developed that encode protein-based materials with desired features. As an example, silk-elastinlike protein polymers (SELPs), composed of tandem repeats of amino acid sequence motifs from Bombyx mori (silkworm) silk and mammalian elastin, have been produced in this approach. SELPs have been studied extensively in the past two decades, however, the fundamental mechanism governing the self-assembly process to date still remains largely unresolved. Further, regardless of the unprecedented success when exploited in areas including drug delivery, gene therapy, and tissue augmentation, SELPs scaffolds as a three-dimensional cell culture model system are complicated by the inability of SELPs to provide the embedded tissue cells with appropriate biochemical stimuli essential for cell survival and function. In this dissertation, it is reported that the self-assembly of silk-elastinlike protein polymers (SELPs) into nanofibers in aqueous solutions can be modulated by tuning the curing temperature, the size of the silk blocks, and the charge of the elastin blocks. A core-sheath model was proposed for nanofiber formation, with the silk blocks in the cores and the hydrated elastin blocks in the sheaths. The folding of the silk blocks into stable cores -- affected by the size of the silk blocks and the charge of the elastin blocks -- plays a critical role in the assembly of silk-elastin nanofibers. The assembled nanofibers further form nanofiber clusters on the microscale, and the nanofiber clusters then coalesce into nanofiber micro-assemblies, interconnection of which eventually leads to the formation of three-dimensional scaffolds with distinct nanoscale and microscale features. SELP-Collagen hybrid scaffolds were also fabricated to enable independent control over the scaffolds' biochemical input and matrix stiffness. It is reported herein that in the hybrid scaffolds, collagen provides essential biochemical cues needed to promote cell attachment and function while SELP imparts matrix stiffness tunability. To obtain tissue-specificity in matrix stiffness that spans over several orders of magnitude covering from soft brain to stiff cartilage, the hybrid SELP-Collagen scaffolds were crosslinked by transglutaminase at physiological conditions compatible for simultaneous cell encapsulation. The effect of the increase in matrix stiffness induced by such enzymatic crosslinking on cellular viability and proliferation was also evaluated using in vitro cell assays.

Multiplex Staining by Sequential Immunostaining and Antibody Removal on Routine Tissue Sections.

PubMed

Bolognesi, Maddalena Maria; Manzoni, Marco; Scalia, Carla Rossana; Zannella, Stefano; Bosisio, Francesca Maria; Faretta, Mario; Cattoretti, Giorgio

2017-08-01

Multiplexing, labeling for multiple immunostains in the very same cell or tissue section in situ, has raised considerable interest. The methods proposed include the use of labeled primary antibodies, spectral separation of fluorochromes, bleaching of the fluorophores or chromogens, blocking of previous antibody layers, all in various combinations. The major obstacles to the diffusion of this technique are high costs in custom antibodies and instruments, low throughput, and scarcity of specialized skills or facilities. We have validated a method based on common primary and secondary antibodies and diffusely available fluorescent image scanners. It entails rounds of four-color indirect immunofluorescence, image acquisition, and removal (stripping) of the antibodies, before another stain is applied. The images are digitally registered and the autofluorescence is subtracted. Removal of antibodies is accomplished by disulfide cleavage and a detergent or by a chaotropic salt treatment, this latter followed by antigen refolding. More than 30 different antibody stains can be applied to one single section from routinely fixed and embedded tissue. This method requires a modest investment in hardware and materials and uses freeware image analysis software. Multiplexing on routine tissue sections is a high throughput tool for in situ characterization of neoplastic, reactive, inflammatory, and normal cells.

Raman Monte Carlo simulation for light propagation for tissue with embedded objects

NASA Astrophysics Data System (ADS)

Periyasamy, Vijitha; Jaafar, Humaira Bte; Pramanik, Manojit

2018-02-01

Monte Carlo (MC) stimulation is one of the prominent simulation technique and is rapidly becoming the model of choice to study light-tissue interaction. Monte Carlo simulation for light transport in multi-layered tissue (MCML) is adapted and modelled with different geometry by integrating embedded objects of various shapes (i.e., sphere, cylinder, cuboid and ellipsoid) into the multi-layered structure. These geometries would be useful in providing a realistic tissue structure such as modelling for lymph nodes, tumors, blood vessels, head and other simulation medium. MC simulations were performed on various geometric medium. Simulation of MCML with embedded object (MCML-EO) was improvised for propagation of the photon in the defined medium with Raman scattering. The location of Raman photon generation is recorded. Simulations were experimented on a modelled breast tissue with tumor (spherical and ellipsoidal) and blood vessels (cylindrical). Results were presented in both A-line and B-line scans for embedded objects to determine spatial location where Raman photons were generated. Studies were done for different Raman probabilities.

Further Studies on the Lyo and Desmo Components of Several Hydrolytic Enzymes and Their Histochemical Significance

PubMed Central

Hannibal, Mark J.; Nachlas, Marvin M.

1959-01-01

This report describes additional studies of the lyo and desmo components of esterase, alkaline phosphatase, acid phosphatase, leucine aminopeptidase, and β-glucuronidase. The techniques used have already been reported (7). Enzyme diffusion occurs to different degrees in different fixatives, and varies somewhat with each enzyme. Loss of enzymatic activity during fixation occurs as a result of both inactivation due to the chemical reaction of the fixative with the enzymic protein, and diffusion of the lyo component into the fixative. The amount of diffusion into formalin can be reduced by the addition of salts, sucrose, or methocel. The pH of the aqueous medium significantly influences the removal of the lyo fraction from the tissue section. A striking similarity can be noted in the proportions of each fraction of enzyme present in the kidney of the rat, dog, and man. The procedure of fixation and paraffin embedding of tissue blocks does not wholly prevent the diffusion of the lyo component from the tissue sections when they are subsequently immersed in the aqueous incubation medium. PMID:13654449

Reliable LC3 and p62 autophagy marker detection in formalin fixed paraffin embedded human tissue by immunohistochemistry.

PubMed

Schläfli, A M; Berezowska, S; Adams, O; Langer, R; Tschan, M P

2015-05-05

Autophagy assures cellular homeostasis, and gains increasing importance in cancer, where it impacts on carcinogenesis, propagation of the malignant phenotype and development of resistance. To date, its tissue-based analysis by immunohistochemistry remains poorly standardized. Here we show the feasibility of specifically and reliably assessing the autophagy markers LC3B and p62 (SQSTM1) in formalin fixed and paraffin embedded human tissue by immunohistochemistry. Preceding functional experiments consisted of depleting LC3B and p62 in H1299 lung cancer cells with subsequent induction of autophagy. Western blot and immunofluorescence validated antibody specificity, knockdown efficiency and autophagy induction prior to fixation in formalin and embedding in paraffin. LC3B and p62 antibodies were validated on formalin fixed and paraffin embedded cell pellets of treated and control cells and finally applied on a tissue microarray with 80 human malignant and non-neoplastic lung and stomach formalin fixed and paraffin embedded tissue samples. Dot-like staining of various degrees was observed in cell pellets and 18/40 (LC3B) and 22/40 (p62) tumors, respectively. Seventeen tumors were double positive for LC3B and p62. P62 displayed additional significant cytoplasmic and nuclear staining of unknown significance. Interobserver-agreement for grading of staining intensities and patterns was substantial to excellent (kappa values 0.60 - 0.83). In summary, we present a specific and reliable IHC staining of LC3B and p62 on formalin fixed and paraffin embedded human tissue. Our presented protocol is designed to aid reliable investigation of dysregulated autophagy in solid tumors and may be used on large tissue collectives.

Identification of tissue-embedded ascarid larvae by ribosomal DNA sequencing.

PubMed

Ishiwata, Kenji; Shinohara, Akio; Yagi, Kinpei; Horii, Yoichiro; Tsuchiya, Kimiyuki; Nawa, Yukifumi

2004-01-01

Polymerase chain reaction (PCR) was applied to identify tissue-embedded ascarid nematode larvae. Two sequences of the internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA), ITS1 and ITS2, of the ascarid parasites were amplified and compared with those of ascarid-nematodes registered in a DNA database (GenBank). The ITS sequences of the PCR products obtained from the ascarid parasite specimen in our laboratory were compatible with those of registered adult Ascaris and Toxocara parasites. PCR amplification of the ITS regions was sensitive enough to detect a single larva of Ascaris suum mixed with porcine liver tissue. Using this method, ascarid larvae embedded in the liver of a naturally infected turkey were identified as Toxocara canis. These results suggest that even a single larva embedded in tissues from patients with larva migrans could be identified by sequencing the ITS regions.

CdSe/CdS semiconductor quantum rods as robust fluorescent probes for paraffin-embedded tissue imaging.

PubMed

Zacheo, Antonella; Quarta, Alessandra; Mangoni, Antonella; Pompa, Pier Paolo; Mastria, Rosanna; Capogrossi, Maurizio C; Rinaldi, Ross; Pellegrino, Teresa

2011-09-01

Immunofluorescence techniques on formalin fixed paraffin-embedded sections allow for the evaluation of the expression and spatial distribution of specific markers in patient tissue specimens or for monitoring the fate of labeled cells after in vivo injection. This technique suffers however from the auto-fluorescence background signal of the embedded tissue that eventually confounds the analysis. Here we show that rod-like semiconductor nanocrystals (QRs), intramuscularly injected in living mice, could be clearly detected by confocal microscopy in formalin fixed paraffin-embedded tissue sections. Despite the low amount of QRs amount injected (25 picomoles), these were clearly visible after 24 h in the muscle sections and their fluorescence signal was stronger than that of CdSe/ZnS quantum dots (QDs) similarly functionalized and in the case of QRs only, the signal lasted even after 21 days after the injection. © 2011 IEEE

Investigating the impact of blood pressure increase to the brain using high resolution serial histology and image processing

NASA Astrophysics Data System (ADS)

Lesage, F.; Castonguay, A.; Tardif, P. L.; Lefebvre, J.; Li, B.

2015-09-01

A combined serial OCT/confocal scanner was designed to image large sections of biological tissues at microscopic resolution. Serial imaging of organs embedded in agarose blocks is performed by cutting through tissue using a vibratome which sequentially cuts slices in order to reveal new tissue to image, overcoming limited light penetration encountered in microscopy. Two linear stages allow moving the tissue with respect to the microscope objective, acquiring a 2D grid of volumes (1x1x0.3 mm) with OCT and a 2D grid of images (1x1mm) with the confocal arm. This process is repeated automatically, until the entire sample is imaged. Raw data is then post-processed to re-stitch each individual acquisition and obtain a reconstructed volume of the imaged tissue. This design is being used to investigate correlations between white matter and microvasculature changes with aging and with increase in pulse pressure following transaortic constriction in mice. The dual imaging capability of the system allowed to reveal different contrast information: OCT imaging reveals changes in refractive indices giving contrast between white and grey matter in the mouse brain, while transcardial perfusion of FITC or pre-sacrifice injection of Evans Blue shows microsvasculature properties in the brain with confocal imaging.

A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA.

PubMed

Ludgate, Jackie L; Wright, James; Stockwell, Peter A; Morison, Ian M; Eccles, Michael R; Chatterjee, Aniruddha

2017-08-31

Formalin fixed paraffin embedded (FFPE) tumor samples are a major source of DNA from patients in cancer research. However, FFPE is a challenging material to work with due to macromolecular fragmentation and nucleic acid crosslinking. FFPE tissue particularly possesses challenges for methylation analysis and for preparing sequencing-based libraries relying on bisulfite conversion. Successful bisulfite conversion is a key requirement for sequencing-based methylation analysis. Here we describe a complete and streamlined workflow for preparing next generation sequencing libraries for methylation analysis from FFPE tissues. This includes, counting cells from FFPE blocks and extracting DNA from FFPE slides, testing bisulfite conversion efficiency with a polymerase chain reaction (PCR) based test, preparing reduced representation bisulfite sequencing libraries and massively parallel sequencing. The main features and advantages of this protocol are: An optimized method for extracting good quality DNA from FFPE tissues. An efficient bisulfite conversion and next generation sequencing library preparation protocol that uses 50 ng DNA from FFPE tissue. Incorporation of a PCR-based test to assess bisulfite conversion efficiency prior to sequencing. We provide a complete workflow and an integrated protocol for performing DNA methylation analysis at the genome-scale and we believe this will facilitate clinical epigenetic research that involves the use of FFPE tissue.

IMPROVEMENTS IN EPOXY RESIN EMBEDDING METHODS

PubMed Central

Luft, John H.

1961-01-01

Epoxy embedding methods of Glauert and Kushida have been modified so as to yield rapid, reproducible, and convenient embedding methods for electron microscopy. The sections are robust and tissue damage is less than with methacrylate embedding. PMID:13764136

Analysis and Comparison of Extended and Unscented Kalman Filtering Methods for Spacecraft Attitude Determination

DTIC Science & Technology

2010-12-01

3)+m*l^2); fncC.m %# eml function y = fncC(x) Bo=0.5; alf=30*pi/180; y=Bo*sin(x(1,1)+alf); 75 Unscented Kalman Filter – Embedded...Matlab Block %# eml function [x_k1,Pxx_k1] = UKF(x_k,Pxx_k,Y_meas,ts,Q,R,kappa) % This block supports the Embedded MATLAB subset. % See the...torque2omegadot.m EML function Wdot = torque2omegadot(T, J, W) % This function takes input of applied torque (T) in component % elements, current angular

Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues

PubMed Central

Steiner, Carine; Ducret, Axel; Tille, Jean-Christophe; Thomas, Marlene; McKee, Thomas A; Rubbia-Brandt, Laura A; Scherl, Alexander; Lescuyer, Pierre; Cutler, Paul

2014-01-01

Proteomic analysis of tissues has advanced in recent years as instruments and methodologies have evolved. The ability to retrieve peptides from formalin-fixed paraffin-embedded tissues followed by shotgun or targeted proteomic analysis is offering new opportunities in biomedical research. In particular, access to large collections of clinically annotated samples should enable the detailed analysis of pathologically relevant tissues in a manner previously considered unfeasible. In this paper, we review the current status of proteomic analysis of formalin-fixed paraffin-embedded tissues with a particular focus on targeted approaches and the potential for this technique to be used in clinical research and clinical diagnosis. We also discuss the limitations and perspectives of the technique, particularly with regard to application in clinical diagnosis and drug discovery. PMID:24339433

Flood-Emplaced Blocks in Holden Crater

NASA Image and Video Library

2010-10-21

This image from NASA Mars Reconnaissance Orbiter shows blocks of bright, layered rock embedded in darker material that are thought to have been deposited by a giant flood that occurred when Uzboi Valles breached the rim of Holden Crater.

Stego on FPGA: An IWT Approach

PubMed Central

Ramalingam, Balakrishnan

2014-01-01

A reconfigurable hardware architecture for the implementation of integer wavelet transform (IWT) based adaptive random image steganography algorithm is proposed. The Haar-IWT was used to separate the subbands namely, LL, LH, HL, and HH, from 8 × 8 pixel blocks and the encrypted secret data is hidden in the LH, HL, and HH blocks using Moore and Hilbert space filling curve (SFC) scan patterns. Either Moore or Hilbert SFC was chosen for hiding the encrypted data in LH, HL, and HH coefficients, whichever produces the lowest mean square error (MSE) and the highest peak signal-to-noise ratio (PSNR). The fixated random walk's verdict of all blocks is registered which is nothing but the furtive key. Our system took 1.6 µs for embedding the data in coefficient blocks and consumed 34% of the logic elements, 22% of the dedicated logic register, and 2% of the embedded multiplier on Cyclone II field programmable gate array (FPGA). PMID:24723794

Effects of soft X-ray radiation damage on paraffin-embedded rat tissues supported on ultralene: a chemical perspective.

PubMed

Bedolla, Diana E; Mantuano, Andrea; Pickler, Arissa; Mota, Carla Lemos; Braz, Delson; Salata, Camila; Almeida, Carlos Eduardo; Birarda, Giovanni; Vaccari, Lisa; Barroso, Regina Cély; Gianoncelli, Alessandra

2018-05-01

Radiation damage is an important aspect to be considered when analysing biological samples with X-ray techniques as it can induce chemical and structural changes in the specimens. This work aims to provide new insights into the soft X-ray induced radiation damage of the complete sample, including not only the biological tissue itself but also the substrate and embedding medium, and the tissue fixation procedure. Sample preparation and handling involves an unavoidable interaction with the sample matrix and could play an important role in the radiation-damage mechanism. To understand the influence of sample preparation and handling on radiation damage, the effects of soft X-ray exposure at different doses on ultralene, paraffin and on paraffin-embedded rat tissues were studied using Fourier-transform infrared (FTIR) microspectroscopy and X-ray microscopy. Tissues were preserved with three different commonly used fixatives: formalin, glutaraldehyde and Karnovsky. FTIR results showed that ultralene and paraffin undergo a dose-dependent degradation of their vibrational profiles, consistent with radiation-induced oxidative damage. In addition, formalin fixative has been shown to improve the preservation of the secondary structure of proteins in tissues compared with both glutaraldehyde and Karnovsky fixation. However, conclusive considerations cannot be drawn on the optimal fixation protocol because of the interference introduced by both substrate and embedding medium in the spectral regions specific to tissue lipids, nucleic acids and carbohydrates. Notably, despite the detected alterations affecting the chemical architecture of the sample as a whole, composed of tissue, substrate and embedding medium, the structural morphology of the tissues at the micrometre scale is essentially preserved even at the highest exposure dose.

Orientation Control in Thin Films of a High-χ Block Copolymer with a Surface Active Embedded Neutral Layer.

PubMed

Zhang, Jieqian; Clark, Michael B; Wu, Chunyi; Li, Mingqi; Trefonas, Peter; Hustad, Phillip D

2016-01-13

Directed self-assembly (DSA) of block copolymers (BCPs) is an attractive advanced patterning technology being considered for future integrated circuit manufacturing. By controlling interfacial interactions, self-assembled microdomains in thin films of polystyrene-block-poly(methyl methacrylate), PS-b-PMMA, can be oriented perpendicular to surfaces to form line/space or hole patterns. However, its relatively weak Flory interaction parameter, χ, limits its capability to pattern sub-10 nm features. Many BCPs with higher interaction parameters are capable of forming smaller features, but these "high-χ" BCPs typically have an imbalance in surface energy between the respective blocks that make it difficult to achieve the required perpendicular orientation. To address this challenge, we devised a polymeric surface active additive mixed into the BCP solution, referred to as an embedded neutral layer (ENL), which segregates to the top of the BCP film during casting and annealing and balances the surface tensions at the top of the thin film. The additive comprises a second BCP with a "neutral block" designed to provide matched surface tensions with the respective polymers of the main BCP and a "surface anchoring block" with very low surface energy that drives the material to the air interface during spin-casting and annealing. The surface anchoring block allows the film to be annealed above the glass transition temperature of the two materials without intermixing of the two components. DSA was also demonstrated with this embedded neutral top layer formulation on a chemical patterned template using a single step coat and simple thermal annealing. This ENL technology holds promise to enable the use of high-χ BCPs in advanced patterning applications.

Detection of EGFR and KRAS mutations in fine-needle aspirates stored on Whatman FTA cards: is this the tool for biobanking cytological samples in the molecular era?

PubMed

da Cunha Santos, Gilda; Liu, Ni; Tsao, Ming-Sound; Kamel-Reid, Suzanne; Chin, Kayu; Geddie, William R

2010-12-25

The aims of this study were to compare the quality of DNA recovered from fine-needle aspirates (FNAs) stored on Whatman FTA cards with that retrieved from corresponding cell blocks and to determine whether the DNA extracted from the cards is suitable for multiple mutation analyses. FNAs collected from 18 resected lung tumors and cell suspensions from 4 lung cancer cell lines were placed on FTA Indicating Micro Cards and further processed to produce paired formalin-fixed paraffin-embedded (FFPE) cell blocks. Fragment analysis was used for the detection of EGFR exon 19 deletion, and direct sequencing for detection of EGFR exon 21 L858R mutation and exon 2 deletion of KRAS. Corresponding FFPE tissue sections from 2 resection specimens were also tested. Analyses were successful with all FNAs and lung cancer-derived cell lines collected on cards. Polymerase chain reaction failed in 2 cell blocks. For FNAs collected on cards, 5 cases showed EGFR and 3 showed KRAS mutations. Eleven cases were wild type. With cell blocks, 4 cases were found to harbor KRAS and 4 harbored EGFR mutations. All lung cancer-derived cell lines tested positive for their respective mutations, and there was complete agreement between card and cell block FNA samples for EGFR exon 21. For EGFR exon 19, 1 of 18 cases showed discordant results between the card and cell block, and for KRAS 1 of 17. The two resection specimens tested gave concordant results with the FTA card. Storage of cytologic material on FTA cards can maximize and simplify sample procurement for multiple mutational analyses with results similar to those from cell blocks.

A Multiple-Window Video Embedding Transcoder Based on H.264/AVC Standard

NASA Astrophysics Data System (ADS)

Li, Chih-Hung; Wang, Chung-Neng; Chiang, Tihao

2007-12-01

This paper proposes a low-complexity multiple-window video embedding transcoder (MW-VET) based on H.264/AVC standard for various applications that require video embedding services including picture-in-picture (PIP), multichannel mosaic, screen-split, pay-per-view, channel browsing, commercials and logo insertion, and other visual information embedding services. The MW-VET embeds multiple foreground pictures at macroblock-aligned positions. It improves the transcoding speed with three block level adaptive techniques including slice group based transcoding (SGT), reduced frame memory transcoder (RFMT), and syntax level bypassing (SLB). The SGT utilizes prediction from the slice-aligned data partitions in the original bitstreams such that the transcoder simply merges the bitstreams by parsing. When the prediction comes from the newly covered area without slice-group data partitions, the pixels at the affected macroblocks are transcoded with the RFMT based on the concept of partial reencoding to minimize the number of refined blocks. The RFMT employs motion vector remapping (MVR) and intra mode switching (IMS) to handle intercoded blocks and intracoded blocks, respectively. The pixels outside the macroblocks that are affected by newly covered reference frame are transcoded by the SLB. Experimental results show that, as compared to the cascaded pixel domain transcoder (CPDT) with the highest complexity, our MW-VET can significantly reduce the processing complexity by 25 times and retain the rate-distortion performance close to the CPDT. At certain bit rates, the MW-VET can achieve up to 1.5 dB quality improvement in peak signal-to-noise-ratio (PSNR).

Evaluation of the presence of Epstein-Barr virus (EBV) in Iranian patients with thyroid papillary carcinoma.

PubMed

Homayouni, Maryam; Mohammad Arabzadeh, Seyed Ali; Nili, Fatemeh; Razi, Farideh; Amoli, Mahsa Mohammad

2017-07-01

Papillary thyroid carcinoma (PTC) is the most common thyroid cancer. EBV is one of the most important viruses related to different types of malignancies. This study investigated the relationship between EBV and papillary thyroid carcinoma. In this study the presence of Epstein-Barr Nuclear Antigen 1 (EBNA1) gene in papillary thyroid carcinoma tissues were examined by nested-PCR method. Paraffin-embedded tissues (N=41) blocks of thyroid cancer were used. DNA was extracted from all samples and then samples were evaluated for the presence of EBV gene. In 41 samples, EBNA1 was detected in 65.8% of patients with papillary thyroid carcinoma which was significantly higher in younger ages. The significant presence of EBV genome in papillary thyroid carcinoma suggests that this virus may play a role in this cancer especially in younger ages. As a result, monitoring of patients with EBV latent infection for PTC can be very important. Copyright © 2017 Elsevier GmbH. All rights reserved.

Staining paraffin embedded sections of scald of barley before paraffin removal.

PubMed

Xi, K; Burnett, P A

1997-07-01

Staining of paraffin embedded sections with periodic acid-Schiff reagent and fast green before paraffin removal resulted in differentiation of barley seed and leaf tissue from fungal structures of Rhynchosporium secalis. Crystal violet, toluidine blue O and antiline blue also successfully stained fungal structures of R. secalis in barley leaf tissues. Staining of embedded sections before paraffin removal allows simple processing of a series of sections, saves time and reduces solvent consumption.

Development and myogenesis of the vermiform Buddenbrockia (Myxozoa) and implications for cnidarian body plan evolution

PubMed Central

2012-01-01

Background The enigmatic wormlike parasite Buddenbrockia plumatellae has recently been shown to belong to the Myxozoa, which are now supported as a clade within Cnidaria. Most myxozoans are morphologically extremely simplified, lacking major metazoan features such as epithelial tissue layers, gut, nervous system, body axes and gonads. This hinders comparisons to free-living cnidarians and thus an understanding of myxozoan evolution and identification of their cnidarian sister group. However, B. plumatellae is less simplified than other myxozoans and therefore is of specific significance for such evolutionary considerations. Methods We analyse and describe the development of major body plan features in Buddenbrockia worms using a combination of histology, electron microscopy and confocal microscopy. Results Early developmental stages develop a primary body axis that shows a polarity, which is manifested as a gradient of tissue development, enabling distinction between the two worm tips. This polarity is maintained in adult worms, which, in addition, often develop a pore at the distal tip. The musculature comprises tetraradially arranged longitudinal muscle blocks consisting of independent myocytes embedded in the extracellular matrix between inner and outer epithelial tissue layers. The muscle fibres are obliquely oriented and in fully grown worms consistently form an angle of 12° with respect to the longitudinal axis of the worm in each muscle block and hence confer chirality. Connecting cells form a link between each muscle block and constitute four rows of cells that run in single file along the length of the worm. These connecting cells are remnants of the inner epithelial tissue layer and are anchored to the extracellular matrix. They are likely to have a biomechanical function. Conclusions The polarised primary body axis represents an ancient feature present in the last common ancestor of Cnidaria and Bilateria. The tetraradial arrangement of musculature is consistent with a medusozoan affinity for Myxozoa. However, the chiral pattern of muscle fibre orientation is apparently novel within Cnidaria and could thus be a specific adaptation. The presence of independent myocytes instead of Cnidaria-like epitheliomuscular cells can be interpreted as further support for the presence of mesoderm in cnidarians, or it may represent convergent evolution to a bilaterian condition. PMID:22594622

Tumoural specimens for forensic purposes: comparison of genetic alterations in frozen and formalin-fixed paraffin-embedded tissues.

PubMed

Ananian, Viviana; Tozzo, Pamela; Ponzano, Elena; Nitti, Donato; Rodriguez, Daniele; Caenazzo, Luciana

2011-05-01

In certain circumstances, tumour tissue specimens are the only DNA resource available for forensic DNA analysis. However, cancer tissues can show microsatellite instability and loss of heterozygosity which, if concerning the short tandem repeats (STRs) used in the forensic field, can cause misinterpretation of the results. Moreover, though formalin-fixed paraffin-embedded tissues (FFPET) represent a large resource for these analyses, the quality of the DNA obtained from this kind of specimen can be an important limit. In this study, we evaluated the use of tumoural tissue as biological material for the determination of genetic profiles in the forensic field, highlighting which STR polymorphisms are more susceptible to tumour genetic alterations and which of the analysed tumours show a higher genetic variability. The analyses were conducted on samples of the same tissues conserved in different storage conditions, to compare genetic profiles obtained by frozen tissues and formalin-fixed paraffin-embedded tissues. The importance of this study is due to the large number of specimens analysed (122), the large number of polymorphisms analysed for each specimen (39), and the possibility to compare, many years after storage, the same tissue frozen and formalin-fixed paraffin-embedded. In the comparison between the genetic profiles of frozen tumour tissues and FFPET, the same genetic alterations have been reported in both kinds of specimens. However, FFPET showed new alterations. We conclude that the use of FFPET requires greater attention than frozen tissues in the results interpretation and great care in both pre-extraction and extraction processes.

Intraoperative Consultation and Macroscopic Handling: The International Society of Urological Pathology (ISUP) Testicular Cancer Consultation Conference Recommendations.

PubMed

Verrill, Clare; Perry-Keene, Joanna; Srigley, John R; Zhou, Ming; Humphrey, Peter A; Lopez-Beltran, Antonio; Egevad, Lars; Ulbright, Thomas M; Tickoo, Satish K; Epstein, Jonathan I; Compérat, Eva; Berney, Daniel M

2018-06-01

The International Society of Urological Pathology held a conference on issues in testicular and penile pathology in Boston in March 2015, which included a presentation by the testis macroscopic features working group. The presentation focused on current published guidance for macroscopic handling of testicular tumors and retroperitoneal lymph node dissections with a summary of results from an online survey of members preceding the conference. The survey results were used to initiate discussions, but decisions on practice were made by expert consensus rather than voting. The importance of comprehensive assessment at the time of gross dissection with confirmation of findings by microscopic assessment was underscored. For example, the anatomic landmarks denoting the distinction of hilar soft tissue invasion (pT2) from spermatic cord invasion (pT3 category) can only be determined by careful macroscopic assessment in many cases. Other recommendations were to routinely sample epididymis, rete testis, hilar soft tissue, and tunica vaginalis in order to confirm macroscopic invasion of these structures or if not macroscopically evident, to exclude subtle microscopic invasion. Tumors 2 cm or less in greatest dimension should be completely embedded. If the tumor is >2 cm in greatest dimension, 10 blocks or a minimum of 1 to 2 additional blocks per centimeter should be taken (whichever is greater).

Mining the archives: a cross-platform analysis of gene ...

EPA Pesticide Factsheets

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 of nucleic acids. Here we evaluated gene expression profiles derived from fresh-frozen (FRO) and FFPE mouse liver tissues using two DNA microarray protocols and two whole transcriptome sequencing (RNA-seq) library preparation methodologies. The ribo-depletion protocol outperformed the other three methods by having the highest correlations of differentially expressed genes (DEGs) and best overlap of pathways between FRO and FFPE groups. We next tested the effect of sample time in formalin (18 hours or 3 weeks) on gene expression profiles. Hierarchical clustering of the datasets indicated that test article treatment, and not preservation method, was the main driver of gene expression profiles. Meta- and pathway analyses indicated that biological responses were generally consistent for 18-hour and 3-week FFPE samples compared to FRO samples. However, clear erosion of signal intensity with time in formalin was evident, and DEG numbers differed by platform and preservation method. Lastly, we investigated the effect of age in FFPE block on genomic profiles. RNA-seq analysis of 8-, 19-, and 26-year-old control blocks using the ribo-depletion protocol resulted in comparable quality metrics, inc

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

PubMed Central

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

An orthodontic bracket embedded in the medial pterygoid surface: a case report.

PubMed

Wilmott, Sheryl E; Ikeagwuani, Okechukwu; McLeod, Niall M H

2016-01-08

There is a potential risk that orthodontic brackets can become dislodged into the aerodigestive tract. This case illustrates the management of an orthodontic bracket, which became embedded in the deep tissues of the oropharynx. We aim to highlight the potential risk misplaced dental instruments and materials pose, including that they may become embedded in the soft tissues of the throat and suggest that that this possibility should be considered when they cannot be localized.

An orthodontic bracket embedded in the medial pterygoid surface: a case report.

PubMed

Wilmott, Sheryl E; Ikeagwuani, Okechukwu; McLeod, Niall M H

2016-03-01

There is a potential risk that orthodontic brackets can become dislodged into the aerodigestive tract. This case illustrates the management of an orthodontic bracket, which became embedded in the deep tissues of the oropharynx. We aim to highlight the potential risk misplaced dental instruments and materials pose, including that they may become embedded in the soft tissues of the throat and suggest that that this possibility should be considered when they cannot be localized.

Post-embedding tem signal-to-noise ratio of S-100

NASA Technical Reports Server (NTRS)

Fermin, C. D.; Lee, D. H.; Martin, D.

1994-01-01

We assessed the reactivity of purified S-100 antiserum in immuno-electron microscopy by counting the number of gold particles per microns 2 over inner ear tissues embedded in different media. Sections containing predominantly Schwann's cell cytoplasm and nucleus, afferent fiber axoplasm and myelin sheath of chick cochleae were reacted with anti-S-100 IgG, an antibody to a calcium binding protein of neuronal tissues, then labeled with anti-IgG-gold conjugate. This investigation was conducted because previously published procedures, unmodified, did not yield acceptable results. Preparation of all specimens was identical. Only the medium (PolyBed 812, Araldite or Spurr epoxies; and LR White, LR Gold or Lowicryl plastics) was changed. The medium was made the changing variable because antigens available in post-embedding immuno-electron microscopy are decreased by heat, either used and/or released during polymerization of the embedding medium. The results indicate that: (a) none of the embedding media above provided optimal signal-to-noise ratio for all parts of the nerve stained in the same section; (b) aggregation of gold particles over cells was highest in embedding media with high background labeling over areas devoid of tissue (noise); (c) aggregation occurred randomly throughout both cellular and acellular regions; and (d) particles aggregated less and were distributed more evenly in tissues from media yielding good ultrastructural integrity.

Experimental and numeric stress analysis of titanium and zirconia one-piece dental implants.

PubMed

Mobilio, Nicola; Stefanoni, Filippo; Contiero, Paolo; Mollica, Francesco; Catapano, Santo

2013-01-01

To compare the stress in bone around zirconia and titanium implants under loading. A one-piece zirconia implant and a replica of the same implant made of commercially pure titanium were embedded in two self-curing acrylic resin blocks. To measure strain, a strain gauge was applied on the surface of the two samples. Loads of 50, 100, and 150 N, with orientations of 30, 45, and 60 degrees with respect to the implant axis were applied on the implant. Strain under all loading conditions on both samples was measured. Three-dimensional virtual replicas of both the implants were reproduced using the finite element method and inserted into a virtual acrylic resin block. All the materials were considered isotropic, linear, and elastic. The same geometry and loading conditions of the experimental setup were used to realize two new models, with the implants embedded within a virtual bone block. Very close values of strain in the two implants embedded in acrylic resin were obtained both experimentally and numerically. The stress states generated by the implants embedded in virtual bone were also very similar, even if the two implants moved differently. Moreover, the stress levels were higher on cortical bone than on trabecular bone. The stress levels in bone, generated by the two implants, appeared to be very similar. From a mechanical point of view, zirconia is a feasible substitute for titanium.

Mast cells and angiogenesis in wound healing.

PubMed

Gaber, Mohamed A; Seliet, Iman A; Ehsan, Nermin A; Megahed, Mohamed A

2014-02-01

To investigate the role of mast cells and vascular endothelial growth factor (VEGF) as a mediator of angiogenesis to promote wound healing in surgical and pathological scars. The study was carried out on 40 patients who presented with active scar lesions. They were subdivided into 4 groups. They included granulation tissue (10 cases), surgical scar (10 cases), hypertrophic scar (10 cases), and keloid scar (10 cases). Also 10 healthy volunteers of the same age and sex were selected as a control group. Skin biopsies were taken from the patients and the control group. Skin biopsies from clinically assessed studied groups were processed for routine histology and embedded in paraffin. Four sections were prepared from each paraffin block. The first section was stained with hematoxylin and eosin for histological evaluation. The second and third sections were processed for immunostaining of mast cells that contain chymase (MCCs) and mast cells that contain tryptase (MCTs). The fourth section was processed for immunostaining of VEGF. MCCs exhibited mild expression in normal tissue, granulation tissue, and surgical, hypertrophic and keloid scars. MCTs exhibited mild expression in normal tissue, granulation tissue and keloid, whereas moderate expression was exhibited in hypertrophic and surgical scars. VEGF expression was absent in normal tissue, mild in keloid, surgical and hypertrophic scars, and moderate in keloids and granulation tissue. Mast cell expression variation among different scar types signals the pathological evolution of the lesion, and hence may guide the need for therapeutic intervention.

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

EPA Science Inventory

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...

Raloxifene microsphere-embedded collagen/chitosan/β-tricalcium phosphate scaffold for effective bone tissue engineering.

PubMed

Zhang, Ming-Lei; Cheng, Ji; Xiao, Ye-Chen; Yin, Ruo-Feng; Feng, Xu

2017-02-25

Engineering novel scaffolds that can mimic the functional extracellular matrix (ECM) would be a great achievement in bone tissue engineering. This paper reports the fabrication of novel collagen/chitosan/β-tricalcium phosphate (CCTP) based tissue engineering scaffold. In order to improve the regeneration ability of scaffold, we have embedded raloxifene (RLX)-loaded PLGA microsphere in the CCTP scaffold. The average pore of scaffold was in the range of 150-200μm with ideal mechanical strength and swelling/degradation characteristics. The release rate of RLX from the microsphere (MS) embedded scaffold was gradual and controlled. Also a significantly enhanced cell proliferation was observed in RLX-MS exposed cell group suggesting that microsphere/scaffold could be an ideal biomaterial for bone tissue engineering. Specifically, RLX-MS showed a significantly higher Alizarin red staining indicating the higher mineralization capacity of this group. Furthermore, a high alkaline phosphatase (ALP) activity for RLX-MS exposed group after 15days incubation indicates the bone regeneration capacity of MC3T3-E1 cells. Overall, present study showed that RLX-loaded microsphere embedded scaffold has the promising potential for bone tissue engineering applications. Copyright © 2016. Published by Elsevier B.V.

Evaluation of laser ablation microtomy for correlative microscopy of hard tissues.

PubMed

Boyde, A

2018-02-27

Laser ablation machining or microtomy (LAM) is a relatively new approach to producing slide mounted sections of translucent materials. We evaluated the method with a variety of problems from the bone, joint and dental tissues fields where we require thin undecalcified and undistorted sections for correlative light microscopy (LM) and backscattered electron scanning electron microscopy (BSE SEM). All samples were embedded in poly-methylmethacrlate (PMMA) and flat block surfaces had been previously studied by BSE-SEM and confocal scanning light microscopy (CSLM). Most were also studied by X-yay microtomography (XMT). The block surface is stuck to a glass slide with cyanoacrylate adhesive. Setting the section thickness and levelling uses inbuilt optical coherence tomographic imaging. Tight focusing of near-infrared laser radiation in the sectioning plane gives extreme intensities causing photodisruption of material at the focal point. The laser beam is moved by a fast scanner to write a cutting line, which is simultaneously moved by an XY positioning unit to create a sectioning plane. The block is thereby released from the slide, leaving the section stuck to the slide. Light, wet polishing on the finest grade (4000 grit) silicon carbide polishing paper is used to remove a 1-2 μm thick damaged layer at the surface of the section. Sections produced by laser cutting are fine in quality and superior to those produced by mechanical cutting and can be thinner than the 'voxel' in most laboratory X-ray microtomography systems. The present extensive pilot studies have shown that it works to produce samples which we can study by both light and electron microscopy. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Morphological changes in the sciatic nerve, skeletal muscle, heart and brain of rabbits receiving continuous sciatic nerve block with 0.2% ropivacaine.

PubMed

Zhou, Yangning; He, Miao; Zou, Tianxiao; Yu, Bin

2015-01-01

To investigate the morphological changes in various tissues of rabbits receiving sciatic nerve block with 0.2% ropivacaine for 48 h. Twenty healthy were randomly assigned to normal saline group (N group) and ropivacaine group (R group). The right sciatic nerve was exposed, and a nerve-blocking trocar cannula embedded. Animals received an injection of 0.5% ropivacaine hydrochloride at a dose of 0.75 ml/kg. Rabbit was then connected to an infusion pump containing 50 ml of normal saline in N group, or to a infusion pump containing 0.2% ropivacaine hydrochloride in R group at 0.25 ml/kg•h-1. In both R group and N group, a small number of nerve cells exhibited pyknotic degeneration. More nerve cells with pyknotic degeneration were found in R group than in N group (P<0.001). At 48 h after surgery, there was a significant correlation between the abnormality of right hind limb and the degree of edema in sciatic nerve (P<0.01). Pyknotic degeneration of sciatic nerve increased after an infusion of 0.2% ropivacaine hydrochloride for 48 h, suggesting the neurotoxicity of ropivacaine. An infusion of 0.2% ropivacaine hydrochloride for 48 h may cause necrosis of skeletal muscle cells. The sciatic nerve edema would greatly affect the hindlimb motor while both pyknotic degeneration of sciatic nerve and skeletal muscle have little influence on the hindlimb movement. After an infusion of 0.2% ropivacaine hydrochloride for 48 h, the morphology of right atrium and brain tissues around the ventriculus tertius and medulla oblongata remained unchanged.

Young investigator challenge: Validation and optimization of immunohistochemistry protocols for use on cellient cell block specimens.

PubMed

Sauter, Jennifer L; Grogg, Karen L; Vrana, Julie A; Law, Mark E; Halvorson, Jennifer L; Henry, Michael R

2016-02-01

The objective of the current study was to establish a process for validating immunohistochemistry (IHC) protocols for use on the Cellient cell block (CCB) system. Thirty antibodies were initially tested on CCBs using IHC protocols previously validated on formalin-fixed, paraffin-embedded tissue (FFPE). Cytology samples were split to generate thrombin cell blocks (TCB) and CCBs. IHC was performed in parallel. Antibody immunoreactivity was scored, and concordance or discordance in immunoreactivity between the TCBs and CCBs for each sample was determined. Criteria for validation of an antibody were defined as concordant staining in expected positive and negative cells, in at least 5 samples each, and concordance in at least 90% of the samples total. Antibodies that failed initial validation were retested after alterations in IHC conditions. Thirteen of the 30 antibodies (43%) did not meet initial validation criteria. Of those, 8 antibodies (calretinin, clusters of differentiation [CD] 3, CD20, CDX2, cytokeratin 20, estrogen receptor, MOC-31, and p16) were optimized for CCBs and subsequently validated. Despite several alterations in conditions, 3 antibodies (Ber-EP4, D2-40, and paired box gene 8 [PAX8]) were not successfully validated. Nearly one-half of the antibodies tested in the current study failed initial validation using IHC conditions that were established in the study laboratory for FFPE material. Although some antibodies subsequently met validation criteria after optimization of conditions, a few continued to demonstrate inadequate immunoreactivity. These findings emphasize the importance of validating IHC protocols for methanol-fixed tissue before clinical use and suggest that optimization for alcohol fixation may be needed to obtain adequate immunoreactivity on CCBs. © 2016 American Cancer Society.

Optimal temperature control of tissue embedded with gold nanoparticles for enhanced thermal therapy based on two-energy equation model.

PubMed

Wang, Shen-Ling; Qi, Hong; Ren, Ya-Tao; Chen, Qin; Ruan, Li-Ming

2018-05-01

Thermal therapy is a very promising method for cancer treatment, which can be combined with chemotherapy, radiotherapy and other programs for enhanced cancer treatment. In order to get a better effect of thermal therapy in clinical applications, optimal internal temperature distribution of the tissue embedded with gold nanoparticles (GNPs) for enhanced thermal therapy was investigated in present research. The Monte Carlo method was applied to calculate the heat generation of the tissue embedded with GNPs irradiated by continuous laser. To have a better insight into the physical problem of heat transfer in tissues, the two-energy equation was employed to calculate the temperature distribution of the tissue in the process of GNPs enhanced therapy. The Arrhenius equation was applied to evaluate the degree of permanent thermal damage. A parametric study was performed to investigate the influence factors on the tissue internal temperature distribution, such as incident light intensity, the GNPs volume fraction, the periodic heating and cooling time, and the incident light position. It was found that period heating and cooling strategy can effectively avoid overheating of skin surface and heat damage of healthy tissue. Lower GNPs volume fraction will be better for the heat source distribution. Furthermore, the ring heating strategy is superior to the central heating strategy in the treatment effect. All the analysis provides theoretical guidance for optimal temperature control of tissue embedded with GNP for enhanced thermal therapy. Copyright © 2018 Elsevier Ltd. All rights reserved.

Screening prostate cancer using a portable near infrared scanning imaging unit with an optical fiber-based rectal probe

NASA Astrophysics Data System (ADS)

Pu, Yang; Wang, Wubao; Tang, Guichen; Budansky, Yury; Sharonov, Mikhail; Xu, Min; Achilefu, Samuel; Eastham, James A.; Alfano, Robert R.

2012-01-01

A portable near infrared scanning polarization imaging unit with an optical fiber-based rectal probe, namely Photonic Finger, was designed and developed o locate the 3D position of abnormal prostate site inside normal prostate tissue. An inverse algorithm, Optical Tomography using Independent Component Analysis (OPTICA) was improved particularly to unmix the signal from targets (cancerous tissue) embedded in a turbid medium (normal tissue) in the backscattering imaging geometry. Photonic Finger combined with OPTICA was tested to characterize different target(s) inside different tissue medium, including cancerous prostate tissue embedded by large piece of normal tissue.

A high-resolution method for the localization of proanthocyanidins in plant tissues

PubMed Central

2011-01-01

Background Histochemical staining of plant tissues with 4-dimethylaminocinnamaldehyde (DMACA) or vanillin-HCl is widely used to characterize spatial patterns of proanthocyanidin accumulation in plant tissues. These methods are limited in their ability to allow high-resolution imaging of proanthocyanidin deposits. Results Tissue embedding techniques were used in combination with DMACA staining to analyze the accumulation of proanthocyanidins in Lotus corniculatus (L.) and Trifolium repens (L.) tissues. Embedding of plant tissues in LR White or paraffin matrices, with or without DMACA staining, preserved the physical integrity of the plant tissues, allowing high-resolution imaging that facilitated cell-specific localization of proanthocyanidins. A brown coloration was seen in proanthocyanidin-producing cells when plant tissues were embedded without DMACA staining and this was likely to have been due to non-enzymatic oxidation of proanthocyanidins and the formation of colored semiquinones and quinones. Conclusions This paper presents a simple, high-resolution method for analysis of proanthocyanidin accumulation in organs, tissues and cells of two plant species with different patterns of proanthocyanidin accumulation, namely Lotus corniculatus (birdsfoot trefoil) and Trifolium repens (white clover). This technique was used to characterize cell type-specific patterns of proanthocyanidin accumulation in white clover flowers at different stages of development. PMID:21595992

Comparison of multivariate analysis methods for extracting the paraffin component from the paraffin-embedded cancer tissue spectra for Raman imaging

NASA Astrophysics Data System (ADS)

Meksiarun, Phiranuphon; Ishigaki, Mika; Huck-Pezzei, Verena A. C.; Huck, Christian W.; Wongravee, Kanet; Sato, Hidetoshi; Ozaki, Yukihiro

2017-03-01

This study aimed to extract the paraffin component from paraffin-embedded oral cancer tissue spectra using three multivariate analysis (MVA) methods; Independent Component Analysis (ICA), Partial Least Squares (PLS) and Independent Component - Partial Least Square (IC-PLS). The estimated paraffin components were used for removing the contribution of paraffin from the tissue spectra. These three methods were compared in terms of the efficiency of paraffin removal and the ability to retain the tissue information. It was found that ICA, PLS and IC-PLS could remove the paraffin component from the spectra at almost the same level while Principal Component Analysis (PCA) was incapable. In terms of retaining cancer tissue spectral integrity, effects of PLS and IC-PLS on the non-paraffin region were significantly less than that of ICA where cancer tissue spectral areas were deteriorated. The paraffin-removed spectra were used for constructing Raman images of oral cancer tissue and compared with Hematoxylin and Eosin (H&E) stained tissues for verification. This study has demonstrated the capability of Raman spectroscopy together with multivariate analysis methods as a diagnostic tool for the paraffin-embedded tissue section.

PATHOLOGY AND MOLECULAR DETECTION OF RABIES VIRUS IN FERRET BADGERS ASSOCIATED WITH A RABIES OUTBREAK IN TAIWAN.

PubMed

Chiou, Hue-Ying; Jeng, Chian-Ren; Wang, Hurng-Yi; Inoue, Satoshi; Chan, Fang-Tse; Liao, Jiunn-Wang; Chiou, Ming-Tang; Pang, Victor Fei

2016-01-01

Until Rabies virus (RABV) infection in Taiwan ferret badgers (TWFB; Melogale moschata subaurantiaca) was diagnosed in mid-June 2013, Taiwan had been considered rabies free for >50 yr. Although rabies has also been reported in ferret badgers in China, the pathologic changes and distribution of viral antigens of ferret badger-associated rabies have not been described. We performed a comprehensive pathologic study and molecular detection of rabies virus in three necropsied rabid TWFBs and evaluated archival paraffin-embedded tissue blocks of six other TWFBs necropsied during 2004 and 2012. As in other RABV-infected species, the characteristic pathologic changes in TWFBs were nonsuppurative meningoencephalomyelitis, ganglionitis, and the formation of typical intracytoplasmic Negri bodies, with the brain stem most affected. There was also variable spongiform degeneration, primarily in the perikaryon of neurons and neuropil, in the cerebral cortex, thalamus, and brain stem. In nonnervous system tissues, representative lesions included adrenal necrosis and lymphocytic interstitial sialadenitis. Immunohistochemical staining and fluorescent antibody test demonstrated viral antigens in the perikaryon of the neurons and axonal or dendritic processes throughout the nervous tissue and in the macrophages in various tissues. Similar to raccoons (Procyon lotor) and skunks (Mephitidae), the nervous tissue of rabid TWFBs displayed widely dispersed lesions, RABV antigens, and large numbers of Negri bodies. We traced the earliest rabid TWFB case back to 2004.

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

PubMed

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.

The Prostate, Lung, Colorectal and Ovarian Cancer (PLCO) Screening Trial Pathology Tissue Resource.

PubMed

Zhu, Claire S; Huang, Wen-Yi; Pinsky, Paul F; Berg, Christine D; Sherman, Mark; Yu, Kelly J; Carrick, Danielle M; Black, Amanda; Hoover, Robert; Lenz, Petra; Williams, Craig; Hawkins, Laura; Chaloux, Matthew; Yurgalevitch, Susan; Mathew, Sunitha; Miller, Amy; Olivo, Vanessa; Khan, Asia; Pretzel, Shannon M; Multerer, Deborah; Beckmann, Patricia; Broski, Karen G; Freedman, Neal D

2016-12-01

Pathology tissue specimens with associated epidemiologic and clinical data are valuable for cancer research. The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial undertook a large-scale effort to create a public resource of pathology tissues from PLCO participants who developed a cancer during the trial. Formalin-fixed paraffin-embedded tissue blocks were obtained from pathology laboratories on a loan basis for central processing of tissue microarrays, with additional free-standing tissue cores collected for nucleic acid extraction. Pathology tissue specimens were obtained for prostate cancer (n = 1,052), lung cancer (n = 434), colorectal cancer (n = 675) and adenoma (n = 658), ovarian cancer and borderline tumors (n = 212), breast cancer (n = 870), and bladder cancer (n = 204). The process of creating this resource was complex, involving multidisciplinary teams with expertise in pathology, epidemiology, information technology, project management, and specialized laboratories. Creating the PLCO tissue resource required a multistep process, including obtaining medical records and contacting pathology departments where pathology materials were stored after obtaining necessary patient consent and authorization. The potential to link tissue biomarkers to prospectively collected epidemiologic information, screening and clinical data, and matched blood or buccal samples offers valuable opportunities to study etiologic heterogeneity, mechanisms of carcinogenesis, and biomarkers for early detection and prognosis. The methods and protocols developed for this effort, and the detailed description of this resource provided here, will be useful for those seeking to use PLCO pathology tissue specimens for their research and may also inform future tissue collection efforts in other settings. Cancer Epidemiol Biomarkers Prev; 25(12); 1635-42. ©2016 AACR. ©2016 American Association for Cancer Research.

Hiding Electronic Patient Record (EPR) in medical images: A high capacity and computationally efficient technique for e-healthcare applications.

PubMed

Loan, Nazir A; Parah, Shabir A; Sheikh, Javaid A; Akhoon, Jahangir A; Bhat, Ghulam M

2017-09-01

A high capacity and semi-reversible data hiding scheme based on Pixel Repetition Method (PRM) and hybrid edge detection for scalable medical images has been proposed in this paper. PRM has been used to scale up the small sized image (seed image) and hybrid edge detection ensures that no important edge information is missed. The scaled up version of seed image has been divided into 2×2 non overlapping blocks. In each block there is one seed pixel whose status decides the number of bits to be embedded in the remaining three pixels of that block. The Electronic Patient Record (EPR)/data have been embedded by using Least Significant and Intermediate Significant Bit Substitution (ISBS). The RC4 encryption has been used to add an additional security layer for embedded EPR/data. The proposed scheme has been tested for various medical and general images and compared with some state of art techniques in the field. The experimental results reveal that the proposed scheme besides being semi-reversible and computationally efficient is capable of handling high payload and as such can be used effectively for electronic healthcare applications. Copyright © 2017. Published by Elsevier Inc.

Observations on the preparation of sections of dental hard and soft tissues without conventional embedding procedures.

PubMed

Mok, Y C; Fearnhead, R W

1985-09-01

Inexpensive thin copper discs loaded with diamonds embedded in small slits around the periphery, may be used to cut sections from unembedded tooth samples without disrupting the cellular and extracellular components intimately associated with hard tissue interfaces. The tissue may be unfixed, fixed or cut using fixation or dye solutions as the lubricant. The use of these discs therefore opens up new avenues of histochemical investigation of hard tissue unrestricted by those artefacts associated with conventional or traditional methods of preparation.

Evaluation of the branched-chain DNA assay for measurement of RNA in formalin-fixed tissues.

PubMed

Knudsen, Beatrice S; Allen, April N; McLerran, Dale F; Vessella, Robert L; Karademos, Jonathan; Davies, Joan E; Maqsodi, Botoul; McMaster, Gary K; Kristal, Alan R

2008-03-01

We evaluated the branched-chain DNA (bDNA) assay QuantiGene Reagent System to measure RNA in formalin-fixed, paraffin-embedded (FFPE) tissues. The QuantiGene Reagent System does not require RNA isolation, avoids enzymatic preamplification, and has a simple workflow. Five selected genes were measured by bDNA assay; quantitative polymerase chain reaction (qPCR) was used as a reference method. Mixed-effect statistical models were used to partition the overall variance into components attributable to xenograft, sample, and assay. For FFPE tissues, the coefficients of reliability were significantly higher for the bDNA assay (93-100%) than for qPCR (82.4-95%). Correlations between qPCR(FROZEN), the gold standard, and bDNA(FFPE) ranged from 0.60 to 0.94, similar to those from qPCR(FROZEN) and qPCR(FFPE). Additionally, the sensitivity of the bDNA assay in tissue homogenates was 10-fold higher than in purified RNA. In 9- to 13-year-old blocks with poor RNA quality, the bDNA assay allowed the correct identification of the overexpression of known cancer genes. In conclusion, the QuantiGene Reagent System is considerably more reliable, reproducible, and sensitive than qPCR, providing an alternative method for the measurement of gene expression in FFPE tissues. It also appears to be well suited for the clinical analysis of FFPE tissues with diagnostic or prognostic gene expression biomarker panels for use in patient treatment and management.

Evaluation of the Branched-Chain DNA Assay for Measurement of RNA in Formalin-Fixed Tissues

PubMed Central

Knudsen, Beatrice S.; Allen, April N.; McLerran, Dale F.; Vessella, Robert L.; Karademos, Jonathan; Davies, Joan E.; Maqsodi, Botoul; McMaster, Gary K.; Kristal, Alan R.

2008-01-01

We evaluated the branched-chain DNA (bDNA) assay QuantiGene Reagent System to measure RNA in formalin-fixed, paraffin-embedded (FFPE) tissues. The QuantiGene Reagent System does not require RNA isolation, avoids enzymatic preamplification, and has a simple workflow. Five selected genes were measured by bDNA assay; quantitative polymerase chain reaction (qPCR) was used as a reference method. Mixed-effect statistical models were used to partition the overall variance into components attributable to xenograft, sample, and assay. For FFPE tissues, the coefficients of reliability were significantly higher for the bDNA assay (93–100%) than for qPCR (82.4–95%). Correlations between qPCRFROZEN, the gold standard, and bDNAFFPE ranged from 0.60 to 0.94, similar to those from qPCRFROZEN and qPCRFFPE. Additionally, the sensitivity of the bDNA assay in tissue homogenates was 10-fold higher than in purified RNA. In 9- to 13-year-old blocks with poor RNA quality, the bDNA assay allowed the correct identification of the overexpression of known cancer genes. In conclusion, the QuantiGene Reagent System is considerably more reliable, reproducible, and sensitive than qPCR, providing an alternative method for the measurement of gene expression in FFPE tissues. It also appears to be well suited for the clinical analysis of FFPE tissues with diagnostic or prognostic gene expression biomarker panels for use in patient treatment and management. PMID:18276773

[Measurement of periapical pressure created by occlusal loading].

PubMed

Dobó, Nagy Csaba; Fejérdy, Pál; Angyal, János; Harasztosi, Lajos; Daróczi, Lajos; Beke, Dezsó; Wesselink, Paul R

2004-04-01

The aim of this study was to develop an in vitro model in which the pressure in the periapical tissues can be measured during loading. Extracted human maxillary central incisors were embedded into resin blocks that had physical characteristics similar to bone and periodontal ligament. Each tooth was loaded with 20, 40, 50, 60, 75, 85, 100, 200, 300 and 450 N vertical forces from the incisal edge of the crown; this procedure was carried out three consecutive times. A minute resistor embedded in the periapical space was used to detect apical pressure changes during occlusal loading. The ratio of apical pressure changes (delta P) to the loading force changes (delta F) was calculated. The periapical pressure detected was in direct proportion to the loading force. The mean value of delta P/delta F was 5.994 kPa/N (SD = 2.04). Direct proportionality was found between the coronal loading and the apical hydrostatic pressure. The (delta P)/(delta F) ratio determined in this study makes it easier to estimate the apical hydrostatic pressure values during occlusal loading of single rooted teeth. In this study the apical pressure generated under occlusal loading was of the same magnitude as that estimated with the finite element method.

Measurement of periapical pressure created by occlusal loading.

PubMed

Dobó-Nagy, C; Fejérdy, P; Angyal, J; Harasztosi, L; Daróczi, L; Beke, D; Wesselink, P R

2003-10-01

To develop an in vitro model in which the pressure in the periapical tissues can be measured during loading. Extracted human maxillary central incisors were embedded in resin blocks that had physical characteristics similar to those of bone and periodontal ligament. Each tooth was loaded with 20, 40, 50, 60, 75, 85, 100, 200, 300 and 450 N vertical forces from the incisal edge of the crown on three consecutive occasions. A minute resistor embedded in the periapical space was used to detect apical pressure changes during occlusal loading. The ratio of apical pressure changes (DeltaP) to the loading force changes (DeltaF) was calculated. The periapical pressure detected was in direct proportion to the loading force. The mean value of DeltaP/DeltaF was 5.994 kPa N-1 (SD = 2.04). Direct proportionality was found between the coronal loading and the apical hydrostatic pressure. The DeltaP/DeltaF ratio determined in this study makes it easier to estimate the apical hydrostatic pressure values during occlusal loading of single-rooted teeth. In this study, the apical pressure generated under occlusal loading was the same magnitude as that estimated with the finite element method.

Cell block samples from malignant pleural effusion might be valid alternative samples for anaplastic lymphoma kinase detection in patients with advanced non-small-cell lung cancer.

PubMed

Zhou, Jianya; Yao, Hongtian; Zhao, Jing; Zhang, Shumeng; You, Qihan; Sun, Ke; Zou, Yinying; Zhou, Caicun; Zhou, Jianying

2015-06-01

To evaluate the clinical value of cell block samples from malignant pleural effusion (MPE) as alternative samples to tumour tissue for anaplastic lymphoma kinase (ALK) detection in patients with advanced non-small-cell lung cancer (NSCLC). Fifty-two matched samples were eligible for analysis. ALK status was detected by Ventana immunohistochemistry (IHC) (with the D5F3 clone), reverse transcription polymerase chain reaction (RT-PCR) and fluorescence in-situ hybridization (FISH) in MPE cell block samples, and by FISH in tumour tissue block samples. In total, ALK FISH results were obtained for 52 tumour tissue samples and 41 MPE cell block samples. Eight cases (15.4%) were ALK-positive in tumour tissue samples by FISH, and among matched MPE cell block samples, five were ALK-positive by FISH, seven were ALK-positive by RT-PCR, and eight were ALK-positive by Ventana IHC. The ALK status concordance rates between tumour tissue and MPE cell block samples were 78.9% by FISH, 98.1% by RT-PCR, and 100% by Ventana IHC. In MPE cell block samples, the sensitivity and specificity of Ventana IHC (100% and 100%) and RT-PCR (87.5% and 100%) were higher than those of FISH (62.5% and 100%). Malignant pleural effusion cell block samples had a diagnostic performance for ALK detection in advanced NSCLC that was comparable to that of tumour tissue samples. MPE cell block samples might be valid alternative samples for ALK detection when tissue is not available. Ventana IHC could be the most suitable method for ALK detection in MPE cell block samples. © 2014 John Wiley & Sons Ltd.

Histological methods to determine blood flow distribution with fluorescent microspheres.

PubMed

Luchtel, D L; Boykin, J C; Bernard, S L; Glenny, R W

1998-11-01

We evaluated several histological methods and determined their advantages and disadvantages for histological studies of tissues and organs perfused with fluorescent microspheres. Microspheres retained their fluorescence in 7-10 microm serial sections with a change in the antimedium from toluene when samples were fixed in formalin and embedded in paraffin. Several antimedia allowed both wax infiltration of tissue and preservation of microsphere fluorescence. Histoclear II was the best substitute for toluene. When samples were fixed in formalin and embedded in glycol methacrylate, thinner (3-5 microm) sections provided greater histological detail but had fewer microspheres per section. Air dried lung tissue followed by Vibratome sectioning provided thick sections (100 microm) that facilitated rapid survey of large volumes of tissue for microspheres but limited histological detail, and the air drying procedure was restricted to lung tissue. Samples fixed in formalin followed by Vibratome sectioning of unembedded tissue provided better histological detail of lung tissue and was also useful for other organs. These sections were more difficult to handle and to mount on slides compared to air dried tissue, whereas fixed tissue embedded in gelatin provided better tissue support for Vibratome sectioning. Rapid freezing followed by cryo-microtome sectioning resulted in frozen sections that were relatively difficult to handle compared to embedded or unembedded tissue; they also deteriorated relatively rapidly with time. Paraffin sections were stained with hematoxylin and eosin or with aqueous methyl green, although tissue autofluorescence by itself was usually sufficient to identify histological features. Methacrylate sections quenched tissue autofluorescence, and Lee's stain or Richardson's stain were used for staining sections. Toluene based mountants such as Cytoseal quenched fluorescence, particularly the red fluorescent microspheres. Aqueous based mountants such as Aquamount, Crystal/Mount, Fluoromount-G were substituted, although such preparations were not as permanent as Cytoseal mounted coverglasses and tended to cause fading of stained sections.

A comparative study to evaluate liquid dish washing soap as an alternative to xylene and alcohol in deparaffinization and hematoxylin and eosin staining.

PubMed

Pandey, Pinki; Dixit, Alok; Tanwar, Aparna; Sharma, Anuradha; Mittal, Sanjeev

2014-07-01

Our study presents a new deparaffinizing and hematoxylin and eosin (H and E) staining method that involves the use of easily available, nontoxic and eco-friendly liquid diluted dish washing soap (DWS) by completely eliminating expensive and hazardous xylene and alcohol from deparaffinizing and rehydration prior to staining, staining and from dehydration prior to mounting. The aim was to evaluate and compare the quality of liquid DWS treated xylene and alcohol free (XAF) sections with that of the conventional H and E sections. A total of 100 paraffin embedded tissue blocks from different tissues were included. From each tissue block, one section was stained with conventional H and E (normal sections) and the other with XAF H and E (soapy sections) staining method. Slides were scored using five parameters: Nuclear, cytoplasmic, clarity, uniformity, and crispness of staining. Z-test was used for statistical analysis. Soapy sections scored better for cytoplasmic (90%) and crisp staining (95%) with a statistically significant difference. Whereas for uniformity of staining, normal sections (88%) scored over soapy sections (72%) (Z = 2.82, P < 0.05). For nuclear (90%) and clarity of staining (90%) total scored favored soapy sections, but the difference was not statistically significant. About 84% normal sections stained adequately for diagnosis when compared with 86% in soapy sections (Z = 0.396, P > 0.05). Liquid DWS is a safe and efficient alternative to xylene and alcohol in deparaffinization and routine H and E staining procedure. We are documenting this project that can be used as a model for other histology laboratories.

A comparative study to evaluate liquid dish washing soap as an alternative to xylene and alcohol in deparaffinization and hematoxylin and eosin staining

PubMed Central

Pandey, Pinki; Dixit, Alok; Tanwar, Aparna; Sharma, Anuradha; Mittal, Sanjeev

2014-01-01

Introduction: Our study presents a new deparaffinizing and hematoxylin and eosin (H and E) staining method that involves the use of easily available, nontoxic and eco-friendly liquid diluted dish washing soap (DWS) by completely eliminating expensive and hazardous xylene and alcohol from deparaffinizing and rehydration prior to staining, staining and from dehydration prior to mounting. The aim was to evaluate and compare the quality of liquid DWS treated xylene and alcohol free (XAF) sections with that of the conventional H and E sections. Materials and Methods: A total of 100 paraffin embedded tissue blocks from different tissues were included. From each tissue block, one section was stained with conventional H and E (normal sections) and the other with XAF H and E (soapy sections) staining method. Slides were scored using five parameters: Nuclear, cytoplasmic, clarity, uniformity, and crispness of staining. Z-test was used for statistical analysis. Results: Soapy sections scored better for cytoplasmic (90%) and crisp staining (95%) with a statistically significant difference. Whereas for uniformity of staining, normal sections (88%) scored over soapy sections (72%) (Z = 2.82, P < 0.05). For nuclear (90%) and clarity of staining (90%) total scored favored soapy sections, but the difference was not statistically significant. About 84% normal sections stained adequately for diagnosis when compared with 86% in soapy sections (Z = 0.396, P > 0.05). Conclusion: Liquid DWS is a safe and efficient alternative to xylene and alcohol in deparaffinization and routine H and E staining procedure. We are documenting this project that can be used as a model for other histology laboratories. PMID:25328332

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

PubMed

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.

A novel image watermarking method based on singular value decomposition and digital holography

NASA Astrophysics Data System (ADS)

Cai, Zhishan

2016-10-01

According to the information optics theory, a novel watermarking method based on Fourier-transformed digital holography and singular value decomposition (SVD) is proposed in this paper. First of all, a watermark image is converted to a digital hologram using the Fourier transform. After that, the original image is divided into many non-overlapping blocks. All the blocks and the hologram are decomposed using SVD. The singular value components of the hologram are then embedded into the singular value components of each block using an addition principle. Finally, SVD inverse transformation is carried out on the blocks and hologram to generate the watermarked image. The watermark information embedded in each block is extracted at first when the watermark is extracted. After that, an averaging operation is carried out on the extracted information to generate the final watermark information. Finally, the algorithm is simulated. Furthermore, to test the encrypted image's resistance performance against attacks, various attack tests are carried out. The results show that the proposed algorithm has very good robustness against noise interference, image cut, compression, brightness stretching, etc. In particular, when the image is rotated by a large angle, the watermark information can still be extracted correctly.

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

NASA Astrophysics Data System (ADS)

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.

Preventing False Negatives for Histochemical Detection of Phenolics and Lignins in PEG-Embedded Plant Tissues

PubMed Central

Ferreira, Bruno G.; Falcioni, Renan; Guedes, Lubia M.; Avritzer, Sofia C.; Antunes, Werner C.; Souza, Luiz A.; Isaias, Rosy M.S.

2016-01-01

Polyethylene glycol (PEG) is a low-cost and advantageous embedding medium, which maintains the majority of cell contents unaltered during the embedding process. Some hard or complex plant materials are better embedded in PEG than in other usual embedding media. However, the histochemical tests for phenolics and lignins in PEG-embedded plant tissues commonly result in false negatives. We hypothesize that these false negatives should be prevented by the use of distinct fixatives, which should avoid the bonds between PEG and phenols. Novel protocols for phenolics and flavanols detection are efficiently tested, with fixation of the samples in ferrous sulfate and formalin or in caffeine and sodium benzoate, respectively. The differentiation of lignin types is possible in safranin-stained sections observed under fluorescence. The Maule’s test faultlessly distinguishes syringyl-rich from guaiacyl- and hydroxyphenyl-rich lignins in PEG-embedded material under light microscopy. Current hypothesis is corroborated, that is, the adequate fixation solves the false-negative results, and the new proposed protocols fill up some gaps on the detection of phenolics and lignins. PMID:28117630

A simplified plastic embedding and immunohistologic technique for immunophenotypic analysis of human hematopoietic and lymphoid tissues.

PubMed Central

Casey, T. T.; Cousar, J. B.; Collins, R. D.

1988-01-01

Routine fixation and paraffin embedding destroys many hematopoietic and lymphoid differentiation antigens detected by flow cytometry or frozen section immunohistochemistry. On the other hand, morphologic evaluation is difficult in flow cytometric or frozen section studies. A simplified three-step plastic embedding system using acetone-fixed tissues embedded in glycol-methacrylate (GMA) resin has been found to provide both excellent morphologic and antigenic preservation. With our system, a wide variety of antigens are detected in plastic sections without trypsinization or prolonged embedding procedures; pan-B (CD19, CD22), pan-T (CD7, CD5, CD3, CD2), T-subset (CD4, CD8, CD1, CD25) markers as well as surface immunoglobulin and markers for myeloid and mononuclear-phagocyte cells are preserved. In summary, modifications of plastic embedding techniques used in this study simplify the procedure, apparently achieve excellent antigenic preservation, and facilitate evaluation of morphologic details in relation to immunocytochemical markers. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:3282442

Method of holding optical elements without deformation during their fabrication

DOEpatents

Hed, P.P.

1997-04-29

An improved method for securing and removing an optical element to and from a blocking tool without causing deformation of the optical element is disclosed. A lens tissue is placed on the top surface of the blocking tool. Dots of UV cement are applied to the lens tissue without any of the dots contacting each other. An optical element is placed on top of the blocking tool with the lens tissue sandwiched therebetween. The UV cement is then cured. After subsequent fabrication steps, the bonded blocking tool, lens tissue, and optical element are placed in a debonding solution to soften the UV cement. The optical element is then removed from the blocking tool. 16 figs.

Method of holding optical elements without deformation during their fabrication

DOEpatents

Hed, P. Paul

1997-01-01

An improved method for securing and removing an optical element to and from a blocking tool without causing deformation of the optical element. A lens tissue is placed on the top surface of the blocking tool. Dots of UV cement are applied to the lens tissue without any of the dots contacting each other. An optical element is placed on top of the blocking tool with the lens tissue sandwiched therebetween. The UV cement is then cured. After subsequent fabrication steps, the bonded blocking tool, lens tissue, and optical element are placed in a debonding solution to soften the UV cement. The optical element is then removed from the blocking tool.

Barium-cross-linked alginate-gelatine microcapsule as a potential platform for stem cell production and modular tissue formation.

PubMed

Alizadeh Sardroud, Hamed; Nemati, Sorour; Baradar Khoshfetrat, Ali; Nabavinia, Mahbobeh; Beygi Khosrowshahi, Younes

2017-08-01

Influence of gelatine concentration and cross-linker ions of Ca 2+ and Ba 2+ was evaluated on characteristics of alginate hydrogels and proliferation behaviours of model adherent and suspendable stem cells of fibroblast and U937 embedded in alginate microcapsules. Increasing gelatine concentration to 2.5% increased extent of swelling to 15% and 25% for barium- and calcium-cross-linked hydrogels, respectively. Mechanical properties also decreased with increasing swelling of hydrogels. Both by increasing gelatine concentration and using barium ions increased considerably the proliferation of encapsulated model stem cells. Barium-cross-linked alginate-gelatine microcapsule tested for bone building block showed a 13.5 ± 1.5-fold expansion for osteoblast cells after 21 days with deposition of bone matrix. The haematopoietic stem cells cultured in the microcapsule after 7 days also showed up to 2-fold increase without adding any growth factor. The study demonstrates that barium-cross-linked alginate-gelatine microcapsule has potential for use as a simple and efficient 3D platform for stem cell production and modular tissue formation.

Alveolar Soft Part Sarcoma.

PubMed

Jaber, Omar I; Kirby, Patricia A

2015-11-01

Alveolar soft part sarcoma is a rare neoplasm usually arising in the soft tissues of the lower limbs in adults and in the head and neck region in children. It presents primarily as a slowly growing mass or as metastatic disease. It is characterized by a specific chromosomal alteration, der(17)t(X:17)(p11:q25), resulting in fusion of the transcription factor E3 (TFE3) with alveolar soft part sarcoma critical region 1 (ASPSCR1) at 17q25. This translocation is diagnostically useful because the tumor nuclei are positive for TFE3 by immunohistochemistry. Real-time polymerase chain reaction to detect the ASPSCR1-TFE3 fusion transcript on paraffin-embedded tissue blocks has been shown to be more sensitive and specific than detection of TFE3 by immunohistochemical stain. Cathepsin K is a relatively recent immunohistochemical stain that can aid in the diagnosis. The recent discovery of the role of the ASPSCR1-TFE3 fusion protein in the MET proto-oncogene signaling pathway promoting angiogenesis and cell proliferation offers a promising targeted molecular therapy.

Human Papilloma Virus Detection by INNOLiPA HPV in Prostate Tissue from Men of Northeast Mexico

PubMed

Dávila-Rodríguez, Martha I; Ignacio Morales, Cesar V; Aragón Tovar, Anel R; Olache Jimenez, Delia; Castelán Maldonado, Edmundo; Lara Miranda, Sandra; Cortés Gutiérrez, Elva I

2016-11-01

Background: Prostatic adenocarcinoma by Prosate cancer (PCa) is the most prevalent cancer and the second cause of cancer-related death among men in the Western world. Human papilloma virus (HPV) may be considered as a preventable risk factor. In this study, we assessed the frequencies of HPV infection in prostatic adenocarcinoma and benign prostatic hyperplasia (BPH) cases in Northeast Mexico. Materials and Methods: A total of 87 paraffin-embedded blocks (from 25 and 62 patients with definite diagnoses of BPH and adenocarcinoma, respectively) were selected and subjected to INNOLiPA HPV Genotyping to detect 28 high- and low-risk HPV types. The rates of infection were compared in the two studied groups. Results: INNOLiPA HPV demonstrated great sensitivity for HPV detection on paraffin-embedded tissue. Global prevalence was 14.9% (13/87). HPV infection was positive in 19.4% (12/62) of patients with adenocarcinoma and 4.0% (1/25) of patients with BPH. HPV-11, which is considered to be low risk, was more prevalent. Interestingly, one patient with BPH and six with prostate cancer showed examples considered to be high risk (HPV-18, -51, -52, and -66). Conclusion: A higher rate of HPV infection among Mexican patients with prostatic carcinoma than among those with BPH was observed. HPV infections may thus contribute to the risk of prostate cancer. Further studies are required to elucidate any roles of HPV infection in prostate disease in Mexico and the effect of prevention and treatment of HPV infection on prostatic adenocarcinoma. Creative Commons Attribution License

Human Papilloma Virus Detection by INNOLiPA HPV in Prostate Tissue from Men of Northeast Mexico

PubMed Central

Rodriguez, Martha I Dávila; Morales, Cesar V Ignacio; Tovar, Anel R Aragón; Jimenez, Delia Olache; Maldonado, Edmundo Castelán; Miranda, Sandra Lara; Gutiérrez, Elva I Cortés

2016-01-01

Background: Prostatic adenocarcinoma by Prosate cancer (PCa) is the most prevalent cancer and the second cause of cancer-related death among men in the Western world. Human papilloma virus (HPV) may be considered as a preventable risk factor. In this study, we assessed the frequencies of HPV infection in prostatic adenocarcinoma and benign prostatic hyperplasia (BPH) cases in Northeast Mexico. Materials and Methods: A total of 87 paraffin-embedded blocks (from 25 and 62 patients with definite diagnoses of BPH and adenocarcinoma, respectively) were selected and subjected to INNOLiPA HPV Genotyping to detect 28 high- and low-risk HPV types. The rates of infection were compared in the two studied groups. Results: INNOLiPA HPV demonstrated great sensitivity for HPV detection on paraffin-embedded tissue. Global prevalence was 14.9% (13/87). HPV infection was positive in 19.4% (12/62) of patients with adenocarcinoma and 4.0% (1/25) of patients with BPH. HPV-11, which is considered to be low risk, was more prevalent. Interestingly, one patient with BPH and six with prostate cancer showed examples considered to be high risk (HPV-18, -51, -52, and -66). Conclusion: A higher rate of HPV infection among Mexican patients with prostatic carcinoma than among those with BPH was observed. HPV infections may thus contribute to the risk of prostate cancer. Further studies are required to elucidate any roles of HPV infection in prostate disease in Mexico and the effect of prevention and treatment of HPV infection on prostatic adenocarcinoma. PMID:28030912

Tuberculosis patients co-infected with Mycobacterium bovis and Mycobacterium tuberculosis in an urban area of Brazil.

PubMed

Silva, Marcio Roberto; Rocha, Adalgiza da Silva; da Costa, Ronaldo Rodrigues; de Alencar, Andrea Padilha; de Oliveira, Vania Maria; Fonseca Júnior, Antônio Augusto; Sales, Mariana Lázaro; Issa, Marina de Azevedo; Filho, Paulo Martins Soares; Pereira, Omara Tereza Vianello; dos Santos, Eduardo Calazans; Mendes, Rejane Silva; Ferreira, Angela Maria de Jesus; Mota, Pedro Moacyr Pinto Coelho; Suffys, Philip Noel; Guimarães, Mark Drew Crosland

2013-05-01

In this cross-sectional study, mycobacteria specimens from 189 tuberculosis (TB) patients living in an urban area in Brazil were characterised from 2008-2010 using phenotypic and molecular speciation methods (pncA gene and oxyR pseudogene analysis). Of these samples, 174 isolates simultaneously grew on Löwenstein-Jensen (LJ) and Stonebrink (SB)-containing media and presented phenotypic and molecular profiles of Mycobacterium tuberculosis, whereas 12 had molecular profiles of M. tuberculosis based on the DNA analysis of formalin-fixed paraffin wax-embedded tissue samples (paraffin blocks). One patient produced two sputum isolates, the first of which simultaneously grew on LJ and SB media and presented phenotypic and molecular profiles of M. tuberculosis, and the second of which only grew on SB media and presented phenotypic profiles of Mycobacterium bovis. One patient provided a bronchial lavage isolate, which simultaneously grew on LJ and SB media and presented phenotypic and molecular profiles of M. tuberculosis, but had molecular profiles of M. bovis from paraffin block DNA analysis, and one sample had molecular profiles of M. tuberculosis and M. bovis identified from two distinct paraffin blocks. Moreover, we found a low prevalence (1.6%) of M. bovis among these isolates, which suggests that local health service procedures likely underestimate its real frequency and that it deserves more attention from public health officials.

Column generation algorithms for virtual network embedding in flexi-grid optical networks.

PubMed

Lin, Rongping; Luo, Shan; Zhou, Jingwei; Wang, Sheng; Chen, Bin; Zhang, Xiaoning; Cai, Anliang; Zhong, Wen-De; Zukerman, Moshe

2018-04-16

Network virtualization provides means for efficient management of network resources by embedding multiple virtual networks (VNs) to share efficiently the same substrate network. Such virtual network embedding (VNE) gives rise to a challenging problem of how to optimize resource allocation to VNs and to guarantee their performance requirements. In this paper, we provide VNE algorithms for efficient management of flexi-grid optical networks. We provide an exact algorithm aiming to minimize the total embedding cost in terms of spectrum cost and computation cost for a single VN request. Then, to achieve scalability, we also develop a heuristic algorithm for the same problem. We apply these two algorithms for a dynamic traffic scenario where many VN requests arrive one-by-one. We first demonstrate by simulations for the case of a six-node network that the heuristic algorithm obtains very close blocking probabilities to exact algorithm (about 0.2% higher). Then, for a network of realistic size (namely, USnet) we demonstrate that the blocking probability of our new heuristic algorithm is about one magnitude lower than a simpler heuristic algorithm, which was a component of an earlier published algorithm.

An Embedded Microretroreflector-Based Microfluidic Immunoassay Platform

PubMed Central

Raja, Balakrishnan; Pascente, Carmen; Knoop, Jennifer; Shakarisaz, David; Sherlock, Tim; Kemper, Steven; Kourentzi, Katerina; Renzi, Ronald F.; Hatch, Anson V.; Olano, Juan; Peng, Bi-Hung; Ruchhoeft, Paul; Willson, Richard

2017-01-01

We present a microfluidic immunoassay platform based on the use of linear microretroreflectors embedded in a transparent polymer layer as an optical sensing surface, and micron-sized magnetic particles as light-blocking labels. Retroreflectors return light directly to its source and are highly detectable using inexpensive optics. The analyte is immuno-magnetically pre-concentrated from a sample and then captured on an antibody-modified microfluidic substrate comprised of embedded microretroreflectors, thereby blocking reflected light. Fluidic force discrimination is used to increase specificity of the assay, following which a difference imaging algorithm that can see single 3 μm magnetic particles without optical calibration is used to detect and quantify signal intensity from each sub-array of retroreflectors. We demonstrate the utility of embedded microretroreflectors as a new sensing modality through a proof-of-concept immunoassay for a small, obligate intracellular bacterial pathogen, Rickettsia conorii, the causative agent of Mediterranean Spotted Fever. The combination of large sensing area, optimized surface chemistry and microfluidic protocols, automated image capture and analysis, and high sensitivity of the difference imaging results in a sensitive immunoassay with a limit of detection of roughly 4000 R. conorii per mL. PMID:27025227

Crystal violet stain as a selective stain for the assessment of mitotic figures in oral epithelial dysplasia and oral squamous cell carcinoma.

PubMed

Jadhav, Kiran B; Ahmed Mujib, B R; Gupta, Nidhi

2012-01-01

Assessment of mitotic figures (MFs) is routinely practiced as prognostic indicator in oral epithelial dysplasia (OED) and oral squamous cell carcinoma (OSCC), but identification of MFs poses a problem in terms of staining characteristics. To evaluate effectiveness of crystal violet stain for staining of MFs and its comparison with hematoxylin and eosin (H and E) stain. Study sample includes archival tissues embedded in paraffin blocks diagnosed as OED (n = 30) and OSCC (n = 30). The control group comprised of tissue specimen from oral mucosa of healthy volunteers (n = 30). Two serial sections of each tissue specimen were stained separately with H and E stain and 1% crystal violet stain. The stained sections were observed under microscope for identification and counting of MFs. Data obtained was statistically analyzed by using the Man-Whitney U test. A significant increase in number of MFs was observed in OED and OSCC in comparison with normal oral mucosa. There was a highly significant increase in number of MFs in crystal violet stained tissue sections when compared with H and E stain. Metaphase is the most commonly observed phase of mitosis in crystal violet stain when compared with H and E stain for all three groups. Crystal violet stain can be considered as selective stain for mitotic figures.

Silicon Carbide Nanoparticles as an Effective Bioadhesive to Bond Collagen Containing Composite Gel Layers for Tissue Engineering Applications.

PubMed

Attalla, Rana; Ling, Celine S N; Selvaganapathy, Ponnambalam Ravi

2018-03-01

Additive manufacturing via layer-by-layer adhesive bonding holds much promise for scalable manufacturing of tissue-like constructs, specifically scaffolds with integrated vascular networks for tissue engineering applications. However, there remains a lack of effective adhesives capable of composite layer fusion without affecting the integrity of patterned features. Here, the use of silicon carbide is introduced as an effective adhesive to achieve strong bonding (0.39 ± 0.03 kPa) between hybrid hydrogel films composed of alginate and collagen. The techniques have allowed us to fabricate multilayered, heterogeneous constructs with embedded high-resolution microchannels (150 µm-1 mm) that are precisely interspaced (500-600 µm). Hydrogel layers are effectively bonded with silicon carbide nanoparticles without blocking the hollow microchannels and high cell viability (90.61 ± 3.28%) is maintained within the scaffold. Nanosilica is also tested and found to cause clogging of smaller microchannels when used for interlayer bonding, but is successfully used to attach synthetic polymers (e.g., Tygon) to the hydrogels (32.5 ± 2.12 mN bond strength). This allows us to form inlet and outlet interconnections to the gel constructs. This ability to integrate hollow channel networks into bulk soft material structures for perfusion can be useful in 3D tissue engineering applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermoreversible Morphology and Conductivity of a Conjugated Polymer Network Embedded in Block Copolymer Self-Assemblies

DOE PAGES

Han, Youngkyu; Carrillo, Jan-Michael Y.; Zhang, Zhe; ...

2016-07-19

Self-assembly of block copolymers provides numerous opportunities to create functional materials, utilizing self-assembled microdomains with a variety of morphology and periodic architectures as templates for functional nanofillers. Here new progress is reported toward the fabrication of thermally responsive and electrically conductive polymeric self-assemblies made from a water-soluble poly(thiophene) derivative with short poly(ethylene oxide) side chains and Pluronic L62 block copolymer solution in water. The structural and electrical properties of conjugated polymer-embedded self-assembled architectures are investigated by combining small-angle neutron and X-ray scattering, coarse-grained molecular dynamics simulations, and impedance spectroscopy. The L62 solution template organizes the conjugated polymers by stably incorporatingmore » them into the hydrophilic domains thus inhibiting aggregation. The changing morphology of L62 during the micellarto- lamellar phase transition defines the embedded conjugated polymer network. As a result, the conductivity is strongly coupled to the structural change of the templating L62 phase and exhibits thermally reversible behavior with no signs of quenching of the conductivity at high temperature. In conclusion, this study shows promise for enabling more flexibility in processing and utilizing water-soluble conjugated polymers in aqueous solutions for self-assembly based fabrication of stimuli-responsive nanostructures and sensory materials.« less

Thermoreversible Morphology and Conductivity of a Conjugated Polymer Network Embedded in Block Copolymer Self-Assemblies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Youngkyu; Carrillo, Jan-Michael Y.; Zhang, Zhe

Self-assembly of block copolymers provides numerous opportunities to create functional materials, utilizing self-assembled microdomains with a variety of morphology and periodic architectures as templates for functional nanofillers. Here new progress is reported toward the fabrication of thermally responsive and electrically conductive polymeric self-assemblies made from a water-soluble poly(thiophene) derivative with short poly(ethylene oxide) side chains and Pluronic L62 block copolymer solution in water. The structural and electrical properties of conjugated polymer-embedded self-assembled architectures are investigated by combining small-angle neutron and X-ray scattering, coarse-grained molecular dynamics simulations, and impedance spectroscopy. The L62 solution template organizes the conjugated polymers by stably incorporatingmore » them into the hydrophilic domains thus inhibiting aggregation. The changing morphology of L62 during the micellarto- lamellar phase transition defines the embedded conjugated polymer network. As a result, the conductivity is strongly coupled to the structural change of the templating L62 phase and exhibits thermally reversible behavior with no signs of quenching of the conductivity at high temperature. In conclusion, this study shows promise for enabling more flexibility in processing and utilizing water-soluble conjugated polymers in aqueous solutions for self-assembly based fabrication of stimuli-responsive nanostructures and sensory materials.« less

Alternative to xylene as a clearing agent in histopathology

PubMed Central

Alwahaibi, Nasar; Aljaradi, Shaima; Alazri, Horiyah

2018-01-01

INTRODUCTION: Clearing is an essential step in processing tissue for light microscopy. Xylene is the clearing agent used most commonly worldwide. Xylene is toxic and therefore a threat to personnel working in histopathology laboratories. We evaluated a safer alternative clearing agent for use in the histopathology laboratory. MATERIALS AND METHODS: We used 230 formalin-fixed, paraffin-embedded tissue blocks from 19 different tissues. Half of the specimens were processed using xylene and half were processed using UltraClear™. Tissues were evaluated for eight parameters: sectioning, nuclear staining, cytoplasmic staining, overall cell morphology, clarity of staining, uniformity of staining, quality of immunohistochemistry (IHC), and cost. RESULTS: Both UltraClear™ and xylene processed sections scored 100% for IHC. Sections processed using UltraClear™ were easy to cut (81.7%) as were xylene processed sections (96.5%). UltraClear™ processed sections showed 67%, 60.9%, 52.2%, 63.5%, and 67% for nuclear staining, cytoplasmic staining, cell morphology, clarity of staining, and uniformity of staining, respectively. UltraClear™ is twice as expensive as xylene. We found that tissues processed using UltraClear™ were easy to cut and worked well for both hematoxylin and eosin and IHC staining. CONCLUSION: UltraClear™ is less toxic, less flammable, friendlier to the environment, and easy to handle, but it is two times expensive than xylene. The findings of this study recommend the use of UltraClear™ solution as a routine clearing agent in histopathology laboratories. However, further studies are required. PMID:29692586

FIB-SEM imaging of carbon nanotubes in mouse lung tissue.

PubMed

Købler, Carsten; Saber, Anne Thoustrup; Jacobsen, Nicklas Raun; Wallin, Håkan; Vogel, Ulla; Qvortrup, Klaus; Mølhave, Kristian

2014-06-01

Ultrastructural characterisation is important for understanding carbon nanotube (CNT) toxicity and how the CNTs interact with cells and tissues. The standard method for this involves using transmission electron microscopy (TEM). However, in particular, the sample preparation, using a microtome to cut thin sample sections for TEM, can be challenging for investigation of regions with agglomerations of large and stiff CNTs because the CNTs cut with difficulty. As a consequence, the sectioning diamond knife may be damaged and the uncut CNTs are left protruding from the embedded block surface excluding them from TEM analysis. To provide an alternative to ultramicrotomy and subsequent TEM imaging, we studied focused ion beam scanning electron microscopy (FIB-SEM) of CNTs in the lungs of mice, and we evaluated the applicability of the method compared to TEM. FIB-SEM can provide serial section volume imaging not easily obtained with TEM, but it is time-consuming to locate CNTs in the tissue. We demonstrate that protruding CNTs after ultramicrotomy can be used to locate the region of interest, and we present FIB-SEM images of CNTs in lung tissue. FIB-SEM imaging was applied to lung tissue from mice which had been intratracheally instilled with two different multiwalled CNTs; one being short and thin, and the other longer and thicker. FIB-SEM was found to be most suitable for detection of the large CNTs (Ø ca. 70 nm), and to be well suited for studying CNT agglomerates in biological samples which is challenging using standard TEM techniques.

Audio Steganography with Embedded Text

NASA Astrophysics Data System (ADS)

Teck Jian, Chua; Chai Wen, Chuah; Rahman, Nurul Hidayah Binti Ab.; Hamid, Isredza Rahmi Binti A.

2017-08-01

Audio steganography is about hiding the secret message into the audio. It is a technique uses to secure the transmission of secret information or hide their existence. It also may provide confidentiality to secret message if the message is encrypted. To date most of the steganography software such as Mp3Stego and DeepSound use block cipher such as Advanced Encryption Standard or Data Encryption Standard to encrypt the secret message. It is a good practice for security. However, the encrypted message may become too long to embed in audio and cause distortion of cover audio if the secret message is too long. Hence, there is a need to encrypt the message with stream cipher before embedding the message into the audio. This is because stream cipher provides bit by bit encryption meanwhile block cipher provide a fixed length of bits encryption which result a longer output compare to stream cipher. Hence, an audio steganography with embedding text with Rivest Cipher 4 encryption cipher is design, develop and test in this project.

Araldite as an Embedding Medium for Electron Microscopy

PubMed Central

Glauert, Audrey M.; Glauert, R. H.

1958-01-01

Epoxy resins are suitable media for embedding for electron microscopy, as they set uniformly with virtually no shrinkage. A mixture of araldite epoxy resins has been developed which is soluble in ethanol, and which yields a block of the required hardness for thin sectioning. The critical modifications to the conventional mixtures are the choice of a plasticized resin in conjunction with an aliphatic anhydride as the hardener. The hardness of the final block can be varied by incorporating additional plasticizer, and the rate of setting can be controlled by the use of an amine accelerator. The properties of the araldite mixture can be varied quite widely by adjusting the proportions of the various constituents. The procedure for embedding biological specimens is similar to that employed with methacrylates, although longer soaking times are recommended to ensure the complete penetration of the more viscous epoxy resin. An improvement in the preservation of the fine structure of a variety of specimens has already been reported, and a typical electron microgram illustrates the present paper. PMID:13525433

Genetics algorithm optimization of DWT-DCT based image Watermarking

NASA Astrophysics Data System (ADS)

Budiman, Gelar; Novamizanti, Ledya; Iwut, Iwan

2017-01-01

Data hiding in an image content is mandatory for setting the ownership of the image. Two dimensions discrete wavelet transform (DWT) and discrete cosine transform (DCT) are proposed as transform method in this paper. First, the host image in RGB color space is converted to selected color space. We also can select the layer where the watermark is embedded. Next, 2D-DWT transforms the selected layer obtaining 4 subband. We select only one subband. And then block-based 2D-DCT transforms the selected subband. Binary-based watermark is embedded on the AC coefficients of each block after zigzag movement and range based pixel selection. Delta parameter replacing pixels in each range represents embedded bit. +Delta represents bit “1” and -delta represents bit “0”. Several parameters to be optimized by Genetics Algorithm (GA) are selected color space, layer, selected subband of DWT decomposition, block size, embedding range, and delta. The result of simulation performs that GA is able to determine the exact parameters obtaining optimum imperceptibility and robustness, in any watermarked image condition, either it is not attacked or attacked. DWT process in DCT based image watermarking optimized by GA has improved the performance of image watermarking. By five attacks: JPEG 50%, resize 50%, histogram equalization, salt-pepper and additive noise with variance 0.01, robustness in the proposed method has reached perfect watermark quality with BER=0. And the watermarked image quality by PSNR parameter is also increased about 5 dB than the watermarked image quality from previous method.

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

PubMed

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.

Changes of Cyanide Content and Linamarase Activity in Wounded Cassava Roots 1

PubMed Central

Kojima, Mineo; Iwatsuki, Norio; Data, Emma S.; Villegas, Cynthia Dolores V.; Uritani, Ikuzo

1983-01-01

When cassava (Manihot esculenta Crantz) root was cut into blocks and incubated under laboratory conditions, the blocks showed more widespread and more even symptoms of physiological deterioration than those under natural conditions. Thus, the tissue block system has potential for biochemical studies of natural deterioration of cassava root. The changes in cyanide content and linamarase (linamarin β-d-glucoside glucohydrolase; EC 3.2.1.21) activity in various tissues during physiological deterioration were investigated. Total cyanide content increased in all parts of block tissue after 3-day incubation. The degree of increase in cyanide was most pronounced in white parenchymal tissue, 2 to 3 millimeters thick, next to the cortex (A-part tissue), where no physiological symptoms appeared. On the other hand, linamarase activity was decreased in all parts of block tissue after a 3-day incubation. A time course analysis of A-part tissue indicated a clear reciprocal relationship between changes in total cyanide and linamarase activity; total cyanide increased, while linamarase activity decreased. Free cyanide constituted a very small portion of the total cyanide and did not change markedly. Images Fig. 2 PMID:16662957

STED super-resolution microscopy of clinical paraffin-embedded human rectal cancer tissue.

PubMed

Ilgen, Peter; Stoldt, Stefan; Conradi, Lena-Christin; Wurm, Christian Andreas; Rüschoff, Josef; Ghadimi, B Michael; Liersch, Torsten; Jakobs, Stefan

2014-01-01

Formalin fixed and paraffin-embedded human tissue resected during cancer surgery is indispensable for diagnostic and therapeutic purposes and represents a vast and largely unexploited resource for research. Optical microscopy of such specimen is curtailed by the diffraction-limited resolution of conventional optical microscopy. To overcome this limitation, we used STED super-resolution microscopy enabling optical resolution well below the diffraction barrier. We visualized nanoscale protein distributions in sections of well-annotated paraffin-embedded human rectal cancer tissue stored in a clinical repository. Using antisera against several mitochondrial proteins, STED microscopy revealed distinct sub-mitochondrial protein distributions, suggesting a high level of structural preservation. Analysis of human tissues stored for up to 17 years demonstrated that these samples were still amenable for super-resolution microscopy. STED microscopy of sections of HER2 positive rectal adenocarcinoma revealed details in the surface and intracellular HER2 distribution that were blurred in the corresponding conventional images, demonstrating the potential of super-resolution microscopy to explore the thus far largely untapped nanoscale regime in tissues stored in biorepositories.

STED Super-Resolution Microscopy of Clinical Paraffin-Embedded Human Rectal Cancer Tissue

PubMed Central

Wurm, Christian Andreas; Rüschoff, Josef; Ghadimi, B. Michael; Liersch, Torsten; Jakobs, Stefan

2014-01-01

Formalin fixed and paraffin-embedded human tissue resected during cancer surgery is indispensable for diagnostic and therapeutic purposes and represents a vast and largely unexploited resource for research. Optical microscopy of such specimen is curtailed by the diffraction-limited resolution of conventional optical microscopy. To overcome this limitation, we used STED super-resolution microscopy enabling optical resolution well below the diffraction barrier. We visualized nanoscale protein distributions in sections of well-annotated paraffin-embedded human rectal cancer tissue stored in a clinical repository. Using antisera against several mitochondrial proteins, STED microscopy revealed distinct sub-mitochondrial protein distributions, suggesting a high level of structural preservation. Analysis of human tissues stored for up to 17 years demonstrated that these samples were still amenable for super-resolution microscopy. STED microscopy of sections of HER2 positive rectal adenocarcinoma revealed details in the surface and intracellular HER2 distribution that were blurred in the corresponding conventional images, demonstrating the potential of super-resolution microscopy to explore the thus far largely untapped nanoscale regime in tissues stored in biorepositories. PMID:25025184

Improved method for analysis of RNA present in long-term preserved thyroid cancer tissue of atomic bomb survivors.

PubMed

Hamatani, Kiyohiro; Eguchi, Hidetaka; Mukai, Mayumi; Koyama, Kazuaki; Taga, Masataka; Ito, Reiko; Hayashi, Yuzo; Nakachi, Kei

2010-01-01

Since many thyroid cancer tissue samples from atomic bomb (A-bomb) survivors have been preserved for several decades as unbuffered formalin-fixed, paraffin-embedded specimens, molecular oncological analysis of such archival specimens is indispensable for clarifying the mechanisms of thyroid carcinogenesis in A-bomb survivors. Although RET gene rearrangements are the most important targets, it is a difficult task to examine all of the 13 known types of RET gene rearrangements with the use of the limited quantity of RNA that has been extracted from invaluable paraffin-embedded tissue specimens of A-bomb survivors. In this study, we established an improved 5' rapid amplification of cDNA ends (RACE) method using a small amount of RNA extracted from archival thyroid cancer tissue specimens. Three archival thyroid cancer tissue specimens from three different patients were used as in-house controls to determine the conditions for an improved switching mechanism at 5' end of RNA transcript (SMART) RACE method; one tissue specimen with RET/PTC1 rearrangement and one with RET/PTC3 rearrangement were used as positive samples. One other specimen, used as a negative sample, revealed no detectable expression of the RET gene tyrosine kinase domain. We established a 5' RACE method using an amount of RNA as small as 10 ng extracted from long-term preserved, unbuffered formalin-fixed, paraffin-embedded thyroid cancer tissue by application of SMART technology. This improved SMART RACE method not only identified common RET gene rearrangements, but also isolated a clone containing a 93-bp insert of rare RTE/PTC8 in RNA extracted from formalin-fixed, paraffin-embedded thyroid cancer specimens from one A-bomb survivor who had been exposed to a high radiation dose. In addition, in the papillary thyroid cancer of another high-dose A-bomb survivor, this method detected one novel type of RET gene rearrangement whose partner gene is acyl coenzyme A binding domain 5, located on chromosome 10p. We conclude that our improved SMART RACE method is expected to prove useful in molecular analyses using archival formalin-fixed, paraffin-embedded tissue samples of limited quantity.

Design and realization of flash translation layer in tiny embedded system

NASA Astrophysics Data System (ADS)

Ren, Xiaoping; Sui, Chaoya; Luo, Zhenghua; Cao, Wenji

2018-05-01

We design a solution of tiny embedded device NAND Flash storage system on the basis of deeply studying the characteristics of widely used NAND Flash in the embedded devices in order to adapt to the development of intelligent interconnection trend and solve the storage problem of large data volume in tiny embedded system. The hierarchical structure and function purposes of the system are introduced. The design and realization of address mapping, error correction, bad block management, wear balance, garbage collection and other algorithms in flash memory transformation layer are described in details. NAND Flash drive and management are realized on STM32 micro-controller, thereby verifying design effectiveness and feasibility.

KRAS detection in colonic tumors by DNA extraction from FTA paper: the molecular touch-prep.

PubMed

Petras, Melissa L; Lefferts, Joel A; Ward, Brian P; Suriawinata, Arief A; Tsongalis, Gregory J

2011-12-01

DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissue is usually more degraded and contains more polymerase chain reaction (PCR) inhibitors than DNA isolated from nonfixed tissue. In addition, the tumor size and cellular heterogeneity found in tissue sections can often impact testing for molecular biomarkers. As a potential remedy to this situation, we evaluated the use of Whatman FTA paper cards for collection of colorectal tumor samples before tissue fixation and for isolation of DNA for use in a real-time PCR-based KRAS mutation assay. Eleven colon tumor samples were collected by making a cut into the fresh tumor and applying the Whatman FTA paper to the cut surface. Matched FFPE tissue blocks from these tumors were also collected for comparison. KRAS mutation analysis was carried out using the Applied Biosystems 7500 Fast Real-time PCR System using 7 independent custom TaqMan PCR assays. Of the 11 colon tumors sampled, 6 were positive for KRAS mutations in both the Whatman FTA paper preparations and corresponding FFPE samples. Whatman FTA paper cards for collection of colorectal tumor samples before tissue fixation and for isolation of DNA have many advantages including ease of use, intrinsic antimicrobial properties, long storage potential (stability of DNA over time), and a faster turnaround time for results. Extracted DNA should be suitable for most molecular diagnostic assays that use PCR techniques. This novel means of DNA preservation from surgical specimens would benefit from additional study and validation as a dependable and practical technique to preserve specimens for molecular testing.

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

NASA Astrophysics Data System (ADS)

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.

Agar Block Smear Preparation: a Novel Method of Slide Preparation for Preservation of Native Fungal Structures for Microscopic Examination and Long-Term Storage▿

PubMed Central

Woo, Patrick C. Y.; Ngan, Antonio H. Y.; Chui, Hon-Kit; Lau, Susanna K. P.; Yuen, Kwok-Yung

2010-01-01

We describe a novel method of fungal slide preparation named “agar block smear preparation.” A total of 510 agar block smears of 25 fungal strains obtained from culture collections, 90 QC fungal strains, and 82 clinical fungal strains from our clinical microbiology laboratory, which included a total of 137 species of yeasts, molds, and thermal dimorphic fungi, were prepared and examined. In contrast to adhesive tape preparation, agar block smears preserved the native fungal structures, such as intact conidiophores of Aspergillus species and arrangements of conidia in Scopulariopsis brevicaulis. Furthermore, agar block smears allowed examination of fungal structures embedded in the agar, such as the ascomata with ascomal hairs in Chaetomium funicola; pycnidium of Phoma glomerata; the intercalary ovoidal chlamydospores arranged in chains of Fusarium dimerum; and the lateral, spherical chlamydospores arranged in pairs of Fusarium solani. After 1 year of storage, morphological integrity was found to have been maintained in 459 (90%) of the 510 agar block smears. After 3 years of storage, morphological integrity was found to have been maintained in 72 (71%) of the 102 smears prepared in 2006. Agar block smear preparation preserves the native fungal structures and allows long-term storage and examination of fungal structures embedded in the agar, hence overcoming the major drawbacks of adhesive tape preparation. The major roles of agar block smear should be diagnosis for difficult cases, accurate identification of fungal species for clinical management of patients and epidemiological studies, and long-term storage for transportation of slides and education purposes. PMID:20660221

Agar block smear preparation: a novel method of slide preparation for preservation of native fungal structures for microscopic examination and long-term storage.

PubMed

Woo, Patrick C Y; Ngan, Antonio H Y; Chui, Hon-Kit; Lau, Susanna K P; Yuen, Kwok-Yung

2010-09-01

We describe a novel method of fungal slide preparation named "agar block smear preparation." A total of 510 agar block smears of 25 fungal strains obtained from culture collections, 90 QC fungal strains, and 82 clinical fungal strains from our clinical microbiology laboratory, which included a total of 137 species of yeasts, molds, and thermal dimorphic fungi, were prepared and examined. In contrast to adhesive tape preparation, agar block smears preserved the native fungal structures, such as intact conidiophores of Aspergillus species and arrangements of conidia in Scopulariopsis brevicaulis. Furthermore, agar block smears allowed examination of fungal structures embedded in the agar, such as the ascomata with ascomal hairs in Chaetomium funicola; pycnidium of Phoma glomerata; the intercalary ovoidal chlamydospores arranged in chains of Fusarium dimerum; and the lateral, spherical chlamydospores arranged in pairs of Fusarium solani. After 1 year of storage, morphological integrity was found to have been maintained in 459 (90%) of the 510 agar block smears. After 3 years of storage, morphological integrity was found to have been maintained in 72 (71%) of the 102 smears prepared in 2006. Agar block smear preparation preserves the native fungal structures and allows long-term storage and examination of fungal structures embedded in the agar, hence overcoming the major drawbacks of adhesive tape preparation. The major roles of agar block smear should be diagnosis for difficult cases, accurate identification of fungal species for clinical management of patients and epidemiological studies, and long-term storage for transportation of slides and education purposes.

Preference for blocking or response redirection during stereotypy treatment.

PubMed

Giles, Aimee F; St Peter, Claire C; Pence, Sacha T; Gibson, Alexandra B

2012-01-01

Response redirection and response blocking reduce stereotypy maintained by automatic reinforcement. The current study evaluated the effects of redirection and response blocking on the stereotypic responding of three elementary-age children diagnosed with autism. During the treatment evaluation, redirection and response blocking were evaluated using an alternating treatment embedded in a reversal design. Both procedures resulted in comparably low levels of motor stereotypy. Following treatment evaluation, a concurrent chain was conducted to evaluate participant preference for redirection or response blocking. All three participants preferred redirection. Practitioners may wish to consider participant preference when developing and implementing treatments for stereotypy. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

PubMed

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.

Fluorescence tomography characterization for sub-surface imaging with protoporphyrin IX

PubMed Central

Kepshire, Dax; Davis, Scott C.; Dehghani, Hamid; Paulsen, Keith D.; Pogue, Brian W.

2009-01-01

Optical imaging of fluorescent objects embedded in a tissue simulating medium was characterized using non-contact based approaches to fluorescence remittance imaging (FRI) and sub-surface fluorescence diffuse optical tomography (FDOT). Using Protoporphyrin IX as a fluorescent agent, experiments were performed on tissue phantoms comprised of typical in-vivo tumor to normal tissue contrast ratios, ranging from 3.5:1 up to 10:1. It was found that tomographic imaging was able to recover interior inclusions with high contrast relative to the background; however, simple planar fluorescence imaging provided a superior contrast to noise ratio. Overall, FRI performed optimally when the object was located on or close to the surface and, perhaps most importantly, FDOT was able to recover specific depth information about the location of embedded regions. The results indicate that an optimal system for localizing embedded fluorescent regions should combine fluorescence reflectance imaging for high sensitivity and sub-surface tomography for depth detection, thereby allowing more accurate localization in all three directions within the tissue. PMID:18545571

Validation of 31 of the most commonly used immunohistochemical antibodies in cytology prepared using the Cellient(®) automated cell block system.

PubMed

Montgomery, Eric; Gao, Chen; de Luca, Julie; Bower, Jessie; Attwood, Kristropher; Ylagan, Lourdes

2014-12-01

The Cellient(®) cell block system has become available as an alternative, partially automated method to create cell blocks in cytology. We sought to show a validation method for immunohistochemical (IHC) staining on the Cellient cell block system (CCB) in comparison with the formalin fixed paraffin embedded traditional cell block (TCB). Immunohistochemical staining was performed using 31 antibodies on 38 patient samples for a total of 326 slides. Split samples were processed using both methods by following the Cellient(®) manufacturer's recommendations for the Cellient cell block (CCB) and the Histogel method for preparing the traditional cell block (TCB). Interpretation was performed by three pathologists and two cytotechnologists. Immunohistochemical stains were scored as: 0/1+ (negative) and 2/3+ (positive). Inter-rater agreement for each antibody was evaluated for CCB and TCB, as well as the intra-rater agreement between TCB and CCB between observers. Interobserver staining concordance for the TCB was obtained with statistical significance (P < 0.05) in 24 of 31 antibodies. Interobserver staining concordance for the CCB was obtained with statistical significance in 27 of 31 antibodies. Intra-observer staining concordance between TCB and CCB was obtained with statistical significance in 24 of 31 antibodies tested. In conclusions, immunohistochemical stains on cytologic specimens processed by the Cellient system are reliable and concordant with stains performed on the same split samples processed via a formalin fixed-paraffin embedded (FFPE) block. The Cellient system is a welcome adjunct to cytology work-flow by producing cell block material of sufficient quality to allow the use of routine IHC. © 2014 Wiley Periodicals, Inc.

Fibrinogen Demonstration in Oral Lichen Planus: An Immunofluorescence Study on Archival Tissues.

PubMed

Shirol, Pallavi D; Naik, Veena; Kale, Alka

2015-10-01

Lichen planus is a premalignant condition with minimal diagnostic aids. This study is an attempt to use paraffin embedded sections of lichen planus with immunofluorescein stain and to evaluate the immunofluorescent sections to establish pattern of fibrinogen deposition. Thirty-five paraffin embedded sections of old and new cases of oral lichen planus (study group) and five normal oral mucosa (control group) were chosen. Two sections of each (H & E) case were taken, one was stained with hematoxylin and eosin and another with fluorescein isothiocynate conjugate (FITC) polyclonal rabbit antibody against fibrinogen. Fluorescent findings were examined with a fluorescent microscope. A high statistical significant correlation was found in respect to fluorescence positivity, intensity of fluorescence and distribution of fluorescence each with p < 0.0001 and fluorescence at blood vessel walls (p = 0.0003). This study suggested that paraffin embedded sections can be successfully used in direct immunofluorescence staining in routine set up where only formalin fixed tissues are received. Paraffin embedded sections can be successfully used in direct immunofluorescence staining when only formalin fixed tissues are received.

Acid-etching technique of non-decalcified bone samples for visualizing osteocyte-lacuno-canalicular network using scanning electron microscope.

PubMed

Lampi, Tiina; Dekker, Hannah; Ten Bruggenkate, Chris M; Schulten, Engelbert A J M; Mikkonen, Jopi J W; Koistinen, Arto; Kullaa, Arja M

2018-01-01

The aim of this study was to define the acid-etching technique for bone samples embedded in polymethyl metacrylate (PMMA) in order to visualize the osteocyte lacuno-canalicular network (LCN) for scanning electron microscopy (SEM). Human jaw bone tissue samples (N = 18) were collected from the study population consisting of patients having received dental implant surgery. After collection, the bone samples were fixed in 70% ethanol and non-decalcified samples embedded routinely into polymethyl metacrylate (PMMA). The PMMA embedded specimens were acid-etched in either 9 or 37% phosphoric acid (PA) and prepared for SEM for further analysis. PMMA embedded bone specimens acid-etched by 9% PA concentration accomplishes the most informative and favorable visualization of the LCN to be observed by SEM. Etching of PMMA embedded specimens is recommendable to start with 30 s or 40 s etching duration in order to find the proper etching duration for the samples examined. Visualizing osteocytes and LCN provides a tool to study bone structure that reflects changes in bone metabolism and diseases related to bone tissue. By proper etching protocol of non-decalcified and using scanning electron microscope it is possible to visualize the morphology of osteocytes and the network supporting vitality of bone tissue.

Prevalence of human papillomavirus genotypes associated with cervical and breast cancers in iran.

PubMed

Hossein, Rassi; Behzad, Salehi; Tahar, Mohammadian; Azadeh, Nahavandi Araghi

2013-12-01

Cancer is a multi-step disease, and infection with a DNA virus could play a role in one or more of the steps in this pathogenic process. High-risk human papillomaviruses (HPV) are the causative agent of several cancers. In this study, we determined the prevalence and genotype distribution of HPV infection among Iranian patients with cervix lesions (CL) and breast cancer (BC). The study group consisted of postoperative tissues from patients diagnosed with cervix lesions and breast cancer. We analyzed 250 formalin-fixed, paraffin-embedded tissue blocks from 100 cervix lesions and 150 breast cancer samples. Verification of each cancer reported in a relative was sought through the pathology reports of the hospital records. Cervix lesions were collected from 100 patients with squamous metaplasia (SM, n=50), cervical intraepithelial neoplasia (CINI, n=18, CINII or III, n=8), and cervical carcinoma (CC, n=24). In this study we evaluated the prevalence of HPV by multiplex PCR in cervix lesions and breast cancer. For paraffin-embedded tissues, DNA extracted by the simple boiling method yielded higher proportions of successful gene amplification (99%) for b-actin gene. Overall prevalence of HPV infection was 6% in the SM group, 34.61% in the CIN group, 75% in the CC group, and 34.66% in the BC group. Furthermore, MY09/11 consensus PCR failed to detect 44 (55.69%) of all HPV infections and interestingly, the predominant genotype detected in all cancers was the oncogenic variant HPV16/18; about 34% of women aged 24 to 54 were infected with at least one type of HPV. Our results demonstrate that DNA derived from archival tissues that archived for less than 8 years could be used successfully for HPV genotyping by multiplex PCR. Infection with HPV was prevalent among Iranian women with CC and BC. The results indicate a likely causal role for high-risk HPV in CC and BC, and also offer the possibility of primary prevention of these cancers by vaccination against HPV in Iran.

Evaluation of HER-2/neu status in breast cancer specimens using immunohistochemistry (IHC) & fluorescence in-situ hybridization (FISH) assay.

PubMed

Goud, Kalal Iravathy; Dayakar, Seetha; Vijayalaxmi, Kolanupaka; Babu, Saidam Jangu; Reddy, P Vijay Anand

2012-03-01

Fluorescence in situ hybridization (FISH) is increasingly being recognized as the most accurate and predictive test for HER 2/neu gene amplification and response to therapy in breast cancer. In the present study we investigated HER-2/neu gene amplification by FISH in breast carcinoma tissue specimens and compared the results with that of immunohistochemical (IHC) analysis. A total of 90 breast carcinoma tissue samples were used for immunohistochemical (IHC) and FISH analysis. IHC was performed by using mouse monoclonal antibody to the intracellular domain of HER-2/neu protein. Each slide was scored in a blinded fashion by two pathologists according to the manufacturer's recommended criteria. FISH analysis was performed on paraffin embedded breast tumour tissue sections. The polysomy for centromere 17 (Spec green signal) was read as green signals less than 4 as moderate polysomy, and more than 4 as highly polysomy. Thirty of the 90 patients had negative results by IHC and FISH. Of the 28 patients with the score of 2+ by IHC, 20 were FISH positive for HER-2/neu gene amplification, three were FISH negative and five patients showed equivocal (1.8-2.2) results by FISH. These five cases were retested for IHC and FISH on different paraffin embedded tissue blocks, and all five were found positive for HER-2/neu gene amplification. Twenty five patients with the score of 3+ by IHC were FISH positive for HER-2/neu gene amplification (>2.2). Seven cases with the score of 3+ by IHC were FISH negative for HER-2/neu gene amplification (>2.2), and showed polysomy of chromosome number 17 high polysomy > 4. Our results indicated that HER-2/neu status by FISH should be performed in all cases of breast tumour with a 2+ score by IHC. Cases demonstrating a 3+ score by IHC may be subjected to FISH to rule out polysomy of chromosome 17 which could be falsely interpreted as HER-2/neu overexpression by IHC analysis. There is also a need for establishing a clinically validated cut-off value for HER-2/neu FISH amplification against IHC which may be further compared and calibrated.

Validation and utilization of a TFE3 break-apart FISH assay for Xp11.2 translocation renal cell carcinoma and alveolar soft part sarcoma.

PubMed

Pradhan, Dinesh; Roy, Somak; Quiroga-Garza, Gabriela; Cieply, Kathleen; Mahaffey, Alyssa L; Bastacky, Sheldon; Dhir, Rajiv; Parwani, Anil V

2015-09-29

Xp11.2 or TFE3 translocation renal cell carcinomas (RCC) and alveolar soft part sarcoma (ASPS) are characterized by chromosome translocations involving the Xp11.2 breakpoint resulting in transcription factor TFE3 gene fusions. The most common translocations documented in TFE3 RCCs are t(X;1) (p11.2;q21) and t(X;17) (p11.2;q25) which leads to fusion of TFE3 gene on Xp11.2 with PRCC or ASPL respectively. TFE3 immunohistochemistry (IHC) has been inconsistent over time due to background staining problems in part related to fixation issues. Karyotyping to detect TFE3 gene rearrangement requires typically unavailable fresh tissue. Reverse transcriptase-polymerase chain reaction (RT-PCR) is generally very challenging due to degradation of RNA in archival material. The study objective was to develop and validate a TFE3 break-apart fluorescence in situ hybridization (FISH) assay to confirm Xp11 translocation RCCs and ASPS. Representative sections of formalin-fixed paraffin-embedded tissue blocks were selected in 40 possible cases. Approximately 60 tumor cells were analyzed in the targeted region. The validation of TFE3 FISH was done with 11 negative and two positive cases. Cut off for a positive result was validated as >7.15 % positive nuclei with any pattern of break-apart signals. FISH evaluation was done blinded of the immunohistochemical or karyotype data. Three out of forty cases were positive for the TFE3 break-apart signals by FISH. The negative cases were reported as clear cell RCC with papillary features (10), clear cell RCC with sarcomatoid areas (2), Papillary RCC with clear cell areas (9), Chromophobe RCC (2), RCC, unclassified type (3) and renal medullary carcinoma (1). 3 of the negative cases were consultation cases for renal tumor with unknown histology. Seven negative cases were soft tissue tumor suspicious for ASPS. Our study validates the utility of TFE3 break-apart FISH on formalin-fixed paraffin-embedded tissue sections for diagnosis and confirmation of Xp11.2 translocation RCCs and ASPS.

CdS/C60 binary nanocomposite films prepared via phase transition of PS-b-P2VP block copolymer.

PubMed

Lee, Jung-Pil; Koh, Haeng-Deog; Shin, Won-Jeong; Kang, Nam-Goo; Park, Soojin; Lee, Jae-Suk

2014-03-01

We demonstrate the well-defined control of phase transition of a polystyrene-b-poly(2-vinylpyridine) (PS-b-P2VP) block copolymer from spherical micelles to lamellar structures, in which CdS and C60 nanoparticles (NPs) are selectively positioned at the P2VP domains. The CdS NPs are in situ synthesized using PS-b-P2VP block copolymer templates that are self-assembled in PS-selective solvents. The CdS-PS-b-P2VP micellar structures are transformed to lamellar phase by adjusting a solvent selectivity for both blocks. In addition, a binary system of CdS/C60 embedded in PS-b-P2VP lamellar structures (CdS/C60-PS-b-P2VP) is fabricated by embedding C60 molecules into P2VP domain though charge-transfer complexation between pyridine units of PS-b-P2VP and C60 molecules. The CdS/C60-PS-b-P2VP nanostructured films are characterized by transmission electron microscopy (TEM) and UV-Vis spectrometer. Copyright © 2013 Elsevier Inc. All rights reserved.

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

PubMed

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 Xpert MTB/RIF system, 15 were found rifampicin-susceptible, and three were rifampicin-resistant. In two samples in which M. tuberculosis DNA was low positive, rifampicin resistance could not be detected. The identification of M.tuberculosis infections in postmortem cases will contribute epidemiological data in Turkey. In these cases, effective sampling and diagnosing of M.tuberculosis infections by acid-fast stain and culture methods are crucial. However, in cases without microbiological sampling the detection of M.tuberculosis DNA in paraffin-embedded tissues with PCR, although there are differences between PCR systems has diagnostic value. In conclusion, our data indicated that Xpert MTB/RIF system is more favourable to detect M.tuberculosis DNA in paraffin-embedded tissues, with the advantages of determination of rifampicin resistance, and detection of more positive results within a shorter time.

High-performance serial block-face SEM of nonconductive biological samples enabled by focal gas injection-based charge compensation.

PubMed

Deerinck, T J; Shone, T M; Bushong, E A; Ramachandra, R; Peltier, S T; Ellisman, M H

2018-05-01

A longstanding limitation of imaging with serial block-face scanning electron microscopy is specimen surface charging. This charging is largely due to the difficulties in making biological specimens and the resins in which they are embedded sufficiently conductive. Local accumulation of charge on the specimen surface can result in poor image quality and distortions. Even minor charging can lead to misalignments between sequential images of the block-face due to image jitter. Typically, variable-pressure SEM is used to reduce specimen charging, but this results in a significant reduction to spatial resolution, signal-to-noise ratio and overall image quality. Here we show the development and application of a simple system that effectively mitigates specimen charging by using focal gas injection of nitrogen over the sample block-face during imaging. A standard gas injection valve is paired with a precisely positioned but retractable application nozzle, which is mechanically coupled to the reciprocating action of the serial block-face ultramicrotome. This system enables the application of nitrogen gas precisely over the block-face during imaging while allowing the specimen chamber to be maintained under high vacuum to maximise achievable SEM image resolution. The action of the ultramicrotome drives the nozzle retraction, automatically moving it away from the specimen area during the cutting cycle of the knife. The device described was added to a Gatan 3View system with minimal modifications, allowing high-resolution block-face imaging of even the most charge prone of epoxy-embedded biological samples. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Multi-Phenotypic subtyping of circulating tumor cells using sequential fluorescent quenching and restaining

NASA Astrophysics Data System (ADS)

Adams, Daniel L.; Alpaugh, R. Katherine; Tsai, Susan; Tang, Cha-Mei; Stefansson, Steingrimur

2016-09-01

In tissue biopsies formalin fixed paraffin embedded cancer blocks are micro-sectioned producing multiple semi-identical specimens which are analyzed and subtyped proteomically, and genomically, with numerous biomarkers. In blood based biopsies (BBBs), blood is purified for circulating tumor cells (CTCs) and clinical utility is typically limited to cell enumeration, as only 2-3 positive fluorescent markers and 1 negative marker can be used. As such, increasing the number of subtyping biomarkers on each individual CTC could dramatically enhance the clinical utility of BBBs, allowing in depth interrogation of clinically relevant CTCs. We describe a simple and inexpensive method for quenching the specific fluors of fluorescently stained CTCs followed by sequential restaining with additional biomarkers. As proof of principle a CTC panel, immunosuppression panel and stem cell panel were used to sequentially subtype individual fluorescently stained patient CTCs, suggesting a simple and universal technique to analyze multiple clinically applicable immunomarkers from BBBs.

Enzyme Histochemistry for Functional Histology in Invertebrates.

PubMed

Cima, Francesca

2017-01-01

In invertebrates, enzyme histochemistry has recently found a renaissance regarding its applications in morphology and ecology. Many enzyme activities are useful for the morphofunctional characterization of cells, as biomarkers of biological and pathologic processes, and as markers of the response to environmental stressors. Here, the adjustments to classic techniques, including the most common enzymes used for digestion, absorption, transport, and oxidation, as well as techniques for azo-coupling, metal salt substitution and oxidative coupling polymerization, are presented in detail for various terrestrial and aquatic invertebrates. This chapter also provides strategies to solve the problems regarding anesthesia, small body size, the presence of an exo- or endoskeleton and the search for the best fixative in relation to the internal fluid osmolarity. These techniques have the aim of obtaining good results for both the pre- and post-embedding labeling of specimens, tissue blocks, sections, and hemolymph smears using both light and transmission electron microscopy.

Simultaneous EGFR and VEGF Alterations in Non-Small Cell Lung Carcinoma Based on Tissue Microarrays

PubMed Central

Tsiambas, Evangelos; Stamatelopoulos, Athanasios; Karameris, Andreas; Panagiotou, Ioannis; Rigopoulos, Dimitrios; Chatzimichalis, Antonios; Bouros, Demosthenes; Patsouris, Efstratios

2007-01-01

Background: Epidermal growth factor receptor (EGFR) overexpression is observed in significant proportions of non-small cell lung carcinomas (NSCLC). Furthermore, overactivation of vascular endothelial growth factor (VEGF) leads to increased angiogenesis implicated as an important factor in vascularization of those tumors. Patients and Methods: Using tissue microarray technology, forty-paraffin (n = 40) embedded, histologically confirmed primary NSCLCs were cored and re-embedded into a recipient block. Immunohistochemistry was performed for the determination of EGFR and VEGF protein levels which were evaluated by the performance of computerized image analysis. EGFR gene amplification was studied by chromogenic in situ hybridization based on the use of EGFR gene and chromosome 7 centromeric probes. Results: EGFR overexpression was observed in 23/40 (57.5%) cases and was correlated to the stage of the tumors (p = 0.001), whereas VEGF was overexpressed in 35/40 (87.5%) cases and was correlated to the stage of the tumors (p = 0.005) and to the smoking history of the patients (p = 0.016). Statistical significance was assessed comparing the protein levels of EGFR and VEGF (p = 0.043, k = 0.846). EGFR gene amplification was identified in 2/40 (5%) cases demonstrating no association to its overall protein levels (p = 0.241), whereas chromosome 7 aneuploidy was detected in 7/40 (17.5%) cases correlating to smoking history of the patients (p = 0.013). Conclusions: A significant subset of NSCLC is characterized by EGFR and VEGF simultaneous overexpression and maybe this is the eligible target group for the application of combined anti-EGFR/VEGF targeted therapies at the basis of genetic deregulation (especially gene amplification for EGFR). PMID:19455247

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dr. Anthony C. James; Stacey L. McCord

The National Radiobiology Archives (NRA) are an archival program, started in 1989, to collect, organize and maintain data, laboratory notebooks, and animal tissue specimens from government (Department of Energy and its predecessor agencies) sponsored radiobiology life-span animal studies. These unique records, histopathology slides and paraffin embedded tissue blocks are maintained in a central facility and are available for further research study. The materials include electronic and paper records for each of more than 6,000 life-span-observations on dogs as well as details of major studies involving nearly 30,000 mice. Although these studies were performed over many years and at different laboratoriesmore » with differing data management systems, the NRA has translated them into a standardized set of relational database tables. These can be distributed to interested individuals on written request. Specific Aims are: (1) To Maintain the Archive of Written Records from the Animal Experiments - The USTUR continued to maintain the NRA archives which consist of approximately 175 storage boxes containing laboratory notebooks, animal exposure records, animal pathologic records, and radiographs. These were stored in a 6,000 square foot leased facility in Richland, WA. Additionally, through a collaboration with Pacific Northwest National Laboratory's (PNNL) Low Dose Program, many of these records were scanned into digital files. These totaled 34 GB of data, which are saved in 2,407 separate PDF files that are organized by box number and animal identification number. (2) To Maintain the Archive of Animal Tissues at Washington State University - The USTUR continued to house the NRA dog tissue collection in the leased facility. The NRA tissue collection consisted of pathology slides and tissue blocks. Approximately 25% of the laboratory facility was dedicated to the storage of the NRA materials. (3) To Organize the Datasets of These Animals in the Context of Other Datasets so That They Can be Used by the Scientific Community at Large - As was reported in the FY2009 NRA progress report, Dr. Chuck Watson (NRA Database Consultant) completed his service as the US representative on the European Radiobiological Archives (ERA) Advisory Board during FY2009. Unfortunately, due to the lack of financial support during FY2010, the NRA was not able to make further contributions to the ERA's efforts.« less

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

PubMed

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.

Automated adipose study for assessing cancerous human breast tissue using optical coherence tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gan, Yu; Yao, Xinwen; Chang, Ernest W.; Bin Amir, Syed A.; Hibshoosh, Hanina; Feldman, Sheldon; Hendon, Christine P.

2017-02-01

Breast cancer is the third leading cause of death in women in the United States. In human breast tissue, adipose cells are infiltrated or replaced by cancer cells during the development of breast tumor. Therefore, an adipose map can be an indicator of identifying cancerous region. We developed an automated classification method to generate adipose map within human breast. To facilitate the automated classification, we first mask the B-scans from OCT volumes by comparing the signal noise ratio with a threshold. Then, the image was divided into multiple blocks with a size of 30 pixels by 30 pixels. In each block, we extracted texture features such as local standard deviation, entropy, homogeneity, and coarseness. The features of each block were input to a probabilistic model, relevance vector machine (RVM), which was trained prior to the experiment, to classify tissue types. For each block within the B-scan, RVM identified the region with adipose tissue. We calculated the adipose ratio as the number of blocks identified as adipose over the total number of blocks within the B-scan. We obtained OCT images from patients (n = 19) in Columbia medical center. We automatically generated the adipose maps from 24 B-scans including normal samples (n = 16) and cancerous samples (n = 8). We found the adipose regions show an isolated pattern that in cancerous tissue while a clustered pattern in normal tissue. Moreover, the adipose ratio (52.30 ± 29.42%) in normal tissue was higher than the that in cancerous tissue (12.41 ± 10.07%).

HB-EGF embedded in PGA/PLLA scaffolds via subcritical CO2 augments the production of tissue engineered intestine.

PubMed

Liu, Yanchun; Nelson, Tyler; Cromeens, Barrett; Rager, Terrence; Lannutti, John; Johnson, Jed; Besner, Gail E

2016-10-01

The ability to deliver sustained-release, biologically active growth factors through custom designed tissue engineering scaffolds at sites of tissue regeneration offers great therapeutic opportunity. Due to the short in vivo half-lives of most growth factors, it is challenging to deliver these proteins to sites of interest where they may be used before being degraded. The application of subcritical CO2 uses gas-phase CO2 at subcritical pressures ranging from 41 to 62 bar (595-913 PSI) which avoids foaming by reducing the amount of CO2 dissolved in the polymer and maintains completely reversible plasticization. In the current study, heparin-binding EGF-like growth factor (HB-EGF) was embedded into polyglycolic acid (PGA)/Poly-l-latic acid (PLLA) scaffolds via subcritical CO2 exposure for the production of tissue engineered intestine (TEI). PGA fiber morphology after subcritical CO2 exposure was examined by scanning electron microscopy (SEM) and the distribution of HB-EGF embedded in the scaffold fibers was detected by HB-EGF immunofluorescent staining. In vivo implantation of HB-EGF-embedded scaffolds confirmed significantly improved TEI structure as a result of local delivery of the trophic growth factor. These findings may be critical for the production of TEI in the treatment of patients with short bowel syndrome in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development of a Plastic Embedding Method for Large-Volume and Fluorescent-Protein-Expressing Tissues

PubMed Central

Yang, Zhongqin; Hu, Bihe; Zhang, Yuhui; Luo, Qingming; Gong, Hui

2013-01-01

Fluorescent proteins serve as important biomarkers for visualizing both subcellular organelles in living cells and structural and functional details in large-volume tissues or organs. However, current techniques for plastic embedding are limited in their ability to preserve fluorescence while remaining suitable for micro-optical sectioning tomography of large-volume samples. In this study, we quantitatively evaluated the fluorescence preservation and penetration time of several commonly used resins in a Thy1-eYFP-H transgenic whole mouse brain, including glycol methacrylate (GMA), LR White, hydroxypropyl methacrylate (HPMA) and Unicryl. We found that HMPA embedding doubled the eYFP fluorescence intensity but required long durations of incubation for whole brain penetration. GMA, Unicryl and LR White each penetrated the brain rapidly but also led to variable quenching of eYFP fluorescence. Among the fast-penetrating resins, GMA preserved fluorescence better than LR White and Unicryl. We found that we could optimize the GMA formulation by reducing the polymerization temperature, removing 4-methoxyphenol and adjusting the pH of the resin solution to be alkaline. By optimizing the GMA formulation, we increased percentage of eYFP fluorescence preservation in GMA-embedded brains nearly two-fold. These results suggest that modified GMA is suitable for embedding large-volume tissues such as whole mouse brain and provide a novel approach for visualizing brain-wide networks. PMID:23577174

Fabrication and characterization of biological tissue phantoms with embedded nanoparticles

NASA Astrophysics Data System (ADS)

Skaptsov, A. A.; Ustalkov, S. O.; Mohammed, A. H. M.; Savenko, O. A.; Novikova, A. S.; Kozlova, E. A.; Kochubey, V. I.

2017-11-01

Phantoms are imitations of biological tissue, which are used for modelling of the light propagation in biological tissues. Carrying out any biophysical experiments requires an indispensable constancy of the initial experiment conditions. The use of solid undegradable phantoms is the basis to obtain reliable reproducible experimental results. The fabrication of biological tissues phantoms containing high absorbance or fluorescence nanoparticles and corresponding to specific mechanical, optical properties is an actual task. This work describes development, fabrication and characterization of such solid tissue phantoms with embedded CdSe/ZnS quantum dots, gold and upconversion nanoparticles. Luminescence of samples with CdSe/ZnS quantum dots and upconversion nanoparticles were recorded. A sample of gold nanorods was analyzed using thermal gravimetric analysis. It can be concluded that the samples are well suited for experiments on laser thermolysis.

Three-dimensional plotting of a cell-laden alginate/methylcellulose blend: towards biofabrication of tissue engineering constructs with clinically relevant dimensions.

PubMed

Schütz, Kathleen; Placht, Anna-Maria; Paul, Birgit; Brüggemeier, Sophie; Gelinsky, Michael; Lode, Anja

2017-05-01

Biofabrication of tissue engineering constructs with tailored architecture and organized cell placement using rapid prototyping technologies is a major research focus in the field of regenerative therapies. This study describes a novel alginate-based material suitable for both cell embedding and fabrication of three-dimensional (3D) structures with predefined geometry by 3D plotting. The favourable printing properties of the material were achieved by using a simple strategy: addition of methylcellulose (MC) to a 3% alginate solution resulted in a strongly enhanced viscosity, which enabled accurate and easy deposition without high technical efforts. After scaffold plotting, the alginate chains were crosslinked with Ca 2+ ; MC did not contribute to the gelation and was released from the scaffolds during the following cultivation. The resulting constructs are characterized by high elasticity and stability, as well as an enhanced microporosity caused by the transient presence of MC. The suitability of the alginate/MC blend for cell embedding was evaluated by direct incorporation of mesenchymal stem cells during scaffold fabrication. The embedded cells showed high viability after 3 weeks of cultivation, which was similar to those of cells within pure alginate scaffolds which served as control. Maintenance of the differentiation potential of embedded cells, as an important requirement for the generation of functional tissue engineering constructs, was proven for adipogenic differentiation as a model for soft tissue formation. In conclusion, the temporary integration of MC into a low-concentrated alginate solution allowed the generation of scaffolds with dimensions in the range of centimetres without loss of the positive properties of low-concentrated alginate hydrogels with regard to cell embedding. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

The application of polyethylene glycol (PEG) to electron microscopy

PubMed Central

1980-01-01

The cytoplasm of cells from a variety of tissues has been viewed in sections (0.25-1 micrometers) devoid of any embedding resin. Glutaraldehyde- and osmium tetroxide-fixed tissues were infiltrated and embedded in a water-miscible wax, polyethylene glycol (PEG), and subsequently sectioned on dry glass or diamond knives. The PEG matrix was removed and the sections were placed on Formvarcarbon-polylysine- coated grids, dehydrated, dried by the critical-point method, and observed in either the high- or low-voltage electron microscope. Stereoscopic views of cells devoid of embedding resin present an image of cell utrastructure unobscured by electron-scattering resins similar to the image of whole, unembedded critical-point-dried or freeze-dried cultured cells observed by transmission electron microscopy. All organelles, including the cytoskeletal structures, are identified and appear not to have been damaged during processing, although membrane components appear somewhat less distinct. The absence of an embedding matrix eliminates the need for additional staining to increase contrast, unlike the situation with specimens embedded in standard electron-scattering resins. The PEG technique thus appears to be a valuable adjunct to conventional methods for ultrastructural analysis. PMID:7400222

The application of polyethylene glycol (PEG) to electron microscopy.

PubMed

Wolosewick, J J

1980-08-01

The cytoplasm of cells from a variety of tissues has been viewed in sections (0.25-1 micrometers) devoid of any embedding resin. Glutaraldehyde- and osmium tetroxide-fixed tissues were infiltrated and embedded in a water-miscible wax, polyethylene glycol (PEG), and subsequently sectioned on dry glass or diamond knives. The PEG matrix was removed and the sections were placed on Formvarcarbon-polylysine-coated grids, dehydrated, dried by the critical-point method, and observed in either the high- or low-voltage electron microscope. Stereoscopic views of cells devoid of embedding resin present an image of cell utrastructure unobscured by electron-scattering resins similar to the image of whole, unembedded critical-point-dried or freeze-dried cultured cells observed by transmission electron microscopy. All organelles, including the cytoskeletal structures, are identified and appear not to have been damaged during processing, although membrane components appear somewhat less distinct. The absence of an embedding matrix eliminates the need for additional staining to increase contrast, unlike the situation with specimens embedded in standard electron-scattering resins. The PEG technique thus appears to be a valuable adjunct to conventional methods for ultrastructural analysis.

Polyester Wax: A New Embedding Medium for the Histopathologic Study of Human Temporal Bones

PubMed Central

Merchant, Saumil N.; Burgess, Barbara; O'Malley, Jennifer; Jones, Diane; Adams, Joe C.

2007-01-01

Background Celloidin and paraffin are the two common embedding mediums used for histopathologic study of the human temporal bone by light microscopy. Although celloidin embedding permits excellent morphologic assessment, celloidin is difficult to remove, and there are significant restrictions on success with immunostaining. Embedding in paraffin allows immunostaining to be performed, but preservation of cellular detail within the membranous labyrinth is relatively poor. Objectives/Hypothesis Polyester wax is an embedding medium that has a low melting point (37°C), is soluble in most organic solvents, is water tolerant, and sections easily. We hypothesized that embedding in polyester wax would permit good preservation of the morphology of the membranous labyrinth and, at the same time, allow the study of proteins by immunostaining. Methods Nine temporal bones from individuals aged 1 to 94 years removed 2 to 31 hours postmortem, from subjects who had no history of otologic disease, were used. The bones were fixed using 10% formalin, decal-cified using EDTA, embedded in polyester wax, and serially sectioned at a thickness of 8 to 12 μm on a rotary microtome. The block and knife were cooled with frozen CO2 (dry ice) held in a funnel above the block. Sections were placed on glass slides coated with a solution of 1% fish gelatin and 1% bovine albumin, followed by staining of selected sections with hematoxylin and eosin (H&E). Immunostaining was also performed on selected sections using antibodies to 200 kD neurofilament and Na-K-ATPase. Results Polyester wax–embedded sections demonstrated good preservation of cellular detail of the organ of Corti and other structures of the membranous labyrinth, as well as the surrounding otic capsule. The protocol described in this paper was reliable and consistently yielded sections of good quality. Immuno-staining was successful with both antibodies. Conclusion The use of polyester wax as an embedding medium for human temporal bones offers the advantage of good preservation of morphology and ease of immunostaining. We anticipate that in the future, polyester wax embedding will also permit other molecular biologic assays on temporal bone sections such as the retrieval of nucleic acids and the study of proteins using mass spectrometry–based proteomic analysis. PMID:16467713

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

PubMed

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.

In vitro terahertz spectroscopy of gelatin-embedded human brain tumors: a pilot study

NASA Astrophysics Data System (ADS)

Chernomyrdin, N. V.; Gavdush, A. A.; Beshplav, S.-I. T.; Malakhov, K. M.; Kucheryavenko, A. S.; Katyba, G. M.; Dolganova, I. N.; Goryaynov, S. A.; Karasik, V. E.; Spektor, I. E.; Kurlov, V. N.; Yurchenko, S. O.; Komandin, G. A.; Potapov, A. A.; Tuchin, V. V.; Zaytsev, K. I.

2018-04-01

We have performed the in vitro terahertz (THz) spectroscopy of human brain tumors. In order to fix tissues for the THz measurements, we have applied the gelatin embedding. It allows for preserving tissues from hydration/dehydration and sustaining their THz response similar to that of the freshly-excised tissues for a long time after resection. We have assembled an experimental setup for the reflection-mode measurements of human brain tissues based on the THz pulsed spectrometer. We have used this setup to study in vitro the refractive index and the amplitude absorption coefficient of 2 samples of malignant glioma (grade IV), 1 sample of meningioma (grade I), and samples of intact tissues. We have observed significant differences between the THz responses of normal and pathological tissues of the brain. The results of this paper highlight the potential of the THz technology in the intraoperative neurodiagnosis of tumors relying on the endogenous labels of tumorous tissues.

RCL2, a New Fixative, Preserves Morphology and Nucleic Acid Integrity in Paraffin-Embedded Breast Carcinoma and Microdissected Breast Tumor Cells

PubMed Central

Delfour, Christophe; Roger, Pascal; Bret, Caroline; Berthe, Marie-Laurence; Rochaix, Philippe; Kalfa, Nicolas; Raynaud, Pierre; Bibeau, Frédéric; Maudelonde, Thierry; Boulle, Nathalie

2006-01-01

Methacarn and RCL2, a new noncrosslinking fixative, were compared to formalin-fixed or frozen tissue samples of the same invasive breast carcinoma and were evaluated for their effects on tissue morphology and immunohistochemistry as well as DNA and RNA integrity. The histomorphology of methacarn- or RCL2-fixed paraffin-embedded tumors was similar to that observed with the matched formalin-fixed tissues. Immunohistochemistry using various antibodies showed comparable results with either fixative, leading to accurate breast tumor diagnosis and determination of estrogen and progesterone receptors, and HER2 status. Methacarn and RCL2 fixation preserved DNA integrity as demonstrated by successful amplification and sequencing of large DNA amplicons. Similarly, high-quality RNA could be extracted from methacarn- or RCL2-fixed paraffin-embedded MCF-7 cells, whole breast tumor tissues, or microdissected breast tumor cells, as assessed by electropherogram profiles and real-time reverse transcriptase-polymerase chain reaction quantification of various genes. Moreover, tissue morphology and RNA integrity were preserved after 8 months of storage. Altogether, these results indicate that methacarn, as previously shown, and RCL2, a promising new fixative, have great potential for performing both morphological and molecular analyses on the same fixed tissue sample, even after laser-capture microdissection, and can open new doors for investigating small target lesions such as premalignant breast lesions. PMID:16645201

Switching theory-based steganographic system for JPEG images

NASA Astrophysics Data System (ADS)

Cherukuri, Ravindranath C.; Agaian, Sos S.

2007-04-01

Cellular communications constitute a significant portion of the global telecommunications market. Therefore, the need for secured communication over a mobile platform has increased exponentially. Steganography is an art of hiding critical data into an innocuous signal, which provide answers to the above needs. The JPEG is one of commonly used format for storing and transmitting images on the web. In addition, the pictures captured using mobile cameras are in mostly in JPEG format. In this article, we introduce a switching theory based steganographic system for JPEG images which is applicable for mobile and computer platforms. The proposed algorithm uses the fact that energy distribution among the quantized AC coefficients varies from block to block and coefficient to coefficient. Existing approaches are effective with a part of these coefficients but when employed over all the coefficients they show there ineffectiveness. Therefore, we propose an approach that works each set of AC coefficients with different frame work thus enhancing the performance of the approach. The proposed system offers a high capacity and embedding efficiency simultaneously withstanding to simple statistical attacks. In addition, the embedded information could be retrieved without prior knowledge of the cover image. Based on simulation results, the proposed method demonstrates an improved embedding capacity over existing algorithms while maintaining a high embedding efficiency and preserving the statistics of the JPEG image after hiding information.

Human Vascular Microphysiological System for in vitro Drug Screening.

PubMed

Fernandez, C E; Yen, R W; Perez, S M; Bedell, H W; Povsic, T J; Reichert, W M; Truskey, G A

2016-02-18

In vitro human tissue engineered human blood vessels (TEBV) that exhibit vasoactivity can be used to test human toxicity of pharmaceutical drug candidates prior to pre-clinical animal studies. TEBVs with 400-800 μM diameters were made by embedding human neonatal dermal fibroblasts or human bone marrow-derived mesenchymal stem cells in dense collagen gel. TEBVs were mechanically strong enough to allow endothelialization and perfusion at physiological shear stresses within 3 hours after fabrication. After 1 week of perfusion, TEBVs exhibited endothelial release of nitric oxide, phenylephrine-induced vasoconstriction, and acetylcholine-induced vasodilation, all of which were maintained up to 5 weeks in culture. Vasodilation was blocked with the addition of the nitric oxide synthase inhibitor L-N(G)-Nitroarginine methyl ester (L-NAME). TEBVs elicited reversible activation to acute inflammatory stimulation by TNF-α which had a transient effect upon acetylcholine-induced relaxation, and exhibited dose-dependent vasodilation in response to caffeine and theophylline. Treatment of TEBVs with 1 μM lovastatin for three days prior to addition of Tumor necrosis factor - α (TNF-α) blocked the injury response and maintained vasodilation. These results indicate the potential to develop a rapidly-producible, endothelialized TEBV for microphysiological systems capable of producing physiological responses to both pharmaceutical and immunological stimuli.

High-resolution Episcopic Microscopy (HREM) - Simple and Robust Protocols for Processing and Visualizing Organic Materials

PubMed Central

Geyer, Stefan H.; Maurer-Gesek, Barbara; Reissig, Lukas F.; Weninger, Wolfgang J.

2017-01-01

We provide simple protocols for generating digital volume data with the high-resolution episcopic microscopy (HREM) method. HREM is capable of imaging organic materials with volumes up to 5 x 5 x 7 mm3 in typical numeric resolutions between 1 x 1 x 1 and 5 x 5 x 5 µm3. Specimens are embedded in methacrylate resin and sectioned on a microtome. After each section an image of the block surface is captured with a digital video camera that sits on the phototube connected to the compound microscope head. The optical axis passes through a green fluorescent protein (GFP) filter cube and is aligned with a position, at which the bock holder arm comes to rest after each section. In this way, a series of inherently aligned digital images, displaying subsequent block surfaces are produced. Loading such an image series in three-dimensional (3D) visualization software facilitates the immediate conversion to digital volume data, which permit virtual sectioning in various orthogonal and oblique planes and the creation of volume and surface rendered computer models. We present three simple, tissue specific protocols for processing various groups of organic specimens, including mouse, chick, quail, frog and zebra fish embryos, human biopsy material, uncoated paper and skin replacement material. PMID:28715372

High-resolution Episcopic Microscopy (HREM) - Simple and Robust Protocols for Processing and Visualizing Organic Materials.

PubMed

Geyer, Stefan H; Maurer-Gesek, Barbara; Reissig, Lukas F; Weninger, Wolfgang J

2017-07-07

We provide simple protocols for generating digital volume data with the high-resolution episcopic microscopy (HREM) method. HREM is capable of imaging organic materials with volumes up to 5 x 5 x 7 mm 3 in typical numeric resolutions between 1 x 1 x 1 and 5 x 5 x 5 µm 3 . Specimens are embedded in methacrylate resin and sectioned on a microtome. After each section an image of the block surface is captured with a digital video camera that sits on the phototube connected to the compound microscope head. The optical axis passes through a green fluorescent protein (GFP) filter cube and is aligned with a position, at which the bock holder arm comes to rest after each section. In this way, a series of inherently aligned digital images, displaying subsequent block surfaces are produced. Loading such an image series in three-dimensional (3D) visualization software facilitates the immediate conversion to digital volume data, which permit virtual sectioning in various orthogonal and oblique planes and the creation of volume and surface rendered computer models. We present three simple, tissue specific protocols for processing various groups of organic specimens, including mouse, chick, quail, frog and zebra fish embryos, human biopsy material, uncoated paper and skin replacement material.

Dual-Level Security based Cyclic18 Steganographic Method and its Application for Secure Transmission of Keyframes during Wireless Capsule Endoscopy.

PubMed

Muhammad, Khan; Sajjad, Muhammad; Baik, Sung Wook

2016-05-01

In this paper, the problem of secure transmission of sensitive contents over the public network Internet is addressed by proposing a novel data hiding method in encrypted images with dual-level security. The secret information is divided into three blocks using a specific pattern, followed by an encryption mechanism based on the three-level encryption algorithm (TLEA). The input image is scrambled using a secret key, and the encrypted sub-message blocks are then embedded in the scrambled image by cyclic18 least significant bit (LSB) substitution method, utilizing LSBs and intermediate LSB planes. Furthermore, the cover image and its planes are rotated at different angles using a secret key prior to embedding, deceiving the attacker during data extraction. The usage of message blocks division, TLEA, image scrambling, and the cyclic18 LSB method results in an advanced security system, maintaining the visual transparency of resultant images and increasing the security of embedded data. In addition, employing various secret keys for image scrambling, data encryption, and data hiding using the cyclic18 LSB method makes the data recovery comparatively more challenging for attackers. Experimental results not only validate the effectiveness of the proposed framework in terms of visual quality and security compared to other state-of-the-art methods, but also suggest its feasibility for secure transmission of diagnostically important keyframes to healthcare centers and gastroenterologists during wireless capsule endoscopy.

A Method to Evaluate Genome-Wide Methylation in Archival Formalin-Fixed, Paraffin-Embedded Ovarian Epithelial Cells

PubMed Central

Li, Qiling; Li, Min; Ma, Li; Li, Wenzhi; Wu, Xuehong; Richards, Jendai; Fu, Guoxing; Xu, Wei; Bythwood, Tameka; Li, Xu; Wang, Jianxin; Song, Qing

2014-01-01

Background 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. Methodology/Principal Findings 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. Conclusions/Significance We have developed an efficient method that allows DNA methylation to be assessed in archival FFPE tissue samples. PMID:25133528

In situ hybridisation for the detection of Leishmania species in paraffin wax-embedded canine tissues using a digoxigenin-labelled oligonucleotide probe

PubMed Central

Dinhopl, N.; Mostegl, M. M.; Richter, B.; Nedorost, N.; Maderner, A.; Fragner, K.; Weissenböck, H.

2011-01-01

The diagnosis of canine leishmaniosis (CanL) is currently predominantly achieved by cytological or histological identification of amastigotes in biopsy samples, demonstration of specific anti-Leishmania antibodies and PCR-based approaches. All these methods have the advantage of being sensitive and more or less specific; nevertheless, most of them also have disadvantages. A chromogenic in situ hybridisation (ISH) procedure with a digoxigenin-labelled probe, targeting a fragment of the 5.8S rRNA was developed for the detection of all species of Leishmania parasites in routinely paraffin wax-embedded canine tissues. This method was validated in comparison with traditional techniques (histology, PCR), on various tissues from three dogs with histological changes consistent with a florid leishmaniosis. Amastigote forms of Leishmania gave clear signals and were easily identified using ISH. Various tissues from 10 additional dogs with clinical suspicion or/and a positive serological test but without histological presence of amastigotes did not show any ISH signals. Potential cross-reactivity of the probe was ruled out by negative outcome of the ISH against selected protozoa (including the related Trypanosoma cruzi) and fungi. Thus, ISH proved to be a powerful tool for unambiguous detection of Leishmania parasites in paraffin wax-embedded tissues. PMID:21921059

Boric acid-enhanced embedding medium for cryomicrotomy.

PubMed

Lim, Jin Ik; Park, Hun-Kuk

2012-05-01

A polyvinyl alcohol (PVA)/polyethylene glycol (PEG)-based resin is commonly used as a cryoembedding medium for the histological analysis of frozen tissue sections. However, it is not easy to obtain sufficient numbers of satisfactory reproducible sections owing to the differences between the mechanical properties of the medium and embedded tissue and the low cohesive force of the medium. We describe a modified PVA-based cryoembedding medium, composed of PVA (10wt% and 15wt%) with the addition of boric acid (from 0 to 5wt%), that can improve the sectioning properties and efficiency of frozen tissue for histological analysis. The amount of load under the same compressive displacement as well as cohesive force increased with increasing boric acid and PVA contents. 15wt% PVA and 3wt% boric acid was determined as an optimal composition for cryoembedding material based on the sectioning efficiency measured by the numbers of unimpaired sectioned slices and the amount of load under the same compressive displacement test. On the basis of the results of routine hematoxylin and eosin staining of cryosections of tissue embedded in a medium with 3wt% boric acid and PVA, it was concluded that the modified PVA cryoembedding medium can improve the efficiency of cryosectioning for subsequent histological or histochemical analysis of various tissues. Copyright © 2011 Elsevier GmbH. All rights reserved.

Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA.

PubMed

Guo, Shicheng; Diep, Dinh; Plongthongkum, Nongluk; Fung, Ho-Lim; Zhang, Kang; Zhang, Kun

2017-04-01

Adjacent CpG sites in mammalian genomes can be co-methylated owing to the processivity of methyltransferases or demethylases, yet discordant methylation patterns have also been observed, which are related to stochastic or uncoordinated molecular processes. We focused on a systematic search and investigation of regions in the full human genome that show highly coordinated methylation. We defined 147,888 blocks of tightly coupled CpG sites, called methylation haplotype blocks, after analysis of 61 whole-genome bisulfite sequencing data sets and validation with 101 reduced-representation bisulfite sequencing data sets and 637 methylation array data sets. Using a metric called methylation haplotype load, we performed tissue-specific methylation analysis at the block level. Subsets of informative blocks were further identified for deconvolution of heterogeneous samples. Finally, using methylation haplotypes we demonstrated quantitative estimation of tumor load and tissue-of-origin mapping in the circulating cell-free DNA of 59 patients with lung or colorectal cancer.

Dental fragment embedded in the lower lip after facial trauma: Brief review literature and report of a case

PubMed Central

Lauritano, Dorina; Petruzzi, Massimo; Sacco, Gerardo; Campus, Guglielmo; Carinci, Francesco; Milillo, Lucio

2012-01-01

Upper incisors are the most frequently involved teeth in traumatic dental injuries. Soft tissues (lips and/or oral mucosa) adjacent to incisal edge can receive direct and/or indirect traumas. Laceration of the lower lip is a not rare eventuality and teeth fragments could be embedded in labial soft tissue. The reattachment of these fragments, if possible, is the elective treatment choice, thanks to the modern adhesive and restorative techniques. The authors present a case of a white Caucasian 10-year-old child, who attended the dental clinic for the treatment of both upper central incisors’ crown fractures. The fragment of the left incisor was retrieved embedded in the lower lip. It was successfully surgically removed and reattached using a composite adhesive technique. A careful clinical and radiographic examination with the surgical removal of tooth fragments could prevent undesirable foreign body reaction, infection and scarring. The authors also reviewed the most relevant literature concerning tooth fragment reattachment after removal from oral soft tissues. PMID:23814592

Application of in-situ hybridization for the detection and identification of avian malaria parasites in paraffin wax-embedded tissues from captive penguins

PubMed Central

Dinhopl, Nora; Mostegl, Meike M.; Richter, Barbara; Nedorost, Nora; Maderner, Anton; Fragner, Karin; Weissenböck, Herbert

2011-01-01

In captive penguins, avian malaria due to Plasmodium parasites is a well-recognized disease problem as these protozoa may cause severe losses among valuable collections of zoo birds. In blood films from naturally infected birds, identification and differentiation of malaria parasites based on morphological criteria are difficult because parasitaemia is frequently light and blood stages, which are necessary for identification of parasites, are often absent. Post-mortem diagnosis by histological examination of tissue samples is sometimes inconclusive due to the difficulties in differentiating protozoal tissue stages from fragmented nuclei in necrotic tissue. The diagnosis of avian malaria would be facilitated by a technique with the ability to specifically identify developmental stages of Plasmodium in tissue samples. Thus, a chromogenic in-situ hybridization (ISH) procedure with a digoxigenin-labelled probe, targeting a fragment of the 18S rRNA, was developed for the detection of Plasmodium parasites in paraffin wax-embedded tissues. This method was validated in comparison with traditional techniques (histology, polymerase chain reaction), on various tissues from 48 captive penguins that died at the zoological garden Schönbrunn, Vienna, Austria. Meronts of Plasmodium gave clear signals and were easily identified using ISH. Potential cross-reactivity of the probe was ruled out by the negative outcome of the ISH against a number of protozoa and fungi. Thus, ISH proved to be a powerful, specific and sensitive tool for unambiguous detection of Plasmodium parasites in paraffin wax-embedded tissue samples. PMID:21711191

Staining Methods for Normal and Regenerative Myelin in the Nervous System.

PubMed

Carriel, Víctor; Campos, Antonio; Alaminos, Miguel; Raimondo, Stefania; Geuna, Stefano

2017-01-01

Histochemical techniques enable the specific identification of myelin by light microscopy. Here we describe three histochemical methods for the staining of myelin suitable for formalin-fixed and paraffin-embedded materials. The first method is conventional luxol fast blue (LFB) method which stains myelin in blue and Nissl bodies and mast cells in purple. The second method is a LBF-based method called MCOLL, which specifically stains the myelin as well the collagen fibers and cells, giving an integrated overview of the histology and myelin content of the tissue. Finally, we describe the osmium tetroxide method, which consist in the osmication of previously fixed tissues. Osmication is performed prior the embedding of tissues in paraffin giving a permanent positive reaction for myelin as well as other lipids present in the tissue.

[A study on the method of DNA extraction from unbuffered formalin-fixed and paraffin-embedded samples].

PubMed

Tian, Zi-Qiang; Liu, Jun-Feng; Zhang, Shao-Wei; Li, Bao-Qing; Wang, Fu-Shun; Zhang, Yue-Feng

2004-03-01

Unbuffered formalin is widely used to fix resected specimens in China. The DNA in unbuffered formalin-fixed and paraffin-embedded tissues is usually degraded seriously, so the extraction of DNA from these samples is difficult. This study was conducted to seek an optimal method to extract DNA from these samples. Fifteen blocks of esophageal carcinoma resected in Fourth Hospital of Hebei Medical University in 2000 were selected. The cells were lyzed by proteinase K digestion or heating under different pH values, then DNA was extracted by phenol:chloroform. After that, four parameters (deparaffined by xylene or histolene; digested for 48 h or 72 h at 37 degrees C or 56 degrees C; extracted by salting-out or phenol:chloroform) were optimized according to the principle of cross design. At last, the quality of obtained DNA was analyzed with electrophoresis and PCR amplification. The quality and quantity of DNA obtained by proteinase K digestion (the average yield is 17.88 microg) were better than that of heating under different pH (7-12)(P< 0.05). The quality and quantity of DNA digested at 56 degrees C were better than that at 37 degrees C, and similarly, digestion for 72 hours was better than that for 48 hours. The methods of deparaffin and extraction had no obvious influence on the quality and quantity of DNA. By means of NaCl salting-out after proteinase K digestion, more reliable quality of DNA can be obtained from unbuffered formalin-fixed and paraffin-embedded samples. Furthermore,digestion for three days at 56 degrees C is more likely to obtain DNA with high quality and quantity.

A Novel Method for Block Size Forensics Based on Morphological Operations

NASA Astrophysics Data System (ADS)

Luo, Weiqi; Huang, Jiwu; Qiu, Guoping

Passive forensics analysis aims to find out how multimedia data is acquired and processed without relying on pre-embedded or pre-registered information. Since most existing compression schemes for digital images are based on block processing, one of the fundamental steps for subsequent forensics analysis is to detect the presence of block artifacts and estimate the block size for a given image. In this paper, we propose a novel method for blind block size estimation. A 2×2 cross-differential filter is first applied to detect all possible block artifact boundaries, morphological operations are then used to remove the boundary effects caused by the edges of the actual image contents, and finally maximum-likelihood estimation (MLE) is employed to estimate the block size. The experimental results evaluated on over 1300 nature images show the effectiveness of our proposed method. Compared with existing gradient-based detection method, our method achieves over 39% accuracy improvement on average.

Engineering Three-dimensional Epithelial Tissues Embedded within Extracellular Matrix.

PubMed

Piotrowski-Daspit, Alexandra S; Nelson, Celeste M

2016-07-10

The architecture of branched organs such as the lungs, kidneys, and mammary glands arises through the developmental process of branching morphogenesis, which is regulated by a variety of soluble and physical signals in the microenvironment. Described here is a method created to study the process of branching morphogenesis by forming engineered three-dimensional (3D) epithelial tissues of defined shape and size that are completely embedded within an extracellular matrix (ECM). This method enables the formation of arrays of identical tissues and enables the control of a variety of environmental factors, including tissue geometry, spacing, and ECM composition. This method can also be combined with widely used techniques such as traction force microscopy (TFM) to gain more information about the interactions between cells and their surrounding ECM. The protocol can be used to investigate a variety of cell and tissue processes beyond branching morphogenesis, including cancer invasion.

Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer

NASA Astrophysics Data System (ADS)

Zhao, Xiaozheng; Huffman, Kenneth E.; Fujimoto, Junya; Canales, Jamie Rodriguez; Girard, Luc; Nie, Guangjun; Heymach, John V.; Wistuba, Igacio I.; Minna, John D.; Yu, Yonghao

2017-10-01

With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient's pathology based diagnosis of "poorly differentiated SqCC". Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic. [Figure not available: see fulltext.

A new method for fabrication of diamond-dust blocking filters

NASA Technical Reports Server (NTRS)

Collard, H. R.; Hogan, R. C.

1986-01-01

Thermal embedding of diamond dust onto a polyethylene-coated Al plate has been used to make a blocking filter for FIR applications. The Al plate is sandwiched between two Mylar 'blankets' and the air between the layers is removed by means of a small vacuum pump. After the polyethylene is heated and softened, the diamond dust is applied to the polyethylene coating using a brush. The optimum diamond dust grain sizes corresponding to polyethylene layer thicknesses of 9-12 microns are given in a table, and the application of the blocking filter to spectrometric measurements in the FIR is described. An exploded view diagram of the layered structure of the blocking filter is provided.

Development of an optimized protocol for the detection of classical swine fever virus in formalin-fixed, paraffin-embedded tissues by seminested reverse transcription-polymerase chain reaction and comparison with in situ hybridization.

PubMed

Ha, S-K; Choi, C; Chae, C

2004-10-01

An optimized protocol was developed for the detection of classical swine fever virus (CSFV) in formalin-fixed, paraffin-embedded tissues obtained from experimentally and naturally infected pigs by seminested reverse transcription-polymerase chain reaction (RT-PCR). The results for seminested RT-PCR were compared with those determined by in situ hybridization. The results obtained show that the use of deparaffinization with xylene, digestion with proteinase K, extraction with Trizol LS, followed by seminested RT-PCR is a reliable detection method. An increase in sensitivity was observed as amplicon size decreased. The highest sensitivity for RT-PCR on formalin-fixed, paraffin-embedded tissues RNA was obtained with amplicon sizes less than approximately 200 base pairs. An hybridization signal for CSFV was detected in lymph nodes from 12 experimentally and 12 naturally infected pigs. The sensitivity of seminested RT-PCR compared with in situ hybridization was 100% for CSFV. When only formalin-fixed tissues are available, seminested RT-PCR and in situ hybridization would be useful diagnostic methods for the detection of CSFV nucleic acid.

Compressed Collagen Enhances Stem Cell Therapy for Corneal Scarring

PubMed Central

Shojaati, Golnar; Khandaker, Irona; Sylakowski, Kyle; Funderburgh, Martha L.; Du, Yiqin

2018-01-01

Abstract Stem cells from human corneal stroma (CSSC) suppress corneal stromal scarring in a mouse wound‐healing model and promote regeneration of native transparent tissue (PMID:25504883). This study investigated efficacy of compressed collagen gel (CCG) as a vehicle to deliver CSSC for corneal therapy. CSSC isolated from limbal stroma of human donor corneas were embedded in soluble rat‐tendon collagen, gelled at 37°C, and partially dehydrated to a thickness of 100 µm by passive absorption. The CCG disks were dimensionally stable, easy to handle, and could be adhered securely to de‐epithelialized mouse cornea with fibrin‐based adhesive. CSSC in CCG maintained >80% viability for >1 week in culture media and could be cryopreserved in 20% fetal bovine serum‐10%DMSO in liquid nitrogen. CCG containing as few as 500 CSSC effectively prevented visible scarring and suppressed expression of fibrotic Col3a1 mRNA. CSSC in CCG were more effective at blocking scarring on a per‐cell basis than CSSC delivered directly in a fibrin gel as previously described. Collagen‐embedded cells retained the ability to suppress corneal scarring after conventional cryopreservation. This study demonstrates use of a common biomaterial that can facilitate storage and handling of stem cells in a manner that may provide off‐the‐shelf delivery of stem cells as a therapy for corneal scarring. stem cells translational medicine 2018;7:487–494 PMID:29654654

Preparation of a non-woven poly(ε-caprolactone) fabric with partially embedded apatite surface for bone tissue engineering applications by partial surface melting of poly(ε-caprolactone) fibers.

PubMed

Kim, In Ae; Rhee, Sang-Hoon

2017-07-01

This article describes a novel method for the preparation of a biodegradable non-woven poly(ε-caprolactone) fabric with a partially embedded apatite surface designed for application as a scaffold material for bone tissue engineering. The non-woven poly(ε-caprolactone) fabric was generated by the electro-spinning technique and then apatite was coated in simulated body fluid after coating the PVA solution containing CaCl 2 ·2H 2 O. The apatite crystals were partially embedded or fully embedded into the thermoplastic poly(ε-caprolactone) fibers by controlling the degree of poly(ε-caprolactone) fiber surface melting in a convection oven. Identical apatite-coated poly(ε-caprolactone) fabric that did not undergo heat-treatment was used as a control. The features of the embedded apatite crystals were evaluated by FE-SEM, AFM, EDS, and XRD. The adhesion strengths of the coated apatite layers and the tensile strengths of the apatite coated fabrics with and without heat-treatment were assessed by the tape-test and a universal testing machine, respectively. The degree of water absorbance was assessed by adding a DMEM droplet onto the fabrics. Moreover, cell penetrability was assessed by seeding preosteoblastic MC3T3-E1 cells onto the fabrics and observing the degrees of cell penetration after 1 and 4 weeks by staining nuclei with DAPI. The non-woven poly(ε-caprolactone) fabric with a partially embedded apatite surface showed good water absorbance, cell penetrability, higher apatite adhesion strength, and higher tensile strength compared with the control fabric. These results show that the non-woven poly(ε-caprolactone) fabric with a partially embedded apatite surface is a potential candidate scaffold for bone tissue engineering due to its strong apatite adhesion strength and excellent cell penetrability. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1973-1983, 2017. © 2017 Wiley Periodicals, Inc.

Immunogold Staining of Ultrathin Thawed Cryosections for Transmission Electron Microscopy (TEM).

PubMed

Skepper, Jeremy N; Powell, Janet M

2008-06-01

INTRODUCTIONA pre-embedding method of immunochemical staining is used if antigens are damaged by resin embedding, or if the best preservation of membranes is required. Applying immunogold reagents to sections of lightly fixed tissue, free of embedding medium, can be a very sensitive method of immunochemical staining. Cells or tissues are fixed as strongly as possible and then treated with a cryoprotectant, which is usually a mixture of sucrose and polyvinylpyrrolidone (PVP). They are frozen onto pins in liquid nitrogen and sectioned at approximately -100°C. The frozen sections are thaw-mounted on to Formvar/nickel film grids and the cryoprotectant is removed by floating the grids on drops of phosphate-buffered saline (PBS). The immunogold staining is performed on the unembedded sections, which are subsequently contrast counterstained and infiltrated with a mixture of methylcellulose and uranyl acetate. In this protocol, samples are sectioned at low temperature, thaw-mounted onto film grids, immunochemically stained, contrast counterstained, and embedded/encapsulated in situ on the grid before viewing by transmission electron microscopy (TEM).

Embedded sensor having an identifiable orientation

DOEpatents

Bennett, Thomas E.; Nelson, Drew V.

2002-01-01

An apparatus and method is described wherein a sensor, such as a mechanical strain sensor, embedded in a fiber core, is "flagged" to identify a preferred orientation of the sensor. The identifying "flag" is a composite material, comprising a plurality of non-woven filaments distributed in a resin matrix, forming a small planar tab. The fiber is first subjected to a stimulus to identify the orientation providing the desired signal response, and then sandwiched between first and second layers of the composite material. The fiber, and therefore, the sensor orientation is thereby captured and fixed in place. The process for achieving the oriented fiber includes, after identifying the fiber orientation, carefully laying the oriented fiber onto the first layer of composite, moderately heating the assembled layer for a short period in order to bring the composite resin to a "tacky" state, heating the second composite layer as the first, and assembling the two layers together such that they merge to form a single consolidated block. The consolidated block achieving a roughly uniform distribution of composite filaments near the embedded fiber such that excess resin is prevented from "pooling" around the periphery of the fiber.

Managing Security in FPGA-Based Embedded Systems

DTIC Science & Technology

2008-01-01

Trans. De- sign Automation of Electronic Systems (TODAES), vol. 13, no. 3, July 2008, article 44. c©2008 ACM with permission.5) of the function would need...in the finished design. In addition, the life cycle can be subverted when engineers inject unintended functionality, some of which might be malicious...cores and a moat size of two. There are several different drawbridge configurations between the cores. (IOB: I/O block; CLB: configuration logic block

Identification of oleoresin in epoxy-embedded slash pine tissue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Birchem, R.; Brown, C.L.

1978-01-01

Sudan black B stains oleoresin blue-black in epoxy-embedded material as well as in living tissue. The Sudan black B staining properties of oleoresin are similar to those of lipid, but it can be distinguished from tannin, which stains brown. Practically all oleoresin present in resin ducts and intercellular spaces, and much of that contained in epithelial and ray cells, is extracted in preparatory procedures for electron microscopy. A fixation procedure is proposed which preserves significantly more oleoresin in situ. The use of Sudan black B enables one to localize oleoresin by light microscopy, and permits direct comparison of adjacent sectionsmore » of epoxy-embedded material at the ultrastructure level. Ultrastructurally oleoresin and lipid possess similar electron densities and can be distinguished from the highly electron-opaque tannin deposits.« less

Biophysical properties of dermal building-blocks affects extra cellular matrix assembly in 3D endogenous macrotissue.

PubMed

Urciuolo, F; Garziano, A; Imparato, G; Panzetta, V; Fusco, S; Casale, C; Netti, P A

2016-01-29

The fabrication of functional tissue units is one of the major challenges in tissue engineering due to their in vitro use in tissue-on-chip systems, as well as in modular tissue engineering for the construction of macrotissue analogs. In this work, we aim to engineer dermal tissue micromodules obtained by culturing human dermal fibroblasts into porous gelatine microscaffold. We proved that such stromal cells coupled with gelatine microscaffolds are able to synthesize and to assemble an endogenous extracellular matrix (ECM) resulting in tissue micromodules, which evolve their biophysical features over the time. In particular, we found a time-dependent variation of oxygen consumption kinetic parameters, of newly formed ECM stiffness and of micromodules self-aggregation properties. As consequence when used as building blocks to fabricate larger tissues, the initial tissue micromodules state strongly affects the ECM organization and maturation in the final macrotissue. Such results highlight the role of the micromodules properties in controlling the formation of three-dimensional macrotissue in vitro, defining an innovative design criterion for selecting tissue-building blocks for modular tissue engineering.

Embedded Hyperchaotic Generators: A Comparative Analysis

NASA Astrophysics Data System (ADS)

Sadoudi, Said; Tanougast, Camel; Azzaz, Mohamad Salah; Dandache, Abbas

In this paper, we present a comparative analysis of FPGA implementation performances, in terms of throughput and resources cost, of five well known autonomous continuous hyperchaotic systems. The goal of this analysis is to identify the embedded hyperchaotic generator which leads to designs with small logic area cost, satisfactory throughput rates, low power consumption and low latency required for embedded applications such as secure digital communications between embedded systems. To implement the four-dimensional (4D) chaotic systems, we use a new structural hardware architecture based on direct VHDL description of the forth order Runge-Kutta method (RK-4). The comparative analysis shows that the hyperchaotic Lorenz generator provides attractive performances compared to that of others. In fact, its hardware implementation requires only 2067 CLB-slices, 36 multipliers and no block RAMs, and achieves a throughput rate of 101.6 Mbps, at the output of the FPGA circuit, at a clock frequency of 25.315 MHz with a low latency time of 316 ns. Consequently, these good implementation performances offer to the embedded hyperchaotic Lorenz generator the advantage of being the best candidate for embedded communications applications.

Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

PubMed Central

Dalmay, Tamas

2018-01-01

RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions. For example, in Drosophila, some tissues contain a highly abundant 30nt rRNA fragment (the 2S rRNA) as well as abundant 5’ and 3’ terminal rRNA fragments. These can pose difficulties for the construction of sRNA libraries as they can swamp the sequencing space and obscure sRNA abundances. Here we addressed this problem and present a modified “rRNA blocking” protocol for the construction of high-definition (HD) adapter sRNA libraries, in D. melanogaster reproductive tissues. The results showed that 2S rRNAs targeted by blocking oligos were reduced from >80% to < 0.01% total reads. In addition, the use of multiple rRNA blocking oligos to bind the most abundant rRNA fragments allowed us to reveal the underlying sRNA populations at increased resolution. Side-by-side comparisons of sequencing libraries of blocked and non-blocked samples revealed that rRNA blocking did not change the miRNA populations present, but instead enhanced their abundances. We suggest that this rRNA blocking procedure offers the potential to improve the in-depth analysis of differentially expressed sRNAs within and across different tissues. PMID:29474379

Dynamic virtual optical network embedding in spectral and spatial domains over elastic optical networks with multicore fibers

NASA Astrophysics Data System (ADS)

Zhu, Ruijie; Zhao, Yongli; Yang, Hui; Tan, Yuanlong; Chen, Haoran; Zhang, Jie; Jue, Jason P.

2016-08-01

Network virtualization can eradicate the ossification of the infrastructure and stimulate innovation of new network architectures and applications. Elastic optical networks (EONs) are ideal substrate networks for provisioning flexible virtual optical network (VON) services. However, as network traffic continues to increase exponentially, the capacity of EONs will reach the physical limitation soon. To further increase network flexibility and capacity, the concept of EONs is extended into the spatial domain. How to map the VON onto substrate networks by thoroughly using the spectral and spatial resources is extremely important. This process is called VON embedding (VONE).Considering the two kinds of resources at the same time during the embedding process, we propose two VONE algorithms, the adjacent link embedding algorithm (ALEA) and the remote link embedding algorithm (RLEA). First, we introduce a model to solve the VONE problem. Then we design the embedding ability measurement of network elements. Based on the network elements' embedding ability, two VONE algorithms were proposed. Simulation results show that the proposed VONE algorithms could achieve better performance than the baseline algorithm in terms of blocking probability and revenue-to-cost ratio.

Detection of PAX3-FKHR and PAX7-FKHR fusion transcripts in rhabdomyosarcoma by reverse transcriptase-polymerase chain reaction using paraffin-embedded tissue.

PubMed

Chen, B F; Chen, M L; Liang, D C; Huang, Y W; Liu, H C; Chen, S H

1999-02-01

Alveolar rhabdomyosarcoma (RMS) is associated with a characteristic chromosomal translocation t(2;13)(q35;q14). The genes involved in this translocation are paired box (PAX)3 on chromosome 2 and forkhead in RMS (FKHR) on chromosome 13. An occasional variant translocation t(1;13)(p36;q14) affecting PAX7 and FKHR on chromosomes 1 and 13, respectively, has also been described. Chromosomal translocations in RMS are detected using conventional cytogenetic analysis, fluorescence in situ hybridization (FISH) or reverse transcriptase-polymerase chain reaction (RT-PCR) on fresh or frozen tissue samples. We describe the results of RT-PCR analysis of PAX3-FKHR and PAX7-FKHR chimeric messages in formalin-fixed, paraffin-embedded tissue samples from 17 RMS cases. RNA was extracted from formalin-fixed, paraffin-embedded RMS tissue. Oligonucleotide primers corresponding to the regions of PAX3, PAX7 and FKHR were used for the detection of PAX3-FKHR and PAX7-FKHR chimeric messages. A seminested PCR of the PCR products was used to increase the sensitivity of detection. The amplified fragments were purified and directly sequenced to confirm the specificity of the methods. The PAX3-FKHR chimeric message was detected in all three cases of alveolar RMS but not in any of the 12 embryonal and two pleomorphic RMS cases. The PAX7-FKHR fusion transcript was detected in one case of embryonal RMS. The results indicate that the RT-PCR assay is a reliable method for the detection of the PAX3-FKHR fusion transcript of alveolar RMS in formalin-fixed, paraffin-embedded tissue. This simple method enables pathologists to identify chromosomal rearrangements in RMS as a diagnostic aid in cases where fresh or frozen tissue is not available.

Impact of Collection and Storage of Lung Tumor Tissue on Whole Genome Expression Profiling

PubMed Central

Freidin, Maxim B.; Bhudia, Neesa; Lim, Eric; Nicholson, Andrew G.; Cookson, William O.; Moffatt, Miriam F.

2012-01-01

Gene expression profiling could assist in revealing biomarkers of lung cancer prognosis and progression. The handling of biological samples may strongly influence global gene expression, a fact that has not been addressed in many studies. We sought to investigate the changes in gene expression that may occur as a result of sample processing time and conditions. Using Illumina Human WG-6 arrays, we quantified gene expression in lung carcinoma samples from six patients obtained at chest opening before and immediately after lung resection with storage in RNAlater [T1a(CO) and T1b(LR)], after receipt of the sample for histopathology, placed in RNAlater [T2a(HP)]; snap frozen [T2b(HP.SF)]; or snap frozen and stored for 1 week [T2c(HP.SFA)], as well as formalin-fixed, paraffin-embedded (FFPE) block samples. Sampling immediately after resection closely represented the tissue obtained in situ, with only 1% of genes differing more than twofold [T1a(CO) versus T1b(LR)]. Delaying tissue harvest for an average of 30 minutes from the operating theater had a significant impact on gene expression, with approximately 25% of genes differing between T1a(CO) and T2a(HP). Many genes previously identified as lung cancer biomarkers were altered during this period. Examination of FFPE specimens showed minimal correlation with fresh samples. This study shows that tissue collection immediately after lung resection with conservation in RNAlater is an optimal strategy for gene expression profiling. PMID:22240448

Increased Expression of ALDH1A1 in Prostate Cancer is Correlated With Tumor Aggressiveness: A Tissue Microarray Study of Iranian Patients.

PubMed

Kalantari, Elham; Saadi, Faezeh H; Asgari, Mojgan; Shariftabrizi, Ahmad; Roudi, Raheleh; Madjd, Zahra

2017-09-01

Subpopulations of prostate cancer (PCa) cells expressing putative stem cell markers possess the ability to promote tumor growth, maintenance, and progression. This study aimed to evaluate the expression patterns and clinical significance of putative stem cell marker aldehyde dehydrogenase 1 A1 (ALDH1A1) in prostate tumor tissues. ALDH1A1 expression was examined in a well-defined series of prostate tissues, including 105 (68%) samples of PCa, 21 (13%) samples of high-grade prostatic intraepithelial neoplasia, and 31 (19%) samples of benign prostate hyperplasia, which were embedded in tissue microarray blocks. The correlation of ALDH1A1 expression with clinicopathologic parameters was also assessed. There was a significant difference between the expression level of ALDH1A1 in PCa compared with the high-grade prostatic intraepithelial neoplasia and benign prostate hyperplasia samples (P<0.001). PCa cells expressing ALDH1A1 were more often seen in samples with advanced Gleason score (P=0.05) and high serum prostate specific antigen level (P=0.02). In addition, a positive correlation was found between ALDH1A1 expression and primary tumor stage and regional lymph node involvement (P=0.04 and 0.03, respectively). The significant association between ALDH1A1 expressions with Gleason score indicates the potential role of this protein in PCa tumorigenesis and aggressive behavior; therefore, this cancer stem cell marker can be used as a promising candidate for targeted therapy of PCa, especially those with high Gleason score.

Recommendations for Collection and Handling of Specimens From Group Breast Cancer Clinical Trials

PubMed Central

Leyland-Jones, Brian R.; Ambrosone, Christine B.; Bartlett, John; Ellis, Matthew J.C.; Enos, Rebecca A.; Raji, Adekunle; Pins, Michael R.; Zujewski, Jo Anne; Hewitt, Stephen M.; Forbes, John F.; Abramovitz, Mark; Braga, Sofia; Cardoso, Fatima; Harbeck, Nadia; Denkert, Carsten; Jewell, Scott D.

2008-01-01

Recommendations for specimen collection and handling have been developed for adoption across breast cancer clinical trials conducted by the Breast International Group (BIG)-sponsored Groups and the National Cancer Institute (NCI)-sponsored North American Cooperative Groups. These recommendations are meant to promote identifiable standards for specimen collection and handling within and across breast cancer trials, such that the variability in collection/handling practices that currently exists is minimized and specimen condition and quality are enhanced, thereby maximizing results from specimen-based diagnostic testing and research. Three working groups were formed from the Cooperative Group Banking Committee, BIG groups, and North American breast cancer cooperative groups to identify standards for collection and handling of (1) formalin-fixed, paraffin-embedded (FFPE) tissue; (2) blood and its components; and (3) fresh/frozen tissue from breast cancer trials. The working groups collected standard operating procedures from multiple group specimen banks, administered a survey on banking practices to those banks, and engaged in a series of discussions from 2005 to 2007. Their contributions were synthesized into this document, which focuses primarily on collection and handling of specimens to the point of shipment to the central bank, although also offers some guidance to central banks. Major recommendations include submission of an FFPE block, whole blood, and serial serum or plasma from breast cancer clinical trials, and use of one fixative and buffer type (10% neutral phosphate-buffered formalin, pH 7) for FFPE tissue across trials. Recommendations for proper handling and shipping were developed for blood, serum, plasma, FFPE, and fresh/frozen tissue. PMID:18955459

[Immunoexpression of c-erbB-2 in intraductal proliferative lesions of the female breast].

PubMed

Oliveira, Agliberto Barbosa de; De Luca, Laurival Antônio; Carvalho, Grigna Teixeira; Arias, Victor Eduardo Arua; Carvalho, Lídia Raquel de; Assunção, Maria do Carmo

2004-01-01

Genetic modifications are related to genesis and development of cancer. Neoplasias in various organs express the c-erbB-2 oncogene. In intraductal proliferations of the breast it has been assessed as a risk factor for subsequent development of carcinoma. The c-erbB-2 immunoexpression in intraductal epithelial proliferations and the relationship with histopathological characteristics of ductal carcinoma in situ (DCIS) were evaluated. File material from 88 women, which were tissue samples formalin-fixed, paraffin-embedded blocks, was used. Of these 51 presented with DCIS and 37 with ductal hyperplasia without atypia. Ages of the women ranged from 35 to 76 years. All cases were reviewed and nuclear grade, presence of necrosis, preponderance of histological subtype and its extension were verified. Specimens were obtained for the c-erB-2 immunohistochemical study of 84 of the women in question. No expression of the oncogene was verified in the hyperplasias without atypias and in tissues adjacent to all tissue samples. Expression of c-erbB-2 was verified in 9 (19.1%) of the DCIS (p = 0.0001). Immunoexpression was not related to the extension of the lesions. The c-erbB-2 immunoexpression in DCIS was correlated to the histological subtype (p = 0.019), necrosis (p = 0.0066), nuclear grade (p = 0.0084) and Van Nuys Classification (p = 0.039). Expression of c-erbB-2 was significant in proliferative lesions with risk (DCIS) and was correlated to histopathological characteristics: high nuclear grade, presence of necrosis and comedy subtype. There was no expression in the hyperplasias without atypias and adjacent tissues.

The Prostate Cancer Biorepository Network (PCBN)

DTIC Science & Technology

2016-10-01

site includes blood (serum, plasma, and buffy coat), prostatectomy tissues (frozen), biopsies and metastatic tissue from rapid autopsies (paraffin...embedded material and tissue microarrays (TMAs)), prostate cancer patient derived xenografts (PDX) and derived specimens (DNA and RNA) from prostate...Genitourinary Cancer Biorepository set up a rapid autopsy program to provide access to metastatic tissue and create patient derived xenograft (PDX

Evaluation of HER-2/neu status in breast cancer specimens using immunohistochemistry (IHC) & fluorescence in-situ hybridization (FISH) assay

PubMed Central

Goud, Kalal Iravathy; Dayakar, Seetha; Vijayalaxmi, Kolanupaka; Babu, Saidam Jangu; Vijay, Anand Reddy P.

2012-01-01

Background & objectives: Fluorescence in situ hybridization (FISH) is increasingly being recognized as the most accurate and predictive test for HER2/neu gene amplification and response to therapy in breast cancer. In the present study we investigated HER-2/neu gene amplification by FISH in breast carcinoma tissue specimens and compared the results with that of immunohistochemical (IHC) analysis. Methods: A total of 90 breast carcinoma tissue samples were used for immunohistochemical (IHC) and FISH analysis. IHC was performed by using mouse monoclonal antibody to the intracellular domain of HER-2/neu protein. Each slide was scored in a blinded fashion by two pathologists according to the manufacturer's recommended criteria. FISH analysis was performed on paraffin embedded breast tumour tissue sections. The polysomy for centromere 17 (Spec green signal) was read as green signals less than 4 as moderate polysomy, and more than 4 as highly polysomy. Results: Thirty of the 90 patients had negative results by IHC and FISH. Of the 28 patients with the score of 2+ by IHC, 20 were FISH positive for HER-2/neu gene amplification, three were FISH negative and five patients showed equivocal (1.8-2.2) results by FISH. These five cases were retested for IHC and FISH on different paraffin embedded tissue blocks, and all five were found positive for HER-2/neu gene amplification. Twenty five patients with the score of 3+ by IHC were FISH positive for HER-2/neu gene amplification (>2.2). Seven cases with the score of 3+ by IHC were FISH negative for HER-2/neu gene amplification (>2.2), and showed polysomy of chromosome number 17 high polysomy > 4. Interpretation & conclusions: Our results indicated that HER-2/neu status by FISH should be performed in all cases of breast tumour with a 2+ score by IHC. Cases demonstrating a 3+ score by IHC may be subjected to FISH to rule out polysomy of chromosome 17 which could be falsely interpreted as HER-2/neu overexpression by IHC analysis. There is also a need for establishing a clinically validated cut-off value for HER-2/neu FISH amplification against IHC which may be further compared and calibrated. PMID:22561616

High-risk human papilloma virus in archival tissues of oral pathosis and normal oral mucosa.

PubMed

Dhanapal, Raghu; Ranganathan, K; Kondaiah, Paturu; Devi, R Uma; Joshua, Elizabeth; Saraswathi, T R

2015-01-01

Oral cancer ranks third among all cancers in the Indian population. Human papilloma virus (HPV) plays a significant role in oral carcinogenesis. Population-based subtype variations are present in the HPV prevalence. This study gives an emphasis on the parameters to be considered in formalin fixed paraffin embedded tissues for polymerase chain reaction (PCR)-based research work. Cross-sectional study on archival paraffin-embedded tissue samples of oral squamous cell carcinoma (OSCC), epithelial dysplasia, and normal oral mucosa surrounding impacted tooth was amplified by PCR for the E6 gene of HPV type 16 and E1 gene of HPV type 18. HPV 18 was positive in three OSCC cases. There was no statistically significant association of the positivity of HPV with the age, gender or habit. The HPV positive patients had a tobacco habit and were of a younger age group. The presence of HPV in carcinomatous tissue highlights the possible role of HPV in carcinogenesis and archival paraffin embedded tissue specimen can be used for this analysis. Recent studies on genomic analyses have highlighted that the HPV positive tumors are a separate subgroup based on genomic sequencing. The results of a larger retrospective study will help further in our understanding of the role of HPV in carcinogenesis, this study could form the baseline for such follow-up studies.

A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies

PubMed Central

Zlobec, Inti; Suter, Guido; Perren, Aurel; Lugli, Alessandro

2014-01-01

Biomarker research relies on tissue microarrays (TMA). TMAs are produced by repeated transfer of small tissue cores from a ‘donor’ block into a ‘recipient’ block and then used for a variety of biomarker applications. The construction of conventional TMAs is labor intensive, imprecise, and time-consuming. Here, a protocol using next-generation Tissue Microarrays (ngTMA) is outlined. ngTMA is based on TMA planning and design, digital pathology, and automated tissue microarraying. The protocol is illustrated using an example of 134 metastatic colorectal cancer patients. Histological, statistical and logistical aspects are considered, such as the tissue type, specific histological regions, and cell types for inclusion in the TMA, the number of tissue spots, sample size, statistical analysis, and number of TMA copies. Histological slides for each patient are scanned and uploaded onto a web-based digital platform. There, they are viewed and annotated (marked) using a 0.6-2.0 mm diameter tool, multiple times using various colors to distinguish tissue areas. Donor blocks and 12 ‘recipient’ blocks are loaded into the instrument. Digital slides are retrieved and matched to donor block images. Repeated arraying of annotated regions is automatically performed resulting in an ngTMA. In this example, six ngTMAs are planned containing six different tissue types/histological zones. Two copies of the ngTMAs are desired. Three to four slides for each patient are scanned; 3 scan runs are necessary and performed overnight. All slides are annotated; different colors are used to represent the different tissues/zones, namely tumor center, invasion front, tumor/stroma, lymph node metastases, liver metastases, and normal tissue. 17 annotations/case are made; time for annotation is 2-3 min/case. 12 ngTMAs are produced containing 4,556 spots. Arraying time is 15-20 hr. Due to its precision, flexibility and speed, ngTMA is a powerful tool to further improve the quality of TMAs used in clinical and translational research. PMID:25285857

No-cost manual method for preparation of tissue microarrays having high quality comparable to semiautomated methods.

PubMed

Foda, Abd Al-Rahman Mohammad

2013-05-01

Manual tissue microarray (TMA) construction had been introduced to avoid the high cost of automated and semiautomated techniques. The cheapest and simplest technique for constructing manual TMA was that of using mechanical pencil tips. This study was carried out to modify this method, aiming to raise its quality to reach that of expensive ones. Some modifications were introduced to Shebl's technique. Two conventional mechanical pencil tips of different diameters were used to construct the recipient blocks. A source of mild heat was used, and blocks were incubated at 38°C overnight. With our modifications, 3 high-density TMA blocks were constructed. We successfully performed immunostaining without substantial tissue loss. Our modifications increased the number of cores per block and improved the stability of the cores within the paraffin block. This new, modified technique is a good alternative for expensive machines in many laboratories.

Periodontal tissue reaction to customized nano-hydroxyapatite block scaffold in one-wall intrabony defect: a histologic study in dogs

PubMed Central

Lee, Jung-Seok; Park, Weon-Yeong; Cha, Jae-Kook; Jung, Ui-Won; Kim, Chang-Sung; Lee, Yong-Keun

2012-01-01

Purpose This study evaluated histologically the tissue responses to and the effects of a customized nano-hydroxyapatite (n-HA) block bone graft on periodontal regeneration in a one-wall periodontal-defect model. Methods A customized block bone for filling in the standardized periodontal defect was fabricated from prefabricated n-HA powders and a polymeric sponge. Bilateral 4×4×5 mm (buccolingual width×mesiodistal width×depth), one-wall, critical-size intrabony periodontal defects were surgically created at the mandibular second and fourth premolars of five Beagle dogs. In each dog, one defect was filled with block-type HA and the other served as a sham-surgery control. The animals were sacrificed following an 8-week healing interval for clinical and histological evaluations. Results Although the sites that received an n-HA block showed minimal bone formation, the n-HA block was maintained within the defect with its original hexahedral shape. In addition, only a limited inflammatory reaction was observed at sites that received an n-HA block, which might have been due to the high stability of the customized block bone. Conclusions In the limitation of this study, customized n-HA block could provide a space for periodontal tissue engineering, with minimal inflammation. PMID:22586523

Periodontal tissue reaction to customized nano-hydroxyapatite block scaffold in one-wall intrabony defect: a histologic study in dogs.

PubMed

Lee, Jung-Seok; Park, Weon-Yeong; Cha, Jae-Kook; Jung, Ui-Won; Kim, Chang-Sung; Lee, Yong-Keun; Choi, Seong-Ho

2012-04-01

This study evaluated histologically the tissue responses to and the effects of a customized nano-hydroxyapatite (n-HA) block bone graft on periodontal regeneration in a one-wall periodontal-defect model. A customized block bone for filling in the standardized periodontal defect was fabricated from prefabricated n-HA powders and a polymeric sponge. Bilateral 4×4×5 mm (buccolingual width×mesiodistal width×depth), one-wall, critical-size intrabony periodontal defects were surgically created at the mandibular second and fourth premolars of five Beagle dogs. In each dog, one defect was filled with block-type HA and the other served as a sham-surgery control. The animals were sacrificed following an 8-week healing interval for clinical and histological evaluations. Although the sites that received an n-HA block showed minimal bone formation, the n-HA block was maintained within the defect with its original hexahedral shape. In addition, only a limited inflammatory reaction was observed at sites that received an n-HA block, which might have been due to the high stability of the customized block bone. In the limitation of this study, customized n-HA block could provide a space for periodontal tissue engineering, with minimal inflammation.

Cascaded VLSI neural network architecture for on-line learning

NASA Technical Reports Server (NTRS)

Thakoor, Anilkumar P. (Inventor); Duong, Tuan A. (Inventor); Daud, Taher (Inventor)

1992-01-01

High-speed, analog, fully-parallel, and asynchronous building blocks are cascaded for larger sizes and enhanced resolution. A hardware compatible algorithm permits hardware-in-the-loop learning despite limited weight resolution. A computation intensive feature classification application was demonstrated with this flexible hardware and new algorithm at high speed. This result indicates that these building block chips can be embedded as an application specific coprocessor for solving real world problems at extremely high data rates.

Cascaded VLSI neural network architecture for on-line learning

NASA Technical Reports Server (NTRS)

Duong, Tuan A. (Inventor); Daud, Taher (Inventor); Thakoor, Anilkumar P. (Inventor)

1995-01-01

High-speed, analog, fully-parallel and asynchronous building blocks are cascaded for larger sizes and enhanced resolution. A hardware-compatible algorithm permits hardware-in-the-loop learning despite limited weight resolution. A comparison-intensive feature classification application has been demonstrated with this flexible hardware and new algorithm at high speed. This result indicates that these building block chips can be embedded as application-specific-coprocessors for solving real-world problems at extremely high data rates.

RT-PCR analysis of RNA extracted from Bouin-fixed and paraffin-embedded lymphoid tissues.

PubMed

Gloghini, Annunziata; Canal, Barbara; Klein, Ulf; Dal Maso, Luigino; Perin, Tiziana; Dalla-Favera, Riccardo; Carbone, Antonino

2004-11-01

In the present study, we have investigated whether RNA can be efficiently isolated from Bouin-fixed or formalin-fixed, paraffin-embedded lymphoid tissue specimens. To this aim, we applied a new and simple method that includes the combination of proteinase K digestion and column purification. By this method, we demonstrated that the amplification of long fragments could be accomplished after a pre-heating step before cDNA synthesis associated with the use of enzymes that work at high temperature. By means of PCR using different primers for two examined genes (glyceraldehyde-3-phosphate dehydrogenase [GAPDH]- and CD40), we amplified segments of cDNA obtained by reverse transcription of the isolated RNA extracted from Bouin-fixed or formalin-fixed paraffin-embedded tissues. Amplified fragments of the expected sizes were obtained for both genes tested indicating that this method is suitable for the isolation of high-quality RNA. To explore the possibility for giving accurate real time quantitative RT-PCR results, cDNA obtained from matched frozen, Bouin-fixed and formalin-fixed neoplastic samples (two diffuse large cell lymphomas, one plasmacytoma) was tested for the following target genes: CD40, Aquaporin-3, BLIMP1, IRF4, Syndecan-1. Delta threshold cycle (DeltaC(T)) values for Bouin-fixed and formalin-fixed paraffin-embedded tissues and their correlation with those for frozen samples showed an extremely high correlation (r > 0.90) for all of the tested genes. These results show that the method of RNA extraction we propose is suitable for giving accurate real time quantitative RT-PCR results.

Simulation study of interaction of pulse laser with tumor-embedded gastric tissue using finite element analysis

NASA Astrophysics Data System (ADS)

Liu, Lantian; Li, Zhifang; Li, Hui

2018-01-01

The study of interaction of laser with tumor-embedded gastric tissue is of great theoretical and practical significance for the laser diagnosis and treatment of gastric cancer in medicine. A finite element (FE)-based simulation model has been developed incorporating light propagation and heat transfer in soft tissues using a commercial FE simulation package, COMSOL Multiphysics. In this study, FE model is composed of three parts of 1) homogeneous background soft tissues submerged in water, 2) tumor tissue inclusion, and 3) different wavelengths of short pulsed laser source (450nm, 550nm, 632nm and 800nm). The laser point source is placed right under the tissues submerged in water. This laser source light propagation through the multi-layer tissues using the diffusion equation and bioheat transfer in tissues is simulated using bioheat equation for temperature change. The simulation results show that the penetration depth and light energy distribution mainly depend on the optical parameters of the different wavelengths of the tissue. In the process of biological heat transfer, the temperature of the tissue decreases exponentially with the depth and the deep tissues are almost unaffected. The results are helpful to optimize the laser source in a photoacoustic imaging system and provide some significance for the further study of the early diagnosis of gastric cancer.

The PAXgene® Tissue System Preserves Phosphoproteins in Human Tissue Specimens and Enables Comprehensive Protein Biomarker Research

PubMed Central

Gündisch, Sibylle; Schott, Christina; Wolff, Claudia; Tran, Kai; Beese, Christian; Viertler, Christian; Zatloukal, Kurt; Becker, Karl-Friedrich

2013-01-01

Precise quantitation of protein biomarkers in clinical tissue specimens is a prerequisite for accurate and effective diagnosis, prognosis, and personalized medicine. Although progress is being made, protein analysis from formalin-fixed and paraffin-embedded tissues is still challenging. In previous reports, we showed that the novel formalin-free tissue preservation technology, the PAXgene Tissue System, allows the extraction of intact and immunoreactive proteins from PAXgene-fixed and paraffin-embedded (PFPE) tissues. In the current study, we focused on the analysis of phosphoproteins and the applicability of two-dimensional gel electrophoresis (2D-PAGE) and enzyme-linked immunosorbent assay (ELISA) to the analysis of a variety of malignant and non-malignant human tissues. Using western blot analysis, we found that phosphoproteins are quantitatively preserved in PFPE tissues, and signal intensities are comparable to that in paired, frozen tissues. Furthermore, proteins extracted from PFPE samples are suitable for 2D-PAGE and can be quantified by ELISA specific for denatured proteins. In summary, the PAXgene Tissue System reliably preserves phosphoproteins in human tissue samples, even after prolonged fixation or stabilization times, and is compatible with methods for protein analysis such as 2D-PAGE and ELISA. We conclude that the PAXgene Tissue System has the potential to serve as a versatile tissue fixative for modern pathology. PMID:23555997

Manifold Embedding and Semantic Segmentation for Intraoperative Guidance With Hyperspectral Brain Imaging.

PubMed

Ravi, Daniele; Fabelo, Himar; Callic, Gustavo Marrero; Yang, Guang-Zhong

2017-09-01

Recent advances in hyperspectral imaging have made it a promising solution for intra-operative tissue characterization, with the advantages of being non-contact, non-ionizing, and non-invasive. Working with hyperspectral images in vivo, however, is not straightforward as the high dimensionality of the data makes real-time processing challenging. In this paper, a novel dimensionality reduction scheme and a new processing pipeline are introduced to obtain a detailed tumor classification map for intra-operative margin definition during brain surgery. However, existing approaches to dimensionality reduction based on manifold embedding can be time consuming and may not guarantee a consistent result, thus hindering final tissue classification. The proposed framework aims to overcome these problems through a process divided into two steps: dimensionality reduction based on an extension of the T-distributed stochastic neighbor approach is first performed and then a semantic segmentation technique is applied to the embedded results by using a Semantic Texton Forest for tissue classification. Detailed in vivo validation of the proposed method has been performed to demonstrate the potential clinical value of the system.

Maximizing RNA yield from archival renal tumors and optimizing gene expression analysis.

PubMed

Glenn, Sean T; Head, Karen L; Teh, Bin T; Gross, Kenneth W; Kim, Hyung L

2010-01-01

Formalin-fixed, paraffin-embedded tissues are widely available for gene expression analysis using TaqMan PCR. Five methods, including 4 commercial kits, for recovering RNA from paraffin-embedded renal tumor tissue were compared. The MasterPure kit from Epicentre produced the highest RNA yield. However, the difference in RNA yield between the kit from Epicenter and Invitrogen's TRIzol method was not significant. Using the top 3 RNA isolation methods, the manufacturers' protocols were modified to include an overnight Proteinase K digestion. Overnight protein digestion resulted in a significant increase in RNA yield. To optimize the reverse transcription reaction, conventional reverse transcription with random oligonucleotide primers was compared to reverse transcription using primers specific for genes of interest. Reverse transcription using gene-specific primers significantly increased the quantity of cDNA detectable by TaqMan PCR. Therefore, expression profiling of formalin-fixed, paraffin-embedded tissue using TaqMan qPCR can be optimized by using the MasterPure RNA isolation kit modified to include an overnight Proteinase K digestion and gene-specific primers during the reverse transcription.

Antigen Masking During Fixation and Embedding, Dissected

PubMed Central

Scalia, Carla Rossana; Boi, Giovanna; Bolognesi, Maddalena Maria; Riva, Lorella; Manzoni, Marco; DeSmedt, Linde; Bosisio, Francesca Maria; Ronchi, Susanna; Leone, Biagio Eugenio; Cattoretti, Giorgio

2016-01-01

Antigen masking in routinely processed tissue is a poorly understood process caused by multiple factors. We sought to dissect the effect on antigenicity of each step of processing by using frozen sections as proxies of the whole tissue. An equivalent extent of antigen masking occurs across variable fixation times at room temperature. Most antigens benefit from longer fixation times (>24 hr) for optimal detection after antigen retrieval (AR; for example, Ki-67, bcl-2, ER). The transfer to a graded alcohol series results in an enhanced staining effect, reproduced by treating the sections with detergents, possibly because of a better access of the polymeric immunohistochemical detection system to tissue structures. A second round of masking occurs upon entering the clearing agent, mostly at the paraffin embedding step. This may depend on the non-freezable water removal. AR fully reverses the masking due both to the fixation time and the paraffin embedding. AR itself destroys some epitopes which do not survive routine processing. Processed frozen sections are a tool to investigate fixation and processing requirements for antigens in routine specimens. PMID:27798289

Chemical reactivation of fluorescein isothiocyanate immunofluorescence-labeled resin-embedded samples

NASA Astrophysics Data System (ADS)

Li, Longhui; Rao, Gong; Lv, Xiaohua; Chen, Ruixi; Cheng, Xiaofeng; Wang, Xiaojun; Zeng, Shaoqun; Liu, Xiuli

2018-02-01

Resin embedding is widely used and facilitates microscopic imaging of biological tissues. In contrast, quenching of fluorescence during embedding process hinders the application of resin embedding for imaging of fluorescence-labeled samples. For samples expressing fluorescent proteins, it has been demonstrated that the weakened fluorescence could be recovered by reactivating the fluorophore with alkaline buffer. We extended this idea to immunofluorescence-labeling technology. We showed that the fluorescence of pH-sensitive fluorescein isothiocyanate (FITC) was quenched after resin embedding but reactivated after treating by alkaline buffer. We observed 138.5% fluorescence preservation ratio of reactivated state, sixfold compared with the quenched state in embedding resin, which indicated its application for fluorescence imaging of high signal-to-background ratio. Furthermore, we analyzed the chemical reactivation mechanism of FITC fluorophore. This work would show a way for high-resolution imaging of immunofluorescence-labeled samples embedded in resin.

Angle-selective optical filter for highly sensitive reflection photoplethysmogram

PubMed Central

Hwang, Chan-Sol; Yang, Sung-Pyo; Jang, Kyung-Won; Park, Jung-Woo; Jeong, Ki-Hun

2017-01-01

We report an angle-selective optical filter (ASOF) for highly sensitive reflection photoplethysmography (PPG) sensors. The ASOF features slanted aluminum (Al) micromirror arrays embedded in transparent polymer resin, which effectively block scattered light under human tissue. The device microfabrication was done by using geometry-guided resist reflow of polymer micropatterns, polydimethylsiloxane replica molding, and oblique angle deposition of thin Al film. The angular transmittance through the ASOF is precisely controlled by the angle of micromirrors. For the mirror angle of 30 degrees, the ASOF accepts an incident light between - 90 to + 50 degrees and the maximum transmittance at - 55 degrees. The ASOF exhibits the substantial reduction of both the in-band noise of PPG signals over a factor of two and the low-frequency noise by three times. Consequently, this filter allows distinguishing the diastolic peak that allows miscellaneous parameters with diverse vascular information. This optical filter provides a new opportunity for highly sensitive PPG monitoring or miscellaneous optical tomography. PMID:29082070

Histological biocompatibility of a stainless steel miniature glaucoma drainage device in humans: a case report.

PubMed

De Feo, Fabio; Jacobson, Stewart; Nyska, Abraham; Pagani, Paola; Traverso, Carlo Enrico

2009-06-01

The purpose of this study was to evaluate the histological biocompatibility of a stainless steel miniature glaucoma drainage device. Twenty-four months before death due to heart failure, this seventy-three-year-old female patient underwent filtration surgery for primary open-angle glaucoma uncontrolled in the right eye. The device was implanted at the limbus under a scleral flap. For histopathological evaluation, two corneoscleral specimens were embedded in methacrylate blocks sectioned to a thickness of 50 microns, polished and stained with periodic acid schiff. Some sections included a longitudinal cross-section of the implant. At the interface between the spur and the flange of the device and the cornea, there was a small shoulder of fibrous tissue. A thin, fibrous capsule covered the remainder of the body of the device up to the distal tip. No inflammatory cells occurred within the fibrous capsule. No material or blockage was noted within the lumen. Our results support the biological inertness of the device.

The Immunoexpression of Glucocorticoid Receptors in Breast Carcinomas, Lactational Change, and Normal Breast Epithelium and Its Possible Role in Mammary Carcinogenesis

PubMed Central

Wazir, Javed Fayyaz; Brahmi, Urmil Prabha; Fakhro, Abdul Rahman

2017-01-01

The role of estrogen and progesterone receptors in breast cancer biology is well established. In contrast, other steroid hormones are less well studied. Glucocorticoids (GCs) are known to play a role in mammary development and differentiation; thus, it is of interest to attempt to delineate their immunoexpression across a spectrum of mammary epithelia. Aim. To delineate the distribution pattern of glucocorticoid receptors (GRs) in malignant versus nonmalignant epithelium with particular emphasis on lactational epithelium. Materials and Methods. Immunohistochemistry (IHC) for GRs was performed on archival formalin-fixed paraffin-embedded tissue blocks of 96 cases comprising 52 invasive carcinomas, 21 cases with lactational change, and 23 cases showing normal mammary tissue histology. Results. Results reveal an overexpression of GRs in mammary malignant epithelium as compared to both normal and lactational groups individually and combined. GR overexpression is significantly more pronounced in HER-2-negative cancers. Discussion. This is the first study to compare GR expression in human lactating epithelium versus malignant and normal epithelium. The article discusses the literature related to the pathobiology of GCs in the breast with special emphasis on breast cancer. Conclusion. The lactational epithelium did not show overexpression of GR, while GR was overexpressed in mammary NST (ductal) carcinoma, particularly HER-2-negative cancers. PMID:29348941

Eclogitic breccia from the Monviso ophiolite complex: new field and petrographic data

NASA Astrophysics Data System (ADS)

Locatelli, Michele; Verlaguet, Anne; Federico, Laura; Agard, Philippe

2015-04-01

The Monviso meta-ophiolite complex (Northern Italy, Western Alps) represents a coherent portion of oceanic lithosphere metamorphosed under eclogite facies conditions during the Alpine orogeny (2.6 GPa - 550°C, Lago Superiore Unit, Angiboust et al., 2011), and exhibits from bottom to top a thick serpentinite sole locally capped by metasediments, Mg-Al-rich metagabbros, then Fe-Ti-metagabbros capped by metabasalts. This section is disrupted by three main shear zones. Our study focusses on the Lower Shear Zone (LSZ), situated between the serpentinite sole (to the East) and the Mg-metagabbro bodies (to the West), and composed of blocks of both Fe-Ti and Mg-Al metagabbros embedded in a talc and tremolite-rich serpentinite matrix. Among these blocks, some were described as eclogitic breccias and interpreted as the result of a seismic rupture plane (Angiboust et al., 2012). These breccias correspond to blocks of Fe-Ti-metagabbros that were brecciated in eclogitic facies conditions (as attested by the omphacite + garnet ± lawsonite cement of the breccia) in a fluid-rich environment, as suggested by the abundance of lawsonite in the cement. Here we present new field data on the distribution and petrographic characterization of these eclogitic blocks in the LSZ. The aim of this work is twofold: (I) detailed mapping of the eclogitic block distribution along the LSZ, in order to determine precisely the extent and representativity of the breccias and (II) characterization of the brecciated blocks, at the outcrop scale, to explore the brecciation processes and structures. Between Pian del Re and Colle di Luca localities, the occurrence of eclogite blocks is uniform along the strike of the shear-zone, resulting in a 16 km-long belt of outcropping eclogitic bodies embedded in serpentinite matrix. The shear-zone width, by contrast, varies from 1.3 km to 0.8 km. Three types of eclogitic blocks can be distinguished: (1) intact (i.e., not brecciated) blocks of Fe-Ti-metagabbros restricted to the lower part of the shear zone, close to the serpentinite sole; (2) numerous brecciated Fe-Ti-metagabbros scattered in the intermediate to upper levels of the LSZ; (3) blocks showing compositional variations and complex structures, with boudins of intact Fe-Ti-metagabbros embedded in highly foliated and folded Mg-rich rocks bounded on one side by Fe-Ti-breccia planes. In some cases the full transition from intact to highly brecciated rock is recorded in the same block. Here, the contacts between intact metagabbros and breccia are characterized by about 1m-wide zones of non rotated clasts with diameter up to 80 cm, almost matrix-absent. The amount of matrix vs clast increases, associated with a reduction in the clast size and increasing clast rotation, over a few meters up to the end of the bodies. These particular blocks give us a unique opportunity to better characterize the brecciation processes. Different kinds of measurements were realized on the brecciated blocks: (1) block size, (2) clasts vs. matrix relative volumetric abundances, (3) dimension and shape ratio of clasts, and angle of misorientation between their elongation axis or internal foliations (for five selected blocks). Preliminary results show that the majority (82%) of mapped blocks have a diameter of less than 10 meters, with only 8% being larger than 20 meters. In the brecciated Fe-Ti gabbros the average content of matrix is 28%, while for blocks showing compositional variation it varies from zero to 30%. The angle of misorientation between clasts' foliation shows, instead, a chaotic distribution. Preliminary field data thus demonstrate that breccia blocks have to be considered as a constant feature along the LSZ rather than as an exception, and that further work is needed to determine whether they formed through pervasive brecciation (and potentially multiple events) or through a localized event and were later disrupted by ductile deformation along the LSZ.

A comparison of classical histology to anatomy revealed by hard x-rays

NASA Astrophysics Data System (ADS)

Richter, Claus-Peter; Tan, Xiaodong; Young, Hunter; Stock, Stuart; Robinson, Alan; Byskosh, Orest; Zheng, Jing; Soriano, Carmen; Xiao, Xianghui; Whitlon, Donna

2016-10-01

Many diseases trigger morphological changes in affected tissue. Today, classical histology is still the "gold standard" used to study and describe those changes. Classical histology, however, is time consuming and requires chemical tissue manipulations that can result in significant tissue distortions. It is sometimes difficult to separate tissue-processing artifacts from changes caused by the disease process. We show that synchrotron X-ray phase-contrast micro-computed tomography (micro-CT) can be used to examine non-embedded, hydrated tissue at a resolution comparable to that obtained with classical histology. The data analysis from stacks of reconstructed micro-CT images is more flexible and faster than when using the classical, physically embedded sections that are by necessity fixed in a particular orientation. We show that in a three-dimensional (3D) structure with meticulous structural details such as the cochlea and the kidney, micro-CT is more flexible, faster and more convenient for morphological studies and disease diagnoses.

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

PubMed

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.

Spectral domain optical coherence tomography for ex vivo brain tumor analysis

NASA Astrophysics Data System (ADS)

Lenz, Marcel; Krug, Robin; Jaedicke, Volker; Stroop, Ralf; Schmieder, Kirsten; Hofmann, Martin R.

2015-07-01

Non-contact imaging methods to distinguish between healthy tissue and brain tumor tissue during surgery would be highly desirable but are not yet available. Optical Coherence Tomography (OCT) is a non-invasive imaging technology with a resolution around 1-15 μm and a penetration depth of 1-2 mm that may satisfy the demands. To analyze its potential, we measured ex vivo human brain tumor tissue samples from 10 patients with a Spectral Domain OCT system (Thorlabs Callisto: center wavelength of 930 nm) and compared the results with standard histology. In detail, three different measurements were made for each sample. First the sample was measured directly after surgery. Then it was embedded in paraffin (also H and E staining) and examined for the second time. At last, the slices of each paraffin block cut by the pathology were measured. Each time a B-scan was created and for a better comparison with the histology a 3D image was generated, in order to get the corresponding en face images. In both, histopathological diagnosis and the analysis of the OCT images, different types of brain tumor showed difference in structure. This has been affirmed by two blinded investigators. Nevertheless the difference between two images of samples taken directly after surgery is less distinct. To enhance the contrast in the images further, we employ Spectroscopic OCT and pattern recognition algorithms and compare these results to the histopathological standard.

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.

PubMed

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.

Deformation partitioning provides insight into elastic, plastic, and viscous contributions to bone material behavior.

PubMed

Ferguson, V L

2009-08-01

The relative contributions of elastic, plastic, and viscous material behavior are poorly described by the separate extraction and analysis of the plane strain modulus, E('), the contact hardness, H(c) (a hybrid parameter encompassing both elastic and plastic behavior), and various viscoelastic material constants. A multiple element mechanical model enables the partitioning of a single indentation response into its fundamental elastic, plastic, and viscous deformation components. The objective of this study was to apply deformation partitioning to explore the role of hydration, tissue type, and degree of mineralization in bone and calcified cartilage. Wet, ethanol-dehydrated, and PMMA-embedded equine cortical bone samples and PMMA-embedded human femoral head tissues were analyzed for contributions of elastic, plastic and viscous deformation to the overall nanoindentation response at each site. While the alteration of hydration state had little effect on any measure of deformation, unembedded tissues demonstrated significantly greater measures of resistance to plastic deformation than PMMA-embedded tissues. The PMMA appeared to mechanically stabilize the tissues and prevent extensive permanent deformation within the bone material. Increasing mineral volume fraction correlated with positive changes in E('), H(c), and resistance to plastic deformation, H; however, the partitioned deformation components were generally unaffected by mineralization. The contribution of viscous deformation was minimal and may only play a significant role in poorly mineralized tissues. Deformation partitioning enables a detailed interpretation of the elastic, plastic, and viscous contributions to the nanomechanical behavior of mineralized tissues that is not possible when examining modulus and contact hardness alone. Varying experimental or biological factors, such as hydration or mineralization level, enables the understanding of potential mechanisms for specific mechanical behavior patterns that would otherwise be hidden within a more complex set of material property parameters.

Hierarchical Biosilicates by the 3-D Replication of Block Copolymer Templates in Supercritical Fluids

DTIC Science & Technology

2009-12-30

Iron Oxide Nanoparticles through Supercritical CO2 Infusion of TEOS into Ferritin Doped Block Copolymers…………………………………………………...4 4.2 Simple...which is doped with ferritin (yellow spheres). The blue PPO domains are removed during calcination as is the apoferritin shell, leaving magnetic...iron oxide particles (black) embedded in the mesoporous silica film. 5 2 TEM images of ferritin -containing samples at the specified ferritin

On the delay analysis of a TDMA channel with finite buffer capacity

NASA Technical Reports Server (NTRS)

Yan, T.-Y.

1982-01-01

The throughput performance of a TDMA channel with finite buffer capacity for transmitting data messages is considered. Each station has limited message buffer capacity and has Poisson message arrivals. Message arrivals will be blocked if the buffers are congested. Using the embedded Markov chain model, the solution procedure for the limiting system-size probabilities is presented in a recursive fashion. Numerical examples are given to demonstrate the tradeoffs between the blocking probabilities and the buffer sizing strategy.

A telepresence robot system realized by embedded object concept

NASA Astrophysics Data System (ADS)

Vallius, Tero; Röning, Juha

2006-10-01

This paper presents the Embedded Object Concept (EOC) and a telepresence robot system which is a test case for the EOC. The EOC utilizes common object-oriented methods used in software by applying them to combined Lego-like software-hardware entities. These entities represent objects in object-oriented design methods, and they are the building blocks of embedded systems. The goal of the EOC is to make the designing embedded systems faster and easier. This concept enables people without comprehensive knowledge in electronics design to create new embedded systems, and for experts it shortens the design time of new embedded systems. We present the current status of a telepresence robot created with second-generation Atomi-objects, which is the name for our implementation of the embedded objects. The telepresence robot is a relatively complex test case for the EOC. The robot has been constructed using incremental device development, which is made possible by the architecture of the EOC. The robot contains video and audio exchange capability and a controlling system for driving with two wheels. The robot is built in two versions, the first consisting of a PC device and Atomi-objects, and the second consisting of only Atomi-objects. The robot is currently incomplete, but most of it has been successfully tested.

Paraffin tissue microarrays constructed with a cutting board and cutting board arrayer.

PubMed

Vogel, Ulrich Felix

2010-05-01

Paraffin tissue microarrays (PTMAs) are blocks of paraffin containing up to 1300 paraffin tissue core biopsies (PTCBs). Normally, these PTCBs are punched from routine paraffin tissue blocks, which contain tissues of differing thicknesses. Therefore, the PTCBs are of different lengths. In consequence, the sections of the deeper portions of the PTMA do not contain all of the desired PTCBs. To overcome this drawback, cutting boards were constructed from panels of plastic with a thickness of 4 mm. Holes were drilled into the plastic and filled completely with at least one PTCB per hole. After being trimmed to a uniform length of 4 mm, these PTCBs were pushed from the cutting board into corresponding holes in a recipient block by means of a plate with steel pins. Up to 1000 sections per PTMA were cut without any significant loss of PTCBs, thereby increasing the efficacy of the PTMA technique.

Tissue Anisotropy Modeling Using Soft Composite Materials.

PubMed

Chanda, Arnab; Callaway, Christian

2018-01-01

Soft tissues in general exhibit anisotropic mechanical behavior, which varies in three dimensions based on the location of the tissue in the body. In the past, there have been few attempts to numerically model tissue anisotropy using composite-based formulations (involving fibers embedded within a matrix material). However, so far, tissue anisotropy has not been modeled experimentally. In the current work, novel elastomer-based soft composite materials were developed in the form of experimental test coupons, to model the macroscopic anisotropy in tissue mechanical properties. A soft elastomer matrix was fabricated, and fibers made of a stiffer elastomer material were embedded within the matrix material to generate the test coupons. The coupons were tested on a mechanical testing machine, and the resulting stress-versus-stretch responses were studied. The fiber volume fraction (FVF), fiber spacing, and orientations were varied to estimate the changes in the mechanical responses. The mechanical behavior of the soft composites was characterized using hyperelastic material models such as Mooney-Rivlin's, Humphrey's, and Veronda-Westmann's model and also compared with the anisotropic mechanical behavior of the human skin, pelvic tissues, and brain tissues. This work lays the foundation for the experimental modelling of tissue anisotropy, which combined with microscopic studies on tissues can lead to refinements in the simulation of localized fiber distribution and orientations, and enable the development of biofidelic anisotropic tissue phantom materials for various tissue engineering and testing applications.

Tissue Anisotropy Modeling Using Soft Composite Materials

PubMed Central

Callaway, Christian

2018-01-01

Soft tissues in general exhibit anisotropic mechanical behavior, which varies in three dimensions based on the location of the tissue in the body. In the past, there have been few attempts to numerically model tissue anisotropy using composite-based formulations (involving fibers embedded within a matrix material). However, so far, tissue anisotropy has not been modeled experimentally. In the current work, novel elastomer-based soft composite materials were developed in the form of experimental test coupons, to model the macroscopic anisotropy in tissue mechanical properties. A soft elastomer matrix was fabricated, and fibers made of a stiffer elastomer material were embedded within the matrix material to generate the test coupons. The coupons were tested on a mechanical testing machine, and the resulting stress-versus-stretch responses were studied. The fiber volume fraction (FVF), fiber spacing, and orientations were varied to estimate the changes in the mechanical responses. The mechanical behavior of the soft composites was characterized using hyperelastic material models such as Mooney-Rivlin's, Humphrey's, and Veronda-Westmann's model and also compared with the anisotropic mechanical behavior of the human skin, pelvic tissues, and brain tissues. This work lays the foundation for the experimental modelling of tissue anisotropy, which combined with microscopic studies on tissues can lead to refinements in the simulation of localized fiber distribution and orientations, and enable the development of biofidelic anisotropic tissue phantom materials for various tissue engineering and testing applications. PMID:29853996

A fully synthetic lung model for wound-ballistic experiments-First results.

PubMed

Bolliger, S A; Poschmann, S A; Thali, M J; Eggert, S

2017-06-01

Today, synthetic models have all but replaced animal and corpse models in examining damage to soft-tissues and skeletal structures by ballistic trauma. As, however, non-solid organs such as the lungs, have not been able to be replaced by a fully synthetic model we attempted to create such a model. 20% ordnance gelatine was frothed with a household mixer and cooled to stable foam. Several of these foam blocks were then stuck together with liquid gelatine and placed between 10% gelatine blocks. As controls, we embedded pig lungs in gelatine and compared the wound channels seen in computed tomography created upon shooting with 9mm Luger. The fully synthetic models displayed radiological and physical densities comparable to real lungs. The wound profile characteristics of the fully synthetic lung models were very similar to the semisynthetic swine-gelatine models regarding the permanent wound cavity. Furthermore, in both semi- and fully synthetic models we detected a ring surrounding the permanent wound channel, most likely representing the remnants of the temporary wound cavity. Our results indicate that this fully synthetic lung model is a viable substitute for ballistic experiments on lungs. We believe that further research on the temporary wound channel in lungs is possible with this model in order to provide more insight into the effect of ballistic trauma to the lungs not seen otherwise. Copyright © 2017 Elsevier B.V. All rights reserved.

A novel edge based embedding in medical images based on unique key generated using sudoku puzzle design.

PubMed

Santhi, B; Dheeptha, B

2016-01-01

The field of telemedicine has gained immense momentum, owing to the need for transmitting patients' information securely. This paper puts forth a unique method for embedding data in medical images. It is based on edge based embedding and XOR coding. The algorithm proposes a novel key generation technique by utilizing the design of a sudoku puzzle to enhance the security of the transmitted message. The edge blocks of the cover image alone, are utilized to embed the payloads. The least significant bit of the pixel values are changed by XOR coding depending on the data to be embedded and the key generated. Hence the distortion in the stego image is minimized and the information is retrieved accurately. Data is embedded in the RGB planes of the cover image, thus increasing its embedding capacity. Several measures including peak signal noise ratio (PSNR), mean square error (MSE), universal image quality index (UIQI) and correlation coefficient (R) are the image quality measures that have been used to analyze the quality of the stego image. It is evident from the results that the proposed technique outperforms the former methodologies.

An improved strategy and a useful housekeeping gene for RNA analysis from formalin-fixed, paraffin-embedded tissues by PCR.

PubMed

Finke, J; Fritzen, R; Ternes, P; Lange, W; Dölken, G

1993-03-01

Specific amplification of nucleic acid sequences by PCR has been extensively used for the detection of gene rearrangements and gene expression. Although successful amplification of DNA sequences has been carried out with DNA prepared from formalin-fixed, paraffin-embedded (FFPE) tissues, there are only a few reports regarding RNA analysis in this kind of material. We describe a procedure for RNA extraction from different types of FFPE tissues, involving digestion with proteinase K followed by guanidinium-thiocyanate acid phenol extraction and DNase I digestion. These RNA preparations are suitable for PCR analysis of mRNA and even of intronless genes. Furthermore, the universally expressed porphobilinogen deaminase mRNA proved to be useful as a positive control because of the lack of pseudogenes.

Expression of programmed cell death protein 1 (PD-1) and indoleamine 2,3-dioxygenase (IDO) in the tumor microenvironment and in tumor-draining lymph nodes of breast cancer.

PubMed

Ye, Qian; Wang, Chenglong; Xian, Jie; Zhang, Ming; Cao, Yijia; Cao, Youde

2018-05-01

Programmed cell death protein 1 (PD-1) and indoleamine 2,3-dioxygenase (IDO) are both immunosuppressive proteins. Here, we investigated the relationship between PD-1 and IDO in the tumor microenvironment (TME) and in tumor-draining lymph nodes (TDLNs) in breast cancer patients. First, the protein and mRNA expression levels of PD-1 and IDO in 20 frozen tissues were examined using Western blotting and real-time polymerase chain reaction. Second, 151 paraffin-embedded breast samples and 52 lymph node samples were analyzed by immunohistochemistry. Third, correlation and survival data for PD-1 and IDO in 963 breast tumor patients were mined using the cBio Cancer Genomics Portal. We found that the protein expression level of IDO was significantly increased in frozen tumor tissues (P = .005). From paraffin-embedded samples in the TME, PD-1 + cells were only located in the stroma, while IDO was expressed in myoepithelial, stromal, and tumor cells. PD-1 and stromal IDO in the TME showed increased expression in tumors (P< .001 and P < .001, respectively). In TDLNs, PD-1 + cells were primarily located in the germinal centers (GCs), and IDO + cells were primarily located in the paracortex. Normal lymph nodes expressed PD-1 and IDO at the same level as non-metastatic and metastatic lymph nodes (P = .151 and P = .812, respectively). According to cBioPortal, the correlation analysis showed that IDO and PD-1 had high correlation coefficients (r = 0.83). These findings suggest that there is a positive correlation between the expression of PD-1 and IDO and that blocking both PD-1 and IDO pathways may represent an attractive therapeutic strategy in breast cancer treatment. Copyright © 2018 Elsevier Inc. All rights reserved.

Advanced Development of TIES-Enhancing Access to Tissue for Cancer Research | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Archived human tissues are an essential resource for translational research. Formalin-fixed, paraffin embedded (FFPE) tissues from cancer patients are used in a wide range of assays, including RT-PCR, SNP profiling, multiplex biomarkers, imaging biomarkers, targeted exome, whole exome, and whole genome sequencing. Remainder FFPE tissues generated during patient care are ‘retrospective'; use of these tissues under specific conditions does not require consent.

Glycol Methacrylate Embedding for the Histochemical Study of the Gastrointestinal Tract of Dogs Naturally Infected with Leishmania Infantum

PubMed Central

Pinto, A.J.W.; de Amorim, I.F.G.; Pinheiro, L.J.; Madeira, I.M.V.M.; Souza, C.C.; Chiarini-Garcia, H.; Caliari, M.V.

2015-01-01

In canine visceral leishmaniasis a diffuse chronic inflammatory exudate and an intense parasite load throughout the gastrointestinal tract (GIT) has been previously reported. However, these studies did not allow a properly description of canine cellular morphology details. The aim of our study was to better characterize these cells in carrying out a qualitative and quantitative histological study in the gastrointestinal tract of dogs naturally infected with Leishmania infantum by examining gut tissues embedded in glycol methacrylate. Twelve infected adult dogs were classified in asymptomatic and symptomatic. Five uninfected dogs were used as controls. After necropsy, three samples of each gut segment, including oesophagus, stomach, duodenum, jejunum, ileum, cecum, colon, and rectum were collected and fixed in Carnoy’s solution for glycol methacrylate protocols. Sections were stained with hematoxylin-eosin, toluidine blue borate, and periodic acid-Schiff stain. Leishmania amastigotes were detected by immunohistochemistry employed in both glycol methacrylate and paraffin embedded tissues. The quantitative histological analysis showed higher numbers of plasma cells, lymphocytes and macrophages in lamina propria of all segments of GIT of infected dogs compared with controls. The parasite load was more intense and cecum and colon, independently of the clinical status of these dogs. Importantly, glycol methacrylate embedded tissue stained with toluidine blue borate clearly revealed mast cell morphology, even after mast cell degranulation. Infected dogs showed lower numbers of mast cells in all gut segments than controls. Despite the glycol methacrylate (GMA) protocol requires more attention and care than the conventional paraffin processing, this embedding procedure proved to be especially suitable for the present histological study, where it allowed to preserve and observe cell morphology in fine detail. PMID:26708180

Using methylene blue as a marker to find and remove tiny metallic foreign bodies embedded in the soft tissues of children: A randomised controlled trial.

PubMed

Su, Yuxi; Nan, Guoxin

2016-05-01

Embedment of metallic foreign bodies in the soft tissues is commonly encountered in the emergency room. Most foreign bodies are easily removed, but removal is difficult if the foreign body is very small or deeply embedded. To determine the usefulness of methylene blue staining in the surgical removal of tiny metallic foreign bodies embedded in the soft tissue. This prospective study involved 41 children treated between May 2007 and May 2012. The patients were randomly divided into a methylene blue group and a control group. In the control group, foreign bodies were located using a C-arm and removed via direct incision. In the methylene blue group, foreign bodies were located using a C-arm, marked with an injection of methylene blue and then removed surgically. The clinical outcomes, complications, operation time, surgical success rate, incision length, frequency of C-arm use, and length and depth of the foreign body were compared between the two groups. The surgical success rate was significantly higher in the methylene blue group. The average operation time was significantly shorter in the methylene blue group. The C-arm was used significantly less frequently in the methylene blue group than in the control group. The incision length was significantly shorter in the methylene blue group than in the control group. Methylene blue staining facilitated the location and removal of tiny metallic foreign bodies from the soft tissue, and significantly reduced operation time, incision length and radiation exposure compared to the conventional method. Copyright © 2016 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

In vitro and in vivo assessment of oral autologous artificial connective tissue characteristics that influence its performance as a graft.

PubMed

Fontanilla, Marta Raquel; Espinosa, Lady Giovanna

2012-09-01

Several studies have evaluated proteins secreted by fibroblasts comprising skin substitutes, finding that they are secreted in combinations and concentrations that promote wound healing. However, assessment of proteins secreted by oral fibroblasts forming a part of oral substitutes is scarce. In our previous work, collagen type-I scaffolds (CSs) and autologous artificial connective tissue (AACT) were produced and implanted in rabbit oral lesions, evidencing that AACT outperforms CS. The present work determined the secreted factor profile of AACT in the time of grafting as well as that of the AACT embedded in the clot. It also evaluated the proliferation and viability of AACT fibroblasts to establish the dwell time of these cells in the grafted area. Finally, it assessed whether CS, AACT, and clot-embedded AACT increase fibroblast recruitment induced by a fibrin clot, because the cell migratory response has been associated with the wound-healing outcome. We found that some of the factors secreted by AACT fibroblasts are significantly different from those secreted by clot-embedded AACT fibroblasts. Also, that the profile of proteins secreted by AACT fibroblasts and clot-embedded AACT fibroblasts is different from already reported protein secretion profiles of other engineered tissues used in treating oral mucosa wounds. It was also found that AACT fibroblasts are viable when grafted and remain in the treated area for almost 2 weeks, and that the migratory response of fibroblasts to tissue-substitute stimulus is significantly less than the migratory response induced by the clot alone. Overall, data suggest that AACT secretion of proteins is modulated by three-dimensionality and environment factors. This bioactivity and the fact that AACT does not increase fibroblast migration can be held accountable for AACT's good performance as a graft.

Heat insulating device for low temperature liquefied gas storage tank

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okamoto, T.; Nishimoto, T.; Sawada, K.

1978-05-02

Hitachi Shipbuilding and Engineering Co., Ltd.'s insulation method for spherical LNG containers solves various problems associated with insulating a sphere's three-dimensional curved surface; equalizing the thickness of the insulation, insulating the junctions between insulation blocks, and preventing seawater or LNG from penetrating the insulation barrier in the event of a rupture in the tank and ship's hull. The design incorporates a number of blocks or plates of rigid foam-insulating material bonded to the outer wall; seats for receiving pressing jigs for the bonding operation are secured to the outer wall in the joints between the insulating blocks. The joints aremore » filled with soft synthetic foam (embedding the seats), a moistureproof layer covers the insulating blocks and joints, and a waterproof material covers the moistureproof layer.« less

Rapid embedding methods into epoxy and LR White resins for morphological and immunological analysis of cryofixed biological specimens.

PubMed

McDonald, Kent L

2014-02-01

A variety of specimens including bacteria, ciliates, choanoflagellates (Salpingoeca rosetta), zebrafish (Danio rerio) embryos, nematode worms (Caenorhabditis elegans), and leaves of white clover (Trifolium repens) plants were high pressure frozen, freeze-substituted, infiltrated with either Epon, Epon-Araldite, or LR White resins, and polymerized. Total processing time from freezing to blocks ready to section was about 6 h. For epoxy embedding the specimens were freeze-substituted in 1% osmium tetroxide plus 0.1% uranyl acetate in acetone. For embedding in LR White the freeze-substitution medium was 0.2% uranyl acetate in acetone. Rapid infiltration was achieved by centrifugation through increasing concentrations of resin followed by polymerization at 100°C for 1.5-2 h. The preservation of ultrastructure was comparable to standard freeze substitution and resin embedding methods that take days to complete. On-section immunolabeling results for actin and tubulin molecules were positive with very low background labeling. The LR White methods offer a safer, quicker, and less-expensive alternative to Lowicryl embedding of specimens processed for on-section immunolabeling without traditional aldehyde fixatives.

Validation of freezing tissues and cells for analysis of DNA strand break levels by comet assay

PubMed Central

Jackson, Petra

2013-01-01

The comet analysis of DNA strand break levels in tissues and cells has become a common method of screening for genotoxicity. The large majority of published studies have used fresh tissues and cells processed immediately after collection. However, we have used frozen tissues and cells for more than 10 years, and we believe that freezing samples improve efficiency of the method. We compared DNA strand break levels measured in fresh and frozen bronchoalveolar cells, and lung and liver tissues from mice exposed to the known mutagen methyl methanesulphonate (0, 25, 75, 112.5mg/kg). We used a high-throughput comet protocol with fully automated scoring of DNA strand break levels. The overall results from fresh and frozen samples were in agreement [R 2 = 0.93 for %DNA in tail (%TDNA) and R 2 = 0.78 for tail length (TL)]. A slightly increased %TDNA was observed in lung and liver tissue from vehicle controls; and TL was slightly reduced in bronchoalveolar lavage cells from the high-dose group. In our comet protocol, a small block of tissue designated for comet analysis is frozen immediately at tissue collection and kept deep frozen until rapidly homogenised and embedded in agarose. To demonstrate the feasibility of long-term freezing of samples, we analysed the day-to-day variation of our internal historical negative and positive comet assay controls collected over a 10-year period (1128 observations, 11 batches of frozen untreated and H2O2-treated A549 lung epithelial cells). The H2O2 treatment explained most of the variation 57–77% and the day-to-day variation was only 2–12%. The presented protocol allows analysis of samples collected over longer time span, at different locations, with reduced variation by reducing number of electrophoreses and is suitable for both toxicological and epidemiological studies. The use of frozen tissues; however, requires great care during preparation before analysis, with handling as a major risk factor. PMID:24136994

Use of lectin microarray to differentiate gastric cancer from gastric ulcer

PubMed Central

Huang, Wei-Li; Li, Yang-Guang; Lv, Yong-Chen; Guan, Xiao-Hui; Ji, Hui-Fan; Chi, Bao-Rong

2014-01-01

AIM: To investigate the feasibility of lectin microarray for differentiating gastric cancer from gastric ulcer. METHODS: Twenty cases of human gastric cancer tissue and 20 cases of human gastric ulcer tissue were collected and processed. Protein was extracted from the frozen tissues and stored. The lectins were dissolved in buffer, and the sugar-binding specificities of lectins and the layout of the lectin microarray were summarized. The median of the effective data points for each lectin was globally normalized to the sum of medians of all effective data points for each lectin in one block. Formalin-fixed paraffin-embedded gastric cancer tissues and their corresponding gastric ulcer tissues were subjected to Ag retrieval. Biotinylated lectin was used as the primary antibody and HRP-streptavidin as the secondary antibody. The glycopatterns of glycoprotein in gastric cancer and gastric ulcer specimens were determined by lectin microarray, and then validated by lectin histochemistry. Data are presented as mean ± SD for the indicated number of independent experiments. RESULTS: The glycosylation level of gastric cancer was significantly higher than that in ulcer. In gastric cancer, most of the lectin binders showed positive signals and the intensity of the signals was stronger, whereas the opposite was the case for ulcers. Significant differences in the pathological score of the two lectins were apparent between ulcer and gastric cancer tissues using the same lectin. For MPL and VVA, all types of gastric cancer detected showed stronger staining and a higher positive rate in comparison with ulcer, especially in the case of signet ring cell carcinoma and intra-mucosal carcinoma. GalNAc bound to MPL showed a significant increase. A statistically significant association between MPL and gastric cancer was observed. As with MPL, there were significant differences in VVA staining between gastric cancer and ulcer. CONCLUSION: Lectin microarray can differentiate the different glycopatterns in gastric cancer and gastric ulcer, and the lectins MPL and VVA can be used as biomarkers. PMID:24833877

Efficacy of Exclusive Lingual Nerve Block versus Conventional Inferior Alveolar Nerve Block in Achieving Lingual Soft-tissue Anesthesia.

PubMed

Balasubramanian, Sasikala; Paneerselvam, Elavenil; Guruprasad, T; Pathumai, M; Abraham, Simin; Krishnakumar Raja, V B

2017-01-01

The aim of this randomized clinical trial was to assess the efficacy of exclusive lingual nerve block (LNB) in achieving selective lingual soft-tissue anesthesia in comparison with conventional inferior alveolar nerve block (IANB). A total of 200 patients indicated for the extraction of lower premolars were recruited for the study. The samples were allocated by randomization into control and study groups. Lingual soft-tissue anesthesia was achieved by IANB and exclusive LNB in the control and study group, respectively. The primary outcome variable studied was anesthesia of ipsilateral lingual mucoperiosteum, floor of mouth and tongue. The secondary variables assessed were (1) taste sensation immediately following administration of local anesthesia and (2) mouth opening and lingual nerve paresthesia on the first postoperative day. Data analysis for descriptive and inferential statistics was performed using SPSS (IBM SPSS Statistics for Windows, Version 22.0, Armonk, NY: IBM Corp. Released 2013) and a P < 0.05 was considered statistically significant. In comparison with the control group, the study group (LNB) showed statistically significant anesthesia of the lingual gingiva of incisors, molars, anterior floor of the mouth, and anterior tongue. Exclusive LNB is superior to IAN nerve block in achieving selective anesthesia of lingual soft tissues. It is technically simple and associated with minimal complications as compared to IAN block.

Efficacy of Exclusive Lingual Nerve Block versus Conventional Inferior Alveolar Nerve Block in Achieving Lingual Soft-tissue Anesthesia

PubMed Central

Balasubramanian, Sasikala; Paneerselvam, Elavenil; Guruprasad, T; Pathumai, M; Abraham, Simin; Krishnakumar Raja, V. B.

2017-01-01

Objective: The aim of this randomized clinical trial was to assess the efficacy of exclusive lingual nerve block (LNB) in achieving selective lingual soft-tissue anesthesia in comparison with conventional inferior alveolar nerve block (IANB). Materials and Methods: A total of 200 patients indicated for the extraction of lower premolars were recruited for the study. The samples were allocated by randomization into control and study groups. Lingual soft-tissue anesthesia was achieved by IANB and exclusive LNB in the control and study group, respectively. The primary outcome variable studied was anesthesia of ipsilateral lingual mucoperiosteum, floor of mouth and tongue. The secondary variables assessed were (1) taste sensation immediately following administration of local anesthesia and (2) mouth opening and lingual nerve paresthesia on the first postoperative day. Results: Data analysis for descriptive and inferential statistics was performed using SPSS (IBM SPSS Statistics for Windows, Version 22.0, Armonk, NY: IBM Corp. Released 2013) and a P < 0.05 was considered statistically significant. In comparison with the control group, the study group (LNB) showed statistically significant anesthesia of the lingual gingiva of incisors, molars, anterior floor of the mouth, and anterior tongue. Conclusion: Exclusive LNB is superior to IAN nerve block in achieving selective anesthesia of lingual soft tissues. It is technically simple and associated with minimal complications as compared to IAN block. PMID:29264294

The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data

PubMed Central

Berman, Jules J; Edgerton, Mary E; Friedman, Bruce A

2003-01-01

Background Tissue Microarrays (TMAs) allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API) hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification. Methods A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs) was established as well as a basic strategy for organizing TMA data in self-describing XML documents. Results The TMA data exchange specification is a well-formed XML document with four required sections: 1) Header, containing the specification Dublin Core identifiers, 2) Block, describing the paraffin-embedded array of tissues, 3)Slide, describing the glass slides produced from the Block, and 4) Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange specification. Anyone using the data exchange specification can validate their TMA files using a software implementation written in Perl and distributed as a supplemental file with this publication. Conclusion The TMA data exchange specification is now available in a draft form with community-approved Common Data Elements and a community-approved general file format and data structure. The specification can be freely used by the scientific community. Efforts sponsored by the Association for Pathology Informatics to refine the draft TMA data exchange specification are expected to continue for at least two more years. The interested public is invited to participate in these open efforts. Information on future workshops will be posted at (API we site). PMID:12769826

Improved method of producing satisfactory sections of whole eyeball by routine histology.

PubMed

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.

Control analysis of lipid biosynthesis in tissue cultures from oil crops shows that flux control is shared between fatty acid synthesis and lipid assembly.

PubMed Central

Ramli, Umi S; Baker, Darren S; Quant, Patti A; Harwood, John L

2002-01-01

Top-Down (Metabolic) Control Analysis (TDCA) was used to examine, quantitatively, lipid biosynthesis in tissue cultures from two commercially important oil crops, olive (Olea europaea L.) and oil palm (Elaeis guineensis Jacq.). A conceptually simplified system was defined comprising two blocks of reactions: fatty acid synthesis (Block A) and lipid assembly (Block B), which produced and consumed, respectively, a common and unique system intermediate, cytosolic acyl-CoA. We manipulated the steady-state levels of the system intermediate by adding exogenous oleic acid and, using two independent assays, measured the effect of the addition on the system fluxes (J(A) and J(B)). These were the rate of incorporation of radioactivity: (i) through Block A from [1-(14)C]acetate into fatty acids and (ii) via Block B from [U-(14)C]glycerol into complex lipids respectively. The data showed that fatty acid formation (Block A) exerted higher control than lipid assembly (Block B) in both tissues with the following group flux control coefficients (C):(i) Oil palm: *C(J(TL))(BlkA)=0.64+/-0.05 and *C(J(TL))(BlkB)=0.36+/-0.05(ii) Olive: *C(J(TL))(BlkA)=0.57+/-0.10 and *C(J(TL))(BlkB)=0.43+/-0.10where *C indicates the group flux control coefficient over the lipid biosynthesis flux (J(TL)) and the subscripts BlkA and BlkB refer to defined blocks of the system, Block A and Block B. Nevertheless, because both parts of the lipid biosynthetic pathway exert significant flux control, we suggest strongly that manipulation of single enzyme steps will not affect product yield appreciably. The present study represents the first use of TDCA to examine the overall lipid biosynthetic pathway in any tissue, and its findings are of immediate academic and economic relevance to the yield and nutritional quality of oil crops. PMID:12023882

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

USDA-ARS?s Scientific Manuscript database

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...

Immunohistochemical analysis of tenascin expression in different grades of oral submucous fibrosis.

PubMed

Tak, Jalaj; Rao, Nirmala N; Chandra, Akhilesh; Gupta, Neha

2015-01-01

Tenascin, a glycoprotein, is one of the major constituents of extracellular matrix, which may function in organizing the stroma in normal and pathological conditions. The study aimed to correlate the structural organization of tenascin with the pathological progression of disease from early, moderate and advanced changes in oral submucous fibrosis (OSMF). A retrospective cross-sectional immunohistochemical (IHC) analysis of OSMF cases was performed. Total 70 slide samples were prepared for the study from 35 formalin-fixed paraffin-embedded tissue blocks with 10 each from histologically proven and graded as early, moderate and advanced OSMF and 5 of normal oral mucosa. The IHC sections were analyzed for the intensity and pattern of tenascin expression at the junction of epithelium and connective tissue (ECJ) and deeper connective tissue (CT), as well as presence or absence of staining around inflammatory cells, fibroblast and endothelial cells using anti-human tenascin. Most of the OSMF cases showed retention of antigen at ECJ and in deeper CT. Its expression varied in different grades as well as around inflammatory cells, fibroblast and endothelial cells in same tissue section. Highly significant P values of 0.001 and 0.003 were obtained for tenascin intensity and pattern, respectively, at ECJ in different OSMF grades. In addition, for the expression of tenascin pattern in deeper CT among different OSMF grades, a significant P value of 0.018 was obtained. A differential expression of tenascin was observed with the progression of disease. The expression of tenascin as bright and continuous deposition at ECJ in early and moderate stages of OSMF signifies either proliferative organization within the overlying epithelium or an epithelial-mesenchymal interaction. However, a weak immunoreactivity of tenascin at ECJ was observed in advanced stage of OSMF.

Iodine Vapor Staining for Atomic Number Contrast in Backscattered Electron and X-ray Imaging

PubMed Central

Boyde, Alan; Mccorkell, Fergus A; Taylor, Graham K; Bomphrey, Richard J; Doube, Michael

2014-01-01

Iodine imparts strong contrast to objects imaged with electrons and X-rays due to its high atomic number (53), and is widely used in liquid form as a microscopic stain and clinical contrast agent. We have developed a simple technique which exploits elemental iodine's sublimation-deposition state-change equilibrium to vapor stain specimens with iodine gas. Specimens are enclosed in a gas-tight container along with a small mass of solid I2. The bottle is left at ambient laboratory conditions while staining proceeds until empirically determined completion (typically days to weeks). We demonstrate the utility of iodine vapor staining by applying it to resin-embedded tissue blocks and whole locusts and imaging them with backscattered electron scanning electron microscopy (BSE SEM) or X-ray microtomography (XMT). Contrast is comparable to that achieved with liquid staining but without the consequent tissue shrinkage, stain pooling, or uneven coverage artefacts associated with immersing the specimen in iodine solutions. Unmineralized tissue histology can be read in BSE SEM images with good discrimination between tissue components. Organs within the locust head are readily distinguished in XMT images with particularly useful contrast in the chitin exoskeleton, muscle and nerves. Here, we have used iodine vapor staining for two imaging modalities in frequent use in our laboratories and on the specimen types with which we work. It is likely to be equally convenient for a wide range of specimens, and for other modalities which generate contrast from electron- and photon-sample interactions, such as transmission electron microscopy and light microscopy. Microsc. Res. Tech. 77:1044–1051, 2014. © 2014 The Authors. Microscopy Research Technique published by Wiley Periodocals, Inc. PMID:25219801

Immunohistochemical evaluation of myofibroblasts in odontogenic cysts and tumors: A comparative study.

PubMed

Syamala, Deepa; Suresh, Rakesh; Janardhanan, Mahija; Savithri, Vindhya; Anand, Prem P; Jose, Amrutha

2016-01-01

Myofibroblasts are fibroblasts with smooth muscle-like features characterized by the presence of a contractile apparatus and found in the connective tissue stroma of normal tissues such as blood vessels and lymph nodes. They are now thought to play a role in the synthesis and reorganization of extracellular matrix, which could contribute to the aggressive biologic behavior of the lesions. To compare the mean number of stromal myofibroblasts in dentigerous cysts (DCs), keratocystic odontogenic tumor (KCOT) and ameloblastoma; and to derive a correlation between the stromal myofibroblasts and the known biologic behavior of the lesions. A cross-sectional immunohistochemical analysis of cases of DC, KCOT and ameloblastoma. Twenty paraffin-embedded tissue blocks each of DC, KCOT and multicystic ameloblastoma were selected for the study and diagnosis confirmed through hematoxylin and eosin staining. Tissue sections were analyzed for the number of myofibroblasts using alpha smooth muscle actin (α-SMA) immunostaining. Differences in the mean number of α-SMA positive cells in each group were analyzed using one-way ANOVA test. Intergroup comparisons of mean values of α-SMA positive cells were performed using Mann-Whitney U-test. Ameloblastoma showed the highest number of myofibroblasts, whereas DC showed the lowest. Among the groups, there were significant differences between the myofibroblast counts among DC and KCOT and between DC and ameloblastoma, whereas the difference in counts was not statistically significant between KCOT and ameloblastoma. A positive correlation was observed between the myofibroblast count and the known biologic behavior of the lesions. Myofibroblasts may act in close association with the epithelial cells to bring about changes in stromal microenvironment, favorable to the growth and progression of the lesion. They may be of great value in predicting the biologic behavior and growth potential of such lesions.

Overexpression of caldesmon is associated with tumor progression in patients with primary non-muscle-invasive bladder cancer

PubMed Central

Lee, Myung-Shin; Lee, Jisu; Kim, Joo Heon; Kim, Won Tae; Kim, Wun-Jae; Ahn, Hanjong; Park, Jinsung

2015-01-01

The expression and function of caldesmon (CAD) in urothelial bladder carcinoma (BC) have not been reported. Here, we investigated the expression, prognostic value, and potential functional mechanism of CAD in primary non-muscle-invasive bladder cancer (NMIBC). Protein profiling of tissue samples using antibody microarrays showed significantly higher CAD expression in muscle-invasive BC tissues compared with NMIBC tissues. We then validated the CAD expression in BC cells by immunohistochemistry analysis using paraffin-embedded tissue blocks and western blots using BC cell lines. In addition, we examined the expression of CAD variants by reverse transcription-polymerase chain reaction, and confirmed the expression of low-molecular-weight isoforms (L-CAD), specifically encoded by WI-38 L-CAD II (transcript variant 2), in BC cells. Survival analysis in an independent primary NMIBC cohort comprising 132 patients showed that positive CAD expression was significantly associated with poorer prognosis than no CAD expression with regard to recurrence- and progression-free survival (p = 0.001 and 0.014, respectively). Multivariate analyses further indicated that positive CAD expression was an independent predictor of progression-free survival (p = 0.032; HR = 5.983). Data obtained from in vitro silencing and overexpression studies indicated that L-CAD promotes migration and invasiveness of BC cells. Immunofluorescence assays showed dramatic structural changes in the actin cytoskeleton of BC cells after L-CAD overexpression. Our findings collectively suggest that L-CAD overexpression in primary NMIBC is significantly associated with tumor progression and that a possible mechanism for L-CAD's activity is implicated in increased cell motility and invasive characteristics through morphological changes in BC cells. PMID:26430961

Immunohistochemical analysis of tenascin expression in different grades of oral submucous fibrosis

PubMed Central

Tak, Jalaj; Rao, Nirmala N; Chandra, Akhilesh; Gupta, Neha

2015-01-01

Aim: Tenascin, a glycoprotein, is one of the major constituents of extracellular matrix, which may function in organizing the stroma in normal and pathological conditions. The study aimed to correlate the structural organization of tenascin with the pathological progression of disease from early, moderate and advanced changes in oral submucous fibrosis (OSMF). Study Design: A retrospective cross-sectional immunohistochemical (IHC) analysis of OSMF cases was performed. Total 70 slide samples were prepared for the study from 35 formalin-fixed paraffin-embedded tissue blocks with 10 each from histologically proven and graded as early, moderate and advanced OSMF and 5 of normal oral mucosa. The IHC sections were analyzed for the intensity and pattern of tenascin expression at the junction of epithelium and connective tissue (ECJ) and deeper connective tissue (CT), as well as presence or absence of staining around inflammatory cells, fibroblast and endothelial cells using anti-human tenascin. Result: Most of the OSMF cases showed retention of antigen at ECJ and in deeper CT. Its expression varied in different grades as well as around inflammatory cells, fibroblast and endothelial cells in same tissue section. Highly significant P values of 0.001 and 0.003 were obtained for tenascin intensity and pattern, respectively, at ECJ in different OSMF grades. In addition, for the expression of tenascin pattern in deeper CT among different OSMF grades, a significant P value of 0.018 was obtained. Conclusion: A differential expression of tenascin was observed with the progression of disease. The expression of tenascin as bright and continuous deposition at ECJ in early and moderate stages of OSMF signifies either proliferative organization within the overlying epithelium or an epithelial-mesenchymal interaction. However, a weak immunoreactivity of tenascin at ECJ was observed in advanced stage of OSMF. PMID:26980955

Engineering of M13 Bacteriophage for Development of Tissue Engineering Materials.

PubMed

Jin, Hyo-Eon; Lee, Seung-Wuk

2018-01-01

M13 bacteriophages have several qualities that make them attractive candidates as building blocks for tissue regenerating scaffold materials. Through genetic engineering, a high density of functional peptides and proteins can be simultaneously displayed on the M13 bacteriophage's outer coat proteins. The resulting phage can self-assemble into nanofibrous network structures and can guide the tissue morphogenesis through proliferation, differentiation and apoptosis. In this manuscript, we will describe methods to develop major coat-engineered M13 phages as a basic building block and aligned tissue-like matrices to develop regenerative nanomaterials.

Evaluation of insertion characteristics of less invasive Si optoneural probe with embedded optical fiber

NASA Astrophysics Data System (ADS)

Morikawa, Takumi; Harashima, Takuya; Kino, Hisashi; Fukushima, Takafumi; Tanaka, Tetsu

2017-04-01

A less invasive Si optoneural probe with an embedded optical fiber was proposed and successfully fabricated. The diameter of the optical fiber was completely controlled by hydrogen fluoride etching, and the thinned optical fiber can propagate light without any leakage. This optical fiber was embedded in a trench formed inside a probe shank, which causes less damage to tissues. In addition, it was confirmed that the optical fiber embedded in the probe shank successfully irradiated light to optically stimulate gene transfected neurons. The electrochemical impedance of the probe did not change despite the light irradiation. Furthermore, probe insertion characteristics were evaluated in detail and less invasive insertion was clearly indicated for the Si optoneural probe with the embedded optical fiber compared with conventional optical neural probes. This neural probe with the embedded optical fiber can be used as a simple and easy tool for optogenetics and brain science.

Plastic Fibre Reinforced Soil Blocks as a Sustainable Building Material

NASA Astrophysics Data System (ADS)

Prasad, C. K. Subramania; Nambiar, E. K. Kunhanandan; Abraham, Benny Mathews

2012-10-01

Solid waste management, especially the huge quantity of waste plastics, is one of the major environmental concerns nowadays. Their employability in block making in the form of fibres, as one of the methods of waste management, can be investigated through a fundamental research. This paper highlights the salient observations from a systematic investigation on the effect of embedded fibre from plastic waste on the performance of stabilised mud blocks. Stabilisation of the soil was done by adding cement, lime and their combination. Plastic fibre in chopped form from carry bags and mineral water bottles were added (0.1% & 0.2% by weight of soil) as reinforcement. The blocks were tested for density, and compressive strength, and observed failure patterns were analysed. Blocks with 0.1% of plastic fibres showed an increase in strength of about 3 to 10%. From the observations of failure pattern it can be concluded that benefits of fibre reinforcement includes both improved ductility in comparison with raw blocks and inhibition of crack propogation after its initial formation.

Protocol for HER2 FISH Using a Non-cross-linking, Formalin-free Tissue Fixative to Combine Advantages of Cryo-preservation and Formalin Fixation

PubMed Central

Loibner, Martina; Oberauner-Wappis, Lisa; Viertler, Christian; Groelz, Daniel; Zatloukal, Kurt

2017-01-01

Morphologic assessment of formalin-fixed, paraffin-embedded (FFPE) tissue samples has been the gold standard for cancer diagnostics for decades due to its excellent preservation of morphology. Personalized medicine increasingly provides individually adapted and targeted therapies for characterized individual diseases enabled by combined morphological and molecular analytical technologies and diagnostics. Performance of morphologic and molecular assays from the same FFPE specimen is challenging because of the negative impact of formalin due to chemical modification and cross-linking of nucleic acids and proteins. A non-cross-linking, formalin-free tissue fixative has been recently developed to fulfil both requirements, i.e., to preserve morphology like FFPE and biomolecules like cryo-preservation. Since FISH is often required in combination with histopathology and molecular diagnostics, we tested the applicability of FISH protocols on tissues treated with this new fixative. We found that formalin post-fixation of histological sections of non-cross-linking, formalin-free and paraffin-embedded (NCFPE) breast cancer tissue generated equivalent results to those with FFPE tissue in human epidermal growth factor receptor 2 (HER2) FISH analysis. This protocol describes how a FISH assay originally developed and validated for FFPE tissue can be used for NCFPE tissues by a simple post-fixation step of histological sections. PMID:29364207

Immunohistochemical Detection of the Autophagy Markers LC3 and p62/SQSTM1 in Formalin-Fixed and Paraffin-Embedded Tissue.

PubMed

Berezowska, Sabina; Galván, José A

2017-01-01

Autophagy is a highly conserved cellular mechanism of "self digestion," ensuring cellular homeostasis, and playing a role in many diseases including cancer. As a stress response mechanism, it may also be involved in cellular response to therapy.LC3 and Sequestosome 1 (p62/SQSTM1) are among the most widely used markers to monitor autophagy, and can be visualized in formalin-fixed and paraffin-embedded tissue by immunohistochemistry. Here we describe a validated staining protocol using an automated staining system available in many routine pathology laboratories, enabling high-throughput staining under standardized conditions.

Codestream-Based Identification of JPEG 2000 Images with Different Coding Parameters

NASA Astrophysics Data System (ADS)

Watanabe, Osamu; Fukuhara, Takahiro; Kiya, Hitoshi

A method of identifying JPEG 2000 images with different coding parameters, such as code-block sizes, quantization-step sizes, and resolution levels, is presented. It does not produce false-negative matches regardless of different coding parameters (compression rate, code-block size, and discrete wavelet transform (DWT) resolutions levels) or quantization step sizes. This feature is not provided by conventional methods. Moreover, the proposed approach is fast because it uses the number of zero-bit-planes that can be extracted from the JPEG 2000 codestream by only parsing the header information without embedded block coding with optimized truncation (EBCOT) decoding. The experimental results revealed the effectiveness of image identification based on the new method.

Nanocomposites based on self-assembly poly(hydroxypropyl methacrylate)-block-poly(N-phenylmaleimide) and Fe3O4-NPs. Thermal stability, morphological characterization and optical properties

NASA Astrophysics Data System (ADS)

Pizarro, Guadalupe del C.; Marambio, Oscar G.; Jeria-Orell, Manuel; Sánchez, Julio; Oyarzún, Diego P.

2018-02-01

The current work presents the synthesis, characterization and preparation of organic-inorganic hybrid polymer films that contain inorganic magnetic nanoparticles (NPs). The block copolymer, prepared by Atom-Transfer Radical Polymerization (ATRP), was used as a nanoreactor for iron oxide NPs. The NPs were embedded in poly(hydroxypropyl methacrylate)-block-poly(N-phenylmaleimide) matrix. The following topographical modifications of the surface of the film were specially analyzed: control of pore features and changes in surface roughness. Finally, the NPs functionality inside the polymer matrix and how it may affect the thermal and optical properties of the films were assessed.

In situ hybridization at the electron microscope level: localization of transcripts on ultrathin sections of Lowicryl K4M-embedded tissue using biotinylated probes and protein A-gold complexes

PubMed Central

1986-01-01

A technique has been developed for localizing hybrids formed in situ on semi-thin and ultrathin sections of Lowicryl K4M-embedded tissue. Biotinylated dUTP (Bio-11-dUTP and/or Bio-16-dUTP) was incorporated into mitochondrial rDNA and small nuclear U1 probes by nick- translation. The probes were hybridized to sections of Drosophila ovaries and subsequently detected with an anti-biotin antibody and protein A-gold complex. On semi-thin sections, probe detection was achieved by amplification steps with anti-protein A antibody and protein A-gold with subsequent silver enhancement. At the electron microscope level, specific labeling was obtained over structures known to be the site of expression of the appropriate genes (i.e., either over mitochondria or over nuclei). The labeling pattern at the light microscope level (semi-thin sections) was consistent with that obtained at the electron microscope level. The described nonradioactive procedures for hybrid detection on Lowicryl K4M-embedded tissue sections offer several advantages: rapid signal detection: superior morphological preservation and spatial resolution; and signal-to-noise ratios equivalent to radiolabeling. PMID:3084498

Microporous silk fibroin scaffolds embedding PLGA microparticles for controlled growth factor delivery in tissue engineering.

PubMed

Wenk, Esther; Meinel, Anne J; Wildy, Sarah; Merkle, Hans P; Meinel, Lorenz

2009-05-01

The development of prototype scaffolds for either direct implantation or tissue engineering purposes and featuring spatiotemporal control of growth factor release is highly desirable. Silk fibroin (SF) scaffolds with interconnective pores, carrying embedded microparticles that were loaded with insulin-like growth factor I (IGF-I), were prepared by a porogen leaching protocol. Treatments with methanol or water vapor induced water insolubility of SF based on an increase in beta-sheet content as analyzed by FTIR. Pore interconnectivity was demonstrated by SEM. Porosities were in the range of 70-90%, depending on the treatment applied, and were better preserved when methanol or water vapor treatments were prior to porogen leaching. IGF-I was encapsulated into two different types of poly(lactide-co-glycolide) microparticles (PLGA MP) using uncapped PLGA (50:50) with molecular weights of either 14 or 35 kDa to control IGF-I release kinetics from the SF scaffold. Embedded PLGA MP were located in the walls or intersections of the SF scaffold. Embedment of the PLGA MP into the scaffolds led to more sustained release rates as compared to the free PLGA MP, whereas the hydrolytic degradation of the two PLGA MP types was not affected. The PLGA types used had distinct effects on IGF-I release kinetics. Particularly the supernatants of the lower molecular weight PLGA formulations turned out to release bioactive IGF-I. Our studies justify future investigations of the developed constructs for tissue engineering applications.

Strategy to Achieve Highly Porous/Biocompatible Macroscale Cell Blocks, Using a Collagen/Genipin-bioink and an Optimal 3D Printing Process.

PubMed

Kim, Yong Bok; Lee, Hyeongjin; Kim, Geun Hyung

2016-11-30

Recently, a three-dimensional (3D) bioprinting process for obtaining a cell-laden structure has been widely applied because of its ability to fabricate biomimetic complex structures embedded with and without cells. To successfully obtain a cell-laden porous block, the cell-delivering vehicle, bioink, is one of the significant factors. Until now, various biocompatible hydrogels (synthetic and natural biopolymers) have been utilized in the cell-printing process, but a bioink satisfying both biocompatibility and print-ability requirements to achieve a porous structure with reasonable mechanical strength has not been issued. Here, we propose a printing strategy with optimal conditions including a safe cross-linking procedure for obtaining a 3D porous cell block composed of a biocompatible collagen-bioink and genipin, a cross-linking agent. To obtain the optimal processing conditions, we modified the 3D printing machine and selected an optimal cross-linking condition (∼1 mM and 1 h) of genipin solution. To show the feasibility of the process, 3D pore-interconnected cell-laden constructs were manufactured using osteoblast-like cells (MG63) and human adipose stem cells (hASCs). Under these processing conditions, a macroscale 3D collagen-based cell block of 21 × 21 × 12 mm 3 and over 95% cell viability was obtained. In vitro biological testing of the cell-laden 3D porous structure showed that the embedded cells were sufficiently viable, and their proliferation was significantly higher; the cells also exhibited increased osteogenic activities compared to the conventional alginate-based bioink (control). The results indicated the fabrication process using the collagen-bioink would be an innovative platform to design highly biocompatible and mechanically stable cell blocks.

Numerical investigation of thermal response of laser-irradiated biological tissue phantoms embedded with gold nanoshells.

PubMed

Phadnis, Akshay; Kumar, Sumit; Srivastava, Atul

2016-10-01

The work presented in this paper focuses on numerically investigating the thermal response of gold nanoshells-embedded biological tissue phantoms with potential applications into photo-thermal therapy wherein the interest is in destroying the cancerous cells with minimum damage to the surrounding healthy cells. The tissue phantom has been irradiated with a pico-second laser. Radiative transfer equation (RTE) has been employed to model the light-tissue interaction using discrete ordinate method (DOM). For determining the temperature distribution inside the tissue phantom, the RTE has been solved in combination with a generalized non-Fourier heat conduction model namely the dual phase lag bio-heat transfer model. The numerical code comprising the coupled RTE-bio-heat transfer equation, developed as a part of the current work, has been benchmarked against the experimental as well as the numerical results available in the literature. It has been demonstrated that the temperature of the optical inhomogeneity inside the biological tissue phantom embedded with gold nanoshells is relatively higher than that of the baseline case (no nanoshells) for the same laser power and operation time. The study clearly underlines the impact of nanoshell concentration and its size on the thermal response of the biological tissue sample. The comparative study concerned with the size and concentration of nanoshells showed that 60nm nanoshells with concentration of 5×10 15 mm -3 result into the temperature levels that are optimum for the irreversible destruction of cancer infected cells in the context of photo-thermal therapy. To the best of the knowledge of the authors, the present study is one of the first attempts to quantify the influence of gold nanoshells on the temperature distributions inside the biological tissue phantoms upon laser irradiation using the dual phase lag heat conduction model. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multiscale assembly for tissue engineering and regenerative medicine

PubMed Central

Inci, Fatih; Tasoglu, Savas; Erkmen, Burcu; Demirci, Utkan

2015-01-01

Our understanding of cell biology and its integration with materials science has led to technological innovations in the bioengineering of tissue-mimicking grafts that can be utilized in clinical and pharmaceutical applications. Bio-engineering of native-like multiscale building blocks provides refined control over the cellular microenvironment, thus enabling functional tissues. In this review, we focus on assembling building blocks from the biomolecular level to the millimeter scale. We also provide an overview of techniques for assembling molecules, cells, spheroids, and microgels and achieving bottom-up tissue engineering. Additionally, we discuss driving mechanisms for self- and guided assembly to create micro-to-macro scale tissue structures. PMID:25796488

Hydrogels for Engineering of Perfusable Vascular Networks

PubMed Central

Liu, Juan; Zheng, Huaiyuan; Poh, Patrina S. P.; Machens, Hans-Günther; Schilling, Arndt F.

2015-01-01

Hydrogels are commonly used biomaterials for tissue engineering. With their high-water content, good biocompatibility and biodegradability they resemble the natural extracellular environment and have been widely used as scaffolds for 3D cell culture and studies of cell biology. The possible size of such hydrogel constructs with embedded cells is limited by the cellular demand for oxygen and nutrients. For the fabrication of large and complex tissue constructs, vascular structures become necessary within the hydrogels to supply the encapsulated cells. In this review, we discuss the types of hydrogels that are currently used for the fabrication of constructs with embedded vascular networks, the key properties of hydrogels needed for this purpose and current techniques to engineer perfusable vascular structures into these hydrogels. We then discuss directions for future research aimed at engineering of vascularized tissue for implantation. PMID:26184185

Fast photoacoustic imaging system based on 320-element linear transducer array.

PubMed

Yin, Bangzheng; Xing, Da; Wang, Yi; Zeng, Yaguang; Tan, Yi; Chen, Qun

2004-04-07

A fast photoacoustic (PA) imaging system, based on a 320-transducer linear array, was developed and tested on a tissue phantom. To reconstruct a test tomographic image, 64 time-domain PA signals were acquired from a tissue phantom with embedded light-absorption targets. A signal acquisition was accomplished by utilizing 11 phase-controlled sub-arrays, each consisting of four transducers. The results show that the system can rapidly map the optical absorption of a tissue phantom and effectively detect the embedded light-absorbing target. By utilizing the multi-element linear transducer array and phase-controlled imaging algorithm, we thus can acquire PA tomography more efficiently, compared to other existing technology and algorithms. The methodology and equipment thus provide a rapid and reliable approach to PA imaging that may have potential applications in noninvasive imaging and clinic diagnosis.

Microscopic fluorescence spectral analysis of basal cell carcinomas

NASA Astrophysics Data System (ADS)

He, Qingli; Lui, Harvey; Zloty, David; Cowan, Bryce; Warshawski, Larry; McLean, David I.; Zeng, Haishan

2007-05-01

Background and Objectives. Laser-induced autofluorescence (LIAF) is a promising tool for cancer diagnosis. This method is based on the differences in autofluorescence spectra between normal and cancerous tissues, but the underlined mechanisms are not well understood. The objective of this research is to study the microscopic origins and intrinsic fluorescence properties of basal cell carcinoma (BCC) for better understanding of the mechanism of in vivo fluorescence detection and margin delineation of BCCs on skin patients. A home-made micro- spectrophotometer (MSP) system was used to image the fluorophore distribution and to measure the fluorescence spectra of various microscopic structures and regions on frozen tissue sections. Materials and Methods. BCC tissue samples were obtained from 14 patients undergoing surgical resections. After surgical removal, each tissue sample was immediately embedded in OCT medium and snap-frozen in liquid nitrogen. The frozen tissue block was then cut into 16-μm thickness sections using a cryostat microtome and placed on microscopic glass slides. The sections for fluorescence study were kept unstained and unfixed, and then analyzed by the MSP system. The adjacent tissue sections were H&E stained for histopathological examination and also served to help identify various microstructures on the adjacent unstained sections. The MSP system has all the functions of a conventional microscope, plus the ability of performing spectral analysis on selected micro-areas of a microscopic sample. For tissue fluorescence analysis, 442nm He-Cd laser light is used to illuminate and excite the unstained tissue sections. A 473-nm long pass filter was inserted behind the microscope objective to block the transmitted laser light while passing longer wavelength fluorescence signal. The fluorescence image of the sample can be viewed through the eyepieces and also recorded by a CCD camera. An optical fiber is mounted onto the image plane of the photograph port of the microscope to collect light from a specific micro area of the sample. The collected light is transmitted via the fiber to a disperserve type CCD spectrometer for spectral analysis. Results. The measurement results showed significant spectral differences between normal and cancerous tissues. For normal tissue regions, the spectral results agreed with our previous findings on autofluorescence of normal skin sections. For the cancerous regions, the epidermis showed very weak fluorescence signal, while the stratum corneum exhibited fluorescence emissions peaking at about 510 nm. In the dermis, the basal cell island and a band of surrounding areas showed very weak fluorescence signal, while distal dermis above and below the basal cell island showed greater fluorescence signal but with different spectral shapes. The very weak autofluorescence from the basal cell island and its surrounding area may be attributed to their degenerative properties that limited the production of collagens. Conclusions. The obtained microscopic results very well explain the in vivo fluorescence properties of BCC lesions in that they have decreased fluorescence intensity compared to the surrounding normal skin. The intrinsic spectra of various microstructures and the microscopic fluorescence images (corresponding fluorophore distribution in tissue) obtained in this study will be used for further theoretical modeling of in vivo fluorescence spectroscopy and imaging of skin cancers.

Detection of hepatitis "C" virus in formalin-fixed liver tissue by nested polymerase chain reaction.

PubMed

Sallie, R; Rayner, A; Portmann, B; Eddleston, A L; Williams, R

1992-08-01

Interpretation of antibody to hepatitis C virus (HCV) in patients with liver disease is difficult due to false-positive reactivity in some conditions. To evaluate the feasibility of HCV in archival material, HCV was sought in formalin-fixed, paraffin-embedded liver biopsy specimens. Nested polymerase chain reaction was used to detect hepatitis C virus in formalin-fixed, paraffin-embedded liver biopsy specimens after total RNA was extracted from tissue by proteinase K digestion and phenol/chloroform purification. The relative efficiency of amplification of HCV RNA from formalin-fixed material was estimated semiquantitatively by serial dilution of cDNA synthesised from RNA extracted from fresh and formalin-fixed sections from the same liver. Although HCV RNA could be detected in formalin-fixed liver tissue by nested PCR in 5/5 cases in which HCV was detected in serum, amplification was approximately 5-fold less efficient than when HCV was amplified from fresh tissue. Nevertheless, nested PCR of HCV from formalin-fixed liver tissue represents a useful technique in addressing some important questions related to the pathogenesis of liver disease.

Distribution of anti-CD68 (EBM11) immunoreactivity in formalin-fixed, paraffin-embedded bovine tissues.

PubMed

Ackermann, M R; DeBey, B M; Stabel, T J; Gold, J H; Register, K B; Meehan, J T

1994-05-01

A commercially acquired anti-human macrophage antibody (anti-CD68; EBM11) was used in an immunocytochemical technique to detect macrophages in formalin-fixed, paraffin-embedded tissues from cattle, pigs, humans, rats, turkeys, dogs, and cats. In healthy cattle, the antibody labeled alveolar macrophages, pulmonary intravascular cells (presumably intravascular macrophages), and macrophage-like cells in other tissues. In bovine lungs infected with Pasteurella haemolytica, EBM11 antibody labeled 95% of alveolar macrophages and macrophages within alveolar septa but only 0-2% of streaming or "oat" leukocytes. Alveolar macrophages were also stained by EBM11 in pigs but not in rats, turkeys, dogs, and cats. The antibody also stained macrophage aggregates in the mesenteric lymph nodes and intestinal lamina propria of Mycobacterium paratuberculosis-infected cattle. This study shows that the anti-CD68 (EBM11) antibody is a useful marker of macrophages in normal bovine tissues or tissues from areas of acute or chronic inflammation that have been routinely processed. The study also adds strength to the growing evidence suggesting that streaming leukocytes seen in pneumonic pasteurellosis are neutrophils.

A New Cell Block Method for Multiple Immunohistochemical Analysis of Circulating Tumor Cells in Patients with Liver Cancer.

PubMed

Nam, Soo Jeong; Yeo, Hyun Yang; Chang, Hee Jin; Kim, Bo Hyun; Hong, Eun Kyung; Park, Joong-Won

2016-10-01

We developed a new method of detecting circulating tumor cells (CTCs) in liver cancer patients by constructing cell blocks from peripheral blood cells, including CTCs, followed by multiple immunohistochemical analysis. Cell blockswere constructed from the nucleated cell pellets of peripheral blood afterremoval of red blood cells. The blood cell blocks were obtained from 29 patients with liver cancer, and from healthy donor blood spikedwith seven cell lines. The cell blocks and corresponding tumor tissues were immunostained with antibodies to seven markers: cytokeratin (CK), epithelial cell adhesion molecule (EpCAM), epithelial membrane antigen (EMA), CK18, α-fetoprotein (AFP), Glypican 3, and HepPar1. The average recovery rate of spiked SW620 cells from blood cell blocks was 91%. CTCs were detected in 14 out of 29 patients (48.3%); 11/23 hepatocellular carcinomas (HCC), 1/2 cholangiocarcinomas (CC), 1/1 combined HCC-CC, and 1/3 metastatic cancers. CTCs from 14 patients were positive for EpCAM (57.1%), EMA (42.9%), AFP (21.4%), CK18 (14.3%), Gypican3 and CK (7.1%, each), and HepPar1 (0%). Patients with HCC expressed EpCAM, EMA, CK18, and AFP in tissue and/or CTCs, whereas CK, HepPar1, and Glypican3 were expressed only in tissue. Only EMA was significantly associated with the expressions in CTC and tissue. CTC detection was associated with higher T stage and portal vein invasion in HCC patients. This cell block method allows cytologic detection and multiple immunohistochemical analysis of CTCs. Our results show that tissue biomarkers of HCC may not be useful for the detection of CTC. EpCAM could be a candidate marker for CTCs in patients with HCC.

Embedded object concept: case balancing two-wheeled robot

NASA Astrophysics Data System (ADS)

Vallius, Tero; Röning, Juha

2007-09-01

This paper presents the Embedded Object Concept (EOC) and a telepresence robot system which is a test case for the EOC. The EOC utilizes common object-oriented methods used in software by applying them to combined Lego-like software-hardware entities. These entities represent objects in object-oriented design methods, and they are the building blocks of embedded systems. The goal of the EOC is to make the designing of embedded systems faster and easier. This concept enables people without comprehensive knowledge in electronics design to create new embedded systems, and for experts it shortens the design time of new embedded systems. We present the current status of a telepresence robot created with Atomi-objects, which is the name for our implementation of the embedded objects. The telepresence robot is a relatively complex test case for the EOC. The robot has been constructed using incremental device development, which is made possible by the architecture of the EOC. The robot contains video and audio exchange capability and a controlling system for driving with two wheels. The robot consists of Atomi-objects, demonstrating the suitability of the EOC for prototyping and easy modifications, and proving the capabilities of the EOC by realizing a function that normally requires a computer. The computer counterpart is a regular PC with audio and video capabilities running with a robot control application. The robot is functional and successfully tested.

Effect of neuromonitor-guided titrated care on brain tissue hypoxia after opioid overdose cardiac arrest.

PubMed

Elmer, Jonathan; Flickinger, Katharyn L; Anderson, Maighdlin W; Koller, Allison C; Sundermann, Matthew L; Dezfulian, Cameron; Okonkwo, David O; Shutter, Lori A; Salcido, David D; Callaway, Clifton W; Menegazzi, James J

2018-04-18

Brain tissue hypoxia may contribute to preventable secondary brain injury after cardiac arrest. We developed a porcine model of opioid overdose cardiac arrest and post-arrest care including invasive, multimodal neurological monitoring of regional brain physiology. We hypothesized brain tissue hypoxia is common with usual post-arrest care and can be prevented by modifying mean arterial pressure (MAP) and arterial oxygen concentration (PaO 2 ). We induced opioid overdose and cardiac arrest in sixteen swine, attempted resuscitation after 9 min of apnea, and randomized resuscitated animals to three alternating 6-h blocks of standard or titrated care. We invasively monitored physiological parameters including brain tissue oxygen (PbtO 2 ). During standard care blocks, we maintained MAP > 65 mmHg and oxygen saturation 94-98%. During titrated care, we targeted PbtO2 > 20 mmHg. Overall, 10 animals (63%) achieved ROSC after a median of 12.4 min (range 10.8-21.5 min). PbtO 2 was higher during titrated care than standard care blocks (unadjusted β = 0.60, 95% confidence interval (CI) 0.42-0.78, P < 0.001). In an adjusted model controlling for MAP, vasopressors, sedation, and block sequence, PbtO 2 remained higher during titrated care (adjusted β = 0.75, 95%CI 0.43-1.06, P < 0.001). At three predetermined thresholds, brain tissue hypoxia was significantly less common during titrated care blocks (44 vs 2% of the block duration spent below 20 mmHg, P < 0.001; 21 vs 0% below 15 mmHg, P < 0.001; and, 7 vs 0% below 10 mmHg, P = .01). In this model of opioid overdose cardiac arrest, brain tissue hypoxia is common and treatable. Further work will elucidate best strategies and impact of titrated care on functional outcomes. Copyright © 2018 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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 < 0.05) between these two approaches in both embedding media. The average Fr was numerically smaller in paraffin compared to resin (86 ± 61 vs. 106 ± 54 oocytes per gram of body mass (mean ± SD)). For both embedding media statistical significant differences (P < 0.05) were seen between Fr results 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.

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

PubMed Central

Esteve-Codina, Anna; Arpi, Oriol; Martinez-García, Maria; Pineda, Estela; Mallo, Mar; Gut, Marta; Carrato, Cristina; Rovira, Anna; Lopez, Raquel; Tortosa, Avelina; Dabad, Marc; Del Barco, Sonia; Heath, Simon; Bagué, Silvia; Ribalta, Teresa; Alameda, Francesc; de la Iglesia, Nuria

2017-01-01

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. PMID:28122052

An indentation depth-force sensing wheeled probe for abnormality identification during minimally invasive surgery.

PubMed

Liu, H; Puangmali, P; Zbyszewski, D; Elhage, O; Dasgupta, P; Dai, J S; Seneviratne, L; Althoefer, K

2010-01-01

This paper presents a novel wheeled probe for the purpose of aiding a surgeon in soft tissue abnormality identification during minimally invasive surgery (MIS), compensating the loss of haptic feedback commonly associated with MIS. Initially, a prototype for validating the concept was developed. The wheeled probe consists of an indentation depth sensor employing an optic fibre sensing scheme and a force/torque sensor. The two sensors work in unison, allowing the wheeled probe to measure the tool-tissue interaction force and the rolling indentation depth concurrently. The indentation depth sensor was developed and initially tested on a homogenous silicone phantom representing a good model for a soft tissue organ; the results show that the sensor can accurately measure the indentation depths occurring while performing rolling indentation, and has good repeatability. To validate the ability of the wheeled probe to identify abnormalities located in the tissue, the device was tested on a silicone phantom containing embedded hard nodules. The experimental data demonstrate that recording the tissue reaction force as well as rolling indentation depth signals during rolling indentation, the wheeled probe can rapidly identify the distribution of tissue stiffness and cause the embedded hard nodules to be accurately located.

The Effect of Ketamine and Dexamethasone in Combination with Lidocaine on the Onset and Duration of Axillary Block in Hand and Forearm Soft Tissue Surgery.

PubMed

Zaman, Behrooz; Hojjati Ashrafi, Siavash; Seyed Siamdoust, Seyedalireza; Hassani, Valiollah; Mohamad Taheri, Siavash; Noorizad, Samad

2017-10-01

Using peripheral nerve block compared to general anesthesia has gained more popularity due to reduced postoperative pain, less need for post-surgery analgesic drugs, reduced incidence of nausea, shortness of PACU time, and increased patient satisfaction. The aim of this study was to compare the effect of ketamine and dexamethasone as additives to lidocaine on duration and onset of axillary block action. In this clinical trial, all patients who referred to Hazrat-e-Fatemeh hospital for forearm and hand soft tissue surgery with informed consent were randomly divided into three groups in order to examine the onset and duration of axillary block: lidocaine + ketamine, lidocaine + dexamethasone in axillary block, and lidocaine alone (control). Then, the onset and duration of sensory and motor blocks were measured and recorded every three minutes and after the surgery. Quantitative and qualitative variables were analyzed using ANOVA or Kruskal-Wallis test and Chi-square or Fisher exact test in SPSS v.22. Duration of sensory and motor block axillary was significantly higher in lidocaine + dexamethasone group than in lidocaine + ketamine group (P < 0.05); it was also significantly higher in lidocaine + ketamine group compared to lidocaine group (P < 0.05). However, there was no significant difference in the onset of sensory and motor block axillary between the three groups (P > 0.05). According to the results of our study, we can conclude that adding dexamethasone or ketamine to lidocaine could improve duration of sensory and motor axillary block in patients undergoing forearm and hand soft tissue surgery. However, dexamethasone had the highest effect on duration of block axillary. We proved that dexamethasone or ketamine added to lidocaine had no effect on the onset of block axillary.

Real-Time Tracking of Implanted Markers During Radiation Treatment by Use of Simultaneous kV and MV Imaging

DTIC Science & Technology

2009-03-01

the MV–kV correlation method by sinusoidally moving a block of solid water (measuring 5 × 5× 10 cm3) containing three embedded BB metallic markers (3 mm...in diameter). A 4D motion platform (Washington University, St Louis, MO) holding the block of solid water (figure 1) was programmed to produce the...Varian Medical Systems, Palo Alto, CA). The SS-IMRT plans were delivered to either the moving pelvic phantom or the cube of solid water attached to the

In situ hybridization and immunofluorescence on resin-embedded tissue to identify the components of Nissl substance.

PubMed

Singhrao, Sim K; Nair-Roberts, Radha G

2010-05-01

It is not clear whether the Nissl substance is present at the axon hillock. To clarify this gap in knowledge, we conducted in situ hybridization (ISH) on mouse brain tissue using 30-microm cryostat and 1-3-microm acrylic resin sections. Cryostat and rehydrated resin sections were exposed to digoxygenin-labeled glutamic acid decarboxylase 1 sense and antisense riboprobes. Consecutive sections from tissue embedded in resin were subjected to the ribosomal protein L26 primary antibody to determine the distribution of the ribo/polysomes. ISH results from the antisense riboprobe in both cryostat and resin-embedded tissue sections demonstrated an abundance of message in the neurons from the substantia nigra pars reticulate. In addition, the resin sections demonstrated hybridization signal in the axon hillock of some neurons. Immunofluorescence labeling of consecutive sections using an antibody to the most abundant ribosomal protein L26 confirmed their distribution in the cell body and the axon hillock of similar neurons. Compared with the 30-microm cryostat sections, the most striking feature of ISH in the thinner resin (2-3 microm) sections was that there was a phenomenal improvement in the overall clarity and spatial resolution. Reexamination of the axon hillock when continuous with the cell body in cryostat sections revealed that the same message was also present, except it was overlooked initially because of overlapping cell populations in thick tissue slices. As ribosomes are a component of Nissl substance, we propose that the axon hillock, like other parts of the neuron, does contain Nissl substance. (c) 2009 Wiley-Liss, Inc.

A hardware-in-the-loop simulation program for ground-based radar

NASA Astrophysics Data System (ADS)

Lam, Eric P.; Black, Dennis W.; Ebisu, Jason S.; Magallon, Julianna

2011-06-01

A radar system created using an embedded computer system needs testing. The way to test an embedded computer system is different from the debugging approaches used on desktop computers. One way to test a radar system is to feed it artificial inputs and analyze the outputs of the radar. More often, not all of the building blocks of the radar system are available to test. This will require the engineer to test parts of the radar system using a "black box" approach. A common way to test software code on a desktop simulation is to use breakpoints so that is pauses after each cycle through its calculations. The outputs are compared against the values that are expected. This requires the engineer to use valid test scenarios. We will present a hardware-in-the-loop simulator that allows the embedded system to think it is operating with real-world inputs and outputs. From the embedded system's point of view, it is operating in real-time. The hardware in the loop simulation is based on our Desktop PC Simulation (PCS) testbed. In the past, PCS was used for ground-based radars. This embedded simulation, called Embedded PCS, allows a rapid simulated evaluation of ground-based radar performance in a laboratory environment.

Freezing without Ice Crystal Damage: Semithin and Ultrathin Frozen Sections of Ethanol-Infiltrated Tissue for Microscopy, with Applications to Immunocytochemistry

NASA Astrophysics Data System (ADS)

Christensen, A. Kent; Lowry, Terry B.

1995-10-01

Ethanol (ethyl alcohol) has long been a standard reagent used in preparing tissues for light and electron microscopy. After fixation, tissues are usually dehydrated with ethanol before being embedded in paraffin or plastic. In this study we show that the ethanol-infiltrated tissue can be frozen and sectioned directly without embedding. When tissue impregnated with ethanol is cooled below about [minus sign]117°C with liquid nitrogen, the ethanol solidifies without appreciable crystallization. The frozen tissue can then be sectioned in a commercial cryoultramicrotome that is set at [minus sign]155 to [minus sign]170°C to produce semithin frozen sections (0.5 to 3 [mu]m thick) for light microscopy or ultrathin frozen sections (50 to 100 nm thick) for electron microscopy. Sections are picked up and mounted on glass slides or EM grids by means that are in current use for ice ultrathin frozen sectioning. Because there is no apparent freezing damage, the morphology in these ethanol frozen sections of unembedded tissue appears generally quite good, often resembling that obtained by conventional EM techniques. Examples are provided that illustrate the use of this material for immunocytochemistry at the light and electron microscope levels.

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

PubMed

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.

Destructive effect of HIFU on rabbit embedded endometrial carcinoma tissues and their vascularities

PubMed Central

Guan, Liming; Xu, Gang

2017-01-01

Objectives To evaluate damage effect of High-intensity focused ultrasound on early stage endometrial cancer tissues and their vascularities. Materials and Methods Rabbit endometrial cancer models were established via tumor blocks implantation for a prospective control study. Ultrasonic ablation efficacy was evaluated by pathologic and imaging changes. The target lesions of experimental rabbits before and after ultrasonic ablation were observed after autopsy. The slides were used for hematoxylin-eosin staining, elastic fiber staining and endothelial cell staining; the slides were observed by optical microscopy. One slide was observed by electron microscopy. Then the target lesions of experimental animals with ultrasonic ablation were observed by vascular imaging, one group was visualized by digital subtract angiography, one group was quantified by color Doppler flow imaging, and one group was detected by dye perfusion. SPSS 19.0 software was used for statistical analyses. Results Histological examination indicated that High-intensity focused ultrasound caused the tumor tissues and their vascularities coagulative necrosis. Tumor vascular structure components including elastic fiber, endothelial cells all were destroyed by ultrasonic ablation. Digital subtract angiography showed tumor vascular shadow were dismissed after ultrasonic ablation. After ultrasonic ablation, gray-scale of tumor nodules enhanced in ultrasonography, tumor peripheral and internal blood flow signals disappeared or significantly reduced in color Doppler flow imaging. Vascular perfusion performed after ultrasonic ablation, tumor vessels could not filled by dye liquid. Conclusion High-intensity focused ultrasound as a noninvasive method can destroy whole endometrial cancer cells and their supplying vascularities, which maybe an alternative approach of targeted therapy and new antiangiogenic strategy for endometrial cancer. PMID:28121624

Destructive effect of HIFU on rabbit embedded endometrial carcinoma tissues and their vascularities.

PubMed

Guan, Liming; Xu, Gang

2017-03-21

To evaluate damage effect of High-intensity focused ultrasound on early stage endometrial cancer tissues and their vascularities. Rabbit endometrial cancer models were established via tumor blocks implantation for a prospective control study. Ultrasonic ablation efficacy was evaluated by pathologic and imaging changes. The target lesions of experimental rabbits before and after ultrasonic ablation were observed after autopsy. The slides were used for hematoxylin-eosin staining, elastic fiber staining and endothelial cell staining; the slides were observed by optical microscopy. One slide was observed by electron microscopy. Then the target lesions of experimental animals with ultrasonic ablation were observed by vascular imaging, one group was visualized by digital subtract angiography, one group was quantified by color Doppler flow imaging, and one group was detected by dye perfusion.SPSS 19.0 software was used for statistical analyses. Histological examination indicated that High-intensity focused ultrasound caused the tumor tissues and their vascularities coagulative necrosis. Tumor vascular structure components including elastic fiber, endothelial cells all were destroyed by ultrasonic ablation. Digital subtract angiography showed tumor vascular shadow were dismissed after ultrasonic ablation. After ultrasonic ablation, gray-scale of tumor nodules enhanced in ultrasonography, tumor peripheral and internal blood flow signals disappeared or significantly reduced in color Doppler flow imaging. Vascular perfusion performed after ultrasonic ablation, tumor vessels could not filled by dye liquid. High-intensity focused ultrasound as a noninvasive method can destroy whole endometrial cancer cells and their supplying vascularities, which maybe an alternative approach of targeted therapy and new antiangiogenic strategy for endometrial cancer.

Extracting DNA from FFPE Tissue Biospecimens Using User-Friendly Automated Technology: Is There an Impact on Yield or Quality?

PubMed

Mathieson, William; Guljar, Nafia; Sanchez, Ignacio; Sroya, Manveer; Thomas, Gerry A

2018-05-03

DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissue blocks is amenable to analytical techniques, including sequencing. DNA extraction protocols are typically long and complex, often involving an overnight proteinase K digest. Automated platforms that shorten and simplify the process are therefore an attractive proposition for users wanting a faster turn-around or to process large numbers of biospecimens. It is, however, unclear whether automated extraction systems return poorer DNA yields or quality than manual extractions performed by experienced technicians. We extracted DNA from 42 FFPE clinical tissue biospecimens using the QiaCube (Qiagen) and ExScale (ExScale Biospecimen Solutions) automated platforms, comparing DNA yields and integrities with those from manual extractions. The QIAamp DNA FFPE Spin Column Kit was used for manual and QiaCube DNA extractions and the ExScale extractions were performed using two of the manufacturer's magnetic bead kits: one extracting DNA only and the other simultaneously extracting DNA and RNA. In all automated extraction methods, DNA yields and integrities (assayed using DNA Integrity Numbers from a 4200 TapeStation and the qPCR-based Illumina FFPE QC Assay) were poorer than in the manual method, with the QiaCube system performing better than the ExScale system. However, ExScale was fastest, offered the highest reproducibility when extracting DNA only, and required the least intervention or technician experience. Thus, the extraction methods have different strengths and weaknesses, would appeal to different users with different requirements, and therefore, we cannot recommend one method over another.

Pathology, immunohistochemistry, and ultrastructural findings associated with neurological sarcocystosis in cattle

USDA-ARS?s Scientific Manuscript database

The case of neurological sarcocystosis in a nine months old bull calf that died in 1982 was restudied. The bull was suspected to have rabies. Therefore, only brain was examined histologically. Thirty four years later, we restudied sections from paraffin-embedded blocks of brain. Numerous schizonts a...

Gold nanorod embedded reduction responsive block copolymer micelle-triggered drug delivery combined with photothermal ablation for targeted cancer therapy.

PubMed

Parida, Sheetal; Maiti, Chiranjit; Rajesh, Y; Dey, Kaushik K; Pal, Ipsita; Parekh, Aditya; Patra, Rusha; Dhara, Dibakar; Dutta, Pranab Kumar; Mandal, Mahitosh

2017-01-01

Gold nanorods, by virtue of surface plasmon resonance, convert incident light energy (NIR) into heat energy which induces hyperthermia. We designed unique, multifunctional, gold nanorod embedded block copolymer micelle loaded with GW627368X for targeted drug delivery and photothermal therapy. Glutathione responsive diblock co-polymer was synthesized by RAFT process forming self-assembled micelle on gold nanorods prepared by seed mediated method and GW627368X was loaded on to the reduction responsive gold nanorod embedded micelle. Photothermal therapy was administered using cwNIR laser (808nm; 4W/cm 2 ). Efficacy of nanoformulated GW627368X, photothermal therapy and combination of both were evaluated in vitro and in vivo. In response to photothermal treatment, cells undergo regulated, patterned cell death by necroptosis. Combining GW627368X with photothermal treatment using single nanoparticle enhanced therapeutic outcome. In addition, these nanoparticles are effective X-ray CT contrast agents, thus, can help in monitoring treatment. Reduction responsive nanorod embedded micelle containing folic acid and lipoic acid when treated on cervical cancer cells or tumour bearing mice, aggregate in and around cancer cells. Due to high glutathione concentration, micelles degrade releasing drug which binds surface receptors inducing apoptosis. When incident with 808nm cwNIR lasers, gold nanorods bring about photothermal effect leading to hyperthermic cell death by necroptosis. Combination of the two modalities enhances therapeutic efficacy by inducing both forms of cell death. Our proposed treatment strategy achieves photothermal therapy and targeted drug delivery simultaneously. It can prove useful in overcoming general toxicities associated with chemotherapeutics and intrinsic/acquired resistance to chemo and radiotherapy. Copyright © 2016 Elsevier B.V. All rights reserved.

Next-gen tissue: preservation of molecular and morphological fidelity in prostate tissue.

PubMed

Gillard, Marc; Tom, Westin R; Antic, Tatjana; Paner, Gladell P; Lingen, Mark W; VanderWeele, David J

2015-01-01

Personalization of cancer therapy requires molecular evaluation of tumor tissue. Traditional tissue preservation involves formalin fixation, which degrades the quality of nucleic acids. Strategies to bank frozen prostate tissue can interfere with diagnostic studies. PAXgene is an alternative fixative that preserves protein and nucleic acid quality. Portions of prostates obtained from autopsy specimens were fixed in either 10% buffered formalin or PAXgene, and processed and embedded in paraffin. Additional sections were immediately embedded in OCT and frozen. DNA and RNA were extracted from the formalin-fixed, PAXgene-fixed, or frozen tissue. Quantitative PCR was used to compare the quality of DNA and RNA obtained from all three tissue types. In addition, 5 μm sections were cut from specimens devoid of cancer and from prostate cancer specimens obtained at prostatectomy and fixed in PAXgene. They were either stained with hematoxylin and eosin or interrogated with antibodies for p63, PSA and p504. Comparable tissue morphology was observed in both the formalin and PAXgene-fixed specimens. Similarly, immunohistochemical expression of the P63, PSA and P504 proteins was comparable between formalin and PAXgene fixation techniques. DNA from the PAXgene-fixed tissue was of similar quality to that from frozen tissue. RNA was also amplified with up to 8-fold greater efficiency in the PAXgene fixed tissue compared to the formalin-fixed tissue. Prostate specimens fixed with PAXgene have preserved histologic morphology, stain appropriately, and have preserved quality of nucleic acids. PAXgene fixation facilitates the use of prostatectomy tissue for molecular biology techniques such as next-generation sequencing.

A Comparative Histopathology, Serology and Molecular Study, on Experimental Ocular Toxocariasis by Toxocara cati in Mongolian Gerbils and Wistar Rats

PubMed Central

Zibaei, Mohammad; Sadjjadi, Seyed Mahmoud; Karamian, Mehdi; Uga, Shoji; Oryan, Ahmad; Jahadi-Hosseini, Seyed Hamidreza

2013-01-01

The aim of this study was to compare the performance of three in-house diagnostic tests, that is, histopathology, enzyme-linked immunosorbent assay (ELISA), and polymerase chain reaction (PCR), for the diagnosis after experimental infection with Toxocara cati. Twenty Mongolian gerbils and Wistar rats were divided into ten groups (n = 2/group). Toxocara cati infections were established in Mongolian gerbils and Wistar rats by administering doses of 240 and 2500 embryonated Toxocara cati eggs by gavage, respectively. Tissue sections were stained with Haematoxylin and Eosin and observed under the light microscope. Sera and vitreous fluid collected from separate infected groups were tested against Toxocara cati antigens, for 92 days postinfection. Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) blocks, and aqueous fluids belong to the animals. The histopathology test gave negative results among the groups of animals examined between 5 and 92 days postinfection. The ELISA results showed that anti-Toxocara antibodies have risen between 7 and 61 days postinfection in sera and vitreous fluid in the animals infected, respectively. Analysis of PCR products revealed positive band (660 bp) in the orbital tissue infected Mongolian gerbils at 5 days postinfection. Of the three evaluated methods, the PCR could be recommended for scientific and laboratory diagnoses of toxocariasis in experimentally infected animals. PMID:24069585

A comparative histopathology, serology and molecular study, on experimental ocular toxocariasis by Toxocara cati in Mongolian gerbils and Wistar rats.

PubMed

Zibaei, Mohammad; Sadjjadi, Seyed Mahmoud; Karamian, Mehdi; Uga, Shoji; Oryan, Ahmad; Jahadi-Hosseini, Seyed Hamidreza

2013-01-01

The aim of this study was to compare the performance of three in-house diagnostic tests, that is, histopathology, enzyme-linked immunosorbent assay (ELISA), and polymerase chain reaction (PCR), for the diagnosis after experimental infection with Toxocara cati. Twenty Mongolian gerbils and Wistar rats were divided into ten groups (n = 2/group). Toxocara cati infections were established in Mongolian gerbils and Wistar rats by administering doses of 240 and 2500 embryonated Toxocara cati eggs by gavage, respectively. Tissue sections were stained with Haematoxylin and Eosin and observed under the light microscope. Sera and vitreous fluid collected from separate infected groups were tested against Toxocara cati antigens, for 92 days postinfection. Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) blocks, and aqueous fluids belong to the animals. The histopathology test gave negative results among the groups of animals examined between 5 and 92 days postinfection. The ELISA results showed that anti-Toxocara antibodies have risen between 7 and 61 days postinfection in sera and vitreous fluid in the animals infected, respectively. Analysis of PCR products revealed positive band (660 bp) in the orbital tissue infected Mongolian gerbils at 5 days postinfection. Of the three evaluated methods, the PCR could be recommended for scientific and laboratory diagnoses of toxocariasis in experimentally infected animals.

[Significance of MUC5B antibody in differential diagnosis between Aspergillus species and Mucorales of fungal sinusitis].

PubMed

Piao, Ying-shi; Liu, Hong-gang; Liu, Xian-jun

2008-04-01

To differentiate between Aspergillus species and Mucorales of fungal sinusitis by immunohistochemistry. Formalin-fixed paraffin-embedded tissue blocks of 66 cases of fungal sinusitis were retrieved from the archival files of Department of Pathology of Beijing Tongren Hospital during the period from 2001 to 2006. The samples included 29 cases of fungal balls, 12 cases of allergic fungal sinusitis, 24 cases of chronic invasive fungal sinusitis and 1 case of acute invasive fungal sinusitis. The types of fungi were 44 Aspergillus species (31 cases of A. fumigatus, 7 cases of A. flavus and 6 cases of A. terreus) and 22 Mucorales (14 cases of Mucor species and 8 cases of Rhizopus species). Immunohistochemistry was performed with MUC2, MUC5AC and MUC5B antibodies. The results were compared with histochemical study for periodic acid-Schiff (PAS) and Grocott methenamine silver (GMS) stains. Immunohistochemical study for MUC5B showed that the positive rate of Aspergillus species was 90.9%, in contrast to 4.5% in Mucorales (P < 0.001). The expression of MUC2 and MUC5AC was completely negative, whereas PAS and GMS stains were positive in all cases. MUC5B antibody appears to be a useful immunohistochemical marker for identifying fungal types in tissue sections, especially in distinguishing between Aspergillus species and Mucorales in fungal sinusitis.

Congenital complete heart block in the newborn associated with maternal systemic lupus erythematosus and other connective tissue disorders.

PubMed Central

Hardy, J D; Solomon, S; Banwell, G S; Beach, R; Wright, V; Howard, F M

1979-01-01

Four babies with complete heart block associated with maternal systemic lupus erythematosus (SLE) are described, together with a 5th baby whose mother had serological abnormalities only. One baby had a rapidly fatal outcome, one has required digoxin for heart failure, and the remaining 3 are asymptomatic but remain in complete heart block. Additional manifestations were present in 2 of them. The spectrum of neonatal abnormalities that may occur in association with maternal SLE and related connective tissue disorders is discussed, together with the possible causes and the prognosis. We conclude that congenital heart block is more common than had previously been appreciated. Images Figure PMID:420526

Kerosene: Contributing agent to xylene as a clearing agent in tissue processing.

PubMed

Shah, Amisha Ashokkumar; Kulkarni, Dinraj; Ingale, Yashwant; Koshy, Ajit V; Bhagalia, Sanjay; Bomble, Nikhil

2017-01-01

Research methodology in oral and maxillofacial pathology has illimitable potential. The tissue processing involves many steps of which one of the most important step is "Clearing," which is a process of replacing dehydrant with a substance which is miscible with embedding medium or paraffin wax. Xylene is one of the common clearing agents used in laboratory, but it is also hazardous. The main aim of this study is to substitute conventionally used xylene by a mixture of kerosene and xylene in clearing steps without altering the morphology and staining characteristics of tissue sections. This will also minimize the toxic effects and tend to be more economical. One hundred and twenty bits of tissue samples were collected, each randomly separated into 4 groups (A, B, C and D) and kept for routine tissue processing till the step of clearing; during the step of clearing instead of conventional xylene, we used mixture of xylene and kerosene in 4 ratios ([A-K:X - 50:50]; [B-K:X - 70:30]; [C - Ab. Kerosene]; [D - Ab. Xylene - as control]) and observed for the light microscopic study adopting H and E staining, IHC (D2-40), Special stains (periodic acid-Schiff and congo red) procedure. The result was subjected to statistical analysis by using Fisher's exact test. The results obtained from the present study were compared with control group, i.e., D and it was observed that Groups A and B were absolutely cleared without altering the morphology of tissue and cellular details; optimum embedding characteristics and better staining characteristics were also noted, whereas Group C presents poor staining characteristics with reduced cellular details. Embedded tissues in Group C presented with rough, irregular surface and also appeared shrunken. Combined mixture of xylene and kerosene as a clearing agent in different ratio, i.e., Group A (K:X - 50:50) and B (K:X - 70:30) can be used without posing any health risk or compromising the cellular integrity.

Electron microscopy of the amphibian model systems Xenopus laevis and Ambystoma mexicanum.

PubMed

Kurth, Thomas; Berger, Jürgen; Wilsch-Bräuninger, Michaela; Kretschmar, Susanne; Cerny, Robert; Schwarz, Heinz; Löfberg, Jan; Piendl, Thomas; Epperlein, Hans H

2010-01-01

In this chapter we provide a set of different protocols for the ultrastructural analysis of amphibian (Xenopus, axolotl) tissues, mostly of embryonic origin. For Xenopus these methods include: (1) embedding gastrulae and tailbud embryos into Spurr's resin for TEM, (2) post-embedding labeling of methacrylate (K4M) and cryosections through adult and embryonic epithelia for correlative LM and TEM, and (3) pre-embedding labeling of embryonic tissues with silver-enhanced nanogold. For the axolotl (Ambystoma mexicanum) we present the following methods: (1) SEM of migrating neural crest (NC) cells; (2) SEM and TEM of extracellular matrix (ECM) material; (3) Cryo-SEM of extracellular matrix (ECM) material after cryoimmobilization; and (4) TEM analysis of hyaluronan using high-pressure freezing and HABP labeling. These methods provide exemplary approaches for a variety of questions in the field of amphibian development and regeneration, and focus on cell biological issues that can only be answered with fine structural imaging methods, such as electron microscopy. Copyright © 2010 Elsevier Inc. All rights reserved.

Towards traceable transient pressure metrology

NASA Astrophysics Data System (ADS)

Hanson, Edward; Olson, Douglas A.; Liu, Haijun; Ahmed, Zeeshan; Douglass, Kevin O.

2018-04-01

We describe our progress in developing the infrastructure for traceable transient measurements of pressure. Towards that end, we have built and characterized a dual diaphragm shock tube that allows us to achieve shock amplitude reproducibility of approximately 2.3% for shocks with Mach speeds ranging from 1.26-1.5. In this proof-of-concept study we use our shock tube to characterize the dynamic response of photonic sensors embedded in polydimethylsiloxane (PDMS), a material of choice for soft tissue phantoms. Our results indicate that the PDMS-embedded photonic sensors response to shock evolves over a tens to hundreds of microseconds time scale making it a useful system for studying transient pressures in soft tissue.

Skin contamination dosimeter

DOEpatents

Hamby, David M [Corvallis, OR; Farsoni, Abdollah T [Corvallis, OR; Cazalas, Edward [Corvallis, OR

2011-06-21

A technique and device provides absolute skin dosimetry in real time at multiple tissue depths simultaneously. The device uses a phoswich detector which has multiple scintillators embedded at different depths within a non-scintillating material. A digital pulse processor connected to the phoswich detector measures a differential distribution (dN/dH) of count rate N as function of pulse height H for signals from each of the multiple scintillators. A digital processor computes in real time from the differential count-rate distribution for each of multiple scintillators an estimate of an ionizing radiation dose delivered to each of multiple depths of skin tissue corresponding to the multiple scintillators embedded at multiple corresponding depths within the non-scintillating material.

Rapid and simple method of photobleaching to reduce background autofluorescence in lung tissue sections.

PubMed

Kumar, B Santhosh; Sandhyamani, S; Nazeer, Shaiju S; Jayasree, R S

2015-02-01

Autofluorescence exhibited by tissues often interferes with immunofluorescence. Using imaging and spectral analysis, we observed remarkable reduction of autofluorescence of formalin fixed paraffin embedded tissues irradiated with light prior to incubation with immunofluorescent dyes. The technique of photobleaching offers significant improvement in the quality and specificity of immunofluorescence. This has the potential for better techniques for disease diagnosis.

Opiate alkaloids in Ascaris suum.

PubMed

Pryor, S C; Putnam, Jennifer; Hoo, Nanyamka

2004-01-01

The parasitic worm Ascaris suum contains the opiate alkaloids morphine and morphine-6-glucuronide as determined by HPLC coupled to electrochemical detection and by gas chromatography/mass spectrometry. The level of morphine in muscle tissue of female and male is 252 +/- 32.68, 1168 +/- 278 and 180 +/- 23.47 (ng/g of wet tissue), respectively. The level of M6G in muscle tissue of female and male is 167 +/- 28.37 and 92 +/- 11.45 (ng/g of wet tissue), respectively. Furthermore, Ascaris maintained for 5 days contained a significant amount of morphine, as did their medium, demonstrating their ability to synthesize the opiate alkaloid. The anatomic distribution of morphine was examined by indirect immunofluorescent staining and HPLC of various tissues dissected from male and female adult worms. Immunofluorescence revealed morphine in the subcuticle layers, in the animals' nerve chords and in the female reproductive organs. Morphine was found to be most prevalent in the muscle tissue and there is significantly more morphine in females than males, probably due to the large amounts in the female uterus. Morphine (10(-9) M) and morphine-6-glucuronide (10(-9) M) stimulated the release of NO from Ascaris muscle tissue. Naloxone (10(-7) M), and L-NAME (10(-6) M) blocked (P < 0.005) morphine-stimulated NO release from A. suum muscle. CTOP (10(-7) M) did not block morphine's NO release. However, naloxone could not block M6G stimulated NO release by muscle tissue, whereas CTOP (10(-7) M) blocked its release. These findings were in seeming contradiction to our inability to isolate a mu opiate receptor messenger RNA by RT-PCR using a human mu primer. This suggests that a novel mu opiate receptor was present and selective toward M6G.

Autogenous bonding of tooth fragment retained in lower lip after trauma

PubMed Central

Lips, Andrea; da Silva, Luciana Pereira; Tannure, Patricia Nivoloni; Farinhas, João Alfredo; Primo, Laura Guimarães; de Araújo Castro, Gloria Fernanda

2012-01-01

In cases of trauma, dental fragments occasionally penetrate into the soft-tissues and may cause severe complications, if neglected. Clinical and radiographic examinations can provide a diagnosis and help in the surgical removal of any dental fragment embedded in soft-tissue. This case report concerns an 8-year-old boy who was diagnosed with a fragment of a fractured permanent central incisor crown located in the lower lip. The patient was seen initially at a general hospital, where the dental fragment went unnoticed. After 2 days, the patient was seen at the pediatric dentistry clinic, where a fragment embedded in the lower lip, causing a large swelling, was diagnosed. The fragment was removed surgically and bonded to the fractured tooth. A mouth guard was prescribed for sports. The importance of soft-tissue exploration even post-trauma was highlighted in this paper. PMID:23633815

Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation

PubMed Central

Einaga, Naoki; Yoshida, Akio; Noda, Hiroko; Suemitsu, Masaaki; Nakayama, Yuki; Sakurada, Akihisa; Kawaji, Yoshiko; Yamaguchi, Hiromi; Sasaki, Yasushi; Tokino, Takashi; Esumi, Mariko

2017-01-01

Formalin-fixed, paraffin-embedded (FFPE) tissues used for pathological diagnosis are valuable for studying cancer genomics. In particular, laser-capture microdissection of target cells determined by histopathology combined with FFPE tissue section immunohistochemistry (IHC) enables precise analysis by next-generation sequencing (NGS) of the genetic events occurring in cancer. The result is a new strategy for a pathological tool for cancer diagnosis: ‘microgenomics’. To more conveniently and precisely perform microgenomics, we revealed by systematic analysis the following three details regarding FFPE DNA compared with paired frozen tissue DNA. 1) The best quality of FFPE DNA is obtained by tissue fixation with 10% neutral buffered formalin for 1 day and heat treatment of tissue lysates at 95°C for 30 minutes. 2) IHC staining of FFPE tissues decreases the quantity and quality of FFPE DNA to one-fourth, and antigen retrieval (at 120°C for 15 minutes, pH 6.0) is the major reason for this decrease. 3) FFPE DNA prepared as described herein is sufficient for NGS. For non-mutated tissue specimens, no artifactual mutation occurs during FFPE preparation, as shown by precise comparison of NGS of FFPE DNA and paired frozen tissue DNA followed by validation. These results demonstrate that even FFPE tissues used for routine clinical diagnosis can be utilized to obtain reliable NGS data if appropriate conditions of fixation and validation are applied. PMID:28498833

Optimization of immunohistochemical and fluorescent antibody techniques for localization of foot-and-mouth disease virus in animal tissues

USDA-ARS?s Scientific Manuscript database

Immunohistochemical (IHC) and immunofluorescent (IF) techniques were optimized for the detection of foot-and-mouth disease virus (FMDV) structural and non-structural proteins in frozen and paraformaldehyde-fixed paraffin embedded (PFPE) tissues of bovine and porcine origin. Immunohistochemical local...

PRESENTATION TYPE: Round Table Discussion (80 minutes) TITLE: Unlocking the ‘Omics Archive: Enabling Toxicogenomic/Proteomic Investigation from Archival Samples

EPA Science Inventory

Formalin fixation and paraffin embedding (FFPE) is a cross-industry gold standard for preparing nonclinical and clinical samples for histopathological assessment which preserves tissue architecture and enables storage of tissue in archival banks. These archival banks are an untap...

Conductive carbon tape used for support and mounting of both whole animal and fragile heat-treated tissue sections for MALDI MS imaging and quantitation.

PubMed

Goodwin, Richard J A; Nilsson, Anna; Borg, Daniel; Langridge-Smith, Pat R R; Harrison, David J; Mackay, C Logan; Iverson, Suzanne L; Andrén, Per E

2012-08-30

Analysis of whole animal tissue sections by MALDI MS imaging (MSI) requires effective sample collection and transfer methods to allow the highest quality of in situ analysis of small or hard to dissect tissues. We report on the use of double-sided adhesive conductive carbon tape during whole adult rat tissue sectioning of carboxymethyl cellulose (CMC) embedded animals, with samples mounted onto large format conductive glass and conductive plastic MALDI targets, enabling MSI analysis to be performed on both TOF and FT-ICR MALDI mass spectrometers. We show that mounting does not unduly affect small molecule MSI detection by analyzing tiotropium abundance and distribution in rat lung tissues, with direct on-tissue quantitation achieved. Significantly, we use the adhesive tape to provide support to embedded delicate heat-stabilized tissues, enabling sectioning and mounting to be performed that maintained tissue integrity on samples that had previously been impossible to adequately prepare section for MSI analysis. The mapping of larger peptidomic molecules was not hindered by tape mounting samples and we demonstrate this by mapping the distribution of PEP-19 in both native and heat-stabilized rat brains. Furthermore, we show that without heat stabilization PEP-19 degradation fragments can detected and identified directly by MALDI MSI analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

FGFR2 alterations in endometrial carcinoma.

PubMed

Gatius, Sonia; Velasco, Ana; Azueta, Ainara; Santacana, Maria; Pallares, Judit; Valls, Joan; Dolcet, Xavier; Prat, Jaime; Matias-Guiu, Xavier

2011-11-01

Fibroblast growth factor receptor 2 (FGFR2) is a tyrosine kinase receptor involved in many biological processes such as embryogenesis, adult tissue homeostasis and cell proliferation. Mutations in FGFR2 have been reported in up to 10-12% of endometrial carcinomas identical to those found in congenital craniofacial disorders. Inhibition of FGFR2 could be a new therapeutic target in endometrial carcinoma. FGFR2 immunostaining was assessed in three tissue microarrays: one constructed from paraffin-embedded blocks of 60 samples of normal endometrium in different phases of menstrual cycle, and two tissue microarrays containing endometrial carcinoma samples (95 and 62 cases). FGFR2 expression was correlated with stage, histological type and grade as well as with immunostaining of PTEN, RASSF1A, estrogen and progesterone receptors, KI67, Cyclin D1, STAT-3 and SPRY2. FGFR2 mutations were assessed by PCR and direct sequencing, with DNA obtained from 31 paraffin-embedded endometrial carcinoma samples. In normal endometrium, FGFR2 expression was higher in the secretory than in the proliferative phase (P=0.001), with an inverse correlation with Ki67 (P=0.00032), suggesting a tumor-suppressor role for FGFR2 in normal endometrium. Cytoplasmic expression of FGFR2 was higher in endometrial carcinoma when compared with the atrophic endometrium from the same patients (P=0.0283), but was lower in comparison with normal endometrium from women in the menstrual cycle. Interestingly, nuclear staining was observed in some cases, and it was less frequent in endometrial carcinoma when compared with the adjacent atrophic endometrium (P=0.0465). There were no statistical differences when comparing superficial and myoinvasive endometrial carcinoma samples. Endometrioid endometrial carcinomas showed higher expression of FGFR2 than nonendometrioid endometrial carcinomas (fold change 2.56; P=0.0015). Grade III endometrioid endometrial carcinomas showed decreased FGFR2 expression when compared with grade II endometrioid endometrial carcinomas (P=0.0055). No differences were found regarding pathological stage. Two missense mutations of FGFR2 gene were detected in exons 6 and 11 (S252W and N549K, respectively; 6.45%). Results support the hypothesis that FGFR2 has a dual role in the endometrium, by inhibiting cell proliferation in normal endometrium during the menstrual cycle, but acting as an oncogene in endometrial carcinoma.

Preventing the infiltration of leukocytes by monoclonal antibody blocks the development of progressive ischemia in rat burns.

PubMed

Choi, M; Rabb, H; Arnaout, M A; Ehrlich, H P

1995-10-01

Tissue loss as a consequence of thermal trauma occurs in two stages. There is immediate necrosis in tissues directly killed by the thermal energy, followed by a delayed secondary necrosis in neighboring tissues. The infiltration of neutrophils into traumatized tissues is a hallmark of the inflammatory response. Neutrophils have the machinery to kill invading microorganisms, but these same weapons have the capacity to destroy the host's viable tissues as well. Leukocyte infiltration requires their adherence to the vascular endothelial cell surface. Masking these adhesion sites on neutrophils will block the adhesion of neutrophils to the endothelium. A monoclonal antibody (mAb) was developed to guinea pig leukocyte adhesion sites CD11b/ CD18, and this mAb cross-reacts with rat leukocytes, blocking their adherence. Rats received a "comb burn" composed of four rectangular full-thickness burns placed in a row and separated by three areas left unburned. The four individual burns convert into a single large wound because the blood flow to the interspaces was terminated, blood vessels were occluded, and leukocytes were present in the extravascular space. The systemic administration of the mAb (50 to 150 microliters) immediately following a comb burn promoted the survival of the interspace, demonstrated by the prevention of loss of blood flow by laser Doppler monitoring, maintained patent vessels by latex vascular casts, blocked extravascular migration of neutrophils histologically at 2 hours, and limited the tissue loss to the original four burns.

Detection of EML4-ALK in Lung Adenocarcinoma Using Pleural Effusion with FISH, IHC, and RT-PCR Methods

PubMed Central

Zhou, Xiaodie; Song, Yong; Zhou, Xiaojun; Yu, Like; Wang, Jiandong

2015-01-01

Anaplastic lymphoma kinase (ALK) and echinoderm microtubule-associated protein-like 4 (EML4) gene rearrangements occur in approximately 5% of non-small-cell lung cancers (NSCLC), leading to the overexpression of anaplastic lymphoma kinase and predicting a response to the targeted inhibitor, crizotinib. Malignant pleural effusion occurs in most patients with advanced lung cancer, especially adenocarcinoma, and tissue samples are not always available from these patients. We attempted to clarify the feasibility of detecting the EML4-ALK fusion gene in pleural effusion cells using different methods. We obtained 66 samples of pleural effusion from NSCLC patients. The pleural effusion fluid was centrifuged, and the cellular components obtained were formalin fixed and paraffin embedded. The EML4-ALK fusion gene status was determined with fluorescent in situ hybridization (FISH), reverse transcription—polymerase chain reaction (RT-PCR), and immunohistochemistry (IHC). EML4-ALK was detected in three of 66 patient samples (4.5%) with RT-PCR. When the RT-PCR data were used as the standard, one false positive and one false negative samples were identified with IHC; and one false negative sample was identified with FISH. These results suggest that a block of pleural effusion cells can be used to detect the EML4-ALK fusion gene. IHC had good sensitivity, but low specificity. FISH had low sensitivity, but high specificity. RT-PCR is a good candidate method for detecting EML4-ALK in blocks of pleural effusion cells from lung cancer patients. PMID:25785456

Detection of EML4-ALK in lung adenocarcinoma using pleural effusion with FISH, IHC, and RT-PCR methods.

PubMed

Liu, Leilei; Zhan, Ping; Zhou, Xiaodie; Song, Yong; Zhou, Xiaojun; Yu, Like; Wang, Jiandong

2015-01-01

Anaplastic lymphoma kinase (ALK) and echinoderm microtubule-associated protein-like 4 (EML4) gene rearrangements occur in approximately 5% of non-small-cell lung cancers (NSCLC), leading to the overexpression of anaplastic lymphoma kinase and predicting a response to the targeted inhibitor, crizotinib. Malignant pleural effusion occurs in most patients with advanced lung cancer, especially adenocarcinoma, and tissue samples are not always available from these patients. We attempted to clarify the feasibility of detecting the EML4-ALK fusion gene in pleural effusion cells using different methods. We obtained 66 samples of pleural effusion from NSCLC patients. The pleural effusion fluid was centrifuged, and the cellular components obtained were formalin fixed and paraffin embedded. The EML4-ALK fusion gene status was determined with fluorescent in situ hybridization (FISH), reverse transcription-polymerase chain reaction (RT-PCR), and immunohistochemistry (IHC). EML4-ALK was detected in three of 66 patient samples (4.5%) with RT-PCR. When the RT-PCR data were used as the standard, one false positive and one false negative samples were identified with IHC; and one false negative sample was identified with FISH. These results suggest that a block of pleural effusion cells can be used to detect the EML4-ALK fusion gene. IHC had good sensitivity, but low specificity. FISH had low sensitivity, but high specificity. RT-PCR is a good candidate method for detecting EML4-ALK in blocks of pleural effusion cells from lung cancer patients.

Au/CdS Hybrid Nanoparticles in Block Copolymer Micellar Shells.

PubMed

Koh, Haeng-Deog; Changez, Mohammad; Lee, Jae-Suk

2010-10-18

A polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP) micellar structure with a P2VP core containing 5 nm CdS nanoparticles (NPs) and a PS shell formed in toluene that is a good solvent for PS block undergoes the core-shell inversion by excess addition of methanol that is a good solvent for P2VP block. It leads to the formation of micellar shell-embedded CdS NPs in the methanol major phase. The spontaneous crystalline growth of Au NPs on the CdS surfaces positioned at micellar shells without a further reduction process is newly demonstrated. The nanostructure of Au/CdS/PS-b-P2VP hybrid NPs is confirmed by transmission electron microscopy, energy-dispersive X-ray, and UV-Vis absorption. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nuclear component horizontal seismic restraint

DOEpatents

Snyder, Glenn J.

1988-01-01

A nuclear component horizontal seismic restraint. Small gaps limit horizontal displacement of components during a seismic occurrence and therefore reduce dynamic loadings on the free lower end. The reactor vessel and reactor guard vessel use thicker section roll-forged rings welded between the vessel straight shell sections and the bottom hemispherical head sections. The inside of the reactor guard vessel ring forging contains local vertical dovetail slots and upper ledge pockets to mount and retain field fitted and installed blocks. As an option, the horizontal displacement of the reactor vessel core support cone can be limited by including shop fitted/installed local blocks in opposing alignment with the reactor vessel forged ring. Beams embedded in the wall of the reactor building protrude into apertures in the thermal insulation shell adjacent the reactor guard vessel ring and have motion limit blocks attached thereto to provide to a predetermined clearance between the blocks and reactor guard vessel ring.

Enabling complex nanoscale pattern customization using directed self-assembly.

PubMed

Doerk, Gregory S; Cheng, Joy Y; Singh, Gurpreet; Rettner, Charles T; Pitera, Jed W; Balakrishnan, Srinivasan; Arellano, Noel; Sanders, Daniel P

2014-12-16

Block copolymer directed self-assembly is an attractive method to fabricate highly uniform nanoscale features for various technological applications, but the dense periodicity of block copolymer features limits the complexity of the resulting patterns and their potential utility. Therefore, customizability of nanoscale patterns has been a long-standing goal for using directed self-assembly in device fabrication. Here we show that a hybrid organic/inorganic chemical pattern serves as a guiding pattern for self-assembly as well as a self-aligned mask for pattern customization through cotransfer of aligned block copolymer features and an inorganic prepattern. As informed by a phenomenological model, deliberate process engineering is implemented to maintain global alignment of block copolymer features over arbitrarily shaped, 'masking' features incorporated into the chemical patterns. These hybrid chemical patterns with embedded customization information enable deterministic, complex two-dimensional nanoscale pattern customization through directed self-assembly.

Three dimensional structure of the distal condyles of the third metacarpal bone of the horse.

PubMed

Boyde, A; Haroon, Y; Jones, S J; Riggs, C M

1999-03-01

This study examined the three-dimensional (3D) microarchitecture of regions of the equine third metacarpal bone (McIII) commonly involved in distal condylar fractures. Limbs were obtained from Thoroughbred horses (neonates to age 24 years) destroyed for inoperable fractures and a variety of other conditions. Beams, blocks and sections were cut in the principal axes, some embedded in PMMA and others examined unembedded. Several methods were used to study the 3D structure, including conventional and confocal optical microscopy, scanning electron microscopy (SEM) and radiography. The mineralised articular cartilage tends to cleave in the sagittal plane. Proximal to the subchondral bone, the main trabeculae are robust plates running in the sagittal direction with less significant mediolateral connections. Small blood vessel canals lie inside the sagittal plates. This structure gives maximum strength and protection in the sagittal plane in which the bone rotates, but offers minimal resistance to fracture propagation in this plane. The anatomical course of the common distal condylar fractures of the third metacarpal bones can be explained by underlying anisotropic structural features of the mineralised tissues.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raja, Shilpa N.; Zherebetskyy, Danylo; Wu, Siva

Nanoscale stress-sensing can be used across fields ranging from detection of incipient cracks in structural mechanics to monitoring forces in biological tissues. We demonstrate how tetrapod quantum dots (tQDs) embedded in block copolymers act as sensors of tensile/compressive stress. Remarkably, tQDs can detect their own composite dispersion and mechanical properties with a switch in optomechanical response when tQDs are in direct contact. Using experimental characterizations, atomistic simulations and finite-element analyses, we show that under tensile stress, densely packed tQDs exhibit a photoluminescence peak shifted to higher energies ("blue-shift") due to volumetric compressive stress in their core; loosely packed tQDs exhibitmore » a peak shifted to lower energies ("red-shift") from tensile stress in the core. The stress shifts result from the tQD's unique branched morphology in which the CdS arms act as antennas that amplify the stress in the CdSe core. Our nanocomposites exhibit excellent cyclability and scalability with no degraded properties of the host polymer. Colloidal tQDs allow sensing in many materials to potentially enable autoresponsive, smart structural nanocomposites that self-predict upcoming fracture.« less

Non-Markovianity in the collision model with environmental block

NASA Astrophysics Data System (ADS)

Jin, Jiasen; Yu, Chang-shui

2018-05-01

We present an extended collision model to simulate the dynamics of an open quantum system. In our model, the unit to represent the environment is, instead of a single particle, a block which consists of a number of environment particles. The introduced blocks enable us to study the effects of different strategies of system–environment interactions and states of the blocks on the non-Markovianities. We demonstrate our idea in the Gaussian channels of an all-optical system and derive a necessary and sufficient condition of non-Markovianity for such channels. Moreover, we show the equivalence of our criterion to the non-Markovian quantum jump in the simulation of the pure damping process of a single-mode field. We also show that the non-Markovianity of the channel working in the strategy that the system collides with environmental particles in each block in a certain order will be affected by the size of the block and the embedded entanglement and the effects of heating and squeezing the vacuum environmental state will quantitatively enhance the non-Markovianity.

An algorithm of a real time image tracking system using a camera with pan/tilt motors on an embedded system

NASA Astrophysics Data System (ADS)

Kim, Hie-Sik; Nam, Chul; Ha, Kwan-Yong; Ayurzana, Odgeral; Kwon, Jong-Won

2005-12-01

The embedded systems have been applied to many fields, including households and industrial sites. The user interface technology with simple display on the screen was implemented more and more. The user demands are increasing and the system has more various applicable fields due to a high penetration rate of the Internet. Therefore, the demand for embedded system is tend to rise. An embedded system for image tracking was implemented. This system is used a fixed IP for the reliable server operation on TCP/IP networks. Using an USB camera on the embedded Linux system developed a real time broadcasting of video image on the Internet. The digital camera is connected at the USB host port of the embedded board. All input images from the video camera are continuously stored as a compressed JPEG file in a directory at the Linux web-server. And each frame image data from web camera is compared for measurement of displacement Vector. That used Block matching algorithm and edge detection algorithm for past speed. And the displacement vector is used at pan/tilt motor control through RS232 serial cable. The embedded board utilized the S3C2410 MPU, which used the ARM 920T core form Samsung. The operating system was ported to embedded Linux kernel and mounted of root file system. And the stored images are sent to the client PC through the web browser. It used the network function of Linux and it developed a program with protocol of the TCP/IP.

Enhanced Circular Dichroism of Gold Bilayered Slit Arrays Embedded with Rectangular Holes.

PubMed

Zhang, Hao; Wang, Yongkai; Luo, Lina; Wang, Haiqing; Zhang, Zhongyue

2017-01-01

Gold bilayered slit arrays with rectangular holes embedded into the metal surface are designed to enhance the circular dichroism (CD) effect of gold bilayered slit arrays. The rectangular holes in these arrays block electric currents and generate localized surface plasmons around these holes, thereby strengthening the CD effect. The CD enhancement factor depends strongly on the rotational angle and the structural parameters of the rectangular holes; this factor can be enhanced further by drilling two additional rectangular holes into the metal surfaces of the arrays. These results help facilitate the design of chiral structures to produce a strong CD effect and large electric fields.

X-ray luminescence imaging of water, air, and tissue phantoms

NASA Astrophysics Data System (ADS)

Lun, Michael C.; Li, Changqing

2018-02-01

X-ray luminescence computed tomography (XLCT) is an emerging hybrid molecular imaging modality. In XLCT, high energy x-ray photons excite phosphors emitting optical photons for tomographic image reconstruction. During XLCT, the optical signal obtained is thought to only originate from the embedded phosphor particles. However, numerous studies have reported other sources of optical photons such as in air, water, and tissue that are generated from ionization. These sources of optical photons will provide background noise and will limit the molecular sensitivity of XLCT imaging. In this study, using a water-cooled electron multiplying charge-coupled device (EMCCD) camera, we performed luminescence imaging of water, air, and several tissue mimicking phantoms including one embedded with a target containing 0.01 mg/mL of europium-doped gadolinium oxysulfide (GOS:Eu3+) particles during x-ray irradiation using a focused x-ray beam with energy less than the Cerenkov radiation threshold. In addition, a spectrograph was used to measure the x-ray luminescence spectrum. The phantom embedded with the GOS:Eu3+ target displayed the greatest luminescence intensity, followed by the tissue phantom, and finally the water phantom. Our results indicate that the x-ray luminescence intensity from a background phantom is equivalent to a GOS:Eu3+ concentration of 0.8 μg/mL. We also found a 3-fold difference in the radioluminescence intensity between liquid water and air. From the measurements of the emission spectra, we found that water produced a broad spectrum and that a tissue-mimicking phantom made from Intralipid had a different x-ray emission spectrum than one made with TiO2 and India ink. The measured spectra suggest that it is better to use Intralipid instead if TiO2 as optical scatterer for future XLCT imaging.

Micromechanics of brain white matter tissue: A fiber-reinforced hyperelastic model using embedded element technique.

PubMed

Yousefsani, Seyed Abdolmajid; Shamloo, Amir; Farahmand, Farzam

2018-04-01

A transverse-plane hyperelastic micromechanical model of brain white matter tissue was developed using the embedded element technique (EET). The model consisted of a histology-informed probabilistic distribution of axonal fibers embedded within an extracellular matrix, both described using the generalized Ogden hyperelastic material model. A correcting method, based on the strain energy density function, was formulated to resolve the stiffness redundancy problem of the EET in large deformation regime. The model was then used to predict the homogenized tissue behavior and the associated localized responses of the axonal fibers under quasi-static, transverse, large deformations. Results indicated that with a sufficiently large representative volume element (RVE) and fine mesh, the statistically randomized microstructure implemented in the RVE exhibits directional independency in transverse plane, and the model predictions for the overall and local tissue responses, characterized by the normalized strain energy density and Cauchy and von Mises stresses, are independent from the modeling parameters. Comparison of the responses of the probabilistic model with that of a simple uniform RVE revealed that only the first one is capable of representing the localized behavior of the tissue constituents. The validity test of the model predictions for the corona radiata against experimental data from the literature indicated a very close agreement. In comparison with the conventional direct meshing method, the model provided almost the same results after correcting the stiffness redundancy, however, with much less computational cost and facilitated geometrical modeling, meshing, and boundary conditions imposing. It was concluded that the EET can be used effectively for detailed probabilistic micromechanical modeling of the white matter in order to provide more accurate predictions for the axonal responses, which are of great importance when simulating the brain trauma or tumor growth. Copyright © 2018 Elsevier Ltd. All rights reserved.

Unsupervised nonlinear dimensionality reduction machine learning methods applied to multiparametric MRI in cerebral ischemia: preliminary results

NASA Astrophysics Data System (ADS)

Parekh, Vishwa S.; Jacobs, Jeremy R.; Jacobs, Michael A.

2014-03-01

The evaluation and treatment of acute cerebral ischemia requires a technique that can determine the total area of tissue at risk for infarction using diagnostic magnetic resonance imaging (MRI) sequences. Typical MRI data sets consist of T1- and T2-weighted imaging (T1WI, T2WI) along with advanced MRI parameters of diffusion-weighted imaging (DWI) and perfusion weighted imaging (PWI) methods. Each of these parameters has distinct radiological-pathological meaning. For example, DWI interrogates the movement of water in the tissue and PWI gives an estimate of the blood flow, both are critical measures during the evolution of stroke. In order to integrate these data and give an estimate of the tissue at risk or damaged; we have developed advanced machine learning methods based on unsupervised non-linear dimensionality reduction (NLDR) techniques. NLDR methods are a class of algorithms that uses mathematically defined manifolds for statistical sampling of multidimensional classes to generate a discrimination rule of guaranteed statistical accuracy and they can generate a two- or three-dimensional map, which represents the prominent structures of the data and provides an embedded image of meaningful low-dimensional structures hidden in their high-dimensional observations. In this manuscript, we develop NLDR methods on high dimensional MRI data sets of preclinical animals and clinical patients with stroke. On analyzing the performance of these methods, we observed that there was a high of similarity between multiparametric embedded images from NLDR methods and the ADC map and perfusion map. It was also observed that embedded scattergram of abnormal (infarcted or at risk) tissue can be visualized and provides a mechanism for automatic methods to delineate potential stroke volumes and early tissue at risk.

A Secure and Robust Compressed Domain Video Steganography for Intra- and Inter-Frames Using Embedding-Based Byte Differencing (EBBD) Scheme

PubMed Central

Idbeaa, Tarik; Abdul Samad, Salina; Husain, Hafizah

2016-01-01

This paper presents a novel secure and robust steganographic technique in the compressed video domain namely embedding-based byte differencing (EBBD). Unlike most of the current video steganographic techniques which take into account only the intra frames for data embedding, the proposed EBBD technique aims to hide information in both intra and inter frames. The information is embedded into a compressed video by simultaneously manipulating the quantized AC coefficients (AC-QTCs) of luminance components of the frames during MPEG-2 encoding process. Later, during the decoding process, the embedded information can be detected and extracted completely. Furthermore, the EBBD basically deals with two security concepts: data encryption and data concealing. Hence, during the embedding process, secret data is encrypted using the simplified data encryption standard (S-DES) algorithm to provide better security to the implemented system. The security of the method lies in selecting candidate AC-QTCs within each non-overlapping 8 × 8 sub-block using a pseudo random key. Basic performance of this steganographic technique verified through experiments on various existing MPEG-2 encoded videos over a wide range of embedded payload rates. Overall, the experimental results verify the excellent performance of the proposed EBBD with a better trade-off in terms of imperceptibility and payload, as compared with previous techniques while at the same time ensuring minimal bitrate increase and negligible degradation of PSNR values. PMID:26963093

A Secure and Robust Compressed Domain Video Steganography for Intra- and Inter-Frames Using Embedding-Based Byte Differencing (EBBD) Scheme.

PubMed

Idbeaa, Tarik; Abdul Samad, Salina; Husain, Hafizah

2016-01-01

This paper presents a novel secure and robust steganographic technique in the compressed video domain namely embedding-based byte differencing (EBBD). Unlike most of the current video steganographic techniques which take into account only the intra frames for data embedding, the proposed EBBD technique aims to hide information in both intra and inter frames. The information is embedded into a compressed video by simultaneously manipulating the quantized AC coefficients (AC-QTCs) of luminance components of the frames during MPEG-2 encoding process. Later, during the decoding process, the embedded information can be detected and extracted completely. Furthermore, the EBBD basically deals with two security concepts: data encryption and data concealing. Hence, during the embedding process, secret data is encrypted using the simplified data encryption standard (S-DES) algorithm to provide better security to the implemented system. The security of the method lies in selecting candidate AC-QTCs within each non-overlapping 8 × 8 sub-block using a pseudo random key. Basic performance of this steganographic technique verified through experiments on various existing MPEG-2 encoded videos over a wide range of embedded payload rates. Overall, the experimental results verify the excellent performance of the proposed EBBD with a better trade-off in terms of imperceptibility and payload, as compared with previous techniques while at the same time ensuring minimal bitrate increase and negligible degradation of PSNR values.

Tissue Fixation and Processing for the Histological Identification of Lipids.

PubMed

Carriel, Víctor; Campos, Fernando; Aneiros-Fernández, José; Kiernan, John A

2017-01-01

Lipids are a heterogeneous group of substances characterized by their solubility in organic solvents and insolubility in water. Lipids can be found as normal components of different tissues and organs, and they can be affected by several pathological conditions. The histochemical identification of lipids plays an important role in histopathological diagnosis and research, but successful staining depends on adequate fixation and processing of the tissue. Here we describe methods to fix and process tissue samples for the histochemical identification of lipids in frozen or paraffin-embedded tissues.

A Fully Integrated Sensor SoC with Digital Calibration Hardware and Wireless Transceiver at 2.4 GHz

PubMed Central

Kim, Dong-Sun; Jang, Sung-Joon; Hwang, Tae-Ho

2013-01-01

A single-chip sensor system-on-a-chip (SoC) that implements radio for 2.4 GHz, complete digital baseband physical layer (PHY), 10-bit sigma-delta analog-to-digital converter and dedicated sensor calibration hardware for industrial sensing systems has been proposed and integrated in a 0.18-μm CMOS technology. The transceiver's building block includes a low-noise amplifier, mixer, channel filter, receiver signal-strength indicator, frequency synthesizer, voltage-controlled oscillator, and power amplifier. In addition, the digital building block consists of offset quadrature phase-shift keying (OQPSK) modulation, demodulation, carrier frequency offset compensation, auto-gain control, digital MAC function, sensor calibration hardware and embedded 8-bit microcontroller. The digital MAC function supports cyclic redundancy check (CRC), inter-symbol timing check, MAC frame control, and automatic retransmission. The embedded sensor signal processing block consists of calibration coefficient calculator, sensing data calibration mapper and sigma-delta analog-to-digital converter with digital decimation filter. The sensitivity of the overall receiver and the error vector magnitude (EVM) of the overall transmitter are −99 dBm and 18.14%, respectively. The proposed calibration scheme has a reduction of errors by about 45.4% compared with the improved progressive polynomial calibration (PPC) method and the maximum current consumption of the SoC is 16 mA. PMID:23698271

Honeycomb-like thin films of polystyrene-block-poly(2-vinylpyridine) embedded with gold or silver nanoparticles formed at the planer liquid/liquid interface.

PubMed

Wang, Di; Ma, Huihui; Chu, Chunxiao; Hao, Jingcheng; Liu, Hong-Guo

2013-07-15

Composite thin films of polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP) decorated with Au or Ag nanoclusters and nanoparticles were fabricated at the interfaces of chloroform solution of PS-b-P2VP and aqueous solutions of HAuCl4 or AgNO3. Transmission electron microscopy (TEM) investigations indicated that large area of a single-layer honeycomb structure was formed, which is composed of polygons (most of them are hexagons) whose walls look like spindles with the length of several hundreds of nanometers. Large amount of Au or Ag nanoparticles are embedded in the walls and the undersides of the honeycomb structures. The formation of these novel composite structures was attributed to the adsorption of block copolymer molecules and inorganic species of AuCl4(-) and Ag(+) ions at the liquid-liquid interface, the combination of the polymer molecules and the inorganic ions, and the self-assembly of the composite molecules. After UV-light irradiation and KBH4 aqueous solution treatment, the inorganic species were reduced completely, as confirmed by UV-vis spectra and X-ray photoelectron spectra. These composite films exhibited high catalytic activities for the reduction of 4-nitrophenol (4-NP) by KBH4 in aqueous solutions. Copyright © 2013 Elsevier Inc. All rights reserved.

Optical architecture design for detection of absorbers embedded in visceral fat.

PubMed

Francis, Robert; Florence, James; MacFarlane, Duncan

2014-05-01

Optically absorbing ducts embedded in scattering adipose tissue can be injured during laparoscopic surgery. Non-sequential simulations and theoretical analysis compare optical system configurations for detecting these absorbers. For absorbers in deep scattering volumes, trans-illumination is preferred instead of diffuse reflectance. For improved contrast, a scanning source with a large area detector is preferred instead of a large area source with a pixelated detector.

Optical architecture design for detection of absorbers embedded in visceral fat

PubMed Central

Francis, Robert; Florence, James; MacFarlane, Duncan

2014-01-01

Optically absorbing ducts embedded in scattering adipose tissue can be injured during laparoscopic surgery. Non-sequential simulations and theoretical analysis compare optical system configurations for detecting these absorbers. For absorbers in deep scattering volumes, trans-illumination is preferred instead of diffuse reflectance. For improved contrast, a scanning source with a large area detector is preferred instead of a large area source with a pixelated detector. PMID:24877008

Gestalt Perception and Local-Global Processing in High-Functioning Autism

ERIC Educational Resources Information Center

Bolte, Sven; Holtmann, Martin; Poustka, Fritz; Scheurich, Armin; Schmidt, Lutz

2007-01-01

This study examined gestalt perception in high-functioning autism (HFA) and its relation to tasks indicative of local visual processing. Data on of gestalt perception, visual illusions (VI), hierarchical letters (HL), Block Design (BD) and the Embedded Figures Test (EFT) were collected in adult males with HFA, schizophrenia, depression and…

Watermarking scheme for authentication of compressed image

NASA Astrophysics Data System (ADS)

Hsieh, Tsung-Han; Li, Chang-Tsun; Wang, Shuo

2003-11-01

As images are commonly transmitted or stored in compressed form such as JPEG, to extend the applicability of our previous work, a new scheme for embedding watermark in compressed domain without resorting to cryptography is proposed. In this work, a target image is first DCT transformed and quantised. Then, all the coefficients are implicitly watermarked in order to minimize the risk of being attacked on the unwatermarked coefficients. The watermarking is done through registering/blending the zero-valued coefficients with a binary sequence to create the watermark and involving the unembedded coefficients during the process of embedding the selected coefficients. The second-order neighbors and the block itself are considered in the process of the watermark embedding in order to thwart different attacks such as cover-up, vector quantisation, and transplantation. The experiments demonstrate the capability of the proposed scheme in thwarting local tampering, geometric transformation such as cropping, and common signal operations such as lowpass filtering.

Real-time depth processing for embedded platforms

NASA Astrophysics Data System (ADS)

Rahnama, Oscar; Makarov, Aleksej; Torr, Philip

2017-05-01

Obtaining depth information of a scene is an important requirement in many computer-vision and robotics applications. For embedded platforms, passive stereo systems have many advantages over their active counterparts (i.e. LiDAR, Infrared). They are power efficient, cheap, robust to lighting conditions and inherently synchronized to the RGB images of the scene. However, stereo depth estimation is a computationally expensive task that operates over large amounts of data. For embedded applications which are often constrained by power consumption, obtaining accurate results in real-time is a challenge. We demonstrate a computationally and memory efficient implementation of a stereo block-matching algorithm in FPGA. The computational core achieves a throughput of 577 fps at standard VGA resolution whilst consuming less than 3 Watts of power. The data is processed using an in-stream approach that minimizes memory-access bottlenecks and best matches the raster scan readout of modern digital image sensors.

Correlated light and electron microscopy observations of the uterine epithelial cell actin cytoskeleton using fluorescently labeled resin-embedded sections.

PubMed

Moore, Chad L; Cheng, Delfine; Shami, Gerald J; Murphy, Christopher R

2016-05-01

In order to perform correlative light and electron microscopy (CLEM) more precisely, we have modified existing specimen preparation protocols allowing fluorescence retention within embedded and sectioned tissue, facilitating direct observation across length scales. We detail a protocol which provides a precise correlation accuracy using accessible techniques in biological specimen preparation. By combining a pre-embedding uranyl acetate staining step with the progressive lowering of temperature (PLT) technique, a methacrylate embedded tissue specimen is ultrathin sectioned and mounted onto a TEM finder grid for immediate viewing in the confocal and electron microscope. In this study, the protocol is applied to rat uterine epithelial cells in vivo during early pregnancy. Correlative overlay data was used to track changes in filamentous actin that occurs in these cells from fertilization (Day 1) to implantation on Day 6 as part of the plasma membrane transformation, a process essential in the development of uterine receptivity in the rat. CLEM confirmed that the actin cytoskeleton is disrupted as apical microvilli are progressively lost toward implantation, and revealed the thick and continuous terminal web is replaced by a thinner and irregular actin band, with individually distinguishable filaments connecting actin meshworks which correspond with remaining plasma membrane protrusions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Fault diagnosis and fault-tolerant finite control set-model predictive control of a multiphase voltage-source inverter supplying BLDC motor.

PubMed

Salehifar, Mehdi; Moreno-Equilaz, Manuel

2016-01-01

Due to its fault tolerance, a multiphase brushless direct current (BLDC) motor can meet high reliability demand for application in electric vehicles. The voltage-source inverter (VSI) supplying the motor is subjected to open circuit faults. Therefore, it is necessary to design a fault-tolerant (FT) control algorithm with an embedded fault diagnosis (FD) block. In this paper, finite control set-model predictive control (FCS-MPC) is developed to implement the fault-tolerant control algorithm of a five-phase BLDC motor. The developed control method is fast, simple, and flexible. A FD method based on available information from the control block is proposed; this method is simple, robust to common transients in motor and able to localize multiple open circuit faults. The proposed FD and FT control algorithm are embedded in a five-phase BLDC motor drive. In order to validate the theory presented, simulation and experimental results are conducted on a five-phase two-level VSI supplying a five-phase BLDC motor. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

SU-E-T-424: Feasibility of 3D Printed Radiological Equivalent Customizable Tissue Like Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, D; Ferreira, C; Ahmad, S

Purpose: To investigate the feasibility of 3D printing CT# specific radiological equivalent tissue like materials. Methods: A desktop 3D printer was utilized to create a series of 3 cm x 3 cm x 2 cm PLA plastic blocks of varying fill densities. The fill pattern was selected to be hexagonal (Figure 1). A series of blocks was filled with paraffin and compared to a series filled with air. The blocks were evaluated with a “GE Lightspeed” 16 slice CT scanner and average CT# of the centers of the materials was determined. The attenuation properties of the subsequent blocks were alsomore » evaluated through their isocentric irradiation via “TrueBeam” accelerator under six beam energies. Blocks were placed upon plastic-water slabs of 4 cm in thickness assuring electronic equilibrium and data was collected via Sun Nuclear “Edge” diode detector. Relative changes in dose were compared with those predicted by Varian “Eclipse” TPS. Results: The CT# of 3D printed blocks was found to be a controllable variable. The fill material was able to narrow the range of variability in each sample. The attenuation of the block tracked with the density of the total fill structure. Assigned CT values in the TPS were seen to fall within an expected range predicted by the CT scans of the 3D printed blocks. Conclusion: We have demonstrated that it is possible to 3D print materials of varying tissue equivalencies, and that these materials have radiological properties that are customizable and predictable.« less

Analysis of complications following augmentation with cancellous block allografts.

PubMed

Chaushu, Gavriel; Mardinger, Ofer; Peleg, Michael; Ghelfan, Oded; Nissan, Joseph

2010-12-01

Bone grafting may be associated with soft and hard tissue complications. Recipient site complications encountered using cancellous block allografts for ridge augmentation are analyzed. A total of 101 consecutive patients (62 females and 39 males; mean age 44 ± 17 years) were treated with implant-supported restoration of 137 severe atrophic alveolar ridges augmented with cancellous bone-block allografts. Alveolar ridge deficiency locations were classified as anterior maxilla (n = 58); posterior maxilla (n = 32 sinuses); posterior mandible (n = 32); and anterior mandible (n = 15). A total of 271 rough-surface implants were placed. Recipient site complications associated with block grafting (infection, membrane exposure, incision line opening, perforation of mucosa over the grafted bone, partial graft failure, total graft failure, and implant failure) were recorded. Partial and total bone-block graft failure occurred in 10 (7%) and 11 (8%) of 137 augmented sites, respectively. Implant failure rate was 12 (4.4%) of 271. Soft tissue complications included membrane exposure (42 [30.7%] of 137); incision line opening (41 [30%] of 137); and perforation of the mucosa over the grafted bone (19 [14%] of 137). Infection of the grafted site occurred in 18 (13%) of 137 bone blocks. Alveolar ridge deficiency location had a statistically significant effect on the outcome of recipient site complications. More complications were noted in the mandible compared to the maxilla. Age and gender had no statistically significant effect. Failures caused by complications were rarely noted in association with cancellous block grafting. The incidence of complications in the mandible was significantly higher. Soft tissue complications do not necessarily result in total loss of cancellous block allograft.

Formation of 2D nanoparticles with block structure in simultaneous electric explosion of conductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kryzhevich, Dmitrij S., E-mail: kryzhev@ispms.ru, E-mail: kost@ispms.ru; Zolnikov, Konstantin P., E-mail: kryzhev@ispms.ru, E-mail: kost@ispms.ru; Abdrashitov, Andrei V.

2014-11-14

A molecular dynamics simulation of nanoparticle formation in simultaneous electric explosion of conductors is performed. Interatomic interaction is described using potentials calculated in the framework of the embedded atom method. High-rate heating results in failure of the conductors with the formation of nanoparticles. The influence of the heating rate, temperature distribution over the specimen cross-section and the distance between simultaneously exploded conductors on the structure of formed nanoparticles is studied. The calculation results show that the electric explosion of conductors allows the formation of nanoparticles with block structure.

Small Private Key PKS on an Embedded Microprocessor

PubMed Central

Seo, Hwajeong; Kim, Jihyun; Choi, Jongseok; Park, Taehwan; Liu, Zhe; Kim, Howon

2014-01-01

Multivariate quadratic ( ) cryptography requires the use of long public and private keys to ensure a sufficient security level, but this is not favorable to embedded systems, which have limited system resources. Recently, various approaches to cryptography using reduced public keys have been studied. As a result of this, at CHES2011 (Cryptographic Hardware and Embedded Systems, 2011), a small public key scheme, was proposed, and its feasible implementation on an embedded microprocessor was reported at CHES2012. However, the implementation of a small private key scheme was not reported. For efficient implementation, random number generators can contribute to reduce the key size, but the cost of using a random number generator is much more complex than computing on modern microprocessors. Therefore, no feasible results have been reported on embedded microprocessors. In this paper, we propose a feasible implementation on embedded microprocessors for a small private key scheme using a pseudo-random number generator and hash function based on a block-cipher exploiting a hardware Advanced Encryption Standard (AES) accelerator. To speed up the performance, we apply various implementation methods, including parallel computation, on-the-fly computation, optimized logarithm representation, vinegar monomials and assembly programming. The proposed method reduces the private key size by about 99.9% and boosts signature generation and verification by 5.78% and 12.19% than previous results in CHES2012. PMID:24651722

Small private key MQPKS on an embedded microprocessor.

PubMed

Seo, Hwajeong; Kim, Jihyun; Choi, Jongseok; Park, Taehwan; Liu, Zhe; Kim, Howon

2014-03-19

Multivariate quadratic (MQ) cryptography requires the use of long public and private keys to ensure a sufficient security level, but this is not favorable to embedded systems, which have limited system resources. Recently, various approaches to MQ cryptography using reduced public keys have been studied. As a result of this, at CHES2011 (Cryptographic Hardware and Embedded Systems, 2011), a small public key MQ scheme, was proposed, and its feasible implementation on an embedded microprocessor was reported at CHES2012. However, the implementation of a small private key MQ scheme was not reported. For efficient implementation, random number generators can contribute to reduce the key size, but the cost of using a random number generator is much more complex than computing MQ on modern microprocessors. Therefore, no feasible results have been reported on embedded microprocessors. In this paper, we propose a feasible implementation on embedded microprocessors for a small private key MQ scheme using a pseudo-random number generator and hash function based on a block-cipher exploiting a hardware Advanced Encryption Standard (AES) accelerator. To speed up the performance, we apply various implementation methods, including parallel computation, on-the-fly computation, optimized logarithm representation, vinegar monomials and assembly programming. The proposed method reduces the private key size by about 99.9% and boosts signature generation and verification by 5.78% and 12.19% than previous results in CHES2012.

Structure-Preserving Smoothing of Biomedical Images

NASA Astrophysics Data System (ADS)

Gil, Debora; Hernàndez-Sabaté, Aura; Burnat, Mireia; Jansen, Steven; Martínez-Villalta, Jordi

Smoothing of biomedical images should preserve gray-level transitions between adjacent tissues, while restoring contours consistent with anatomical structures. Anisotropic diffusion operators are based on image appearance discontinuities (either local or contextual) and might fail at weak inter-tissue transitions. Meanwhile, the output of block-wise and morphological operations is prone to present a block structure due to the shape and size of the considered pixel neighborhood.

Defect reduction of SiNx embedded m-plane GaN grown by hydride vapor phase epitaxy

NASA Astrophysics Data System (ADS)

Woo, Seohwi; Kim, Minho; So, Byeongchan; Yoo, Geunho; Jang, Jongjin; Lee, Kyuseung; Nam, Okhyun

2014-12-01

Nonpolar (1 0 -1 0) m-plane GaN has been grown on m-plane sapphire substrates by hydride vapor phase epitaxy (HVPE). We studied the defect reduction of m-GaN with embedded SiNx interlayers deposited by ex-situ metal organic chemical vapor deposition (MOCVD). The full-width at half-maximum values of the X-ray rocking curves for m-GaN with embedded SiNx along [1 1 -2 0]GaN and [0 0 0 1]GaN were reduced to 528 and 1427 arcs, respectively, as compared with the respective values of 947 and 3170 arcs, of m-GaN without SiNx. Cross-section transmission electron microscopy revealed that the basal stacking fault density was decreased by approximately one order to 5×104 cm-1 due to the defect blocking of the embedded SiNx. As a result, the near band edge emission intensities of the room-temperature and low-temperature photoluminescence showed approximately two-fold and four-fold improvement, respectively.

Comparison of Different Buffers for Protein Extraction from Formalin-Fixed and Paraffin-Embedded Tissue Specimens.

PubMed

Shen, Kaini; Sun, Jian; Cao, Xinxin; Zhou, Daobin; Li, Jian

2015-01-01

We determined the best extraction buffer for proteomic investigation using formalin-fixation and paraffin-embedded (FFPE) specimens. A Zwittergent 3-16 based buffer, sodium dodecyl sulfate (SDS)-containing buffer with/without polyethylene glycol 20000 (PEG20000), urea-containing buffer, and FFPE-FASP protein preparation kit were compared for protein extraction from different types of rat FFPE tissues, including the heart, brain, liver, lung, and kidney. All of the samples were divided into two groups of laser microdissected (LMD) and non-LMD specimens. For both kinds of specimens, Zwittergent was the most efficient buffer for identifying peptides and proteins, was broadly applicable to different tissues without impairing the enzymatic digestion, and was well compatible with mass spectrometry analysis. As a high molecular weight carrier substance, PEG20000 improved the identification of peptides and proteins; however, such an advantage is limited to tissues containing submicrograms to micrograms of protein. Considering its low lytic strength, urea-containing buffer would not be the first alternative for protein recovery. In conclusion, Zwittergent 3-16 is an effective buffer for extracting proteins from FFPE specimens for downstream proteomics analysis.

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

PubMed

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.

Optimized protocol for quantitative multiple reaction monitoring-based proteomic analysis of formalin-fixed, paraffin embedded tissues

PubMed Central

Kennedy, Jacob J.; Whiteaker, Jeffrey R.; Schoenherr, Regine M.; Yan, Ping; Allison, Kimberly; Shipley, Melissa; Lerch, Melissa; Hoofnagle, Andrew N.; Baird, Geoffrey Stuart; Paulovich, Amanda G.

2016-01-01

Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin embedded (FFPE) tissues. While the feasibility of using targeted, multiple reaction monitoring-mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e. 9 processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R2 = 0.94) and immuno-MRM (R2 = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens. PMID:27462933

Systematic evaluation of RNA quality, microarray data reliability and pathway analysis in fresh, fresh frozen and formalin-fixed paraffin-embedded tissue samples.

PubMed

Wimmer, Isabella; Tröscher, Anna R; Brunner, Florian; Rubino, Stephen J; Bien, Christian G; Weiner, Howard L; Lassmann, Hans; Bauer, Jan

2018-04-20

Formalin-fixed paraffin-embedded (FFPE) tissues are valuable resources commonly used in pathology. However, formalin fixation modifies nucleic acids challenging the isolation of high-quality RNA for genetic profiling. Here, we assessed feasibility and reliability of microarray studies analysing transcriptome data from fresh, fresh-frozen (FF) and FFPE tissues. We show that reproducible microarray data can be generated from only 2 ng FFPE-derived RNA. For RNA quality assessment, fragment size distribution (DV200) and qPCR proved most suitable. During RNA isolation, extending tissue lysis time to 10 hours reduced high-molecular-weight species, while additional incubation at 70 °C markedly increased RNA yields. Since FF- and FFPE-derived microarrays constitute different data entities, we used indirect measures to investigate gene signal variation and relative gene expression. Whole-genome analyses revealed high concordance rates, while reviewing on single-genes basis showed higher data variation in FFPE than FF arrays. Using an experimental model, gene set enrichment analysis (GSEA) of FFPE-derived microarrays and fresh tissue-derived RNA-Seq datasets yielded similarly affected pathways confirming the applicability of FFPE tissue in global gene expression analysis. Our study provides a workflow comprising RNA isolation, quality assessment and microarray profiling using minimal RNA input, thus enabling hypothesis-generating pathway analyses from limited amounts of precious, pathologically significant FFPE tissues.

DNA extraction from formalin-fixed, paraffin-embedded tissues: protein digestion as a limiting step for retrieval of high-quality DNA.

PubMed

Díaz-Cano, S J; Brady, S P

1997-12-01

Several DNA extraction methods have been used for formalin-fixed, paraffin-embedded tissues, with variable results being reported regarding the suitability of DNA obtained from such sources to serve as template in polymerase chain reaction (PCR)-based genetic analyses. We present a method routinely used for archival material in our laboratory that reliably yields DNA of sufficient quality for PCR studies. This method is based on extended proteinase K digestion (250 micrograms/ml in an EDTA-free calcium-containing buffer supplemented with mussel glycogen) followed by phenol-chloroform extraction. Agarose gel electrophoresis of both digestion buffer aliquots and PCR amplification of the beta-globin gene tested the suitability of the retrieved DNA for PCR amplification.

Ber-H2 (CD30) immunohistochemical staining in malignant melanoma.

PubMed

Polski, J M; Janney, C G

1999-09-01

Malignant melanoma can be included in the differential diagnosis of Hodgkin's disease, anaplastic large cell lymphoma, or embryonal carcinoma These malignancies express CD30, a marker of diagnostic value. A retrospective immunohistochemical study was undertaken to determine the frequency of immunoreactivity of Ber-H2 (anti-CD30 monoclonal antibody) in malignant melanoma Archival paraffin-embedded tissue from 24 primary and metastatic lesions was used. No Ber-H2 labeling was observed in the majority of the studied cases. Variable weak cytoplasmic staining was present in only one case. The findings are compared with the previous reports claiming frequent CD30 expression in malignant melanoma. We discuss issues pertaining to the interpretation of the Ber-H2 IHC staining in formalin-fixed, paraffin-embedded tissue.

Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue

PubMed Central

2014-01-01

Background Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on “rescue karyotyping”, wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). Methods A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). Results Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p = 0.14) or gestational age at pregnancy loss (p = 0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. Conclusions Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss. PMID:24589081

A novel immuno-gold labeling protocol for nanobody-based detection of HER2 in breast cancer cells using immuno-electron microscopy.

PubMed

Kijanka, M; van Donselaar, E G; Müller, W H; Dorresteijn, B; Popov-Čeleketić, D; El Khattabi, M; Verrips, C T; van Bergen En Henegouwen, P M P; Post, J A

2017-07-01

Immuno-electron microscopy is commonly performed with the use of antibodies. In the last decade the antibody fragment indicated as nanobody (VHH or single domain antibody) has found its way to different applications previously done with conventional antibodies. Nanobodies can be selected to bind with high affinity and specificity to different antigens. They are small (molecular weight ca. 15kDa) and are usually easy to produce in microorganisms. Here we have evaluated the feasibility of a nanobody binding to HER2 for application in immuno-electron microscopy. To obtain highest labeling efficiency combined with optimal specificity, different labeling conditions were analysed, which included nanobody concentration, fixation and blocking conditions. The obtained optimal protocol was applied for post-embedment labeling of Tokuyasu cryosections and for pre-embedment labeling of HER2 for fluorescence microscopy and both transmission and scanning electron microscopy. We show that formaldehyde fixation after incubation with the anti-HER2 nanobody, improves labeling intensity. Among all tested blocking agents the best results were obtained with a mixture of cold water fish gelatine and acetylated bovine serum albumin, which prevented a-specific interactions causing background labeling while preserving specific interactions at the same time. In conclusion, we have developed a nanobody-based protocol for immuno-gold labeling of HER2 for Tokuyasu cryosections in TEM as well as for pre-embedment gold labeling of cells for both TEM and SEM. Copyright © 2017. Published by Elsevier Inc.

TaqMan real-time RT-PCR detection of infectious salmon anaemia virus (ISAV) from formalin-fixed paraffin-embedded Atlantic salmon Salmo salar tissues.

PubMed

Godoy, M G; Kibenge, F S; Kibenge, M J; Olmos, P; Ovalle, L; Yañez, A J; Avendaño-Herrera, R

2010-05-18

The objective of this study was to evaluate the application of a TaqMan real-time reverse transcriptase PCR (RT-PCR) assay for the detection of infectious salmon anaemia virus (ISAV) in formalin-fixed paraffin-embedded (FFPE) fish tissues from Atlantic salmon Salmo salar with and without clinical signs of infection, and to compare it with histological and immunohistochemical (IHC) techniques. Sixteen fish samples obtained in 2007 and 2008 from 4 different farms in Chile were examined. The real-time RT-PCR allowed the detection of ISAV in FFPE samples from 9 of 16 fish, regardless of the organs analyzed, whereas 4 of the real-time RT-PCR negative fish were positive as indicated by histological examination and 3 of the real-time RT-PCR positive fish were negative as indicated by immunohistochemistry evaluation. The presence of ISAV in RT-PCR positive samples was confirmed by amplicon sequencing. This work constitutes the first report on the use of real-time RT-PCR for the detection of ISAV in FFPE sections. The assay is very useful for the examination of archival wax-embedded tissues, and allows for both prospective and retrospective evaluation of tissue samples for the presence of ISAV. However, the method only confirms the presence of the pathogen and should be used in combination with histopathology, which is a more precise tool. The combination of both techniques would be invaluable for confirmatory diagnosis of infectious salmon anaemia (ISA), which is essential for solving salmon farm problems.

Unilateral cervical plexus block for prosthetic laryngoplasty in the standing horse.

PubMed

Campoy, L; Morris, T B; Ducharme, N G; Gleed, R D; Martin-Flores, M

2018-04-20

Locoregional anaesthetic techniques can facilitate certain surgeries being performed under standing procedural sedation. The second and third spinal cervical nerves (C2, C3) are part of the cervical plexus and provide sensory innervation to the peri-laryngeal structures in people; block of these nerves might permit laryngeal lateralisation surgery in horses. To describe the anatomical basis for an ultrasound-guided cervical plexus block in horses. To compare this block with conventional local anaesthetic tissue infiltration in horses undergoing standing prosthetic laryngoplasty. Cadaveric study followed by a double-blinded prospective clinical trial. A fresh equine cadaver was dissected to characterise the distribution of C2 and C3 to the perilaryngeal structures on the left side. A second cadaver was utilised to correlate ultrasound images with the previously identified structures; a tissue marker was injected to confirm the feasibility of an ultrasound-guided approach to the cervical plexus. In the clinical study, horses were assigned to two groups, CP (n = 17; cervical plexus block) and INF (n = 17; conventional tissue infiltration). Data collection and analyses included time to completion of surgical procedure, sedation time, surgical field conditions and surgeon's perception of block quality. We confirmed that C2 and C3 provided innervation to the perilaryngeal structures. The nerve root of C2 was identified ultrasonographically located between the longus capitis and the cleidomastoideus muscles, caudal to the parotid gland. The CP group was deemed to provide better (P<0.0002) surgical conditions with no differences in the other variables measured. Further studies with larger numbers of horses may be necessary to detect smaller differences in surgical procedure completion time based on the improved surgical filed conditions. For standing unilateral laryngeal surgery, a cervical plexus block is a viable alternative to tissue infiltration and it improves the surgical field conditions. © 2018 EVJ Ltd.

Exchange bias of Ni nanoparticles embedded in an antiferromagnetic IrMn matrix.

PubMed

Kuerbanjiang, Balati; Wiedwald, Ulf; Haering, Felix; Biskupek, Johannes; Kaiser, Ute; Ziemann, Paul; Herr, Ulrich

2013-11-15

The magnetic properties of Ni nanoparticles (Ni-NPs) embedded in an antiferromagnetic IrMn matrix were investigated. The Ni-NPs of 8.4 nm mean diameter were synthesized by inert gas aggregation. In a second processing step, the Ni-NPs were in situ embedded in IrMn films or SiOx films under ultrahigh vacuum (UHV) conditions. Findings showed that Ni-NPs embedded in IrMn have an exchange bias field HEB = 821 Oe at 10 K, and 50 Oe at 300 K. The extracted value of the exchange energy density is 0.06 mJ m(-2) at 10 K, which is in good accordance with the results from multilayered thin film systems. The Ni-NPs embedded in SiOx did not show exchange bias. As expected for this particle size, they are superparamagnetic at T = 300 K. A direct comparison of the Ni-NPs embedded in IrMn or SiOx reveals an increase of the blocking temperature from 210 K to around 400 K. The coercivity of the Ni-NPs exchange coupled to the IrMn matrix at 10 K is 8 times larger than the value for Ni-NPs embedded in SiOx. We studied time-dependent remanent magnetization at different temperatures. The relaxation behavior is described by a magnetic viscosity model which reflects a rather flat distribution of energy barriers. Furthermore, we investigated the effects of different field cooling processes on the magnetic properties of the embedded Ni-NPs. Exchange bias values fit to model calculations which correlate the contribution of the antiferromagnetic IrMn matrix to its grain size.

Simplified versus geometrically accurate models of forefoot anatomy to predict plantar pressures: A finite element study.

PubMed

Telfer, Scott; Erdemir, Ahmet; Woodburn, James; Cavanagh, Peter R

2016-01-25

Integration of patient-specific biomechanical measurements into the design of therapeutic footwear has been shown to improve clinical outcomes in patients with diabetic foot disease. The addition of numerical simulations intended to optimise intervention design may help to build on these advances, however at present the time and labour required to generate and run personalised models of foot anatomy restrict their routine clinical utility. In this study we developed second-generation personalised simple finite element (FE) models of the forefoot with varying geometric fidelities. Plantar pressure predictions from barefoot, shod, and shod with insole simulations using simplified models were compared to those obtained from CT-based FE models incorporating more detailed representations of bone and tissue geometry. A simplified model including representations of metatarsals based on simple geometric shapes, embedded within a contoured soft tissue block with outer geometry acquired from a 3D surface scan was found to provide pressure predictions closest to the more complex model, with mean differences of 13.3kPa (SD 13.4), 12.52kPa (SD 11.9) and 9.6kPa (SD 9.3) for barefoot, shod, and insole conditions respectively. The simplified model design could be produced in <1h compared to >3h in the case of the more detailed model, and solved on average 24% faster. FE models of the forefoot based on simplified geometric representations of the metatarsal bones and soft tissue surface geometry from 3D surface scans may potentially provide a simulation approach with improved clinical utility, however further validity testing around a range of therapeutic footwear types is required. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rapid detection of metastatic melanoma in lymph nodes using proton magnetic resonance spectroscopy of fine needle aspiration biopsy specimens.

PubMed

Lean, Cynthia L; Bourne, Roger; Thompson, John F; Scolyer, Richard A; Stretch, Jonathan; Li, Ling-Xi Lawrence; Russell, Peter; Mountford, Carolyn

2003-06-01

Accurate staging of patients with primary cutaneous melanoma includes assessment of regional lymph nodes for the presence of micrometastatic disease. Sentinel lymph node biopsy is highly accurate but is an invasive surgical procedure with a 5-10% complication rate, and requires labour-intensive and expensive histological examination to identify disease. A rapid, accurate and cost-effective non-surgical technique able to detect micrometastatic deposits of melanoma in regional lymph nodes would be of great benefit. Fine needle aspiration biopsies and tissue specimens were obtained from lymph nodes from 18 patients undergoing node resection for metastatic melanoma and five patients undergoing radical retropubic prostatectomy. One-dimensional proton magnetic resonance spectroscopy was undertaken at 360 MHz (8.5 T). Lymph nodes were cut into 3 mm thick slices and embedded. Four sequential 5 microm tissue sections were cut from each block and stained, with haematoxylin and eosin, for S100 protein, for HMB45, and again with haematoxylin and eosin, respectively. Proton magnetic resonance spectroscopy distinguished between benign and malignant lymph node tissue (P < 0.001, separate t-test) and benign and malignant lymph node fine needle aspiration biopsy (P < 0.012) based on the ratio of the integrals of resonances from lipid/other metabolites (1.8-2.5 p.p.m. region) and 'choline' (3.1-3.3 p.p.m. region). In conclusion, one-dimensional proton magnetic resonance spectroscopy on a simple fine needle aspiration biopsy can distinguish lymph nodes containing metastatic melanoma from uninvolved nodes, providing a rapid, accurate and cost-effective non-surgical technique to assess regional lymph nodes in patients with melanoma.

Comparison of porcine thorax to gelatine blocks for wound ballistics studies.

PubMed

Mabbott, A; Carr, D J; Champion, S; Malbon, C

2016-09-01

Tissue simulants are typically used in ballistic testing as substitutes for biological tissues. Many simulants have been used, with gelatine amongst the most common. While two concentrations of gelatine (10 and 20 %) have been used extensively, no agreed standard exists for the preparation of either. Comparison of ballistic damage produced in both concentrations is lacking. The damage produced in gelatine is also questioned, with regards to what it would mean for specific areas of living tissue. The aim of the work discussed in this paper was to consider how damage caused by selected pistol and rifle ammunition varied in different simulants. Damage to gelatine blocks 10 and 20 % in concentration were tested with 9 mm Luger (9 × 19 full metal jacket; FMJ) rounds, while damage produced by .223 Remington (5.56 × 45 Federal Premium® Tactical® Bonded®) rounds to porcine thorax sections (skin, underlying tissue, ribs, lungs, ribs, underlying tissue, skin; backed by a block of 10 % gelatine) were compared to 10 and 20 % gelatine blocks. Results from the .223 Remington rifle round, which is one that typically expands on impact, revealed depths of penetration in the thorax arrangement were significantly different to 20 % gelatine, but not 10 % gelatine. The level of damage produced in the simulated thoraxes was smaller in scale to that witnessed in both gelatine concentrations, though greater debris was produced in the thoraxes.

Fluorescence in situ hybridization for phytoplasma and endophytic bacteria localization in plant tissues.

PubMed

Bulgari, Daniela; Casati, Paola; Faoro, Franco

2011-11-01

In the present study, we developed a rapid and efficient fluorescence in situ hybridization assay (FISH) in non-embedded tissues of the model plant Catharanthus roseus for co-localizing phytoplasmas and endophytic bacteria, opening new perspectives for studying the interaction between these microorganisms. Copyright © 2011 Elsevier B.V. All rights reserved.

Fossil Ridge School Intermediate: Restructure the Culture--Transform the School

ERIC Educational Resources Information Center

Principal Leadership, 2013

2013-01-01

Ask a room full of sixth and seventh graders at Fossil Ridge Intermediate School in St. George, UT, to name their favorite part of the day and the answer is, in unison, always the same: REAL (respect, explore, achieve, lead) Time. This 35-minute block embedded into the school's schedule three days each week provides immediate, specific…

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

PubMed Central

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

Precision of Multiple Reaction Monitoring Mass Spectrometry Analysis of Formalin-Fixed, Paraffin-Embedded Tissue

PubMed Central

2012-01-01

We compared the reproducibility of multiple reaction monitoring (MRM) mass spectrometry-based peptide quantitation in tryptic digests from formalin-fixed, paraffin-embedded (FFPE) and frozen clear cell renal cell carcinoma tissues. The analyses targeted a candidate set of 114 peptides previously identified in shotgun proteomic analyses, of which 104 were detectable in FFPE and frozen tissue. Although signal intensities for MRM of peptides from FFPE tissue were on average 66% of those in frozen tissue, median coefficients of variation (CV) for measurements in FFPE and frozen tissues were nearly identical (18–20%). Measurements of lysine C-terminal peptides and arginine C-terminal peptides from FFPE tissue were similarly reproducible (19.5% and 18.3% median CV, respectively). We further evaluated the precision of MRM-based quantitation by analysis of peptides from the Her2 receptor in FFPE and frozen tissues from a Her2 overexpressing mouse xenograft model of breast cancer and in human FFPE breast cancer specimens. We obtained equivalent MRM measurements of HER2 receptor levels in FFPE and frozen mouse xenografts derived from HER2-overexpressing BT474 cells and HER2-negative Sum159 cells. MRM analyses of 5 HER2-positive and 5 HER-negative human FFPE breast tumors confirmed the results of immunohistochemical analyses, thus demonstrating the feasibility of HER2 protein quantification in FFPE tissue specimens. The data demonstrate that MRM analyses can be performed with equal precision on FFPE and frozen tissues and that lysine-containing peptides can be selected for quantitative comparisons, despite the greater impact of formalin fixation on lysine residues. The data further illustrate the feasibility of applying MRM to quantify clinically important tissue biomarkers in FFPE specimens. PMID:22530795

Expression of matrix metalloproteinases 9 and 12 in actinic cheilitis

PubMed Central

Poulopoulos, Athanasios K; Andreadis, Dimitrios; Markopoulos, Anastasios K

2013-01-01

AIM: To investigate the role of matrix-degrading metalloproteinases 9, 12 (MMPs), as mediators of functional connective tissue damage in actinic cheilitis. METHODS: Thirty five formalin-fixed, paraffin embedded specimens of actinic cheilitis, and twelve specimens of normal lower lip vermillion, which were obtained by the archives of the Department of Oral Medicine and Maxillofacial Pathology, were examined. From each block, 5 μm thick sections were cut and routinely stained with Hematoxylin and Eosin. Immunohistochemical studies were performed on 4-μm thick sections of formalin-fixed paraffin embedded actinic cheilitis lesions and of normal lower lip vermillion, for MMP-9 and MMP-12 in serial sections of our specimens. Appropriate positive and negative controls were performed to confirm the specificity of the staining reaction. MMP immunohistochemistry was evaluated using a semiquantitative immunoreactive score. RESULTS: Haematoxylin and eosin staining revealed in actinic cheilitis lesions atrophic stratified squamous cell epithelium, or focally and irregularly hyperplastic of variable thickness, in some areas was observed marked keratin production. Varying degrees of epithelial dysplasia were noticed with a wide spectrum of change within the same specimen. Characteristic was the appearance of chronic inflammatory infiltration, and a band of amorphous acellular, basophilic change like solar elastosis (elastin replacement of collagen). In normal lower lip specimens weak and scanty positive expression of MMP-9 and MMP-12 was observed. Anti-MMP-9 antibody showed a weak reaction, in actinic cheilitis lesions, focal in the elastotic material, in chronic inflammatory cells and mostly in macrophages and neutrophils. Strong and in some cases diffused immunohistochemical expression of MMP-12 was detected in actinic cheilitis lesions in the areas of the fragmented, distorted and thickened elastic fibers. MMP-12 was also expressed in chronic inflammatory cells and mostly macrophages. MMP-12 was significantly higher in actinic cheilitis specimens compared with the normal lower lip specimens (P = 0.0029). CONCLUSION: Our results suggest that especially MMP-12 may play an important role in remodeling events occurring in the connective tissue during long-term exposure to sunlight in the actinic cheilitis lesions. PMID:24520545

Embedded object concept with a telepresence robot system

NASA Astrophysics Data System (ADS)

Vallius, Tero; Röning, Juha

2005-10-01

This paper presents the Embedded Object Concept (EOC) and a telepresence robot system which is a test case for the EOC. The EOC utilizes common object-oriented methods used in software by applying them to combined Lego-like software-hardware entities. These entities represent objects in object-oriented design methods, and they are the building blocks of embedded systems. The goal of the EOC is to make the designing of embedded systems faster and easier. This concept enables people without comprehensive knowledge in electronics design to create new embedded systems, and for experts it shortens the design time of new embedded systems. We present the current status of the EOC, including two generations of embedded objects named Atomi objects. The first generation of the Atomi objects has been tested with different applications, and found to be functional, but not optimal. The second generation aims to correct the issues found with the first generation, and it is being tested in a relatively complex test case. The test case is a telepresence robot consisting of a two wheeled human height robot and its computer counter part. The robot has been constructed using incremental device development, which is made possible by the architecture of the EOC. The robot contains video and audio exchange capability, and a controlling and balancing system for driving with two wheels. The robot is built in two versions, the first consisting of a PDA device and Atomi objects, and the second consisting of only Atomi objects. The robot is currently incomplete, but for the most part it has been successfully tested.

Evaluation of fibrin-gelatin hydrogel as biopaper for application in skin bioprinting: An in-vitro study.

PubMed

Hakam, Mohammad Sadjad; Imani, Rana; Abolfathi, Nabiollah; Fakhrzadeh, Hossein; Sharifi, Ali Mohammad

2016-01-01

Recent advances in tissue engineering have led to the development of the concept of bioprinting as an interesting alternative to traditional tissue engineering approaches. Biopaper, a biomimetic hydrogel, is an essential component of the bioprinting process. The aim of this work was to synthesize a biopaper made of fibrin-gelatin hybrid hydrogel for application in skin bioprinting. Different composition percentages of the two biopolymer hydrogels, fibrin-gelatin, have been studied for the construction of the biopaper and were examined in terms of water absorption, biodegradability, glucose absorption, mechanical properties and water vapor transmission. Subsequently, tissue fusion study was performed on prepared 3T3 fibroblast cell line pellets embedded into the hydrogel. Based on the obtained results, fibrin-gelatin blend hydrogel with the same proportion of two components provides a natural scaffold for fibroblast-based bioink embedding and culture. The suggested optimized hydrogel was a suitable candidate as a biopaper for skin bioprinting technology.

Epoxy Resins in Electron Microscopy

PubMed Central

Finck, Henry

1960-01-01

A method of embedding biological specimens in araldite 502 (Ciba) has been developed for materials available in the United States. Araldite-embedded tissues are suitable for electron microscopy, but the cutting qualities of the resin necessitates more than routine attention during microtomy. The rather high viscosity of araldite 502 also seems to be an unnecessary handicap. The less viscous epoxy epon 812 (Shell) produces specimens with improved cutting qualities, and has several features—low shrinkage and absence of specimen damage during cure, minimal compression of sections, relative absence of electron beam-induced section damage, etc.—which recommends it as a routine embedding material. The hardness of the cured resin can be easily adjusted by several methods to suit the materials embedded in it. Several problems and advantages of working with sections of epoxy resins are also discussed. PMID:13822825

Developing 3D SEM in a broad biological context

PubMed Central

Kremer, A; Lippens, S; Bartunkova, S; Asselbergh, B; Blanpain, C; Fendrych, M; Goossens, A; Holt, M; Janssens, S; Krols, M; Larsimont, J-C; Mc Guire, C; Nowack, MK; Saelens, X; Schertel, A; Schepens, B; Slezak, M; Timmerman, V; Theunis, C; Van Brempt, R; Visser, Y; GuÉRin, CJ

2015-01-01

When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions. Lay Description Life happens in three dimensions. For many years, first light, and then EM struggled to image the smallest parts of cells in 3D. With recent advances in technology and corresponding improvements in computing, scientists can now see the 3D world of the cell at the nanoscale. In this paper we present the results of high resolution 3D imaging in a number of diverse cells and tissues from multiple species. 3D reconstructions of cell structures often revealed them to be significantly more complex when compared to extrapolations made from 2D studies. Correlating functional 3D LM studies with 3D EM results opens up the possibility of making new strides in our understanding of how cell structure is connected to cell function. PMID:25623622

[Molecular mechanisms of lung cancer development at its different stages in nuclear industry workers].

PubMed

Rusinova, G G; Vyazovskaya, N S; Azizova, T V; Revina, V S; Glazkova, I V; Generozov, E V; Zakharzhevskaya, N B; Guryanov, M Yu; Belosokhov, M V; Osovets, S V

2015-01-01

to assess mutational events in exons 5, 7, and 8 of the p53 gene and to reveal mutant p53 protein in verified cases of morphologically altered (proliferative and precancerous changes, lung cancer) and histologically unaltered, lung tissues in workers exposed to occupational radiation. The investigation used formalin-fixed paraffin-embedded unaltered and altered lung tissue blocks (FFPBs) obtained from the human radiobiological tissue repository. The shelf-life of FFPBs was 5-31 years. An immunohistochemical technique using mouse antibodies against p53 protein (, Denmark), stained with diaminobenzidine (DAB) chromogen, was employed to determine p53 protein. DNA was isolated from lung tissue FFPBs with QIAmp DNA FFPE Tissue Kit, (, USA). Polymerase chain reaction (PCR) was performed to amplify the p53 gene exons 5, 7, and 8 selected for examination, by applying the sequences of genes and primers, the specificity of which was checked using the online resource (http://www.ncbi.nlm.nih.gov/blast). PCR products were detected by temporal temperature gradient gel-electrophoresis and the Sanger sequencing method. The obtained DNA fragments were analyzed on a sequencer ABI Prism 3100 Genetic Analizer (, USA). Computer-aided DNA analysis was made using the BLAST program. A package of applied Statistica 6.0 programs was employed for statistical data processing. Results. Immunohistochemical analysis showed that mutant p53 protein was absent in the cells of unaltered lung tissue and the number of cells with mutant p53 protein increased in all the patients with proliferative and precancerous changes and lung cancer, suggesting p53 protein dysfunction. The total number of p53 gene mutations in exons 5, 7, and 8, if there were proliferative and precancerous lung tissue changes and lung cancer, were 25, 20, and 40%, respectively. All the found mutations were transversions (the substitution of purine for pyrimidine or, conversely), indicating the action of exogenous mutagens. The results of this investigation have confirmed other investigators' data showing that p53 gene mutations in lung cancer are observed in 40-70% of cases. The differences in the number of cases of altered lung tissue with mutations in the p53 gene (not more than 40%) and in those of p53 protein expression were found in 100%, suggesting the regulation of p53 gene function in the cell at multiple levels.

On-chip self-assembly of cell embedded microstructures to vascular-like microtubes.

PubMed

Yue, Tao; Nakajima, Masahiro; Takeuchi, Masaru; Hu, Chengzhi; Huang, Qiang; Fukuda, Toshio

2014-03-21

Currently, research on the construction of vascular-like tubular structures is a hot area of tissue engineering, since it has potential applications in the building of artificial blood vessels. In this paper, we report a fluidic self-assembly method using cell embedded microstructures to construct vascular-like microtubes. A novel 4-layer microfluidic device was fabricated using polydimethylsiloxane (PDMS), which contains fabrication, self-assembly and extraction areas inside one channel. Cell embedded microstructures were directly fabricated using poly(ethylene glycol) diacrylate (PEGDA) in the fabrication area, namely on-chip fabrication. Self-assembly of the fabricated microstructures was performed in the assembly area which has a micro well. Assembled tubular structures (microtubes) were extracted outside the channel into culture dishes using a normally closed (NC) micro valve in the extraction area. The self-assembly mechanism was experimentally demonstrated. The performance of the NC micro valve and embedded cell concentration were both evaluated. Fibroblast (NIH/3T3) embedded vascular-like microtubes were constructed inside this reusable microfluidic device.

Handling, storage, and preparation of human tissues.

PubMed

Dressler, L G; Visscher, D

2001-05-01

Human tissue for flow cytometry must be prepared as an adequate single-cell suspension. The appropriate methods for tissue collection, transport, storage, and dissociation depend on the cell parameters being measured and the localization of the markers. This unit includes a general method for collecting and transporting human tissue and preparing a tissue imprint. Protocols are supplied for tissue disaggregation by either mechanical or enzymatic means and for preparation of single-cell suspensions of whole cells from fine-needle aspirates, pleural effusions, abdominal fluids, or other body fluids. Other protocols detail preparation of intact nuclei from fresh, frozen, or paraffin-embedded tissue. Support protocols cover fixation, cryospin preparation, cryopreservation, and removal of debris.

Polymer-based platform for microfluidic systems

DOEpatents

Benett, William [Livermore, CA; Krulevitch, Peter [Pleasanton, CA; Maghribi, Mariam [Livermore, CA; Hamilton, Julie [Tracy, CA; Rose, Klint [Boston, MA; Wang, Amy W [Oakland, CA

2009-10-13

A method of forming a polymer-based microfluidic system platform using network building blocks selected from a set of interconnectable network building blocks, such as wire, pins, blocks, and interconnects. The selected building blocks are interconnectably assembled and fixedly positioned in precise positions in a mold cavity of a mold frame to construct a three-dimensional model construction of a microfluidic flow path network preferably having meso-scale dimensions. A hardenable liquid, such as poly (dimethylsiloxane) is then introduced into the mold cavity and hardened to form a platform structure as well as to mold the microfluidic flow path network having channels, reservoirs and ports. Pre-fabricated elbows, T's and other joints are used to interconnect various building block elements together. After hardening the liquid the building blocks are removed from the platform structure to make available the channels, cavities and ports within the platform structure. Microdevices may be embedded within the cast polymer-based platform, or bonded to the platform structure subsequent to molding, to create an integrated microfluidic system. In this manner, the new microfluidic platform is versatile and capable of quickly generating prototype systems, and could easily be adapted to a manufacturing setting.

A bio-inspired, microchanneled hydrogel with controlled spacing of cell adhesion ligands regulates 3D spatial organization of cells and tissue.

PubMed

Lee, Min Kyung; Rich, Max H; Lee, Jonghwi; Kong, Hyunjoon

2015-07-01

Bioactive hydrogels have been extensively studied as a platform for 3D cell culture and tissue regeneration. One of the key desired design parameters is the ability to control spatial organization of biomolecules and cells and subsequent tissue in a 3D matrix. To this end, this study presents a simple but advanced method to spatially organize microchanneled, cell adherent gel blocks and non-adherent ones in a single construct. This hydrogel system was prepared by first fabricating a bimodal hydrogel in which the microscale, alginate gel blocks modified with cell adhesion peptides containing Arg-Gly-Asp sequence (RGD peptides), and those free of RGD peptides, were alternatingly presented. Then, anisotropically aligned microchannels were introduced by uniaxial freeze-drying of the bimodal hydrogel. The resulting gel system could drive bone marrow stromal cells to adhere to and differentiate into neuron and glial cells exclusively in microchannels of the alginate gel blocks modified with RGD peptides. Separately, the bimodal gel loaded with microparticles releasing vascular endothelial growth factor stimulated vascular growth solely into microchannels of the RGD-alginate gel blocks in vivo. These results were not attained by the bimodal hydrogel fabricated to present randomly oriented micropores. Overall, the bimodal gel system could regulate spatial organization of nerve-like tissue or blood vessels at sub-micrometer length scale. We believe that the hydrogel assembly demonstrated in this study will be highly useful in developing a better understanding of diverse cellular behaviors in 3D tissue and further improve quality of a wide array of engineered tissues. Copyright © 2015 Elsevier Ltd. All rights reserved.

Diagnostic segregation of human brain tumours using Fourier-transform infrared and/or Raman spectroscopy coupled with discriminant analysis†

PubMed Central

Gajjar, Ketan; Heppenstall, Lara D.; Pang, Weiyi; Ashton, Katherine M.; Trevisan, Júlio; Patel, Imran I.; Llabjani, Valon; Stringfellow, Helen F.; Martin-Hirsch, Pierre L.; Dawson, Timothy; Martin, Francis L.

2013-01-01

The most common initial treatment received by patients with a brain tumour is surgical removal of the growth. Precise histopathological diagnosis of brain tumours is to some extent subjective. Furthermore, currently available diagnostic imaging techniques to delineate the excision border during cytoreductive surgery lack the required spatial precision to aid surgeons. We set out to determine whether infrared (IR) and/or Raman spectroscopy combined with multivariate analysis could be applied to discriminate between normal brain tissue and different tumour types (meningioma, glioma and brain metastasis) based on the unique spectral “fingerprints” of their biochemical composition. Formalin-fixed paraffin-embedded tissue blocks of normal brain and different brain tumours were de-waxed, mounted on low-E slides and desiccated before being analyzed using attenuated total reflection Fourier-transform IR (ATR-FTIR) and Raman spectroscopy. ATR-FTIR spectroscopy showed a clear segregation between normal and different tumour subtypes. Discrimination of tumour classes was also apparent with Raman spectroscopy. Further analysis of spectral data revealed changes in brain biochemical structure associated with different tumours. Decreased tentatively-assigned lipid-to-protein ratio was associated with increased tumour progression. Alteration in cholesterol esters-to-phenylalanine ratio was evident in grade IV glioma and metastatic tumours. The current study indicates that IR and/or Raman spectroscopy have the potential to provide a novel diagnostic approach in the accurate diagnosis of brain tumours and have potential for application in intra-operative diagnosis. PMID:24098310

[Attrition, dentin apposition and protein synthesis in the pulp and desmodont of young and old rats].

PubMed

Schroeder, H E; Münzel-Pedrazzoli, S

1994-01-01

Occlusal attrition and responsive adaptations in the pulp-dentinal unit are still problematic. In this study, up to 2 years-old rats were used to measure the amount of occlusal attrition, of dentin apposition and of the incorporation of 3H-proline into the pulpal and periodontal ligament tissues. Two to four SIV-rats each, 45, 365 and 730 days of age, were once injected with 3H-proline 2 hours or 5 days prior to exitus. After cardiac perfusion, the molar blocks of both jaws were decalcified in EDTA and divided into bucco-oral and mesio-distal slices. The latter were embedded in Epon. Semithin sections served to measure the amount of attrition and of tertiary dentin apposition, as well as for autoradiographic labelling and determination of the rate of dentin apposition and proline incorporation in pulpal and periodontal ligament tissues. The results show that (1) the molar cusps lost up to 40% of their initial height during the two years of life, (2) occlusal dentin apposition in the intercuspal region led to an increase in dentinal thickness by 50 to 70%, while in the pulp horn region dentinal apposition occurred early in life and later did not keep phase with attrition, and (3) protein synthesis in pulp and periodontal ligament essentially did not change within the two years of life. These findings are related to that of other authors and discussed in connection with dentinal innervation.

Lava ultimate resin nano ceramic for CAD/ CAM: customization case study.

PubMed

Koller, M; Arnetzl, G V; Holly, L; Arnetzl, G

2012-01-01

Lava Ultimate Resin Nano Ceramic (RNC) blocks are innovative new CAD/CAM materials that make it possible to achieve superior esthetic results in easy steps. The blocks are made of nano ceramic particles embedded in a highly cured resin matrix. Therefore, composite materials can be used to characterize and adjust resin nano ceramic restorations after milling. The milled RNC restorations can be individualized intra-orally or extra-orally, either before or after insertion. Unlike conventional ceramic restorations, customization and glaze firing is neither necessary nor possible with RNC restorations. This opens up the opportunity for intraoral individualization and adaptation of the restorations.

Microvascular complications associated with injection of cosmetic facelift dermal fillers

NASA Astrophysics Data System (ADS)

Yousefi, Siavash; Prendes, Mark; Chang, Shu-Hong; Wang, Ruikang K.

2015-02-01

Minimally-invasive cosmetic surgeries such as injection of subdermal fillers have become very popular in the past decade. Although rare, some complications may follow injections such as tissue necrosis and even blindness. There exist two hypothesis regarding source of these complications both of which include microvasculature. The first hypothesis is that fillers in between the tissue structures and compress microvasculature that causes blockage of tissue neutrition and oxygen exchange in the tissue. In another theory, it is hypothesized that fillers move inside major arteries and block the arteries/veins. In this paper, we study these hypotheses using optical coherence tomography and optical microangiography technologies with different hyaluronic-acid fillers in a mouse ear model. Based on our observations, the fillers eventually block arteries/veins if injected directly into them that eventually causes tissue necrosis.

Validation of a robust proteomic analysis carried out on formalin-fixed paraffin-embedded tissues of the pancreas obtained from mouse and human.

PubMed

Kojima, Kyoko; Bowersock, Gregory J; Kojima, Chinatsu; Klug, Christopher A; Grizzle, William E; Mobley, James A

2012-11-01

A number of reports have recently emerged with focus on extraction of proteins from formalin-fixed paraffin-embedded (FFPE) tissues for MS analysis; however, reproducibility and robustness as compared to flash frozen controls is generally overlooked. The goal of this study was to identify and validate a practical and highly robust approach for the proteomics analysis of FFPE tissues. FFPE and matched frozen pancreatic tissues obtained from mice (n = 8) were analyzed using 1D-nanoLC-MS(MS)(2) following work up with commercially available kits. The chosen approach for FFPE tissues was found to be highly comparable to that of frozen. In addition, the total number of unique peptides identified between the two groups was highly similar, with 958 identified for FFPE and 1070 identified for frozen, with protein identifications that corresponded by approximately 80%. This approach was then applied to archived human FFPE pancreatic cancer specimens (n = 11) as compared to uninvolved tissues (n = 8), where 47 potential pancreatic ductal adenocarcinoma markers were identified as significantly increased, of which 28 were previously reported. Further, these proteins share strongly overlapping pathway associations to pancreatic cancer that include estrogen receptor α. Together, these data support the validation of an approach for the proteomic analysis of FFPE tissues that is straightforward and highly robust, which can also be effectively applied toward translational studies of disease. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Expression of the cytoskeleton regulatory protein Mena in human gastric carcinoma and its prognostic significance

PubMed Central

Xu, Lihua; Tan, Huo; Liu, Ruiming; Huang, Qungai; Zhang, Nana; Li, Xi; Wang, Jiani

2017-01-01

The cytoskeleton regulatory protein Mena is reportedly overexpressed in breast cancer; however, data regarding its expression level and clinical significance in gastric carcinoma (GC) is limited. The aim of the present study was to investigate Mena expression levels and prognostic significance in GC. Mena mRNA expression level was determined by reverse transcription-quantitative polymerase chain reaction in 10 paired GC and adjacent normal tissues. The Mena protein expression level was analyzed in paraffin-embedded GC samples and adjacent normal tissues by immunohistochemistry. Statistical analyses were also performed to evaluate the clinicopathological significance of Mena. The results revealed that the mRNA expression level of Mena was significantly higher in G Ct issues compared with in adjacent normal tissues from10 paired samples. In the paraffin-embedded tissue samples, the protein expression level of Mena was higher in G Ct issues compared with in adjacent normal tissues. Compared with adjacent normal tissues, Mena overexpression was observed in 52.83% (56/106) of patients. The overexpression of Mena was significantly associated with the T stage (P=0.033), tumor-node-metastasis (TNM) stage (P<0.001) and decreased overall survival (P<0.001). Based on a multivariate analysis, Mena expression level was an independent prognostic factor for overall survival time. In conclusion, Mena wasoverexpressed in G C tissues and significantly associated with the T stage, TNM stage and overall survival time. Mena may therefore be suitable as a prognostic indicator for patients with GC. PMID:29113241

Expression of the cytoskeleton regulatory protein Mena in human gastric carcinoma and its prognostic significance.

PubMed

Xu, Lihua; Tan, Huo; Liu, Ruiming; Huang, Qungai; Zhang, Nana; Li, Xi; Wang, Jiani

2017-11-01

The cytoskeleton regulatory protein Mena is reportedly overexpressed in breast cancer; however, data regarding its expression level and clinical significance in gastric carcinoma (GC) is limited. The aim of the present study was to investigate Mena expression levels and prognostic significance in GC. Mena mRNA expression level was determined by reverse transcription-quantitative polymerase chain reaction in 10 paired GC and adjacent normal tissues. The Mena protein expression level was analyzed in paraffin-embedded GC samples and adjacent normal tissues by immunohistochemistry. Statistical analyses were also performed to evaluate the clinicopathological significance of Mena. The results revealed that the mRNA expression level of Mena was significantly higher in G Ct issues compared with in adjacent normal tissues from10 paired samples. In the paraffin-embedded tissue samples, the protein expression level of Mena was higher in G Ct issues compared with in adjacent normal tissues. Compared with adjacent normal tissues, Mena overexpression was observed in 52.83% (56/106) of patients. The overexpression of Mena was significantly associated with the T stage (P=0.033), tumor-node-metastasis (TNM) stage (P<0.001) and decreased overall survival (P<0.001). Based on a multivariate analysis, Mena expression level was an independent prognostic factor for overall survival time. In conclusion, Mena wasoverexpressed in G C tissues and significantly associated with the T stage, TNM stage and overall survival time. Mena may therefore be suitable as a prognostic indicator for patients with GC.

Intraoperative Nerve Blocks Fail to Improve Quality of Recovery after Tissue Expander Breast Reconstruction: A Prospective, Double-Blinded, Randomized, Placebo-Controlled Clinical Trial.

PubMed

Lanier, Steven T; Lewis, Kevin C; Kendall, Mark C; Vieira, Brittany L; De Oliveira, Gildasio; Nader, Anthony; Kim, John Y S; Alghoul, Mohammed

2018-03-01

The authors' study represents the first level I evidence to assess whether intraoperative nerve blocks improve the quality of recovery from immediate tissue expander/implant breast reconstruction. A prospective, randomized, double-blinded, placebo-controlled clinical trial was conducted in which patients undergoing immediate tissue expander/implant breast reconstruction were randomized to either (1) intraoperative intercostal and pectoral nerve blocks with 0.25% bupivacaine with 1:200,000 epinephrine and 4 mg of dexamethasone or (2) sham nerve blocks with normal saline. The 40-item Quality of Recovery score, pain score, and opioid use in the postoperative period were compared statistically between groups. Power analysis ensured 80 percent power to detect a 10-point (clinically significant) difference in the 40-item Quality of Recovery score. Forty-seven patients were enrolled. Age, body mass index, laterality, mastectomy type, and lymph node dissection were similar between groups. There were no statistical differences in quality of recovery, pain burden as measured by visual analogue scale, opioid consumption, antiemetic use, or length of hospital stay between groups at 24 hours after surgery. Mean global 40-item Quality of Recovery scores were 169 (range, 155 to 182) for the treatment arm and 165 (range, 143 to 179) for the placebo arm (p = 0.36), indicating a high quality of recovery in both groups. Although intraoperative nerve blocks can be a safe adjunct to a comprehensive postsurgical recovery regimen, the authors' results indicate no effect on overall quality of recovery from tissue expander/implant breast reconstruction. Therapeutic, I.

Immunohistochemical evaluation of myofibroblasts in odontogenic cysts and tumors: A comparative study

PubMed Central

Syamala, Deepa; Suresh, Rakesh; Janardhanan, Mahija; Savithri, Vindhya; Anand, Prem P; Jose, Amrutha

2016-01-01

Context: Myofibroblasts are fibroblasts with smooth muscle-like features characterized by the presence of a contractile apparatus and found in the connective tissue stroma of normal tissues such as blood vessels and lymph nodes. They are now thought to play a role in the synthesis and reorganization of extracellular matrix, which could contribute to the aggressive biologic behavior of the lesions. Aims: To compare the mean number of stromal myofibroblasts in dentigerous cysts (DCs), keratocystic odontogenic tumor (KCOT) and ameloblastoma; and to derive a correlation between the stromal myofibroblasts and the known biologic behavior of the lesions. Settings and Design: A cross-sectional immunohistochemical analysis of cases of DC, KCOT and ameloblastoma. Materials and Methods: Twenty paraffin-embedded tissue blocks each of DC, KCOT and multicystic ameloblastoma were selected for the study and diagnosis confirmed through hematoxylin and eosin staining. Tissue sections were analyzed for the number of myofibroblasts using alpha smooth muscle actin (α-SMA) immunostaining. Statistical Analysis: Differences in the mean number of α-SMA positive cells in each group were analyzed using one-way ANOVA test. Intergroup comparisons of mean values of α-SMA positive cells were performed using Mann-Whitney U-test. Results: Ameloblastoma showed the highest number of myofibroblasts, whereas DC showed the lowest. Among the groups, there were significant differences between the myofibroblast counts among DC and KCOT and between DC and ameloblastoma, whereas the difference in counts was not statistically significant between KCOT and ameloblastoma. A positive correlation was observed between the myofibroblast count and the known biologic behavior of the lesions. Conclusion: Myofibroblasts may act in close association with the epithelial cells to bring about changes in stromal microenvironment, favorable to the growth and progression of the lesion. They may be of great value in predicting the biologic behavior and growth potential of such lesions. PMID:27601810

Electrostatically screened, voltage-controlled electrostatic chuck

DOEpatents

Klebanoff, Leonard Elliott

2001-01-01

Employing an electrostatically screened, voltage-controlled electrostatic chuck particularly suited for holding wafers and masks in sub-atmospheric operations will significantly reduce the likelihood of contaminant deposition on the substrates. The electrostatic chuck includes (1) an insulator block having a outer perimeter and a planar surface adapted to support the substrate and comprising at least one electrode (typically a pair of electrodes that are embedded in the insulator block), (2) a source of voltage that is connected to the at least one electrode, (3) a support base to which the insulator block is attached, and (4) a primary electrostatic shield ring member that is positioned around the outer perimeter of the insulator block. The electrostatic chuck permits control of the voltage of the lithographic substrate; in addition, it provides electrostatic shielding of the stray electric fields issuing from the sides of the electrostatic chuck. The shielding effectively prevents electric fields from wrapping around to the upper or front surface of the substrate, thereby eliminating electrostatic particle deposition.

Acoustic radiation force due to arbitrary incident fields on spherical particles in soft tissue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Treweek, Benjamin C., E-mail: btreweek@utexas.edu; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.

Acoustic radiation force is of interest in a wide variety of biomedical applications ranging from tissue characterization (e.g. elastography) to tissue treatment (e.g. high intensity focused ultrasound, kidney stone fragment removal). As tissue mechanical properties are reliable indicators of tissue health, the former is the focus of the present contribution. This is accomplished through an investigation of the acoustic radiation force on a spherical scatterer embedded in tissue. Properties of both the scatterer and the surrounding tissue are important in determining the magnitude and the direction of the force. As these properties vary, the force computation shows changes in magnitudemore » and direction, which may enable more accurate noninvasive determination of tissue properties.« less

Acoustic radiation force due to arbitrary incident fields on spherical particles in soft tissue

NASA Astrophysics Data System (ADS)

Treweek, Benjamin C.; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.; Hamilton, Mark F.

2015-10-01

Acoustic radiation force is of interest in a wide variety of biomedical applications ranging from tissue characterization (e.g. elastography) to tissue treatment (e.g. high intensity focused ultrasound, kidney stone fragment removal). As tissue mechanical properties are reliable indicators of tissue health, the former is the focus of the present contribution. This is accomplished through an investigation of the acoustic radiation force on a spherical scatterer embedded in tissue. Properties of both the scatterer and the surrounding tissue are important in determining the magnitude and the direction of the force. As these properties vary, the force computation shows changes in magnitude and direction, which may enable more accurate noninvasive determination of tissue properties.

Productivity standards for histology laboratories.

PubMed

Buesa, René J

2010-04-01

The information from 221 US histology laboratories (histolabs) and 104 from 24 other countries with workloads from 600 to 116 000 cases per year was used to calculate productivity standards for 23 technical and 27 nontechnical tasks and for 4 types of work flow indicators. The sample includes 254 human, 40 forensic, and 31 veterinary pathology services. Statistical analyses demonstrate that most productivity standards are not different between services or worldwide. The total workload for the US human pathology histolabs averaged 26 061 cases per year, with 54% between 10 000 and less than 30 000. The total workload for 70% of the histolabs from other countries was less than 20 000, with an average of 15 226 cases per year. The fundamental manual technical tasks in the histolab and their productivity standards are as follows: grossing (14 cases per hour), cassetting (54 cassettes per hour), embedding (50 blocks per hour), and cutting (24 blocks per hour). All the other tasks, each with their own productivity standards, can be completed by auxiliary staff or using automatic instruments. Depending on the level of automation of the histolab, all the tasks derived from a workload of 25 cases will require 15.8 to 17.7 hours of work completed by 2.4 to 2.7 employees with 18% of their working time not directly dedicated to the production of diagnostic slides. This article explains how to extrapolate this productivity calculation for any workload and different levels of automation. The overall performance standard for all the tasks, including 8 hours for automated tissue processing, is 3.2 to 3.5 blocks per hour; and its best indicator is the value of the gross work flow productivity that is essentially dependent on how the work is organized. This article also includes productivity standards for forensic and veterinary histolabs, but the staffing benchmarks for histolabs will be the subject of a separate article. Copyright 2010 Elsevier Inc. All rights reserved.

Tissues from the irradiated dog/mouse archive

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gayle Woloschak

The purpose of this project is to organize the databases/information and organize and move the tissues from the long-term dog (4,000 dogs) and mouse (over 30,000 mice) radiation experiments done at Argonne National Laboratory during the 1970's and 80's to Northwestern University. These studies were done with the intention of understanding the effects of exposure to radiation at a variety of different doses, dose-rates, and radiation qualities on end-points such as life-shortening, carcinogenesis, cause of death, shifts in disease incidence and other biological parameters. Organ and tissue samples from these animals including cancers, metastases and other significant degenerative and inflammatorymore » lesions and those in a regular protocol of normal tissues were preserved in paraffin blocks, tissue impressions and sections and represent a great resource for the radiation biology community. These collections are particularly significant since these experiments are not likely to be repeated because of the extreme cost of monies and time for such large-scale animal studies. The long-term goal is to make these tissues and databases available to the wider scientific community so that questions such as tissue sensitivity, early and late effects, low dose and protracted dose responses of normal and tumor tissues, etc. can be examined and defined. Recent advances in biology particularly at the subcellular and molecular level now permit microarray-based gene expression array analyses from paraffin-embedded tissues (where RNA samples are significantly degraded), synchrotron-based studies of metal and other elemental distribution patterns in tissues, PCR-based analyses for mutation detection, and other similar approaches that were not available when the long¬ term animal studies were designed and initiated. Understanding the basis and progression of radiation damage should also permit rational approaches to prevention and mitigation of those damages. Therefore, as stated earlier, these tissues and their related documentation, represent a significant resource for future studies. For this project, we propose to accomplish the following objectives: (1) inventory and organize the tissues, blood smears, wet-tissues and paper-¬based information that is available in the tissue bank at Argonne National Laboratory; (2) convert the existing Oracle database of the mouse studies to MS Access( the dog data is already in this format which is far more user friendly and widely used in business and research) , (3) move the remaining samples and documentation from dogs that had been transferred from ANL to New Mexico (in Dr. F. Hahn's care) to Northwestern University and add these to the inventory; (4) move the tissues and Access database at Argonne National Laboratory to Northwestern University.« less

On fragmenting, densely mineralised acellular protrusions into articular cartilage and their possible role in osteoarthritis

PubMed Central

Boyde, A; Davis, G R; Mills, D; Zikmund, T; Cox, T M; Adams, V L; Niker, A; Wilson, P J; Dillon, J P; Ranganath, L R; Jeffery, N; Jarvis, J C; Gallagher, J A

2014-01-01

High density mineralised protrusions (HDMP) from the tidemark mineralising front into hyaline articular cartilage (HAC) were first described in Thoroughbred racehorse fetlock joints and later in Icelandic horse hock joints. We now report them in human material. Whole femoral heads removed at operation for joint replacement or from dissection room cadavers were imaged using magnetic resonance imaging (MRI) dual echo steady state at 0.23 mm resolution, then 26-μm resolution high contrast X-ray microtomography, sectioned and embedded in polymethylmethacrylate, blocks cut and polished and re-imaged with 6-μm resolution X-ray microtomography. Tissue mineralisation density was imaged using backscattered electron SEM (BSE SEM) at 20 kV with uncoated samples. HAC histology was studied by BSE SEM after staining block faces with ammonium triiodide solution. HDMP arise via the extrusion of an unknown mineralisable matrix into clefts in HAC, a process of acellular dystrophic calcification. Their formation may be an extension of a crack self-healing mechanism found in bone and articular calcified cartilage. Mineral concentration exceeds that of articular calcified cartilage and is not uniform. It is probable that they have not been reported previously because they are removed by decalcification with standard protocols. Mineral phase morphology frequently shows the agglomeration of many fine particles into larger concretions. HDMP are surrounded by HAC, are brittle, and show fault lines within them. Dense fragments found within damaged HAC could make a significant contribution to joint destruction. At least larger HDMP can be detected with the best MRI imaging ex vivo. PMID:25132002

Spectral triangulation: a 3D method for locating single-walled carbon nanotubes in vivo

NASA Astrophysics Data System (ADS)

Lin, Ching-Wei; Bachilo, Sergei M.; Vu, Michael; Beckingham, Kathleen M.; Bruce Weisman, R.

2016-05-01

Nanomaterials with luminescence in the short-wave infrared (SWIR) region are of special interest for biological research and medical diagnostics because of favorable tissue transparency and low autofluorescence backgrounds in that region. Single-walled carbon nanotubes (SWCNTs) show well-known sharp SWIR spectral signatures and therefore have potential for noninvasive detection and imaging of cancer tumours, when linked to selective targeting agents such as antibodies. However, such applications face the challenge of sensitively detecting and localizing the source of SWIR emission from inside tissues. A new method, called spectral triangulation, is presented for three dimensional (3D) localization using sparse optical measurements made at the specimen surface. Structurally unsorted SWCNT samples emitting over a range of wavelengths are excited inside tissue phantoms by an LED matrix. The resulting SWIR emission is sampled at points on the surface by a scanning fibre optic probe leading to an InGaAs spectrometer or a spectrally filtered InGaAs avalanche photodiode detector. Because of water absorption, attenuation of the SWCNT fluorescence in tissues is strongly wavelength-dependent. We therefore gauge the SWCNT-probe distance by analysing differential changes in the measured SWCNT emission spectra. SWCNT fluorescence can be clearly detected through at least 20 mm of tissue phantom, and the 3D locations of embedded SWCNT test samples are found with sub-millimeter accuracy at depths up to 10 mm. Our method can also distinguish and locate two embedded SWCNT sources at distinct positions.Nanomaterials with luminescence in the short-wave infrared (SWIR) region are of special interest for biological research and medical diagnostics because of favorable tissue transparency and low autofluorescence backgrounds in that region. Single-walled carbon nanotubes (SWCNTs) show well-known sharp SWIR spectral signatures and therefore have potential for noninvasive detection and imaging of cancer tumours, when linked to selective targeting agents such as antibodies. However, such applications face the challenge of sensitively detecting and localizing the source of SWIR emission from inside tissues. A new method, called spectral triangulation, is presented for three dimensional (3D) localization using sparse optical measurements made at the specimen surface. Structurally unsorted SWCNT samples emitting over a range of wavelengths are excited inside tissue phantoms by an LED matrix. The resulting SWIR emission is sampled at points on the surface by a scanning fibre optic probe leading to an InGaAs spectrometer or a spectrally filtered InGaAs avalanche photodiode detector. Because of water absorption, attenuation of the SWCNT fluorescence in tissues is strongly wavelength-dependent. We therefore gauge the SWCNT-probe distance by analysing differential changes in the measured SWCNT emission spectra. SWCNT fluorescence can be clearly detected through at least 20 mm of tissue phantom, and the 3D locations of embedded SWCNT test samples are found with sub-millimeter accuracy at depths up to 10 mm. Our method can also distinguish and locate two embedded SWCNT sources at distinct positions. Electronic supplementary information (ESI) available: Details concerning instrumental design, experimental procedures, related experiments, and triangulation computations, plus a video showing operation of the scanner. See DOI: 10.1039/c6nr01376g

Foreign Body in the Oral Cavity Mimicking a Benign Connective Tissue Tumor

PubMed Central

Ram, Saravanan; Sedghizadeh, Parish P.

2013-01-01

Foreign bodies may be embedded in the oral cavity either by traumatic injury or iatrogenically. The commonly encountered iatrogenic foreign bodies are restorative materials like amalgam, obturation materials, broken instruments, needles, and impression materials. This paper describes an asymptomatic presentation of a foreign body in the oral mucosa which clinically appeared like a benign connective tissue tumor. PMID:23634307

Foreign body in the oral cavity mimicking a benign connective tissue tumor.

PubMed

Puliyel, Divya; Balouch, Amir; Ram, Saravanan; Sedghizadeh, Parish P

2013-01-01

Foreign bodies may be embedded in the oral cavity either by traumatic injury or iatrogenically. The commonly encountered iatrogenic foreign bodies are restorative materials like amalgam, obturation materials, broken instruments, needles, and impression materials. This paper describes an asymptomatic presentation of a foreign body in the oral mucosa which clinically appeared like a benign connective tissue tumor.

Direct fluorescent antibody technique for the detection of bacterial kidney disease in paraffin-embedded tissues

USGS Publications Warehouse

Ochiai, T.; Yasutake, W.T.; Gould, R.W.

1985-01-01

The direct fluorescent antibody technique (FAT) was successfully used to detect the causative agent of bacterial kidney disease (BKD), Renibacterium salmoninarum, in Bouin's solution flexed and paraffinembedded egg and tissue sections. This method is superior to gram stain and may be particularly useful in detecting the BKD organism in fish with low-grade infection.

A strategy to analyse activity-based profiling of tyrosine kinase substrates in OCT-embedded lung cancer tissue.

PubMed

Arni, Stephan; de Wijn, Rik; Garcia-Villegas, Refugio; Bitanihirwe, Byron K Y; Caviezel, Claudio; Weder, Walter; Hillinger, Sven

2018-04-15

The use of optimal cutting temperature (OCT) medium has served to improve the long-term preservation of surgical tissue specimens. Unfortunately, the presence of polymers in OCT has been found to generate signal interference in proteomic-based techniques. Indeed the presence of OCT medium in tissue lysates precludes the analysis of activity based proteomic profiles obtained from lung adenocarcinoma (LuAdCa) resection specimens. In order to probe this question further tissue lysates were prepared from 47 lung non-neoplastic and tumour, node, metastasis (TNM) stage 1 LuAdCa resection specimens embedded with or without OCT, and data of activity based multiplex profiles of protein tyrosine kinase peptide substrates were obtained. We found that changes in overall phosphorylation level coincided with the use of OCT and subsequently developed an OCT per peptide median correcting strategy by performing median centering on the values of each peptide. Application of this post-analytical strategy not only can identify changes in kinase activity but can also assist in identifying novel targets for therapeutic intervention against LuAdCa. Copyright © 2018 Elsevier Inc. All rights reserved.

Comparison of methods for extracting DNA from formalin-fixed paraffin sections for nonisotopic PCR.

PubMed

Frank, T S; Svoboda-Newman, S M; Hsi, E D

1996-09-01

DNA was extracted from unstained 5-microns sections of neutral buffered 10% formalin-fixed paraffin-embedded tissue by proteinase K digestion without detergents followed by boiling, proteinase K digestion with ionic detergents with and without phenol chloroform extraction and ethanol precipitation, sonication with proteinase K followed by boiling, or boiling alone. Serial 1:10 dilutions of the extracted DNA were subject to polymerase chain reaction (PCR) amplification of a 255-bp portion of the p53 gene. Digestion with proteinase K without ionic detergents followed by boiling (without phenol chloroform extraction) gave the best yield, enabling visualization of ethidium bromide-stained PCR product from a DNA dilution corresponding to 0.1 mm2 of tissue containing of the order of 10(3) nuclear profiles. Proteinase K digestion with detergents followed by phenol-chloroform extraction was no more effective than simple boiling. Although the success of PCR from preserved tissue will vary with the fixative and size of the amplified fragment, DNA extracted with this optimized method can be used for identification of viruses, loss of heterozygosity, and immunoglobulin gene rearrangements in paraffin-embedded tissue without radioisotopes.

Comparison of Different Buffers for Protein Extraction from Formalin-Fixed and Paraffin-Embedded Tissue Specimens

PubMed Central

Shen, Kaini; Sun, Jian; Cao, Xinxin; Zhou, Daobin; Li, Jian

2015-01-01

We determined the best extraction buffer for proteomic investigation using formalin-fixation and paraffin-embedded (FFPE) specimens. A Zwittergent 3–16 based buffer, sodium dodecyl sulfate (SDS)-containing buffer with/without polyethylene glycol 20000 (PEG20000), urea-containing buffer, and FFPE-FASP protein preparation kit were compared for protein extraction from different types of rat FFPE tissues, including the heart, brain, liver, lung, and kidney. All of the samples were divided into two groups of laser microdissected (LMD) and non-LMD specimens. For both kinds of specimens, Zwittergent was the most efficient buffer for identifying peptides and proteins, was broadly applicable to different tissues without impairing the enzymatic digestion, and was well compatible with mass spectrometry analysis. As a high molecular weight carrier substance, PEG20000 improved the identification of peptides and proteins; however, such an advantage is limited to tissues containing submicrograms to micrograms of protein. Considering its low lytic strength, urea-containing buffer would not be the first alternative for protein recovery. In conclusion, Zwittergent 3–16 is an effective buffer for extracting proteins from FFPE specimens for downstream proteomics analysis. PMID:26580073

Embedded fragments from U.S. military personnel--chemical analysis and potential health implications.

PubMed

Centeno, José A; Rogers, Duane A; van der Voet, Gijsbert B; Fornero, Elisa; Zhang, Lingsu; Mullick, Florabel G; Chapman, Gail D; Olabisi, Ayodele O; Wagner, Dean J; Stojadinovic, Alexander; Potter, Benjamin K

2014-01-23

The majority of modern war wounds are characterized by high-energy blast injuries containing a wide range of retained foreign materials of a metallic or composite nature. Health effects of retained fragments range from local or systemic toxicities to foreign body reactions or malignancies, and dependent on the chemical composition and corrosiveness of the fragments in vivo. Information obtained by chemical analysis of excised fragments can be used to guide clinical decisions regarding the need for fragment removal, to develop therapeutic interventions, and to better anticipate future medical problems from retained fragment related injuries. In response to this need, a new U.S Department of Defense (DoD) directive has been issued requiring characterization of all removed fragments to provide a database of fragment types occurring in combat injuries. The objective of this study is to determine the chemical composition of retained embedded fragments removed from injured military personnel, and to relate results to histological findings in tissue adjacent to fragment material. We describe an approach for the chemical analysis and characterization of retained fragments and adjacent tissues, and include case examples describing fragments containing depleted uranium (DU), tungsten (W), lead (Pb), and non-metal foreign bodies composed of natural and composite materials. Fragments obtained from four patients with penetrating blast wounds to the limbs were studied employing a wide range of chemical and microscopy techniques. Available adjacent tissues from three of the cases were histologically, microscopically, and chemically examined. The physical and compositional properties of the removed foreign material surfaces were examined with energy dispersive x-ray fluorescence spectrometry (EDXRF), scanning electron microscopy (SEM), laser ablation inductively-coupled plasma mass-spectrometry (LA-ICP-MS), and confocal laser Raman microspectroscopy (CLRM). Quantitative chemical analysis of both fragments and available tissues was conducted employing ICP-MS. Over 800 fragments have been characterized and included as part of the Joint Pathology Center Embedded Fragment Registry. Most fragments were obtained from penetrating wounds sustained to the extremities, particularly soft tissue injuries. The majority of the fragments were primarily composed of a single metal such as iron, copper, or aluminum with traces of antimony, titanium, uranium, and lead. One case demonstrated tungsten in both the fragment and the connected tissue, together with lead. Capsular tissue and fragments from a case from the 1991 Kuwait conflict showed evidence of uranium that was further characterized by uranium isotopic ratios analysis to contain depleted uranium. The present study provides a systematic approach for obtaining a full chemical characterization of retained embedded fragments. Given the vast number of combat casualties with retained fragments, it is expected that fragment analysis will have significant implications for the optimal short and long-term care of wounded service members.

Embedded Fragments from U.S. Military Personnel—Chemical Analysis and Potential Health Implications

PubMed Central

Centeno, José A.; Rogers, Duane A.; van der Voet, Gijsbert B.; Fornero, Elisa; Zhang, Lingsu; Mullick, Florabel G.; Chapman, Gail D.; Olabisi, Ayodele O.; Wagner, Dean J.; Stojadinovic, Alexander; Potter, Benjamin K.

2014-01-01

Background: The majority of modern war wounds are characterized by high-energy blast injuries containing a wide range of retained foreign materials of a metallic or composite nature. Health effects of retained fragments range from local or systemic toxicities to foreign body reactions or malignancies, and dependent on the chemical composition and corrosiveness of the fragments in vivo. Information obtained by chemical analysis of excised fragments can be used to guide clinical decisions regarding the need for fragment removal, to develop therapeutic interventions, and to better anticipate future medical problems from retained fragment related injuries. In response to this need, a new U.S Department of Defense (DoD) directive has been issued requiring characterization of all removed fragments to provide a database of fragment types occurring in combat injuries. Objectives: The objective of this study is to determine the chemical composition of retained embedded fragments removed from injured military personnel, and to relate results to histological findings in tissue adjacent to fragment material. Methods: We describe an approach for the chemical analysis and characterization of retained fragments and adjacent tissues, and include case examples describing fragments containing depleted uranium (DU), tungsten (W), lead (Pb), and non-metal foreign bodies composed of natural and composite materials. Fragments obtained from four patients with penetrating blast wounds to the limbs were studied employing a wide range of chemical and microscopy techniques. Available adjacent tissues from three of the cases were histologically, microscopically, and chemically examined. The physical and compositional properties of the removed foreign material surfaces were examined with energy dispersive x-ray fluorescence spectrometry (EDXRF), scanning electron microscopy (SEM), laser ablation inductively-coupled plasma mass-spectrometry (LA-ICP-MS), and confocal laser Raman microspectroscopy (CLRM). Quantitative chemical analysis of both fragments and available tissues was conducted employing ICP-MS. Results: Over 800 fragments have been characterized and included as part of the Joint Pathology Center Embedded Fragment Registry. Most fragments were obtained from penetrating wounds sustained to the extremities, particularly soft tissue injuries. The majority of the fragments were primarily composed of a single metal such as iron, copper, or aluminum with traces of antimony, titanium, uranium, and lead. One case demonstrated tungsten in both the fragment and the connected tissue, together with lead. Capsular tissue and fragments from a case from the 1991 Kuwait conflict showed evidence of uranium that was further characterized by uranium isotopic ratios analysis to contain depleted uranium. Conclusions: The present study provides a systematic approach for obtaining a full chemical characterization of retained embedded fragments. Given the vast number of combat casualties with retained fragments, it is expected that fragment analysis will have significant implications for the optimal short and long-term care of wounded service members. PMID:24464236

Detection of Newcastle disease virus RNA by reverse transcription-polymerase chain reaction using formalin-fixed, paraffin-embedded tissue and comparison with immunohistochemistry and in situ hybridization.

PubMed

Wakamatsu, Nobuko; King, Daniel J; Seal, Bruce S; Brown, Corrie C

2007-07-01

The usefulness of reverse transcription-polymerase chain reaction (RT-PCR) from formalin-fixed, paraffin-embedded (FFPE) tissues was examined and compared to the immunohistochemistry (IHC) and in situ hybridization (ISH) assays for detection of Newcastle disease virus (NDV). Spleen and lung tissues were collected from chickens experimentally infected with either of 2 NDV isolates: a low virulent virus (LaSota) and a virulent virus (from the 2002-2003 California outbreak). The tissues were harvested immediately postmortem and fixed in 10% neutral buffered formalin for approximately 52 hours. Also, just before euthanasia, oral and cloacal swabs were collected for virus isolation. RNA was obtained from the FFPE tissues by digestion with proteinase K and subsequent extraction with phenol, chloroform, and isoamyl alcohol. By seminested RT-PCR with primers for the NDV matrix gene, a 232-base pair (bp) product was generated and visualized by electrophoresis. The results of PCR were compared to those of IHC for viral nucleoprotein and ISH for matrix gene (850 bp) on 3-microm sections and to those of virus isolation from swabs. All samples from infected chickens were positive by RT-PCR, including samples that were negative by both IHC and ISH. The RT-PCR positives included tissue from chickens that were no longer shedding virus detectable by virus isolation. The RT-PCR was an effective and sensitive method to detect NDV in FFPE tissues. To the authors' knowledge, this is the first report of NDV detection in FFPE tissues as a diagnostic approach possibly suitable for archival materials.

Analysis of iron, zinc, selenium and cadmium in paraffin-embedded prostate tissue specimens using inductively coupled plasma mass-spectrometry

USGS Publications Warehouse

Sarafanov, A.G.; Todorov, T.I.; Kajdacsy-Balla, A.; Gray, Michael A.; MacIas, V.; Centeno, J.A.

2008-01-01

Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a valuable and abundant resource of pathologic material for various biomedical studies. In the present study, we report the application of high-resolution inductively coupled mass-spectrometry (ICP-MS) for quantification of Fe, Zn, Se and Cd in FFPE prostate tissue. These elements have a possible role in the development of prostate diseases: while Zn and Se are needed for a healthy prostate, Cd shows multiple toxic and carcinogenic effects. Excessive accumulation of Fe induces the production of highly reactive hydroxyl radical species, which may play a role in cancer etiopathogenesis. To assess whether the levels of these metals in the FFPE prostate tissue represent their original content, we compared their levels with those in the fresh tissue (on dry weight basis) in samples obtained from 15 patients. We found that in FFPE tissue, the recoveries of Se, Fe, Cd and Zn were progressively decreased, 97??11% (r=0.88), 82??22% (r=0.86), 59??23% (r=0.69) and 24??11% (r=0.38), respectively. Thus, the use of correction factors, determined as k=0.16 for Se, k=0.20 for Fe, k=0.27 for Cd and k=0.67 for Zn, is required to estimate the retrospective levels of these elements in the parental non-processed fresh (wet) prostate tissue. The technique used in this study enables the analysis of archival FFPE prostate tissue for the concentrations of Fe, Zn, Se and Cd to study association between the levels of these metals and prostate disease. ?? 2008.

3D imaging of cells and tissues by focused ion beam/scanning electron microscopy (FIB/SEM).

PubMed

Drobne, Damjana

2013-01-01

Integration of a scanning electron microscope (SEM) and focused ion beam (FIB) technology into a single FIB/SEM system permits use of the FIB as a nano-scalpel to reveal site-specific subsurface microstructures which can be examined in great detail by SEM. The FIB/SEM technology is widely used in the semiconductor industry and material sciences, and recently its use in the life sciences has been initiated. Samples for FIB/SEM investigation can be either embedded in a plastic matrix, the traditional means of preparation of transmission electron microscopy (TEM) specimens, or simply dried as in samples prepared for SEM imaging. Currently, FIB/SEM is used in the life sciences for (a) preparation by the lift-out technique of lamella for TEM analysis, (b) tomography of samples embedded in a matrix, and (c) in situ site-specific FIB milling and SEM imaging using a wide range of magnifications. Site-specific milling and imaging has attracted wide interest as a technique in structural research of single eukaryotic and prokaryotic cells, small animals, and different animal tissue, but it still remains to be explored more thoroughly. In the past, preparation of samples for site-specific milling and imaging by FIB/SEM has typically adopted the embedding techniques used for TEM samples, and which have been very well described in the literature. Sample preparation protocols for the use of dried samples in FIB/SEM have been less well investigated. The aim of this chapter is to encourage application of FIB/SEM on dried biological samples. A detailed description of conventional dried sample preparation and FIB/SEM investigation of dried biological samples is presented. The important steps are described and illustrated, and direct comparison between embedded and dried samples of same tissues is provided. The ability to discover links between gross morphology of the tissue or organ, surface characteristics of any selected region, and intracellular structural details on the nanometer scale is an appealing application of electron microscopy in the life sciences and merits further exploration.

Predictors of favorable soft tissue profile outcomes following Class II Twin-block treatment.

PubMed

Kim, Ji-Eun; Mah, Su-Jung; Kim, Tae-Woo; Kim, Su-Jung; Park, Ki-Ho; Kang, Yoon-Goo

2018-01-01

The aim of this study was to determine cephalometric factors that help predict favorable soft-tissue profile outcomes following treatment with the Class II Twin-block appliance. Pre- and post-treatment lateral cephalograms of 45 patients treated with the Class II Twin-block appliance were retrospectively analyzed. Profile silhouettes were drawn from the cephalograms and evaluated by three orthodontists in order to determine the extent of improvement. Samples were divided into a favorable group (upper 30% of visual analogue scale [VAS] scores, n = 14) and an unfavorable group (lower 30% of VAS scores, n = 14). Skeletal and soft-tissue measurements were performed on the cephalograms and an intergroup comparison was conducted. An independent t -test revealed that the following pre-treatment values were lower in the favorable group compared to the unfavorable group: lower incisor to mandibular plane angle, lower incisor to pogonion distance, point A-nasion-point B angle, sella-nasion line (SN) to maxillary plane angle, SN to mandibular plane angle, gonial angle, and symphysis inclination. The favorable group had a larger incisor inclination to occlusal plane. Moreover, the favorable group showed larger post-treatment changes in gonial angle, B point projection, and pogonion projection than did the unfavorable group. Class II malocclusion patients with a low divergent skeletal pattern and reduced lower incisor protrusions are likely to show more improvement in soft-tissue profile outcomes following Class II Twin-block treatment.

Color pictorial serpentine halftone for secure embedded data

NASA Astrophysics Data System (ADS)

Curry, Douglas N.

1998-04-01

This paper introduces a new rotatable glyph shape for trusted printing applications that has excellent image rendering, data storage and counterfeit deterrence properties. Referred to as a serpentine because it tiles into a meandering line screen, it can produce high quality images independent of its ability to embed data. The hafltone cell is constructed with hyperbolic curves to enhance its dynamic range, and generates low distortion because of rotational tone invariance with its neighbors. An extension to the process allows the data to be formatted into human readable text patterns, viewable with a magnifying glass, and therefore not requiring input scanning. The resultant embedded halftone patterns can be recognized as simple numbers (0 - 9) or alphanumerics (a - z). The pattern intensity can be offset from the surrounding image field intensity, producing a watermarking effect. We have been able to embed words such as 'original' or license numbers into the background halftone pattern of images which can be readily observed in the original image, and which conveniently disappear upon copying. We have also embedded data blocks with self-clocking codes and error correction data which are machine-readable. Finally, we have successfully printed full color images with both the embedded data and text, simulating a trusted printing application.

PtRu nanoparticles embedded in nitrogen doped carbon with highly stable CO tolerance and durability

NASA Astrophysics Data System (ADS)

Ling, Ying; Yang, Zehui; Yang, Jun; Zhang, Yunfeng; Zhang, Quan; Yu, Xinxin; Cai, Weiwei

2018-02-01

As is well known, the lower durability and sluggish methanol oxidation reaction (MOR) of PtRu alloy electrocatalyst blocks the commercialization of direct methanol fuel cells (DMFCs). Here, we design a new PtRu electrocatalyst, with highly stable CO tolerance and durability, in which the PtRu nanoparticles are embedded in nitrogen doped carbon layers derived from carbonization of poly(vinyl pyrrolidone). The newly fabricated electrocatalyst exhibits no loss in electrochemical surface area (ECSA) and MOR activity after potential cycling from 0.6-1.0 V versus reversible hydrogen electrode, while commercial CB/PtRu retains only 50% of its initial ECSA. Meanwhile, due to the same protective layers, the Ru dissolution is decelerated, resulting in stable CO tolerance. Methanol oxidation reaction (MOR) testing indicates that the activity of newly fabricated electrocatalyst is two times higher than that of commercial CB/PtRu, and the fuel cell performance of the embedded PtRu electrocatalyst was comparable to that of commercial CB/PtRu. The embedded PtRu electrocatalyst is applicable in real DMFC operation. This study offers important and useful information for the design and fabrication of durable and CO tolerant electrocatalysts.

Cross-Layer Modeling Framework for Energy-Efficient Resilience

DTIC Science & Technology

2014-04-01

functional block diagram of the software architecture of PEARL, which stands for: Power Efficient and Resilient Embedded Processing with Real - Time ... DVFS ). The goal of the run- time manager is to minimize power consumption, while maintaining system resilience targets (on average) and meeting... real - time performance targets. The integrated performance, power and resilience models are nothing but the analytical modeling toolkit described in

Escape from the Island: Grammaticality and (Reduced) Acceptability of "Wh"-Island Violations in Danish

ERIC Educational Resources Information Center

Christensen, Ken Ramshoj; Kizach, Johannes; Nyvad, Anne Mette

2013-01-01

In the syntax literature, it is commonly assumed that a constraint on linguistic competence blocks extraction of "wh-"expressions (e.g. "what" or "which book") from embedded questions, referred to as "wh-"islands. Furthermore, it is assumed that there is an argument/adjunct asymmetry in extraction from "wh-"islands. We report results from two…

Imaging the Material Properties of Bone Specimens using Reflection-Based Infrared Microspectroscopy

PubMed Central

Acerbo, Alvin S.; Carr, G. Lawrence; Judex, Stefan; Miller, Lisa M.

2012-01-01

Fourier Transform InfraRed Microspectroscopy (FTIRM) is a widely used method for mapping the material properties of bone and other mineralized tissues, including mineralization, crystallinity, carbonate substitution, and collagen cross-linking. This technique is traditionally performed in a transmission-based geometry, which requires the preparation of plastic-embedded thin sections, limiting its functionality. Here, we theoretically and empirically demonstrate the development of reflection-based FTIRM as an alternative to the widely adopted transmission-based FTIRM, which reduces specimen preparation time and broadens the range of specimens that can be imaged. In this study, mature mouse femurs were plastic-embedded and longitudinal sections were cut at a thickness of 4 μm for transmission-based FTIRM measurements. The remaining bone blocks were polished for specular reflectance-based FTIRM measurements on regions immediately adjacent to the transmission sections. Kramers-Kronig analysis of the reflectance data yielded the dielectric response from which the absorption coefficients were directly determined. The reflectance-derived absorbance was validated empirically using the transmission spectra from the thin sections. The spectral assignments for mineralization, carbonate substitution, and collagen cross-linking were indistinguishable in transmission and reflection geometries, while the stoichiometric/non-stoichiometric apatite crystallinity parameter shifted from 1032 / 1021 cm−1 in transmission-based to 1035 / 1025 cm−1 in reflection-based data. This theoretical demonstration and empirical validation of reflection-based FTIRM eliminates the need for thin sections of bone and more readily facilitates direct correlations with other methods such nanoindentation and quantitative backscatter electron imaging (qBSE) from the same specimen. It provides a unique framework for correlating bone’s material and mechanical properties. PMID:22455306

Performance and Challenges of Point of Use Devices for Lead ...

EPA Pesticide Factsheets

this presentation summarizes the performance of POU devices for the removal of lead and some other metals, in Flint, Michigan. The mechanism of POU filters for metal removal is described as being a combination of physical filtration with surface sorption and adherence to embedded functional groups in the carbon block, along with the certification process and how to find certified products from the web listings. Finally, there is a discussion of several alternative approaches for possible improvement of the NSF/ANSI 53 and 42 standards to improve the amount of protection afforded by the devices, in the future. this presentation summarizes the performance of POU devices for the removal of lead and some other metals, in Flint, Michigan. The mechanism of POU filters for metal removal is described as being a combination of physical filtration with surface sorption and adherence to embedded functional groups in the carbon block, along with the certification process and how to find certified products from the web listings. Finally, there is a discussion of several alternative approaches for possible improvement of the NSF/ANSI 53 and 42 standards to improve the amount of protection afforded by the devices, in the future.

Low-Power Embedded DSP Core for Communication Systems

NASA Astrophysics Data System (ADS)

Tsao, Ya-Lan; Chen, Wei-Hao; Tan, Ming Hsuan; Lin, Maw-Ching; Jou, Shyh-Jye

2003-12-01

This paper proposes a parameterized digital signal processor (DSP) core for an embedded digital signal processing system designed to achieve demodulation/synchronization with better performance and flexibility. The features of this DSP core include parameterized data path, dual MAC unit, subword MAC, and optional function-specific blocks for accelerating communication system modulation operations. This DSP core also has a low-power structure, which includes the gray-code addressing mode, pipeline sharing, and advanced hardware looping. Users can select the parameters and special functional blocks based on the character of their applications and then generating a DSP core. The DSP core has been implemented via a cell-based design method using a synthesizable Verilog code with TSMC 0.35[InlineEquation not available: see fulltext.]m SPQM and 0.25[InlineEquation not available: see fulltext.]m 1P5M library. The equivalent gate count of the core area without memory is approximately 50 k. Moreover, the maximum operating frequency of a[InlineEquation not available: see fulltext.] version is 100 MHz (0.35[InlineEquation not available: see fulltext.]m) and 140 MHz (0.25[InlineEquation not available: see fulltext.]m).

Robust and Blind 3D Mesh Watermarking in Spatial Domain Based on Faces Categorization and Sorting

NASA Astrophysics Data System (ADS)

Molaei, Amir Masoud; Ebrahimnezhad, Hossein; Sedaaghi, Mohammad Hossein

2016-06-01

In this paper, a 3D watermarking algorithm in spatial domain is presented with blind detection. In the proposed method, a negligible visual distortion is observed in host model. Initially, a preprocessing is applied on the 3D model to make it robust against geometric transformation attacks. Then, a number of triangle faces are determined as mark triangles using a novel systematic approach in which faces are categorized and sorted robustly. In order to enhance the capability of information retrieval by attacks, block watermarks are encoded using Reed-Solomon block error-correcting code before embedding into the mark triangles. Next, the encoded watermarks are embedded in spherical coordinates. The proposed method is robust against additive noise, mesh smoothing and quantization attacks. Also, it is stout next to geometric transformation, vertices and faces reordering attacks. Moreover, the proposed algorithm is designed so that it is robust against the cropping attack. Simulation results confirm that the watermarked models confront very low distortion if the control parameters are selected properly. Comparison with other methods demonstrates that the proposed method has good performance against the mesh smoothing attacks.

Maintaining clinical tissue archives and supporting human research: challenges and solutions.

PubMed

Giannini, Caterina; Oelkers, Michael M; Edwards, William D; Aubry, Marie Christine; Muncil, Maureen M; Mohamud, Koshin H; Sandleback, Sara G; Nowak, John M; Bridgeman, Andrew; Brown, Marie E; Cheville, John C

2011-03-01

The increasing number of requests for use of clinically archived tissue in translational research poses unique challenges. Conflicts may arise between pathologists who are responsible for overseeing and preserving the tissues and investigators who need these materials for research purposes. To evaluate the status of our institution's Tissue Registry Archive and to develop updated written policies and procedures to support a new modern and robust tracking system with features of a library loan system. An observational study was performed. We found the existing process for managing loans of tissue (slides and paraffin blocks) to be insufficient for the complexity and volume of this task. After extensive customization, a new tracking system was implemented in January 2008. Analysis of the first year of the system's use (2008) showed that of the 206,330 slides and 51,416 blocks loaned out in 2008, 92% and 94%, respectively, were returned by the due date. These rates were markedly improved from those before the new system: 61% and 47%, respectively, in 2005. Material permanently "lost" in 2008 represented only 0.02% of slides and 0.05% of blocks, none of which was the only diagnostic material for the case. With expanding needs for archived tissues for clinical care and growing demands for translational research, it is essential that pathology departments at institutions with large tissue-based research endeavors have a tracking and management system in place to meet clinical, educational, and research needs, as well as legal requirements.

Compact FPGA hardware architecture for public key encryption in embedded devices

PubMed Central

Morales-Sandoval, Miguel; Cumplido, René; Feregrino-Uribe, Claudia; Algredo-Badillo, Ignacio

2018-01-01

Security is a crucial requirement in the envisioned applications of the Internet of Things (IoT), where most of the underlying computing platforms are embedded systems with reduced computing capabilities and energy constraints. In this paper we present the design and evaluation of a scalable low-area FPGA hardware architecture that serves as a building block to accelerate the costly operations of exponentiation and multiplication in GF(p), commonly required in security protocols relying on public key encryption, such as in key agreement, authentication and digital signature. The proposed design can process operands of different size using the same datapath, which exhibits a significant reduction in area without loss of efficiency if compared to representative state of the art designs. For example, our design uses 96% less standard logic than a similar design optimized for performance, and 46% less resources than other design optimized for area. Even using fewer area resources, our design still performs better than its embedded software counterparts (190x and 697x). PMID:29360824

Computation of multi-dimensional viscous supersonic jet flow

NASA Technical Reports Server (NTRS)

Kim, Y. N.; Buggeln, R. C.; Mcdonald, H.

1986-01-01

A new method has been developed for two- and three-dimensional computations of viscous supersonic flows with embedded subsonic regions adjacent to solid boundaries. The approach employs a reduced form of the Navier-Stokes equations which allows solution as an initial-boundary value problem in space, using an efficient noniterative forward marching algorithm. Numerical instability associated with forward marching algorithms for flows with embedded subsonic regions is avoided by approximation of the reduced form of the Navier-Stokes equations in the subsonic regions of the boundary layers. Supersonic and subsonic portions of the flow field are simultaneously calculated by a consistently split linearized block implicit computational algorithm. The results of computations for a series of test cases relevant to internal supersonic flow is presented and compared with data. Comparison between data and computation are in general excellent thus indicating that the computational technique has great promise as a tool for calculating supersonic flow with embedded subsonic regions. Finally, a User's Manual is presented for the computer code used to perform the calculations.

Compact FPGA hardware architecture for public key encryption in embedded devices.

PubMed

Rodríguez-Flores, Luis; Morales-Sandoval, Miguel; Cumplido, René; Feregrino-Uribe, Claudia; Algredo-Badillo, Ignacio

2018-01-01

Security is a crucial requirement in the envisioned applications of the Internet of Things (IoT), where most of the underlying computing platforms are embedded systems with reduced computing capabilities and energy constraints. In this paper we present the design and evaluation of a scalable low-area FPGA hardware architecture that serves as a building block to accelerate the costly operations of exponentiation and multiplication in [Formula: see text], commonly required in security protocols relying on public key encryption, such as in key agreement, authentication and digital signature. The proposed design can process operands of different size using the same datapath, which exhibits a significant reduction in area without loss of efficiency if compared to representative state of the art designs. For example, our design uses 96% less standard logic than a similar design optimized for performance, and 46% less resources than other design optimized for area. Even using fewer area resources, our design still performs better than its embedded software counterparts (190x and 697x).

Profiling of potential driver mutations in sarcomas by targeted next generation sequencing.

PubMed

Andersson, Carola; Fagman, Henrik; Hansson, Magnus; Enlund, Fredrik

2016-04-01

Comprehensive genetic profiling by massively parallel sequencing, commonly known as next generation sequencing (NGS), is becoming the foundation of personalized oncology. For sarcomas very few targeted treatments are currently in routine use. In clinical practice the preoperative diagnostic workup of soft tissue tumours largely relies on core needle biopsies. Although mostly sufficient for histopathological diagnosis, only very limited amounts of formalin fixated paraffin embedded tissue are often available for predictive mutation analysis. Targeted NGS may thus open up new possibilities for comprehensive characterization of scarce biopsies. We therefore set out to search for driver mutations by NGS in a cohort of 55 clinically and morphologically well characterized sarcomas using low input of DNA from formalin fixated paraffin embedded tissues. The aim was to investigate if there are any recurrent or targetable aberrations in cancer driver genes in addition to known chromosome translocations in different types of sarcomas. We employed a panel covering 207 mutation hotspots in 50 cancer-associated genes to analyse DNA from nine gastrointestinal stromal tumours, 14 synovial sarcomas, seven myxoid liposarcomas, 22 Ewing sarcomas and three Ewing-like small round cell tumours at a large sequencing depth to detect also mutations that are subclonal or occur at low allele frequencies. We found nine mutations in eight different potential driver genes, some of which are potentially actionable by currently existing targeted therapies. Even though no recurrent mutations in driver genes were found in the different sarcoma groups, we show that targeted NGS-based sequencing is clearly feasible in a diagnostic setting with very limited amounts of paraffin embedded tissue and may provide novel insights into mesenchymal cell signalling and potentially druggable targets. Interestingly, we also identify five non-synonymous sequence variants in 4 established cancer driver genes in DNA from normal tissue from sarcoma patients that may possibly predispose or contribute to neoplastic development. Copyright © 2016 Elsevier Inc. All rights reserved.

Linking cases of illegal shootings of the endangered California condor using stable lead isotope analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Finkelstein, Myra E., E-mail: myraf@ucsc.edu; Kuspa, Zeka E.; Welch, Alacia

Lead poisoning is preventing the recovery of the critically endangered California condor (Gymnogyps californianus) and lead isotope analyses have demonstrated that ingestion of spent lead ammunition is the principal source of lead poisoning in condors. Over an 8 month period in 2009, three lead-poisoned condors were independently presented with birdshot embedded in their tissues, evidencing they had been shot. No information connecting these illegal shooting events existed and the timing of the shooting(s) was unknown. Using lead concentration and stable lead isotope analyses of feathers, blood, and recovered birdshot, we observed that: i) lead isotope ratios of embedded shot frommore » all three birds were measurably indistinguishable from each other, suggesting a common source; ii) lead exposure histories re-constructed from feather analysis suggested that the shooting(s) occurred within the same timeframe; and iii) two of the three condors were lead poisoned from a lead source isotopically indistinguishable from the embedded birdshot, implicating ingestion of this type of birdshot as the source of poisoning. One of the condors was subsequently lead poisoned the following year from ingestion of a lead buckshot (blood lead 556 µg/dL), illustrating that ingested shot possess a substantially greater lead poisoning risk compared to embedded shot retained in tissue (blood lead ∼20 µg/dL). To our knowledge, this is the first study to use lead isotopes as a tool to retrospectively link wildlife shooting events. - Highlights: • We conducted a case-based analysis of illegal shootings of California condors. • Blood and feather Pb isotopes were used to reconstruct the illegal shooting events. • Embedded birdshot from the three condors had the same Pb isotope ratios. • Feather and blood Pb isotopes indicated that the condors were shot in a common event. • Ingested shot causes substantially greater lead exposure compared to embedded shot.« less

The quaternary lidocaine derivative QX-314 in combination with bupivacaine for long-lasting nerve block: Efficacy, toxicity, and the optimal formulation in rats

PubMed Central

Zheng, Qingshan; Yang, Xiaolin; Lv, Rong; Ma, Longxiang; Liu, Jin; Zhu, Tao; Zhang, Wensheng

2017-01-01

Objective The quaternary lidocaine derivative (QX-314) in combination with bupivacaine can produce long-lasting nerve blocks in vivo, indicating potential clinical application. The aim of the study was to investigate the efficacy, safety, and the optimal formulation of this combination. Methods QX-314 and bupivacaine at different concentration ratios were injected in the vicinity of the sciatic nerve in rats; bupivacaine and saline served as controls (n = 6~10). Rats were inspected for durations of effective sensory and motor nerve blocks, systemic adverse effects, and histological changes of local tissues. Mathematical models were established to reveal drug-interaction, concentration-effect relationships, and the optimal ratio of QX-314 to bupivacaine. Results 0.2~1.5% QX-314 with 0.03~0.5% bupivacaine produced 5.8~23.8 h of effective nerve block; while 0.5% bupivacaine alone was effective for 4 h. No systemic side effects were observed; local tissue reactions were similar to those caused by 0.5% bupivacaine if QX-314 were used < 1.2%. The weighted modification model was successfully established, which revealed that QX-314 was the main active ingredient while bupivacaine was the synergist. The formulation, 0.9% QX-314 plus 0.5% bupivacaine, resulted in 10.1 ± 0.8 h of effective sensory and motor nerve blocks. Conclusion The combination of QX-314 and bupivacaine facilitated prolonged sciatic nerve block in rats with a satisfactory safety profile, maximizing the duration of nerve block without clinically important systemic and local tissue toxicity. It may emerge as an alternative approach to post-operative pain treatment. PMID:28334014

The quaternary lidocaine derivative QX-314 in combination with bupivacaine for long-lasting nerve block: Efficacy, toxicity, and the optimal formulation in rats.

PubMed

Yin, Qinqin; Li, Jun; Zheng, Qingshan; Yang, Xiaolin; Lv, Rong; Ma, Longxiang; Liu, Jin; Zhu, Tao; Zhang, Wensheng

2017-01-01

The quaternary lidocaine derivative (QX-314) in combination with bupivacaine can produce long-lasting nerve blocks in vivo, indicating potential clinical application. The aim of the study was to investigate the efficacy, safety, and the optimal formulation of this combination. QX-314 and bupivacaine at different concentration ratios were injected in the vicinity of the sciatic nerve in rats; bupivacaine and saline served as controls (n = 6~10). Rats were inspected for durations of effective sensory and motor nerve blocks, systemic adverse effects, and histological changes of local tissues. Mathematical models were established to reveal drug-interaction, concentration-effect relationships, and the optimal ratio of QX-314 to bupivacaine. 0.2~1.5% QX-314 with 0.03~0.5% bupivacaine produced 5.8~23.8 h of effective nerve block; while 0.5% bupivacaine alone was effective for 4 h. No systemic side effects were observed; local tissue reactions were similar to those caused by 0.5% bupivacaine if QX-314 were used < 1.2%. The weighted modification model was successfully established, which revealed that QX-314 was the main active ingredient while bupivacaine was the synergist. The formulation, 0.9% QX-314 plus 0.5% bupivacaine, resulted in 10.1 ± 0.8 h of effective sensory and motor nerve blocks. The combination of QX-314 and bupivacaine facilitated prolonged sciatic nerve block in rats with a satisfactory safety profile, maximizing the duration of nerve block without clinically important systemic and local tissue toxicity. It may emerge as an alternative approach to post-operative pain treatment.

Evaluation of Protein Profiles From Treated Xenograft Tumor Models Identifies an Antibody Panel for Formalin-fixed and Paraffin-embedded (FFPE) Tissue Analysis by Reverse Phase Protein Arrays (RPPA)*

PubMed Central

Bader, Sabine; Zajac, Magdalena; Friess, Thomas; Ruge, Elisabeth; Rieder, Natascha; Gierke, Berthold; Heubach, Yvonne; Thomas, Marlene; Pawlak, Michael

2015-01-01

Reverse phase protein arrays (RPPA) are an established tool for measuring the expression and activation status of multiple proteins in parallel using only very small amounts of tissue. Several studies have demonstrated the value of this technique for signaling pathway analysis using proteins extracted from fresh frozen (FF) tissue in line with validated antibodies for this tissue type; however, formalin fixation and paraffin embedding (FFPE) is the standard method for tissue preservation in the clinical setting. Hence, we performed RPPA to measure profiles for a set of 300 protein markers using matched FF and FFPE tissue specimens to identify which markers performed similarly using the RPPA technique in fixed and unfixed tissues. Protein lysates were prepared from matched FF and FFPE tissue specimens of individual tumors taken from three different xenograft models of human cancer. Materials from both untreated mice and mice treated with either anti-HER3 or bispecific anti-IGF-1R/EGFR monoclonal antibodies were analyzed. Correlations between signals from FF and FFPE tissue samples were investigated. Overall, 60 markers were identified that produced comparable profiles between FF and FFPE tissues, demonstrating significant correlation between the two sample types. The top 25 markers also showed significance after correction for multiple testing. The panel of markers covered several clinically relevant tumor signaling pathways and both phosphorylated and nonphosphorylated proteins were represented. Biologically relevant changes in marker expression were noted when RPPA profiles from treated and untreated xenografts were compared. These data demonstrate that, using appropriately selected antibodies, RPPA analysis from FFPE tissue is well feasible and generates biologically meaningful information. The identified panel of markers that generate similar profiles in matched fixed and unfixed tissue samples may be clinically useful for pharmacodynamic studies of drug effect using FFPE tissues. PMID:26106084

Effect of Antigen Retrieval Methods on Nonspecific Binding of Antibody-Metal Nanoparticle Conjugates on Formalin-Fixed Paraffin-Embedded Tissue.

PubMed

Zhang, Yuying; Wang, Xin-Ping; Perner, Sven; Bankfalvi, Agnes; Schlücker, Sebastian

2018-01-02

Immunohistochemical analysis of formalin-fixed paraffin-embedded (FFPE) tissues provides important diagnostic and prognostic information in pathology. Metal nanoparticles (NPs) and, in particular, surface-enhanced Raman scattering (SERS) nanotags as a new class of labeling reagents are promising to be used for multiplexed protein profiling on tissue sections. However, nonspecific binding of NPs onto the tissue specimens greatly hampers their clinical applications. In this study, we found that the antigen retrieval method strongly influences the extent of nonspecific binding of the antibody-SERS NP conjugates to the tissue. Our SERS labels comprised ca. 70 nm Au nanostars coated with ethylene glycol-modified Raman reporter molecules for hydrophilic stabilization and subsequent covalent bioconjugation to antibodies. We systematically investigated the influence of heat- and protease-induced epitope retrieval (HIER and PIER, respectively) on the immunostaining quality of prostate-specific antigen (PSA) on human prostate tissue sections. The best staining results were obtained with PIER. Pretreatment of the tissue sections by HIER led to selective but nonspecific adsorption of the antibody-Au nanostar conjugates onto epithelial cells, while enzymatic treatment within PIER did not. In addition to gold nanostars, also other types of metal NPs with different shapes and sizes (including ca. 20 nm quasi-spherical Au NPs and ca. 60 nm quasi-spherical Au/Ag nanoshells) as well as tissue sections from different organs (including prostate and breast) were tested; in each case the same tendency was observed, i.e., PIER yielded better results than HIER. Therefore, we recommend PIER for future NP-based tissue immunostaining such as immuno-SERS microscopy. Alternatively, for antigens that can only be unmasked by heating, PEGylation of the NPs is recommended to avoid nonspecific binding.

Effects of a Multidisciplinary Approach to Improve Volume of Diagnostic Material in CT-Guided Lung Biopsies.

PubMed

Ferguson, Philip E; Sales, Catherine M; Hodges, Dalton C; Sales, Elizabeth W

2015-01-01

Recent publications have emphasized the importance of a multidisciplinary strategy for maximum conservation and utilization of lung biopsy material for advanced testing, which may determine therapy. This paper quantifies the effect of a multidisciplinary strategy implemented to optimize and increase tissue volume in CT-guided transthoracic needle core lung biopsies. The strategy was three-pronged: (1) once there was confidence diagnostic tissue had been obtained and if safe for the patient, additional biopsy passes were performed to further increase volume of biopsy material, (2) biopsy material was placed in multiple cassettes for processing, and (3) all tissue ribbons were conserved when cutting blocks in the histology laboratory. This study quantifies the effects of strategies #1 and #2. This retrospective analysis comparing CT-guided lung biopsies from 2007 and 2012 (before and after multidisciplinary approach implementation) was performed at a single institution. Patient medical records were reviewed and main variables analyzed include biopsy sample size, radiologist, number of blocks submitted, diagnosis, and complications. The biopsy sample size measured was considered to be directly proportional to tissue volume in the block. Biopsy sample size increased 2.5 fold with the average total biopsy sample size increasing from 1.0 cm (0.9-1.1 cm) in 2007 to 2.5 cm (2.3-2.8 cm) in 2012 (P<0.0001). The improvement was statistically significant for each individual radiologist. During the same time, the rate of pneumothorax requiring chest tube placement decreased from 15% to 7% (P = 0.065). No other major complications were identified. The proportion of tumor within the biopsy material was similar at 28% (23%-33%) and 35% (30%-40%) for 2007 and 2012, respectively. The number of cases with at least two blocks available for testing increased from 10.7% to 96.4% (P<0.0001). The effect of this multidisciplinary strategy to CT-guided lung biopsies was effective in significantly increasing tissue volume and number of blocks available for advanced diagnostic testing.

Combination therapy efficacy of catgut embedding acupuncture and diet intervention on interleukin-6 levels and body mass index in obese patients

NASA Astrophysics Data System (ADS)

Tjan, P. M.; Srilestari, A.; Abdurrohim, K.; Kresnawan, T.

2017-08-01

Obesity is a major health problem worldwide, affecting more than 500 million adults with an additional 1.5 billion adults classified as overweight. Acupuncture has been recognized as an adjunctive therapy for obesity, and recent evidence suggests its potential to reduce the inflammatory response in adipose tissue, a condition believed to be responsible for obesity-related health problems. Interleukin-6 (IL-6) has been proposed as an important mediator of the inflammatory response in adipose tissue, but the number of studies addressing the issue is still limited. A double-blind, randomized, placebo-controlled trial was conducted with36 obese patients currently receiving dietary intervention. The patients were randomly allocated into the catgut embedding acupuncture group with diet intervention or the sham (placebo) embedding acupuncture group with diet intervention. Catgut embedding therapy was given twice at CV12 Zhongwan, ST25 Tianshu, CV6 Qihai, and SP6 Sanyinjiao acupoints with two week intervals between procedures. The study endpoints were the IL-6 levels in the blood plasma and body mass index (BMI), measured before and after the intervention. We observed a reduction in the IL-6 levels (mean reduction 0.13 pg/mL, 95% CI: 0.03-0.23) and BMI (mean reduction 0.66, 95% CI 0.43-0.88) in the accupuncture group. The average difference in mean reduction of BMI between the accupuncture and sham groups was 0.34 (95% CI: 0.17-0.52). No difference was found in mean IL-6 reduction between the two groups (95% CI: -0.17 to 0.06). The results suggest that acupoint catgut embedding therapy may help reduce IL-6 levels and BMI in obese patients receiving dietary intervention.

[Effect of Medicated-catgut Embedding at "Changqiang" (GV 1) on Mechanical Pain Threshold and P 38 MAPK Expression in Spinal Cord Tissue in Anus Incisional Pain Rats].

PubMed

Shu, Tao; Zhang, Shi-Ti; Yan, Feng; Ke, Yu-Pei; Wang, Jun

2017-10-25

To observe the effect of medicated-catgut embedding at "Changqiang"(GV 1) on regional pain reaction and expression of p 38 MAPK in the dorsal horn of spinal cord in anus incisional pain rats, so as to explore its analgesic mechanism. Forty male SD rats were randomly divided into control, model, GV 1-embedding and sham acupoint embedding groups ( n =10 rats in each group). The anus incisional pain model was established by making a radial incision (about 10 mm length) at the left lithotomy position of the anus with a surgical knife, and the mechanical pain threshold (PT) was measured by using a Von Frey before and 4, 8, 12, 24 h after operation. The medicated-catgut (about 12.5 mm length/kg body weight) was implanted in the subcutaneous tissue of GV 1 region. The immunoactivity of p 38 MAPK was determined by immunohistochemistry. Compared with the control group, the mechanical PTs were significantly decreased 4, 8, 12 and 24 h after operation both at the site of incision and about 15 mm proximal to the site of incision in the model group ( P <0.05), and the immunoactivity of phosphorylated (p)-p 38 MAPK in the superficial layer of dorsal horns of lumbar spinal cord was significantly increased(24 h)after operation( P <0.05). Compared with the model group, the PTs were significantly increased 8, 12 and 24 h after operation at the site of incision, and 12 h and 24 h at the site about 15 mm proximal to the incision region ( P <0.05), and the immunoactivity level of p-p 38 MAPK was significantly down-regulated in the GV 1-embedding group ( P <0.05). No significant changes were found in the PT and p-p 38 MAPK immunoactivity levels in the sham acupoint embedding group ( P <0.05). Medicated-catgut embedding at "Changqiang"(GV 1) has an analgesic effect in anus incisional pain model rats, which may be related to its effect in down-regulating the expression of p 38 MAPK in the dorsal horn of lumbar spinal cord.

Ruxolitinib

MedlinePlus

... by scar tissue and causes decreased blood cell production). Ruxolitinib is in a class of medications called kinase inhibitors. It works by blocking an enzyme that causes scar tissue to form in the bone marrow.

Comparative analysis of nonlinear dimensionality reduction techniques for breast MRI segmentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akhbardeh, Alireza; Jacobs, Michael A.; Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205

2012-04-15

Purpose: Visualization of anatomical structures using radiological imaging methods is an important tool in medicine to differentiate normal from pathological tissue and can generate large amounts of data for a radiologist to read. Integrating these large data sets is difficult and time-consuming. A new approach uses both supervised and unsupervised advanced machine learning techniques to visualize and segment radiological data. This study describes the application of a novel hybrid scheme, based on combining wavelet transform and nonlinear dimensionality reduction (NLDR) methods, to breast magnetic resonance imaging (MRI) data using three well-established NLDR techniques, namely, ISOMAP, local linear embedding (LLE), andmore » diffusion maps (DfM), to perform a comparative performance analysis. Methods: Twenty-five breast lesion subjects were scanned using a 3T scanner. MRI sequences used were T1-weighted, T2-weighted, diffusion-weighted imaging (DWI), and dynamic contrast-enhanced (DCE) imaging. The hybrid scheme consisted of two steps: preprocessing and postprocessing of the data. The preprocessing step was applied for B{sub 1} inhomogeneity correction, image registration, and wavelet-based image compression to match and denoise the data. In the postprocessing step, MRI parameters were considered data dimensions and the NLDR-based hybrid approach was applied to integrate the MRI parameters into a single image, termed the embedded image. This was achieved by mapping all pixel intensities from the higher dimension to a lower dimensional (embedded) space. For validation, the authors compared the hybrid NLDR with linear methods of principal component analysis (PCA) and multidimensional scaling (MDS) using synthetic data. For the clinical application, the authors used breast MRI data, comparison was performed using the postcontrast DCE MRI image and evaluating the congruence of the segmented lesions. Results: The NLDR-based hybrid approach was able to define and segment both synthetic and clinical data. In the synthetic data, the authors demonstrated the performance of the NLDR method compared with conventional linear DR methods. The NLDR approach enabled successful segmentation of the structures, whereas, in most cases, PCA and MDS failed. The NLDR approach was able to segment different breast tissue types with a high accuracy and the embedded image of the breast MRI data demonstrated fuzzy boundaries between the different types of breast tissue, i.e., fatty, glandular, and tissue with lesions (>86%). Conclusions: The proposed hybrid NLDR methods were able to segment clinical breast data with a high accuracy and construct an embedded image that visualized the contribution of different radiological parameters.« less

Embedded top-coat for reducing the effect out of band radiation in EUV lithography

NASA Astrophysics Data System (ADS)

Du, Ke; Siauw, Meiliana; Valade, David; Jasieniak, Marek; Voelcker, Nico; Trefonas, Peter; Thackeray, Jim; Blakey, Idriss; Whittaker, Andrew

2017-03-01

Out of band (OOB) radiation from the EUV source has significant implications for the performance of EUVL photoresists. Here we introduce a surface-active polymer additive, capable of partitioning to the top of the resist film during casting and annealing, to protect the underlying photoresist from OOB radiation. Copolymers were prepared using reversible addition-fragmentation chain transfer (RAFT) polymerization, and rendered surface active by chain extension with a block of fluoro-monomer. Films were prepared from the EUV resist with added surface-active Embedded Barrier Layer (EBL), and characterized using measurements of contact angles and spectroscopic ellipsometry. Finally, the lithographic performance of the resist containing the EBL was evaluated using Electron Beam Lithography exposure

PRCC-TFE3 dual-fusion FISH assay: A new method for identifying PRCC-TFE3 renal cell carcinoma in paraffin-embedded tissue

PubMed Central

Liu, Ning; Wang, Zhen; Miao, Baolei; Li, Dongmei; Guo, Hongqian

2017-01-01

PRCC-TFE3 renal cell carcinoma (RCC) is one of the most common types of Xp11.2 translocation renal cell carcinoma (tRCC), of which the diagnosis mainly relies on reverse transcription-polymerase chain reaction (RT-PCR) or chromosomal analysis in fresh frozen samples. Herein, we developed a new dual-fusion fluorescence in situ hybridization (FISH) probe to succinctly identify PRCC-TFE3 RCC in paraffin-embedded tissue. We immunohistochemically analyzed TFE3 and cathepsin K expression in 23 cases of Xp11.2 tRCC which had been confirmed by break-apart TFE3 FISH probe. Next, the dual-fusion FISH assay was performed on these selected cases. Twenty typical cases of clear renal cell carcinoma and 20 cases of papillary renal cell carcinoma were collected as control groups. Seven cases were finally confirmed as PRCC-TFE3 RCC by FISH detection, emerging dual-fusion signals, of which 2 cases were identified as PRCC-TFE3 RCC by RT-PCR previously. All remaining cases were negative for the PRCC-TFE3 rearrangement by FISH. The TFE3 immunohistochemistry was positive in 22/23 cases and the cathepsin K was positive in 16/23 cases. All 7 PRCC-TFE3 RCCs showed positive cathepsin K immunoreactivity. Our results reveal that PRCC-TFE3 dual-fusion FISH probe is an efficient and concise technique for diagnosing PRCC-TFE3 RCC in paraffin-embedded tissue. PMID:28949976

Clearing a Pile of Unknown Objects using Interactive Perception

DTIC Science & Technology

2012-11-01

blocks and the shampoo . The robot now decides to grasp the bottle of shampoo . Next, the tissue box and the chunk of wood are pushed and grasped. The...20 seconds. Poking an object requires 12 (a) Initial pile (b) Poking macaroni box (c) After poking (d) Grasping shampoo (e) After grasping (f) Pooking...objects: a tissue box, a chunk of wood, a bottle of shampoo , a box of macaroni, and toy blocks. The algorithm switches between pushing to verify

No evidence for Helicobacter pylori in oral lichen planus.

PubMed

Hulimavu, Shwetha R; Mohanty, Leeky; Tondikulam, Narayan V; Shenoy, Sadhana; Jamadar, Saleha; Bhadranna, Abhishek

2014-09-01

Oral lichen planus is a T-cell-mediated mucosal disease of unknown etiology. Numerous predisposing factors have been put forward in the etiology of this disease. This includes stress, drugs, genetic susceptibility, certain viruses, and bacterial infections. Recently, there have been studies published on possible role of Helicobacter pylori infection in pathogenesis of mucocutaneous diseases including oral lichen planus (OLP). The aim of this study was to detect immunohistochemically the presence of Helicobacter pylori in oral lichen planus. Paraffin-embedded tissue blocks of 50 cases of OLP and 10 cases of normal buccal mucosal biopsies and 6 endoscopic biopsies of patients with peptic ulcer (control group) were sectioned and stained by hematoxylin and eosin. Serial sections of same were stained immunohistochemically using Anti-Helicobacter pylori antibody and observed under microscope for presence or absence of Helicobacter pylori. Except for the control group, none of the cases of OLP and normal buccal mucosal biopsies showed positivity for Helicobacter pylori. As we did not detect the presence of Helicobacter pylori in any of the OLP cases, we question the role of these organisms in the pathogenesis of OLP planus if any. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

[Roles of histologic examination and polymerase chain reaction in diagnosis of toxoplasmic lymphadenitis].

PubMed

Dai, Lin; Huang, Juan; Tang, Yuan; Liao, Dian-ying; Dong, Dan-dan; Xu, Gang; Li, Gan-di

2010-06-01

To study the roles of histologic examination and polymerase chain reaction in diagnosis of toxoplasmic lymphadenitis (TL). Forty-six archival cases of histologically diagnosed TL, encountered during the period from April, 1999 to September, 2009 and with the paraffin-embedded lymph node tissue blocks available, were enrolled into the study. The presence of genome fragments of Toxoplasma gondii (T. gondii) was analyzed using semi-nested polymerase chain reaction (PCR). Thirty cases of one or two histopathologic triad of TL as the controls. The positive rate of PCR in TL group was 76.1% (35/46), as compared to 10.0% (3/30) in the control group. The difference was of statistical significance. The sensitivity and specificity of the histologic triad in diagnosing TL was 92.1% (35/38) and 71.1% (27/38), respectively. The predictive value of positive and negative PCR results was 76.1% (35/46) and 90.0% (27/30). respectively. The high specificity but low sensitivity of applying the histologic triad in diagnosing TL cases may be due to the occurrence of atypical histologic pattern. The sensitivity is improved with the use of semi-nested PCR in detecting T. gondii DNA.

Mechanisms of Local Stress Sensing in Multifunctional Polymer Films Using Fluorescent Tetrapod Nanocrystals

DOE PAGES

Raja, Shilpa N.; Zherebetskyy, Danylo; Wu, Siva; ...

2016-07-13

Nanoscale stress-sensing can be used across fields ranging from detection of incipient cracks in structural mechanics to monitoring forces in biological tissues. We demonstrate how tetrapod quantum dots (tQDs) embedded in block copolymers act as sensors of tensile/compressive stress. Remarkably, tQDs can detect their own composite dispersion and mechanical properties with a switch in optomechanical response when tQDs are in direct contact. Using experimental characterizations, atomistic simulations and finite-element analyses, we show that under tensile stress, densely packed tQDs exhibit a photoluminescence peak shifted to higher energies ("blue-shift") due to volumetric compressive stress in their core; loosely packed tQDs exhibitmore » a peak shifted to lower energies ("red-shift") from tensile stress in the core. The stress shifts result from the tQD's unique branched morphology in which the CdS arms act as antennas that amplify the stress in the CdSe core. Our nanocomposites exhibit excellent cyclability and scalability with no degraded properties of the host polymer. Colloidal tQDs allow sensing in many materials to potentially enable autoresponsive, smart structural nanocomposites that self-predict upcoming fracture.« less

The Prevalence of Human Papilloma Virus in Esophageal Squamous Cell Carcinoma

PubMed Central

Noori, Sadat; Monabati, Ahmad; Ghaderi, Abbasali

2012-01-01

Background: Carcinomas of esophagus, mostly squamous cell carcinomas, occur throughout the world. There are a number of suspected genetic or environmental etiologies. Human papilloma virus (HPV) is said to be a major etiology in areas with high incidence of esophageal carcinoma, while it is hardly detectable in low incidence regions. This study was designed to evaluate the prevalence of HPV in esophageal squamous cell carcinoma (ESCC) cases diagnosed in Pathology Department, Medical School, Shiraz University of Medical Sciences. Methods: DNA material for PCR amplification of HPV genome was extracted from formalin-fixed paraffin-embedded tissue blocks of 92 cases of ESCC, diagnosed during 20 years from 1982 to 2002. Polymerase chain reaction was performed for amplification and detection of common HPV and type specific HPV-16 and HPV-18 genomic sequences in the presence of positive control (HPV-18 and HPV positive biopsies of uterine exocervix) and additional internal controls i.e. beta-globin and cytotoxic T lymphocyte antigen 4 (CTLA4). Result: Good amplification of positive control and internal controls was observed. However, no amplification of HPV genome was observed. Conclusion: There is no association between HPV infection and the development of esophageal squamous cell carcinoma in the cases evaluated. PMID:23115442

Chlorella vulgaris triggers apoptosis in hepatocarcinogenesis-induced rats*

PubMed Central

Mohd Azamai, Emey Suhana; Sulaiman, Suhaniza; Mohd Habib, Shafina Hanim; Looi, Mee Lee; Das, Srijit; Abdul Hamid, Nor Aini; Wan Ngah, Wan Zurinah; Mohd Yusof, Yasmin Anum

2009-01-01

Chlorella vulgaris (CV) has been reported to have antioxidant and anticancer properties. We evaluated the effect of CV on apoptotic regulator protein expression in liver cancer-induced rats. Male Wistar rats (200~250 g) were divided into eight groups: control group (normal diet), CDE group (choline deficient diet supplemented with ethionine in drinking water to induce hepatocarcinogenesis), CV groups with three different doses of CV (50, 150, and 300 mg/kg body weight), and CDE groups treated with different doses of CV (50, 150, and 300 mg/kg body weight). Rats were sacrificed at various weeks and liver tissues were embedded in paraffin blocks for immunohistochemistry studies. CV, at increasing doses, decreased the expression of anti-apoptotic protein, Bcl-2, but increased the expression of pro-apoptotic protein, caspase 8, in CDE rats, which was correlated with decreased hepatoctyes proliferation and increased apoptosis as determined by bromodeoxy-uridine (BrdU) labeling and terminal deoxynucleotidyl transferase mediated dUTP nick-end labeling (TUNEL) assay, respectively. Our study shows that CV has definite chemopreventive effect by inducing apoptosis via decreasing the expression of Bcl-2 and increasing the expression of caspase 8 in hepatocarcinogenesis-induced rats. PMID:19198018

Effects of the conjugated equine estrogen/bazedoxifene tissue-selective estrogen complex (TSEC) on mammary gland and breast cancer in mice.

PubMed

Song, Yan; Santen, Richard J; Wang, Ji-ping; Yue, Wei

2012-12-01

A tissue-selective estrogen complex (TSEC), combining a selective estrogen receptor modulator, bazedoxifene (BZA), with conjugated equine estrogen (CEE), represents a novel strategy of menopausal hormone therapy without involving a progestin. We hypothesized that the antiestrogenic properties of BZA can also block the estrogenic effects of CEE on breast tissue and thereby prevent breast cancer in women. To test our hypothesis, the effects of estradiol (E(2)), CEE, and BZA on mammary gland and breast cancer xenografts were assessed in mouse models. In immature castrate mice, BZA completely blocked CEE- or E(2)-stimulated ductal and terminal end bud growth of mammary gland as well as estrogen-responsive gene expression. As a positive control, E(2) stimulated tumor growth in nude mice bearing MCF-7 xenografts. This effect was completely blocked by BZA as were E(2)-stimulated expression of PR, pS2 (trefoil factor 1), cMyc, and AREG; the enhancement of Ki67 and proliferating cell nuclear antigen (PCNA); and the antiapoptotic effect. CEE was much less potent than E(2) in stimulating Ki67, reducing apoptosis, and stimulating gene expression, but all effects were blocked by BZA. Unexpectedly, CEE alone, even at high doses, did not stimulate tumor growth. As confirmation of its absorption and deconjugation, CEE caused a 6-fold increase in uterine weight and stimulation of gene expression. These data support our hypothesis that the net effect of the CEE/BZA TSEC is to block estrogen action in benign and malignant breast tissue. These findings provide a rationale for a clinical study to determine whether this TSEC prevents breast cancer in women.

Clean image synthesis and target numerical marching for optical imaging with backscattering light

PubMed Central

Pu, Yang; Wang, Wubao

2011-01-01

Scanning backscattering imaging and independent component analysis (ICA) are used to probe targets hidden in the subsurface of a turbid medium. A new correction procedure is proposed and used to synthesize a “clean” image of a homogeneous host medium numerically from a set of raster-scanned “dirty” backscattering images of the medium with embedded targets. The independent intensity distributions on the surface of the medium corresponding to individual targets are then unmixed using ICA of the difference between the set of dirty images and the clean image. The target positions are localized by a novel analytical method, which marches the target to the surface of the turbid medium until a match with the retrieved independent component is accomplished. The unknown surface property of the turbid medium is automatically accounted for by this method. Employing clean image synthesis and target numerical marching, three-dimensional (3D) localization of objects embedded inside a turbid medium using independent component analysis in a backscattering geometry is demonstrated for the first time, using as an example, imaging a small piece of cancerous prostate tissue embedded in a host consisting of normal prostate tissue. PMID:21483608

Characterization of an Adhesion-Associated Tumor Suppressor in Breast Cancer

DTIC Science & Technology

2001-08-01

Western blot analysis were invasive and associated with fibrous connective tissue (Fig. 4, B of whole cell lysates resolved by SDS-PAGE was...of breast cancer. Immunohistochemical analyses of archival, formalin-fixed paraffin-embedded specimens of benign and malignant breast tissues confirm...10A cells. In particular, EphA2 destabilizes cell-cell attachments while increasing cell interactions with extracellular matrix (ECM proteins). We have

Role of Macrophage-Induced Inflammation in Mesothelioma

DTIC Science & Technology

2010-07-01

in human mesothelioma tumors and correlate immune cell infiltration with histopathologic subtype (months 1-6). Using tumor tissue microarrays of... histopathologic subtype (months 1-6). • Acquired 71 fixed and paraffin-embedded mesothelioma tumor samples • Prepared mesothelioma tumor tissue...Biol., 2008. 84: p. 1-8. 5. Dave, S.S., et al., Prediction of survival in follicular lymphoma based on molecular features of tumor-infiltrating

Ultrasonographic diagnosis of porcupine quill foreign bodies in the plantar flexor tendon sheath region in a heifer

PubMed Central

Mulon, Pierre-Yves; Achard, Damien; Babkine, Marie

2010-01-01

A 17-month-old Holstein heifer was presented for persistent enlargement above the right hind fetlock of 1-month’s duration. Diffuse plantar soft tissue swelling was present on the radiographs and ultrasonography revealed the presence of multiple porcupine quill extremities embedded in the subcutaneous tissue within the flexor tendon sheath wall. Surgical removal was performed. PMID:21037892

Chondrogenic induction of mesenchymal stromal/stem cells from Wharton's jelly embedded in alginate hydrogel and without added growth factor: an alternative stem cell source for cartilage tissue engineering.

PubMed

Reppel, Loïc; Schiavi, Jessica; Charif, Naceur; Leger, Léonore; Yu, Hao; Pinzano, Astrid; Henrionnet, Christel; Stoltz, Jean-François; Bensoussan, Danièle; Huselstein, Céline

2015-12-30

Due to their intrinsic properties, stem cells are promising tools for new developments in tissue engineering and particularly for cartilage tissue regeneration. Although mesenchymal stromal/stem cells from bone marrow (BM-MSC) have long been the most used stem cell source in cartilage tissue engineering, they have certain limits. Thanks to their properties such as low immunogenicity and particularly chondrogenic differentiation potential, mesenchymal stromal/stem cells from Wharton's jelly (WJ-MSC) promise to be an interesting source of MSC for cartilage tissue engineering. In this study, we propose to evaluate chondrogenic potential of WJ-MSC embedded in alginate/hyaluronic acid hydrogel over 28 days. Hydrogels were constructed by the original spraying method. Our main objective was to evaluate chondrogenic differentiation of WJ-MSC on three-dimensional scaffolds, without adding growth factors, at transcript and protein levels. We compared the results to those obtained from standard BM-MSC. After 3 days of culture, WJ-MSC seemed to be adapted to their new three-dimensional environment without any detectable damage. From day 14 and up to 28 days, the proportion of WJ-MSC CD73(+), CD90(+), CD105(+) and CD166(+) decreased significantly compared to monolayer marker expression. Moreover, WJ-MSC and BM-MSC showed different phenotype profiles. After 28 days of scaffold culture, our results showed strong upregulation of cartilage-specific transcript expression. WJ-MSC exhibited greater type II collagen synthesis than BM-MSC at both transcript and protein levels. Furthermore, our work highlighted a relevant result showing that WJ-MSC expressed Runx2 and type X collagen at lower levels than BM-MSC. Once seeded in the hydrogel scaffold, WJ-MSC and BM-MSC have different profiles of chondrogenic differentiation at both the phenotypic level and matrix synthesis. After 4 weeks, WJ-MSC, embedded in a three-dimensional environment, were able to adapt to their environment and express specific cartilage-related genes and matrix proteins. Today, WJ-MSC represent a real alternative source of stem cells for cartilage tissue engineering.

Dynamic culture yields engineered myocardium with near-adult functional output

PubMed Central

Jackman, Christopher P.; Carlson, Aaron L.; Bursac, Nenad

2016-01-01

Engineered cardiac tissues hold promise for cell therapy and drug development, but exhibit inadequate function and maturity. In this study, we sought to significantly improve the function and maturation of rat and human engineered cardiac tissues. We developed dynamic, free-floating culture conditions for engineering “cardiobundles”, 3-dimensional cylindrical tissues made from neonatal rat cardiomyocytes or human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) embedded in fibrin-based hydrogel. Compared to static culture, 2-week dynamic culture of neonatal rat cardiobundles significantly increased expression of sarcomeric proteins, cardiomyocyte size (~2.1-fold), contractile force (~3.5-fold), and conduction velocity of action potentials (~1.4-fold). The average contractile force per cross-sectional area (59.7 mN/mm2) and conduction velocity (52.5 cm/sec) matched or approached those of adult rat myocardium, respectively. The inferior function of statically cultured cardiobundles was rescued by transfer to dynamic conditions, which was accompanied by an increase in mTORC1 activity and decline in AMPK phosphorylation and was blocked by rapamycin. Furthermore, dynamic culture effects did not stimulate ERK1/2 pathway and were insensitive to blockers of mechanosensitive channels, suggesting increased nutrient availability rather than mechanical stimulation as the upstream activator of mTORC1. Direct comparison with phenylephrine treatment confirmed that dynamic culture promoted physiological cardiomyocyte growth rather than pathological hypertrophy. Optimized dynamic culture conditions also augmented function of human cardiobundles made reproducibly from cardiomyocytes derived from multiple hPSC lines, resulting in significantly increased contraction force (~2.5-fold) and conduction velocity (~1.4-fold). The average specific force of 23.2 mN/mm2 and conduction velocity of 25.8 cm/sec approached the functional metrics of adult human myocardium. In conclusion, we have developed a versatile methodology for engineering cardiac tissues with a near-adult functional output without the need for exogenous electrical or mechanical stimulation, and have identified mTOR signaling as an important mechanism for advancing tissue maturation and function in vitro. PMID:27723557

Dynamic culture yields engineered myocardium with near-adult functional output.

PubMed

Jackman, Christopher P; Carlson, Aaron L; Bursac, Nenad

2016-12-01

Engineered cardiac tissues hold promise for cell therapy and drug development, but exhibit inadequate function and maturity. In this study, we sought to significantly improve the function and maturation of rat and human engineered cardiac tissues. We developed dynamic, free-floating culture conditions for engineering "cardiobundles", 3-dimensional cylindrical tissues made from neonatal rat cardiomyocytes or human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) embedded in fibrin-based hydrogel. Compared to static culture, 2-week dynamic culture of neonatal rat cardiobundles significantly increased expression of sarcomeric proteins, cardiomyocyte size (∼2.1-fold), contractile force (∼3.5-fold), and conduction velocity of action potentials (∼1.4-fold). The average contractile force per cross-sectional area (59.7 mN/mm 2 ) and conduction velocity (52.5 cm/s) matched or approached those of adult rat myocardium, respectively. The inferior function of statically cultured cardiobundles was rescued by transfer to dynamic conditions, which was accompanied by an increase in mTORC1 activity and decline in AMPK phosphorylation and was blocked by rapamycin. Furthermore, dynamic culture effects did not stimulate ERK1/2 pathway and were insensitive to blockers of mechanosensitive channels, suggesting increased nutrient availability rather than mechanical stimulation as the upstream activator of mTORC1. Direct comparison with phenylephrine treatment confirmed that dynamic culture promoted physiological cardiomyocyte growth rather than pathological hypertrophy. Optimized dynamic culture conditions also augmented function of human cardiobundles made reproducibly from cardiomyocytes derived from multiple hPSC lines, resulting in significantly increased contraction force (∼2.5-fold) and conduction velocity (∼1.4-fold). The average specific force of 23.2 mN/mm 2 and conduction velocity of 25.8 cm/s approached the functional metrics of adult human myocardium. In conclusion, we have developed a versatile methodology for engineering cardiac tissues with a near-adult functional output without the need for exogenous electrical or mechanical stimulation, and have identified mTOR signaling as an important mechanism for advancing tissue maturation and function in vitro. Copyright © 2016 Elsevier Ltd. All rights reserved.

Computational Design of Biomimetic Gels With Properties of Human Tissues

DTIC Science & Technology

2008-12-01

poly(styrene-block- isoprene -block-styrene) copolymer or SIS in the I-selective solvent has been chosen as a model triblock copolymer for this study...our model. A A B B B RC Fig. 2. Schematic representation of A1B3A1 triblock copolymer mapped on DPD model. Poly(styrene-block- isoprene -block...Pa making G 2.25 times higher for c changes from 0.16 to 0.33 (density of styrene and isoprene blocks are taken to be 1.04 and 0.913 g/cm3

Two methods for proteomic analysis of formalin-fixed, paraffin embedded tissue result in differential protein identification, data quality, and cost.

PubMed

Luebker, Stephen A; Wojtkiewicz, Melinda; Koepsell, Scott A

2015-11-01

Formalin-fixed paraffin-embedded (FFPE) tissue is a rich source of clinically relevant material that can yield important translational biomarker discovery using proteomic analysis. Protocols for analyzing FFPE tissue by LC-MS/MS exist, but standardization of procedures and critical analysis of data quality is limited. This study compared and characterized data obtained from FFPE tissue using two methods: a urea in-solution digestion method (UISD) versus a commercially available Qproteome FFPE Tissue Kit method (Qkit). Each method was performed independently three times on serial sections of homogenous FFPE tissue to minimize pre-analytical variations and analyzed with three technical replicates by LC-MS/MS. Data were evaluated for reproducibility and physiochemical distribution, which highlighted differences in the ability of each method to identify proteins of different molecular weights and isoelectric points. Each method replicate resulted in a significant number of new protein identifications, and both methods identified significantly more proteins using three technical replicates as compared to only two. UISD was cheaper, required less time, and introduced significant protein modifications as compared to the Qkit method, which provided more precise and higher protein yields. These data highlight significant variability among method replicates and type of method used, despite minimizing pre-analytical variability. Utilization of only one method or too few replicates (both method and technical) may limit the subset of proteomic information obtained. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Histochemical detection of lead and zinc in plant tissues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tung, G.; Temple, P.J.

1975-01-01

Histochemical studies on uptake and localization of lead and zinc in plant tissues were carried out. A histochemical stain technique was developed to differentiate zinc from lead. Lead was detected in plant tissues by soaking fresh plant materials in freshly prepared sodium rhodizonate stain (0.2% Na rhodizonate acidified to pH3 with glacial acetic acid). Samples were evacuated 5 min and soaked for 30 min before embedding in the congealed stain, then sectioned with a cryostat and examined under a light microscope. Lead particles in plant tissues were stained scarlet-red. Gelatinous, proteinaceous or saccharic embedding materials normally used to prepare plantmore » sampled for sectioning in the cryostat interfered with the color reaction. Sectioning plant samples without staining whole tissues resulted in a weakened response to the stain. Color of stained sample materials were retained for several months if stored in a frozen condition. This technique was used to detect lead both inside and on the surface of plant samples collected in the vicinity of highway and industrial lead sources and to trace the pathways of lead uptake from the air or from contaminated soils. A sodium rhodizonate technique was also developed to be specific for zinc in plant tissues. Plant samples were soaked in a neutral Na-rhodizonate in phosphate buffer at pH 7.5 for observation. The color of zinc developed to produce a purplish or reddish-brown color.« less

A review of room temperature storage of biospecimen tissue and nucleic acids for anatomic pathology laboratories and biorepositories

PubMed Central

Lou, Jerry J; Mirsadraei, Leili; Sanchez, Desiree E; Wilson, Ryan W; Shabihkhani, Maryam; Lucey, Gregory M; Wei, Bowen; Singer, Elyse J; Mareninov, Sergey; Yong, William H

2014-01-01

Frozen biospecimens are crucial for translational research and contain well preserved nucleic acids and protein. However, the risk for catastrophic freezer failure as well as space, cost, and environmental concerns argue for evaluating long-term room temperature storage alternatives. Formalin-fixed paraffin embedded (FFPE) tissues have great value but their use is limited by cross-linking and fragmentation of nucleic acids, as well as loss of enzymatic activity. Stabilization solutions can now robustly preserve fresh tissue for up to 7 days at room temperature. For longer term storage, commercial vendors of chemical matrices claim real time stability of nucleic acids of over 2 years and their accelerated aging studies to date suggest stability for 12 years for RNA and 60 years for DNA. However, anatomic pathology biorepositories store mostly frozen tissue rather than nucleic acids. Small quantities of tissue can be directly placed on some chemical matrices to stabilize DNA, however RNA and proteins are not preserved. Current lyophilization approaches can preserve histomorphology, DNA, RNA, and proteins though RNA shows moderate degradation after 1–2 years. Formalin free fixatives show improved but varying abilities to preserve nucleic acids and face validation as well as cost barriers in replacing FFPE specimens. The paraffin embedding process can degrade RNA. Development of robust long-term room temperature biospecimen tissue storage technology can potentially reduce costs for the biomedical community in the face of growing targeted therapy needs and decreasing budgets. PMID:24362270

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing.

PubMed

Shah, Sheel; Lubeck, Eric; Schwarzkopf, Maayan; He, Ting-Fang; Greenbaum, Alon; Sohn, Chang Ho; Lignell, Antti; Choi, Harry M T; Gradinaru, Viviana; Pierce, Niles A; Cai, Long

2016-08-01

Accurate and robust detection of mRNA molecules in thick tissue samples can reveal gene expression patterns in single cells within their native environment. Preserving spatial relationships while accessing the transcriptome of selected cells is a crucial feature for advancing many biological areas - from developmental biology to neuroscience. However, because of the high autofluorescence background of many tissue samples, it is difficult to detect single-molecule fluorescence in situ hybridization (smFISH) signals robustly in opaque thick samples. Here, we draw on principles from the emerging discipline of dynamic nucleic acid nanotechnology to develop a robust method for multi-color, multi-RNA imaging in deep tissues using single-molecule hybridization chain reaction (smHCR). Using this approach, single transcripts can be imaged using epifluorescence, confocal or selective plane illumination microscopy (SPIM) depending on the imaging depth required. We show that smHCR has high sensitivity in detecting mRNAs in cell culture and whole-mount zebrafish embryos, and that combined with SPIM and PACT (passive CLARITY technique) tissue hydrogel embedding and clearing, smHCR can detect single mRNAs deep within thick (0.5 mm) brain slices. By simultaneously achieving ∼20-fold signal amplification and diffraction-limited spatial resolution, smHCR offers a robust and versatile approach for detecting single mRNAs in situ, including in thick tissues where high background undermines the performance of unamplified smFISH. © 2016. Published by The Company of Biologists Ltd.

Non-contact thermoacoustic detection of embedded targets using airborne-capacitive micromachined ultrasonic transducers

NASA Astrophysics Data System (ADS)

Nan, Hao; Boyle, Kevin C.; Apte, Nikhil; Aliroteh, Miaad S.; Bhuyan, Anshuman; Nikoozadeh, Amin; Khuri-Yakub, Butrus T.; Arbabian, Amin

2015-02-01

A radio frequency (RF)/ultrasound hybrid imaging system using airborne capacitive micromachined ultrasonic transducers (CMUTs) is proposed for the remote detection of embedded objects in highly dispersive media (e.g., water, soil, and tissue). RF excitation provides permittivity contrast, and ultra-sensitive airborne-ultrasound detection measures thermoacoustic-generated acoustic waves that initiate at the boundaries of the embedded target, go through the medium-air interface, and finally reach the transducer. Vented wideband CMUTs interface to 0.18 μm CMOS low-noise amplifiers to provide displacement detection sensitivity of 1.3 pm at the transducer surface. The carefully designed vented CMUT structure provides a fractional bandwidth of 3.5% utilizing the squeeze-film damping of the air in the cavity.

Investigate The Role Of Cells To Cell Adhesion During Wound Healing

NASA Astrophysics Data System (ADS)

Montes, D. R.; Rodriguez, A. J.; Uyoh, E.; Antwi, P.; Olusegun, S.; Murray, P.

2017-12-01

Improvements in wound healing can save living organism and cut misery in health care centers and on the military battlefield. Microscopic examination of how Madin-Darby Canine Kidney (MDCK) epithelial cells respond to wounds under various treatments that block general calcium absorption and e-cadherin mechanics may yield novel wound treatment insights. We used MDCK cells as our tissue model for this experiment.Each tissue was grown on mattek dishes at high, middle, and low densities. Next, we incubated the tissue at 37 degrees celsius overnight. The next day, we wounded the MDCK tissue by scratching them with a 21G1 ½(38.1 mm) syringe needle. Before the scratch we took an image of the tissues. With the tissue wound we made a time-lapse movie of about 3 hours long with a interval of 1 min. Afterward, we compared each MDCK tissue by adding a calcium chelator named EGTA. As so, this will sequester calcium use as well to block e-cadherin mechanics. We then looked at the relationship between a wounded tissue and a healthy tissue. As such, wound dynamics can be observed. We asked ourselves, will EGTA prevent wound closure?

Gene expression analysis of immunostained endothelial cells isolated from formaldehyde-fixated paraffin embedded tumors using laser capture microdissection--a technical report.

PubMed

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

2009-12-01

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 reverse transcription-PCR (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 degrees 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. Glyceraldehyde-3-phosphate dehydrogenase 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.

Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression.

PubMed

Patel, Vyomesh; Hood, Brian L; Molinolo, Alfredo A; Lee, Norman H; Conrads, Thomas P; Braisted, John C; Krizman, David B; Veenstra, Timothy D; Gutkind, J Silvio

2008-02-15

Squamous cell carcinoma of the head and neck (HNSCC), the sixth most prevalent cancer among men worldwide, is associated with poor prognosis, which has improved only marginally over the past three decades. A proteomic analysis of HNSCC lesions may help identify novel molecular targets for the early detection, prevention, and treatment of HNSCC. Laser capture microdissection was combined with recently developed techniques for protein extraction from formalin-fixed paraffin-embedded (FFPE) tissues and a novel proteomics platform. Approximately 20,000 cells procured from FFPE tissue sections of normal oral epithelium and well, moderately, and poorly differentiated HNSCC were processed for mass spectrometry and bioinformatic analysis. A large number of proteins expressed in normal oral epithelium and HNSCC, including cytokeratins, intermediate filaments, differentiation markers, and proteins involved in stem cell maintenance, signal transduction, migration, cell cycle regulation, growth and angiogenesis, matrix degradation, and proteins with tumor suppressive and oncogenic potential, were readily detected. Of interest, the relative expression of many of these molecules followed a distinct pattern in normal squamous epithelia and well, moderately, and poorly differentiated HNSCC tumor tissues. Representative proteins were further validated using immunohistochemical studies in HNSCC tissue sections and tissue microarrays. The ability to combine laser capture microdissection and in-depth proteomic analysis of FFPE tissues provided a wealth of information regarding the nature of the proteins expressed in normal squamous epithelium and during HNSCC progression, which may allow the development of novel biomarkers of diagnostic and prognostic value and the identification of novel targets for therapeutic intervention in HNSCC.

High-Throughput Sequencing and Copy Number Variation Detection Using Formalin Fixed Embedded Tissue in Metastatic Gastric Cancer

PubMed Central

Hong, Min Eui; Do, In-Gu; Kang, So Young; Ha, Sang Yun; Kim, Seung Tae; Park, Se Hoon; Kang, Won Ki; Choi, Min-Gew; Lee, Jun Ho; Sohn, Tae Sung; Bae, Jae Moon; Kim, Sung; Kim, Duk-Hwan; Kim, Kyoung-Mee

2014-01-01

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. PMID:25372287

Thermodynamic confinement and alpha-helix persistence length in poly(gamma-benzyl-L-glutamate)-b-poly(dimethyl siloxane)-b-poly(gamma-benzyl-L-glutamate) triblock copolymers.

PubMed

Papadopoulos, P; Floudas, G; Schnell, I; Lieberwirth, I; Nguyen, T Q; Klok, H-A

2006-02-01

The structure and the associated dynamics of a series of poly(gamma-benzyl-L-glutamate)-b-poly(dimethyl siloxane)-b-poly(gamma-benzyl-L-glutamate) (PBLG-b-PDMS-b-PBLG) triblock copolymers were investigated using small- and wide-angle X-ray scattering, NMR, transmission electron microscopy, and dielectric spectroscopy, respectively. The structural analysis revealed phase separation in the case of the longer blocks with defected alpha-helical segments embedded within the block copolymer nanodomains. The alpha-helical persistence length was found to depend on the degree of segregation; thermodynamic confinement and chain stretching results in the partial annihilation of helical defects.

Young Investigator Challenge: A novel, simple method for cell block preparation, implementation, and use over 2 years.

PubMed

Lindsey, Kathryn G; Houser, Patricia M; Shotsberger-Gray, Wanda; Chajewski, Olga S; Yang, Jack

2016-12-01

The cell block is an essential adjunct to conventional cytopreparatory techniques. The need for molecular analysis and immunostains will increase the need for successful cell block preparation. Even with this need, to the authors' knowledge very little has changed regarding the way in which cell blocks are produced. The authors developed A Formalin-Fixed, paraffin Embedded Cytology cell block Technique (AFFECT) that uses a cytospin centrifuge and funnel to deposit a cell pellet into a well on a piece of open-cell, absorbent foam. The foam and the pellet are then sent through normal processing. Herein, the authors present the implementation of this method and some of their experience with its performance over the course of 2 years. Although a comparison of the methods indicated good correlation for the production of a cell block between AFFECT and the agarose method, the AFFECT blocks demonstrated markedly improved cellular morphology. Over the first 6 months of use, AFFECT produced a successful cell block in 74% of cases overall, and in 65% of cases with a cell pellet measuring ≤0.1 mL. The year preceding the implementation of AFFECT and its first year of use were compared for endoscopic and bronchoscopic ultrasound-guided fine-needle aspiration specimens, and demonstrated an improved success rate. The authors developed a novel method of cell block preparation that demonstrates improved histology and has increased the success rate of cell block production compared with the agarose method. Cancer Cytopathol 2016;124:885-892. © 2016 American Cancer Society. © 2016 American Cancer Society.

Real-time three-dimensional ultrasound-assisted axillary plexus block defines soft tissue planes.

PubMed

Clendenen, Steven R; Riutort, Kevin; Ladlie, Beth L; Robards, Christopher; Franco, Carlo D; Greengrass, Roy A

2009-04-01

Two-dimensional (2D) ultrasound is commonly used for regional block of the axillary brachial plexus. In this technical case report, we described a real-time three-dimensional (3D) ultrasound-guided axillary block. The difference between 2D and 3D ultrasound is similar to the difference between plain radiograph and computer tomography. Unlike 2D ultrasound that captures a planar image, 3D ultrasound technology acquires a 3D volume of information that enables multiple planes of view by manipulating the image without movement of the ultrasound probe. Observation of the brachial plexus in cross-section demonstrated distinct linear hyperechoic tissue structures (loose connective tissue) that initially inhibited the flow of the local anesthesia. After completion of the injection, we were able to visualize the influence of arterial pulsation on the spread of the local anesthesia. Possible advantages of this novel technology over current 2D methods are wider image volume and the capability to manipulate the planes of the image without moving the probe.

Extraneous tissue in surgical pathology: a College of American Pathologists Q-Probes study of 275 laboratories.

PubMed

Gephardt, G N; Zarbo, R J

1996-11-01

To develop a multi-institutional reference database of extraneous tissue (contaminants) in surgical pathology. In 1994, participants in the College of American Pathologists Q-Probes quality improvement program performed prospective and retrospective evaluations of extraneous tissue found in surgical pathology microscopic sections for a period of 4 weeks or until 1000 slides were reviewed in each participating laboratory. Two hundred seventy-five surgical pathology laboratories institutions, predominantly from North America. Extraneous tissue contamination rate for slides in prospective and retrospective reviews; staffing and practice procedures; location of extraneous tissue on slides; type of extraneous tissue (normal, abnormal, nonneoplastic, neoplasm, microorganisms, etc); class of extraneous tissue (slide or block contaminants); source of extraneous tissue (different or same case); origin of extraneous tissue (pathology laboratory, physician's office or operating room); and degree of diagnostic difficulty caused by extraneous tissue. Three hundred twenty-one thousand seven hundred fifty-seven slides were reviewed in the prospective study and 57083 slides in the retrospective study. There was an overall extraneous tissue rate of 0.6% of slides (2074/321757) in the prospective study and 2.9% of slides (1653/57083) in the retrospective study. Of those slides with extraneous tissue, the extraneous tissue was located near diagnostic tissue sections in 59.5% of the slides reviewed prospectively and in 25.3% of slides reviewed retrospectively; deeper sections were performed to evaluate extraneous tissue in 12.2% of prospective cases and in 3.1% of retrospective cases. Of the laboratories, 98% had written guidelines for changing solution in tissue processors, and 64.9% had guidelines for maintaining water baths free of extraneous tissue. A total of 98.9% used lens paper, filter bags, or sponges for processing fragmented and small specimens. Written protocols for documentation of extraneous tissue in surgical pathology reports were established in 6.1% of laboratories, for removal of extraneous tissue from blocks in 5.7%, and for removal of extraneous tissue from microscopic slides in 4.7%. In 24% of laboratories no comment or record was kept to document extraneous tissue. Extraneous tissue consisted of neoplasm in 12.7% of the prospectively reviewed slides and in 6.0% of the retrospectively reviewed slides. For the prospective study, 59.4% of extraneous tissue was classified as slide contaminants, and 28.4% was found to be contaminants within the paraffin block; for the retrospective study, 72.9% was classified as slide contaminants and 15.9% as block contaminants. For the prospective study, 63.2% of extraneous tissue was presumed to be from a different case, and in the retrospective study, 48.5% was presumed to be from a different case. Over 90% of extraneous tissue was thought to originate from the pathology laboratory. The degree of diagnostic difficulty caused by extraneous tissue was judged to be severe in 0.4% of slides in the prospective study and 0.1% of slides in the retrospective study. In the prospective study, it could not be determined whether the tissue in the diagnostic sections was extraneous in 0.6% of slides, and in the retrospective study, it could not be determined whether tissue in the diagnostic sections was extraneous in 0.1%. This study has documented the frequency, type, origin, source, and diagnostic difficulty of extraneous tissue and presents benchmarks of extraneous tissue experienced in the general practice of surgical pathology.

Effect of Occult Metastases on Survival in Node-Negative Breast Cancer

PubMed Central

Weaver, Donald L.; Ashikaga, Takamaru; Krag, David N.; Skelly, Joan M.; Anderson, Stewart J.; Harlow, Seth P.; Julian, Thomas B.; Mamounas, Eleftherios P.; Wolmark, Norman

2011-01-01

BACKGROUND Retrospective and observational analyses suggest that occult lymph-node metastases are an important prognostic factor for disease recurrence or survival among patients with breast cancer. Prospective data on clinical outcomes from randomized trials according to sentinel-node involvement have been lacking. METHODS We randomly assigned women with breast cancer to sentinel-lymph-node biopsy plus axillary dissection or sentinel-lymph-node biopsy alone. Paraffin-embedded tissue blocks of sentinel lymph nodes obtained from patients with pathologically negative sentinel lymph nodes were centrally evaluated for occult metastases deeper in the blocks. Both routine staining and immunohistochemical staining for cytokeratin were used at two widely spaced additional tissue levels. Treating physicians were unaware of the findings, which were not used for clinical treatment decisions. The initial evaluation at participating sites was designed to detect all macrometastases larger than 2 mm in the greatest dimension. RESULTS Occult metastases were detected in 15.9% (95% confidence interval [CI], 14.7 to 17.1) of 3887 patients. Log-rank tests indicated a significant difference between patients in whom occult metastases were detected and those in whom no occult metastases were detected with respect to overall survival (P = 0.03), disease-free survival (P = 0.02), and distant-disease–free interval (P = 0.04). The corresponding adjusted hazard ratios for death, any outcome event, and distant disease were 1.40 (95% CI, 1.05 to 1.86), 1.31 (95% CI, 1.07 to 1.60), and 1.30 (95% CI, 1.02 to 1.66), respectively. Five-year Kaplan-Meier estimates of overall survival among patients in whom occult metastases were detected and those without detectable metastases were 94.6% and 95.8%, respectively. CONCLUSIONS Occult metastases were an independent prognostic variable in patients with sentinel nodes that were negative on initial examination; however, the magnitude of the difference in outcome at 5 years was small (1.2 percentage points). These data do not indicate a clinical benefit of additional evaluation, including immunohistochemical analysis, of initially negative sentinel nodes in patients with breast cancer. (Funded by the National Cancer Institute; ClinicalTrials.gov number, NCT00003830.) PMID:21247310

Enhanced detection of Rickettsia species in Ixodes pacificus using highly sensitive fluorescence in situ hybridization coupled with Tyramide Signal Amplification.

PubMed

Bagheri, Ghazaleh; Lehner, Jeremy D; Zhong, Jianmin

2017-10-01

Ixodes pacificus is a host of many bacteria including Rickettsia species phylotypes G021 and G022. As part of the overall goal of understanding interactions of phylotypes with their tick host, this study focused on molecular detection of rickettsiae in ovarian and midgut tissue of I. pacificus by fluorescent in situ hybridization (FISH), PCR, and ultrastructural analysis. Of three embedding media (Technovit 8100, Unicryl, and paraffin) tested for generating thin sections, tissues embedded in paraffin resulted in the visualization of bacteria with low autofluorescence in FISH. Digoxigenin-labeled probes were used in FISH to intensify bacterial hybridization signals using Tyramide Signal Amplification reaction. Using this technique, rickettsiae were detected in the cytoplasm of oocytes of I. pacificus. The presence of rickettsiae in the ovary and midgut was further confirmed by PCR and transmission electron microscopic analysis. Overall, the methods in this study can be used to identify locations of tick-borne bacteria in tick tissues and understand transmission routes of bacterial species in ticks. Copyright © 2017 Elsevier GmbH. All rights reserved.

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.

PubMed

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.

3D bioprinting: A new insight into the therapeutic strategy of neural tissue regeneration.

PubMed

Hsieh, Fu-Yu; Hsu, Shan-hui

2015-01-01

Acute traumatic injuries and chronic degenerative diseases represent the world's largest unmet medical need. There are over 50 million people worldwide suffering from neurodegenerative diseases. However, there are only a few treatment options available for acute traumatic injuries and neurodegenerative diseases. Recently, 3D bioprinting is being applied to regenerative medicine to address the need for tissues and organs suitable for transplantation. In this commentary, the newly developed 3D bioprinting technique involving neural stem cells (NSCs) embedded in the thermoresponsive biodegradable polyurethane (PU) bioink is reviewed. The thermoresponsive and biodegradable PU dispersion can form gel near 37 °C without any crosslinker. NSCs embedded within the water-based PU hydrogel with appropriate stiffness showed comparable viability and differentiation after printing. Moreover, in the zebrafish embryo neural deficit model, injection of the NSC-laden PU hydrogels promoted the repair of damaged CNS. In addition, the function of adult zebrafish with traumatic brain injury was rescued after implantation of the 3D-printed NSC-laden constructs. Therefore, the newly developed 3D bioprinting technique may offer new possibilities for future therapeutic strategy of neural tissue regeneration.

Velocity and attenuation of shear waves in the phantom of a muscle-soft tissue matrix with embedded stretched fibers

NASA Astrophysics Data System (ADS)

Rudenko, O. V.; Tsyuryupa, S. N.; Sarvazyan, A. P.

2016-09-01

We develop a theory of the elasticity moduli and dissipative properties of a composite material: a phantom simulating muscle tissue anisotropy. The model used in the experiments was made of a waterlike polymer with embedded elastic filaments imitating muscle fiber. In contrast to the earlier developed phenomenological theory of the anisotropic properties of muscle tissue, here we obtain the relationship of the moduli with characteristic sizes and moduli making up the composite. We introduce the effective elasticity moduli and viscosity tensor components, which depend on stretching of the fibers. We measure the propagation velocity of shear waves and the shear viscosity of the model for regulated tension. Waves were excited by pulsed radiation pressure generated by modulated focused ultrasound. We show that with increased stretching of fibers imitating muscle contraction, an increase in both elasticity and viscosity takes place, and this effect depends on the wave propagation direction. The results of theoretical and experimental studies support our hypothesis on the protective function of stretched skeletal muscle, which protects bones and joints from trauma.