Tissue processing

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Compound fixatives in microwave assisted tissue processing: A step towards formalin free laboratory practice

Compound fixatives in microwave assisted tissue processing: A step towards formalin free laboratory practice

Quick processing of histopathological tissues is an imperative need of the hour to accomplish the requirements of clinicians attending to intensely ailing patients. Turn-around time is a vital concern in tissue processing. At first, steps were taken to reduce the tissue processing time for intra-operative frozen sections and specimens where a swift diagnosis and quick commencement of treatment based on the histopathology findings were required. In this era of decreased health care costs and modern diagnostic procedures, it is imperative to reduce the turn-around time for routine histopathological specimens as well.
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Original Article New tissue processing protocol for better long-fragment DNA preservation

Original Article New tissue processing protocol for better long-fragment DNA preservation

sue autolysis, stabilize proteins and limit anti- gen and nucleic acids degradation thereby nicely preserve the tissue morphology. But for- malin introduce protein-protein and proteins- nucleic cross-linking, as well as chemical modi- fications of nucleic acids [9]. These reactions lead to significant degradation of nucleic acids in FFPE blocks. Further fragmentation of DNA and RNA can be caused by suboptimal fixation, prolonged storage of FFPE blocks, tissue pro- cessing, sectioning and staining procedures [10, 11]. With the development of molecular biology and genetics, requirements for nucleic acids preservation in clinical specimens be- come high. Besides, increased applications of minimal invasive surgery and biopsy produce much smaller pieces of pathology specimens. Therefore, finding better ways for pathological specimen processing and storage are of great necessity. Many groups from worldwide had published various papers aiming at nucleic preservation for molecular diagnosis. But these studies were mainly focus on testing different types of fixatives or DNA isolation methods [12- 14]. Whereas different tissue processing proto- cols are not given enough attention.
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Comparing the efficiency of coconut oil and palm oil with xylene as a clearing agent in conventional hematoxylin and eosin histopathological staining procedure

Comparing the efficiency of coconut oil and palm oil with xylene as a clearing agent in conventional hematoxylin and eosin histopathological staining procedure

On account of the Occupational Safety and Health Administration (OSHA) regulations, various xylene substitutes, such as, limonene reagents, aliphatic hydrocarbons, vegetable oils and mineral oils were tried in the past to avoid xylene in the laboratory. However, these substitutes were found to be less effective and more expensive 5 . Coconut oil is a commonly used vegetable oil, available throughout the tropical world. It is non-toxic, heat stable, slow to oxidize and has highest resistance to rancidity 6 . Palm oil promises to be widely available and safe substitute for xylene. Hence, here we attempt to check the use of coconut oil and palm oil as a clearing agent during tissue processing and as a dewaxing agent during Hematoxylin and Eosin staining procedure has any effect when compared with the xylene processed tissue.
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Current perspectives on Mohs micrographic surgery for melanoma

Current perspectives on Mohs micrographic surgery for melanoma

2-hour method for preparing permanent sections of MIS for MMS through microwave tissue processing with comparable results – whether or not this has gained widespread use is yet to be seen. Despite its time-consuming nature, permanent sectioning has long been considered the gold standard for melanocytic lesion evaluation for the reasons previously described. However, fast and reliable immunohistochemi- cal stains are now increasingly being used as an adjunct to H&E-stained frozen sections 3,8,35,36,38 and can provide identical

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Simulating the histology laboratory : evaluation of organizational interventions for the histology laboratory through the development of a generalizable Discrete Event simulation model

Simulating the histology laboratory : evaluation of organizational interventions for the histology laboratory through the development of a generalizable Discrete Event simulation model

Although many technological innovations were introduced in the histopathological laboratory during the previous century, the workflow of the conventional histopathological laboratory essentially stayed the same until the turn of the century (Buesa, 2007a; Vernon, 2005). All tissue was left to fixate on formaldehyde overnight, followed by grossing the next day before spending another night being processed in the tissue processor. As such, tissue was accumulated in large batches throughout the day, which had to be completely processed during the morning. This resulted in long turnaround times and skewed workloads throughout the day (Buesa, 2007a; Vernon, 2005). Since 1997 however, continuous throughput rapid tissue processing machines have been in development, using common histologic reagents and microwave energy to rapidly process tissue (Morales et al., 2002). This allows tissue to be processed much faster allowing for tissue processing during the day, which has a large impact on the planning of the histological process (Buesa, 2007b; Morales et al., 2002). In modern days, the continuous throughput processing machines have been adapted by most histology laboratories and have revolutionized the workflow by making it possible to shorten turnaround times by up to one day (Vernon, 2005).
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THE RESIN-EMBEDDED CORNEA PREPARED VIA RAPID PROCESSING PROTOCOL : A GOOD HISTOMORPHOMETRIC TARGET FOR CLINICAL INVESTIGATION IN OPHTHALMOLOGY AND OPTOMETRY

THE RESIN-EMBEDDED CORNEA PREPARED VIA RAPID PROCESSING PROTOCOL : A GOOD HISTOMORPHOMETRIC TARGET FOR CLINICAL INVESTIGATION IN OPHTHALMOLOGY AND OPTOMETRY

This study illustrates and quantifies the changes on corneal tissue between the paraffin-embedded and resin-embedded blocks and thus, selects a better target in investigational ophthalmology and optometry via light microscopy. Corneas of two cynomolgus monkeys (Macaca fascicularis) were used in this study. The formalin-fixed cornea was prepared in paraffin block via the conventional tissue processing protocol (4-day protocol) and stained with haematoxylin and eosin. The glutaraldehyde-fixed cornea was prepared in resin block via the rapid and modified tissue processing procedure (1.2-day protocol) and stained with toluidine blue. The paraffin-embedded sample exhibits various undesired tissue damage and artifact such as thinner epithelium (due to the substantial volumic extraction from the tissue), thicker stroma layer (due to the separation of lamellae and the presence of voids) and the distorted endothelium. In contrast, the resin-embedded corneal tissue has demonstrated satisfactory corneal ultrastructural preservation. The rapid and modified tissue processing method for preparing the resin-embedded is particularly beneficial to accelerate the microscopic evaluation in ophthalmology and optometry.
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Designing a knowledge-based intelligent assistant for diagnosis of atrophy in small intestine on the basis of processing the tissue images

Designing a knowledge-based intelligent assistant for diagnosis of atrophy in small intestine on the basis of processing the tissue images

A knowledge-based expert system is suggested as the intelligent assistant of specialist for diagnosis of intestinal tissue atrophy. The facts of system are prepared as the input of inferential engine based on the expert knowledge, tests, physical examination and processing the images of damaged tissue. Processing the images of damaged tissue provides a new method based on processing the endoscopic images of atrophy tissues in small intestine through the new morphological structures. These masks move on the images with almost 85% of similarity and adaptation, and then track and estimate the density of designed objects in masks on the image. The
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The role of the pathology department in the preanalytical phase of molecular analyses

The role of the pathology department in the preanalytical phase of molecular analyses

degradation is quite different from the degradation of nucleic acids, current international pathology practice protocols require that the used protocols for tissue processing take into consideration DNA and/or RNA degradation. Thus, in order to also achieve a good tissue quality for molecular testing, the decalcification time is between 16 and 24 hours and the used substance is 14% ethylenediaminetetraacetic acid. Shorten- ing this time is only acceptable for morphology assessment. In case the laboratory also requires molecular, cytogenetic,

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Bleached Palm Oil as a Bio-friendly Substitute for Xylene:A Comparitive Study

Bleached Palm Oil as a Bio-friendly Substitute for Xylene:A Comparitive Study

its highly volatile nature, makes it a difficult compound for laboratories to handle. The aim of the present study is to utilize eco-friendly substitutes which are nontoxic, less biohazardous, and economical. Bleached palm oil promises to be a widely available and safe substitute. The present study evaluates the efficacy of bleached palm oil as a clearing agent during tissue processing, the effects on the transparency and production of serial sections, and as a deparaffinizing agent, and to compare staining characteristics with that of tissue processed and the sec- tions deparaffinized using xylene.
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Translational Research in Pediatrics IV: Solid Tissue Collection and Processing

Translational Research in Pediatrics IV: Solid Tissue Collection and Processing

concentrations. Tissue pH and tryptophan levels are 2 methods to judge the quality of solid tissue collected for research purposes; however, the RNA integrity number, together with analyses of housekeeping genes, is the new standard. A comprehensive clinical data set accompanying all tissue samples is imperative. In this review, we examined: the ethical standards relating to solid tissue procurement from children; potential sources of solid tissues; optimal practices for solid tissue processing, handling, and storage; and reliable markers of solid tissue quality.
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Title: A Classification Approach for Predicting Plant Leaf Diseases in Digital Image Processing

Title: A Classification Approach for Predicting Plant Leaf Diseases in Digital Image Processing

The segmentation was to find the value of pixels that separates healthy and diseased tissue. The diseased tissue tends to generate peaks towards the (left end of the histogram) lower value bins. The healthier the leaf as the more pronounced are the higher peaks. Due to differences in color, shades and illumination, the position of those peaks may vary substantially from sample to sample. CNN learned the accuracy and bin values of diseased and healthier leaf histograms and generated the class label. Then based on the color and bins of test image, diseased as well as healthier part of an image is automatically segmented and improves the detection accuracy.
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Spontaneous Bacterial Peritonitis and Henoch-Schönlein Purpura in a Patient with Liver Cirrhosis

Spontaneous Bacterial Peritonitis and Henoch-Schönlein Purpura in a Patient with Liver Cirrhosis

Despite further labs to exclude viral, autoimmune, and other causes, Table 1(b), the etiology of his liver cirrhosis remained unclear, attributable to NASH versus alcohol given his history of uncontrolled diabetes and chronic etoh abuse, Table 1(b). Diagnostic paracentesis was performed, showing glucose 182, LDH 79, albumin 0.9, and protein 1.7 with 6400 RBCs and 1850 nucleated cells (51% granulocytes, 17% lymphocytes, and 32% tissue cells), Table 1(c). Cytopatholog- ical examination revealed no neoplastic cells, and bacterial culture was negative. The corrected neutrophil count of 917 and serum-ascites albumin gradient of 2.1 were consistent with SBP and portal hypertension, Table 1(c).
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Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification

Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification

Here, we demonstrate our ABPP protocol by identification of the in vivo targets of the diacylglycerol lipase inhibitor DH376 in four mouse tissues (brain, kidney, liver and testis) using two biotinylated probes (FP-biotin and THL-biotin (MB108)). In a nutshell, tissue lysates of mice treated with DH376 or vehicle are compared by competitive ABPP (heat-inactivated vehicle sam- ples are used as a control) (Fig. 1b). After tissue lysis (Steps 1–9), enzymes are labeled by incubation with a cocktail of the two bioti- nylated ABPs (Steps 10–13), enriched using affinity chromatog- raphy (avidin–agarose pulldown, Steps 15–34), and digested with trypsin (Steps 35–37). The resulting tryptic peptides are meas- ured using LC–IMS–MS (Steps 38–44). Label-free quantification is used to compare the different conditions (vehicle versus heat inactivated, vehicle versus inhibitor and the relative enzyme activ- ity across the different tissues) (Steps 45–67). The comparison of these different conditions would not have been possible with dimethyl labeling as a quantification method, because of the lack of multiplicity.
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Special Issue on Computer-Assisted Craniofacial Reconstruction and Modeling

Special Issue on Computer-Assisted Craniofacial Reconstruction and Modeling

The reconstruction of facial soft tissue is an essential processing phase in the fields of forensics, anthropology as well as maxillofacial surgery. In the first two areas the working subject is a skull find of a deceased where the soft tissue needs to be reconstructed. In forensics, this work helps to identify skeletons from open cases of death. In anthropology, the comparison of facial features between modern and ancient human beings is the main focus of research. Finally, in the case of maxillofacial surgery, a face must be reconstructed after, for example, cancer surgery. The goals of forensics, anthropology and maxillofacial surgery differ substantially. However, the mathematical basis of computer-aided soft facial reconstruction is effectively the same.
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Efficient semi-automatic segmentation for creating patient specific models for virtual environments

Efficient semi-automatic segmentation for creating patient specific models for virtual environments

positioning is replaced by seed fronts representing a good approximation to the original structures. Consequently only 50 to 70 iterations are needed to propagate to the structure boundaries. This dramatically decreases processing time and reduces the risks of leaking at the weak boundaries, without compromising the accuracy of segmentation. Currently, the default parameters used by our system work well in a variety of image modalities, such that adjustment of these parameters for each case which is common in other level set based methods tends not to be necessary. The evaluation will be extended to other image modalities as manual segmentations become available.
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Energy limitation as a selective pressure on the evolution of sensory systems

Energy limitation as a selective pressure on the evolution of sensory systems

Although similar relationships can be envisaged for other peripheral sensory structures, the relationship between information processing, energy consumption and the size of higher centres remains unclear. The efficacy of energy-efficient coding schemes can change with size (e.g. graded versus action potentials, sparse coding), making direct comparisons difficult. Thus, direct quantification of the energetic costs, performance and size of a particular sensory system is essential for understanding the cost–benefit trade-offs that have influenced its evolution. This is particularly important in comparisons of phylogenetically distant species, among which it is not reasonable to assume that a specific volume of neural tissue consumes similar amounts of energy. For example, elasmobranchs have a larger relative brain size when compared to teleost fish of the same body mass (Nilsson et al., 2000) (Fig. 11A). Early studies assumed that elasmobranch brains consumed considerably more energy than those of teleosts with similar body mass. However, measurements from elasmobranch and teleost neural tissue have shown that they have very different specific rates of energy consumption but that overall their brains consume similar amounts of energy (Fig. 11B,C).
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A three-dimensional multivariate image processing technique for the analysis of FTIR spectroscopic images of multiple tissue sections

A three-dimensional multivariate image processing technique for the analysis of FTIR spectroscopic images of multiple tissue sections

The high correlation of spectral clusters with anatomical and histopathological features has been conclusively demonstrated for a number of different tissue types including cervical [2,3], breast [10,15], liver [4,7], brain [5], mouth [6], intestine [8,16], skin [17], bone [18,19], cornea [20] and prostate [21]. Hitherto FTIR multivariate imaging has been mainly restricted to the generation of 2D cluster maps. The exception is Mendelsohn and cow- orkers [22] who constructed a 3D univariate map of corti- cal bone based on peak ratios from serial two- dimensional sections. By interfacing two types of software namely Cytospec [14] and SCIRun [23] and writing a sim- ple "stitching" algorithm we are able to generate 3D mul- tivariate cluster maps from multiple tissue sections. The ability to visualize 3D FTIR cluster maps provides a new avenue to assess variation in multiple tissue sections and to determine the penetration of histopathological struc- tures based on the underlying macromolecular structure of the diseased tissue.
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Planning and designing of a stem cell centre in a tertiary care hospital

Planning and designing of a stem cell centre in a tertiary care hospital

Stem cells are derived from embryos, fetal and adult tissues. Today, they have acquired mystical status as they are master organizer of all the living organisms and can give rise to any tissue in the body being the carriers of the immortal DNA. The stem cells center is the nerve center of research, storage and therapy and involves almost all branches of medical sciences. However, the only clinical therapy approved is bone marrow therapy and no other stem cell therapy involving adult, fetal and embryonic cells has been approved world over. Although much hype and exaggeration exist, the estimate of market size of 90 billion by 2015, gives hope to million not responding to conventional treatment.
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New Technique to Produce Large Amount of Flat Silk by Biospinning

New Technique to Produce Large Amount of Flat Silk by Biospinning

Another new technique related was observed in the wild Saturniid silkworm Antheraea mylitta denominated “biospinning” [13]. This was the only technique present in the literature, until now, using a natural method to biofabricate a silk fiber matrices that can be used for future applications as a biomaterial. This method consists in A. mylitta larvae spinning fibers and fabricating matrices with linear or mixed orientations on coverslip sur- faces measuring 20 × 25 mm. In the randomly aligned only one silkworm were placed on Teflon-coated glass plates and spun layer by layer on it, while in the technique of B. mori silk tissue, many larvae produced a largest tissue in a cheaper surface.
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Volume segmentation and visualisation for a 3D ultrasound acquisition system

Volume segmentation and visualisation for a 3D ultrasound acquisition system

determ ination of the heart. This work, due to M cCann et al [28], produced some very pleasing in vitro images of a dog heart by both compound B-scanning a set of parallel slices, and using a stepper m otor to ro tate a transducer in order to gain a set of 2D slice images sharing a common axis. The com pound nature of the B-scan images elim inated a great deal of the noise associated with ultrasound images, and the surface-rendered 3D reconstructions of this d a ta shows some surprisingly clear anatom ical detail of epicardial and endocardial surfaces. The ro tatin g tra n s­ ducer scans show comparable anatom ical detail, although much interpolation and sm oothing of the images was necessary in order to create a series of parallel slices as a 3D d a ta set; these being produced orthogonal to the original axial 2D images. This in vitro rotating scan study was carried out to test the feasibility of in vivo clinical scans of the same form at. The in vivo results presented show a surface-rendered representation of the endocardium , the epicardium being alm ost impossible to segment accurately from the surrounding tissue.
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