Quantitative characterization of domes in primary mouse mammary epithelial tumor cell cultures

Summary Dome populations from primary cultures of mouse mammary tumor cells were quantitatively studied in regard to size, distribution, density and the area occupied by light-diffusion photography and image analysis. The effects of fetal bovine serum, insulin and hydrocortisone were analyzed. Quantitative characterization documented dome diameter (mode diameter 0.26 to 0.52 mm), dome area occupied (average 23%, maximum 38.7%), and density (average 78 domes per cm², maximum 117 domes per cm²) for standard culture conditions. Insulin and hydrocortisone had a primary effect on dome density whereas 15% fetal bovine serum had a minimal effect. However, insulin and hydrocortisone had a synergistic optimal effect on dome population. Time-lapse cinematography revealed that the dome population is not static, but a very dynamic one. Domes underwent irregular pulsations of expansion and contraction. Dome enlargement was either by a series of expansions and contractions, by lateral involvement of other cells, or by coalescence of two or more domes. Domes have been considered to be the in vitro counterpart of the in vivo acinus of the mouse mammary gland. However, quantitative dome population characterization has not been available. Dome analysis by light-diffraction photography and image analysis lends itself towards correlative studies of domes and their differentiative products. Supported in part by Public Health Service Contract NO1-CP 61013 within the Virus Cancer Program of the National Cancer Institute and by Public Health Service Training Grant CA05245 from the National Cancer Institute.     

Evaluation of mesh- and binary-based contour propagation methods in 4D thoracic radiotherapy treatments using patient 4D CT images

Based on four dimensional (4D) computed tomography (CT) images, mesh- and binary-based contour propagation algorithms for 4D thoracic radiotherapy treatments were evaluated. Gross tumor volumes (GTVs), lungs, hearts and spinal cords on the CT images at the end-exhale and end-inhale phases for six patients were delineated by the physician. All volumes of interest (VOIs) were automatically propagated from the end-exhale phase to the end-inhale phase using two propagation methods. The propagated VOIs were quantitatively compared with the VOIs contoured at the end-inhale phase by the physician using Dice Similarity Coefficient (DSC), Mean Slicewise Hausdorff Distance (MSHD), Center Of Mass (COM) displacement and volume difference. A two-sided Student’s t test was implemented to examine the significance of the differences between the results obtained from the two algorithms. For GTVs, statistically significant differences between the two algorithms were not observed. For all the other VOIs, the mesh-based method showed higher mean DSCs for the heart, left lung, right lung and spinal cord, lower mean MSHD for the spinal cord, lower mean COM displacement for the heart, and lower mean volume differences for the left lung, right lung and spinal cord with statistically significant differences than the binary-based method. The running time for propagation was approximately 3 s and 3 min for the mesh- and binary-based methods, respectively. Collectively, the mesh-based algorithm provides superiorities in running time and reliability for contour propagation in 4D radiotherapy.     

Classification and Reconstruction of a Heterogeneous Set of Electron Microscopic Images: A Case Study of GroEL–Substrate Complexes

Image analysis methods were used to separate images of a large macromolecular complex, the chaperonin GroEL, in a preparation in which it is partially liganded to a nonnative protein substrate, glutamine synthetase. The relatively small difference (6%) in size between the chaperonin in its free and complexed forms, and the absence of gross changes in overall conformation, made separation of the two types of particles challenging. Different approaches were evaluated and used for alignment and classification of images, both in two common projections and in three dimensions, yielding 2D averages and a 3D reconstruction. The results of 3D analysis describe the conformational changes effected by binding of this particular protein substrate and demonstrate the utility of 2D analysis as an indicator of structural change in this system.     

Quantification of polyacrylamide gel bands by digital image processing

A method of quantifying bands on polyacrylamide gels based on image processing of digitized photographic negatives is presented.     

Validation of a deformable image registration produced by a commercial treatment planning system in head and neck

In recent years one of the areas of interest in radiotherapy has been adaptive radiation therapy (ART), with the most efficient way of performing ART being the use of deformable image registration (DIR). In this paper we use the distances between points of interest (POIs) in the computed tomography (CT) and the cone beam computed tomography (CBCT) acquisition images and the inverse consistence (IC) property to validate the RayStation treatment planning system (TPS) DIR algorithm. This study was divided into two parts: Firstly the distance-accuracy of the TPS DIR algorithm was ascertained by placing POIs on anatomical features in the CT and CBCT images from five head and neck cancer patients. Secondly, a method was developed for studying the implication of these distances on the dose by using the IC. This method compared the dose received by the structures in the CT, and the structures that were quadruply-deformed. The accuracy of the TPS was 1.7 ± 0.8 mm, and the distance obtained with the quadruply-deformed IC method was 1.7 ± 0.9 mm, i.e. the difference between the IC method multiplied by two, and that of the TPS validation method, was negligible. Moreover, the IC method shows very little variation in the dose-volume histograms when comparing the original and quadruply-deformed structures. This indicates that this algorithm is useful for planning adaptive radiation treatments using CBCT in head and neck cancer patients, although these variations must be taken into account when making a clinical decision to adapt a treatment plan.     

Structural changes in the innercortex cells of soybean root nodules are induced by short-term exposure to high salt or oxygen concentrations

After a 2 h exposure of intact soybean nodules to high concentrations of NaCl (100mol m_?3) or oxygen (8OkPa O₂), morphometric computations carried out using an image analysis technique on semi-thin sections showed that both treatments induced a decrease in the area of the inner-cortex cells, which were then characterized by a tangential elongation. In contrast, no significant change in area occurred in the middle-cortex cells although their elongation decreased. Electron microscopic observations showed that in the inner-cortex cells changes included the presence of wall infoldings, an enlarged periplasmic space and a lobate nucleus whose chromatin distribution differed from that of the control. Structural changes also occurred in the endoplasmic reticulum, microbodies, mitochondria and plastids. From several of these changes, which are similar to those noted in osmocontractil cells in response to external stimuli, it can be hypothesized that the inner cortex may provide a potential mechanism for the control of oxygen diffusion through the nodules.     

The use of digital images to evaluate the interobserver agreement on cervical smear readings in Italian cervical cancer screening

G. Tinacci, A. Biggeri, A. Pellegrini, M.P. Cariaggi, M.L. Schiboni and M. Confortini The use of digital images to evaluate the interobserver agreement on cervical smear readings in Italian cervical cancer screening Objective: The aim of this study was to measure interobserver agreement among cytologists on using a set of digital images. Methods: A set of 90 selected Papanicolaou‐stained cervical smears were digitalized and the digital images circulated among 117 readers, from laboratories spread across almost all Italian regions. Three representative fields of each smear were displayed at 20× and 40× magnification (overall six images for each case). The diagnoses made by the cytologists who provided the images were taken as target diagnoses. Results: The κ values were: very low for the categories atypical squamous cells of undetermined significance (ASC‐US), and atypical squamous cells – cannot exclude high‐grade squamous intraepithelial lesion (ASC‐H); poor for the categories atypical glandular cells (AGC), high‐grade squamous intraepithelial lesion (HSIL) and invasive cancer; and fair to good for the categories negative and low‐grade squamous intraepithelial lesion (LSIL). However, we found a cluster of 42 best concordant readers. The overall κ value and overall weighted κ with the target diagnosis for these 42 readers were 0.45 and 0.66, respectively. This finding is in contrast with the overall κ value and overall weighted κ for the other readers of 0.39 and 0.59, respectively. Conclusions: As this finding is an estimate of the accuracy of the readers, we can infer that it will be very important to reach this level of concordance for all the participating readers. Future effort will facilitate common experiences in order to improve the reproducibility of diagnostic criteria. Digital images could be the key to reach this aim.     

Phylogeny and mechanisms of shared hierarchical patterns in birdsong

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Detection and Analysis of DNA Damage in Mouse Skeletal Muscle In Situ Using the TUNEL Method

Terminal deoxynucleotidyl transferase (TdT) deoxyuridine triphosphate (dUTP) nick end labeling (TUNEL) is the method of using the TdT enzyme to covalently attach a tagged form of dUTP to 3’ ends of double- and single-stranded DNA breaks in cells. It is a reliable and useful method to detect DNA damage and cell death in situ. This video describes dissection, tissue processing, sectioning, and fluorescence-based TUNEL labeling of mouse skeletal muscle. It also describes a method of semi-automated TUNEL signal quantitation. Inherent normal tissue features and tissue processing conditions affect the ability of the TdT enzyme to efficiently label DNA. Tissue processing may also add undesirable autofluorescence that will interfere with TUNEL signal detection. Therefore, it is important to empirically determine tissue processing and TUNEL labeling methods that will yield the optimal signal-to-noise ratio for subsequent quantitation. The fluorescence-based assay described here provides a way to exclude autofluorescent signal by digital channel subtraction. The TUNEL assay, used with appropriate tissue processing techniques and controls, is a relatively fast, reproducible, quantitative method for detecting apoptosis in tissue. It can be used to confirm DNA damage and apoptosis as pathological mechanisms, to identify affected cell types, and to assess the efficacy of therapeutic treatments in vivo.