An application of mathematical morphology to analysis of the size and shape of nuclei in tissue sections of non-Hodgkin's lymphoma

Using principles from the theory of mathematical morphology, a semiautomatic analysis of the size and shape of cell nuclei on tissue sections was carried out on a Leitz Texture Analysis System (Leitz-TAS). The four parameters proposed here are more discriminatory than conventional shape evaluation by the form factor (FF), which is based on the ratio of perimeter squared to area. The parameters quantified, respectively, nuclear elongation (ND), narrow (R1) and wide (R2) irregularities, and the distribution of R1 and R2 along the nuclear contour (ID). The properties of these parameters were tested nucleus-by-nucleus on 24 nuclear models. The methodology was then illustrated by a study of lymph node nuclei in non-Hodgkin's lymphoma (NHL). Prior to analysis, 45 lymphomas were classified into five categories of nuclear size and shape according to the International Working Formulation (IWF). Two hundred nuclei were measured on each lymph node section. Statistical interpretation was based upon an analysis of the nuclear surface area on sections and upon the mean values of R1, R2, and ND, the standard deviations of R1 and R2, and the percentage of cleaved nuclei detected by ID. The mean value of R2 discriminated best between the two sets of populations with regular and irregular nuclear contours, respectively. Parameters R1, ND, and ID permitted the distinction of certain NHL cases among populations with irregular nuclei. Nuclear invaginations decreased in depth as the nuclear area became greater. The median surface area was well correlated to the IWF, and the skewness coefficient (third statistical moment of the nuclear surface area distribution) was related to the number of nuclear size or shape subpopulations.     

Statistical region-based active contours for segmentation: An overview

In this paper we propose a brief survey on geometric variational approaches and more precisely on statistical region-based active contours for medical image segmentation. In these approaches, image features are considered as random variables whose distribution may be either parametric, and belongs to the exponential family, or non-parametric estimated with a kernel density method. Statistical region-based terms are listed and reviewed showing that these terms can depict a wide spectrum of segmentation problems. A shape prior can also be incorporated to the previous statistical terms. A discussion of some optimization schemes available to solve the variational problem is also provided. Examples on real medical images are given to illustrate some of the given criteria.     

Morphometric discrimination between syndromic (Gorlin) and nonsyndromic keratocysts.

OBJECTIVE: To search for morphologic nuclear features in the epithelial lining of odontogenic keratocysts to differentiate simple from Gorlin syndrome cysts. STUDY DESIGN: Five cases of syndrome-associated keratocysts and five of simple ones were studied. Thirty nuclei from the epithelial basal layer for each case were analyzed by the shape analytical morphometry (SAM) software system to quantitatively evaluate nuclear dimensions (area, perimeter, diameter), contour irregularities and nuclear shape asymmetries. Results were subjected to Student's t test and cluster analysis. RESULTS: Values of nuclear dimensions were very close in both groups of keratocysts, without any significant statistical differences. The variables related to nuclear profile irregularities, as well as those describing nuclear asymmetry, showed significantly higher values (P < .001) in syndromic cysts. Cluster analysis produced two different clusters by using variables related to nuclear contour irregularities. CONCLUSION: Preliminary results indicate the existence of nuclear morphologic differences between simple and syndromic cysts.     

The acute effects of different stretching exercises on jump performance

The purpose of this study was to demonstrate the short-term effects of different stretching exercises during the warm-up period on the lower limbs. A controlled, crossover clinical study involving 49 volunteers (14 women and 35 men; mean age: 20.4 years) enrolled in a "physical and sporting activities monitor" program. The explosive force was assessed using the Bosco test. The protocol was as follows: The test involved a (pre) jump test, general warm-up, intervention and (post) jump test. Each volunteer was subjected to each of the 5 interventions (no stretching [NS] and stretching: static passive stretching [P]; proprioceptive neuromuscular facilitation [PNF] techniques; static active stretching in passive tension [PT]; static active stretching in active tension [AT]) in a random order. The jump test was used to assess the squat jump, countermovement jump (CMJ), elasticity index (EI), and drop jump. An intragroup statistical analysis was performed before and after each intervention to compare the differences between the different stretching exercises. An intergroup analysis was also performed. Significant differences (p < 0.05) were found between all variables for the interventions "P," "PNF," and "TA" in the intragroup analysis, with each value being higher in the postjump test. Only the "P" intervention showed a significant difference (p = 0.046) for "EI," with the postvalue being lower. Likewise, significant differences (p < 0.05) were observed for the "CMJ" measurements during the intergroup analysis, especially between "NS" and the interventions "P," "PNF," "AT," and "PT," with each value, particularly that for "AT," being higher after stretching. The results of this study suggest that static active stretching in AT can be recommended during the warm-up for explosive force disciplines.     

Worker rehabilitation programs. Separating fact from fiction.

A few worker rehabilitation programs have had outstanding success in improving ability to function for persons with occupational back pain. Local programs must show that they have similar success. Because the definitions of terms such as "back school," "work hardening," and "functional restoration" are blurred at a local level, the choice of a program for an individual patient must depend primarily on the program''s demonstrated success rate with similar patients. The chances of returning to work decrease as a function of time after injury. Therefore, referring physicians, insurers, and employers must be provided with information regarding results in terms of acute (0 to 6 weeks), subacute (7 to 12 weeks), and chronic (more than 12 weeks) back pain. Other important variables include selection criteria, program cost, and dropout rate. We advocate standardized reporting of such data for all worker rehabilitation programs. A model "report to consumers," described here, is a minimal obligation. The validity of a number of important internal quality assurance issues is uncertain. Ethical and legal pressures must be recognized.     

Morphometric distinction of granulomas in tuberculosis and sarcoidosis. Difference in nuclear profiles

Morphometric measurements were carried out on epithelioid-cell nuclei of noncaseating granulomas in paraffin-embedded sections of lymph node biopsy specimens originating from 15 patients with sarcoidosis and from 18 patients with tuberculosis. The results, which were obtained with the help of a computer-assisted tracing device, established highly significant differences in shape and size of epithelioid-cell nuclear profiles in these two diseases. Direct measurements and computations on these results showed that epithelioid-cell nuclear profiles in sarcoidosis have a smaller mean and median perimeter (boundary length), area and long diameter (maximum length of the nuclear profile) and exhibit a more plump, elliptical-like shape than do those in tuberculous granulomas. Epithelioid-cell nuclear profiles of the latter, as a whole, show more irregular contours, resembling those, e.g., of the sole of a shoe or other elongated patterns. Differences in shape of nuclear profiles were best demonstrated by a size-independent form factor (4 pi *area/perimeter2).     

Nuclear morphometry and estrogen receptors in infiltrating ductal carcinoma of the breast

In this study ten cases of breast infiltrating ductal carcinoma have been considered. In all of them the content of ER has been evaluated by using monoclonal antibodies. Five of them were ER positive and five were ER negative. For the morphometric study ten nuclei of each case have been considered. By using the S.A.M. (Shape Analytical Morphometry) work-station an analytical study of the nuclear shape was performed. The first step was the extraction of fundamental shape which describes the basic shape of original contour without its irregularities. It was obtained by using two parametric equations. The second step was the evaluation of shape asymmetry by S.A.E. (Shape Asymmetry Evaluator). Finally the contour irregularities were evaluated by Fourier analysis. Along with analytical parameters, dimensions (area, perimeter and maximum diameter) were considered too. All obtained data were submitted to univariate statistical analysis (Student's T test) to compare the two groups (ER positive and ER negative tumors). Area, perimeter and maximum diameter were significatively greater in ER negative cases while analytical parameters were not discriminant between the two groups.     

Analysis of Clostridium botulinum Toxigenic Types A, B, and E for Fatty and Carbohydrate Content

Lyophilized, 48-hr log-phase vegetative cells were extracted with chloroform-methanol (2:1, v/v) and ethanol-ether (3:1, v/v) and then saponified with methanolic KOH. Gas-liquid chromatography of the methyl esters of extractable fatty acids revealed distinctive "pattern profiles" of Clostridium botulinum toxigenic types "A," "B," and "E." C. perfringens type "A" and Escherichia coli strain "B" were also studied in a similar manner and were found to give pattern profiles which were distinct even from those obtained for the C. botulinum microorganisms. Amino sugar content of the five microorganisms was determined by using a Beckman amino acid analyzer. The molar ratio of glucosamine to that of galactosamine was found to be of further assistance in distinguishing the individual microorganisms.     

jModelTest: phylogenetic model averaging

jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.     

Differentiating benign nevi from malignant melanoma using DNA microdensitometry and karyometry and maturation: a zonal comparison,correlation and multivariate analysis

OBJECTIVE: To evaluate the diagnostic effectiveness of cytometric features of DNA microdensitometry, karyometry (nuclear morphometry) and maturation and their combinations in separating benign nevi from malignant melanomas. STUDY DESIGN: Tumor cells were measured from each of the superficial, middle and deep zones of 81 melanocytic lesions using video image analysis for nuclear DNA content, chromatin compactness, and nuclear size and shape variables. There were 27 banal compound melanocytic nevi, 20 dysplastic compound nevi, 10 Spitz nevi and 24 malignant melanomas (MM). Maturation of cells with depth into the dermis was also studied by comparing cells from superficial to deep zones. RESULTS: MM showed distinct characteristics of DNA microdensitometry, karyometry and maturation as compared to all groups of benign nevi. There were overall close correlations between nuclear DNA content variables and nuclear size parameters in the total group of 81 lesions. However, there were fewer significant correlations between the various indices in the group of melanomas alone. Using multivariate discriminant analysis, up to 97% of the lesions could be correctly separated as benign or malignant by a combination of five key microdensitometric, karyometric and maturation parameters. CONCLUSION: DNA microdensitometry, karyometry and maturation parameters have independent abilities in identifying individual malignant melanomas. Coevaluation of various cytometric features and maturation profiles offers better diagnostic ability in separating benign nevi from MM.     

Towards 3-D modelling of epithelia by computer simulation.

The present work is a preliminary step towards dynamic 3-D modelling by computer graphics simulation of the structure of normal and pathological epithelia, using an expert system. In its present state, Esexsy (Epithelium Simulation by EXpert SYstem) allows the construction, through iterative steps, of a simple 3-D representation of the nasal epithelium, based on the positions, sizes and shapes of nuclei. The iterative process is based on statistical comparisons between distributions of parameter values calculated from real (2-D) histological sections and those issued from an equivalent computer 'section' through the simulated 3-D image. We show the results of attempts at simulating normal, metaplastic and dysplastic states of the nasal epithelium, the latter two being characterized by a progressive architectural disorganization, accompanied by nuclear size/shape alterations. The representation takes into account the size, shape, orientation and spatial arrangement of nuclei, with one or several layers from the basal lamina to the lumen. A modified Poisson point process is used at present to position the nuclei, which are modelled by bi-axial spheroids (from prolate to oblate through spherical), with random orientation and size/shape deviations. It should be possible to use the same computer program to simulate other types of epithelia and to achieve increasingly realistic representations by incorporating, notably, nuclear deformations and chromatin texture.     

Automated nuclear image morphometry on fine needle aspiration smears of malignant round cell tumors

OBJECTIVE: To analyze nuclear image morphometry in fine needle aspiration cytology smears of different groups of malignant round cell tumors (MRCTs) to evaluate its diagnostic role. STUDY DESIGN: In this study there were 55 cases of MRCT, consisting of 18 Ewing's sarcoma (EW), 10 neuroblastoma (NB), 5 non-Hodgkin's lymphoma (NHL), 6 rhabdomyosarcoma (RMS), 4 peripheral neuroectodermal tumor (PNET), 8 Wilm's tumor (WT), 2 retinoblastoma (RB) and 2 undifferentiated round cell tumor (URCT). A Leica image cytometer with Quantimet 600 software (Leica, Cambridge, U.K) was used to measure nuclear area, nuclear diameter, nuclear perimeter, nuclear convex perimeter (CP), nuclear roundness and nuclear convex area on hematoxylin and eosin-stained cytologic smears. At least 100 cells were studied in each case. RESULTS: The RB group of tumors showed the highest mean nuclear area (NA), convex area (CA), CP, diameter (D), perimeter (P) and roundness (R). RMS had the highest mean CA, and URCT had the highest mean roundness. ANOVA was performed on the tumors and showed significant differences for all the variables in all the groups (P < .000). All the morphometric data (except roundness) were significantly different in RMS versus all other MRCTs except RB. Similarly, morphometric data on WT were also significantly different from that on NHL. Most of the morphometric data (except CA and R) showed significant differences between RB and all other MRCTs except RMS. PNET, EW and NB could not be differentiated with those variables. CONCLUSION: RMS and RB could successfully be differentiated from all other MRCTs with the help of morphometry. It was not possible to differentiate RMS and RB by image cytometry (ICM) since the ICM data overlapped in those two groups. It was possible to differentiate WT and NHL with ICM. Nuclear ICM was not significantly different in the NB, PNET and ES groups, and probably ICM would not be very helpful to differentiate these groups of MRCT.     

Ecoinformatics for integrated pest management: expanding the applied insect ecologist's tool-kit

Experimentation has been the cornerstone of much of integrated pest management (IPM) research. Here, we aim to open a discussion on the possible merits of expanding the use of observational studies, and in particular the use of data from farmers or private pest management consultants in "ecoinformatics" studies, as tools that might complement traditional, experimental research. The manifold advantages of experimentation are widely appreciated: experiments provide definitive inferences regarding causal relationships between key variables, can produce uniform and high-quality data sets, and are highly flexible in the treatments that can be evaluated. Perhaps less widely considered, however, are the possible disadvantages of experimental research. Using the yield-impact study to focus the discussion, we address some reasons why observational or ecoinformatics approaches might be attractive as complements to experimentation. A survey of the literature suggests that many contemporary yield-impact studies lack sufficient statistical power to resolve the small, but economically important, effects on crop yield that shape pest management decision-making by farmers. Ecoinformatics-based data sets can be substantially larger than experimental data sets and therefore hold out the promise of enhanced power. Ecoinformatics approaches also address problems at the spatial and temporal scales at which farming is conducted, can achieve higher levels of "external validity," and can allow researchers to efficiently screen many variables during the initial, exploratory phases of research projects. Experimental, observational, and ecoinformatics-based approaches may, if used together, provide more efficient solutions to problems in pest management than can any single approach, used in isolation.     

LoCoH: nonparameteric kernel methods for constructing home ranges and utilization distributions

Parametric kernel methods currently dominate the literature regarding the construction of animal home ranges (HRs) and utilization distributions (UDs). These methods frequently fail to capture the kinds of hard boundaries common to many natural systems. Recently a local convex hull (LoCoH) nonparametric kernel method, which generalizes the minimum convex polygon (MCP) method, was shown to be more appropriate than parametric kernel methods for constructing HRs and UDs, because of its ability to identify hard boundaries (e.g., rivers, cliff edges) and convergence to the true distribution as sample size increases. Here we extend the LoCoH in two ways: "fixed sphere-of-influence," or r-LoCoH (kernels constructed from all points within a fixed radius r of each reference point), and an "adaptive sphere-of-influence," or a-LoCoH (kernels constructed from all points within a radius a such that the distances of all points within the radius to the reference point sum to a value less than or equal to a), and compare them to the original "fixed-number-of-points," or k-LoCoH (all kernels constructed from k-1 nearest neighbors of root points). We also compare these nonparametric LoCoH to parametric kernel methods using manufactured data and data collected from GPS collars on African buffalo in the Kruger National Park, South Africa. Our results demonstrate that LoCoH methods are superior to parametric kernel methods in estimating areas used by animals, excluding unused areas (holes) and, generally, in constructing UDs and HRs arising from the movement of animals influenced by hard boundaries and irregular structures (e.g., rocky outcrops). We also demonstrate that a-LoCoH is generally superior to k- and r-LoCoH (with software for all three methods available at http://locoh.cnr.berkeley.edu).     

SEXUAL DIMORPHISM OF SHELL SHAPE AND GROWTH OF VILLOSA VILLOSA (WRIGHT) AND ELLIPTIO ICTERINA (CONRAD) (BIVALVIA: UNIONIDAE)

Shell shape and growth of two unionacean species, Villosa villosaand Elliptio icterina, are analyzed with univariate and multivariatetechniques. The relationship of shape variables to size variablesis examined. Under the lognormal assumption, parametric testsof these allometric relationships are valid. Variables describingthe ventro-posterior region of the shell are shown to be thebest of those tested for discriminating between the sexes ofboth species regardless of statistical method. Neither speciesexhibits size sexual dimorphism. Shape sexual dimorphism ofV. villosa is constant during adult growth, but the more subtledimorphism of E. icterina changes as adults continue to grow. (Received 20 January 1986;     

Disordered development of macrophages in non-Hodgkin's lymphoma

Macrophage development in 20 untreated patients with non-Hodgkin's lymphoma (NHL) has been studied and compared with that in 20 normal subjects. Morphometric measurements were carried out on ultrastructural features of cell, nucleus and mitochondria during 6 days suspension culture of blood monocytes in the presence of autologous serum and lymphocytes. The results were subjected to multivariate and univariate analysis of variance. Statistically significant differences were found between the subject groups with respect to the volumes and surface areas of cell, nucleus and mitochondria, to the excess surface membrane of cell and nucleus (as compared with equivalent spheres) and to the number of mitochondrial profiles per section. It would appear that the patients' cell grew less, showed less elaboration of surface features and had reduced nuclear and mitochondrial development, the latter affecting mitochondrial numbers rather than individual size. The findings provide further evidence that mononuclear phagocytes are deranged in NHL.     

High-dimensional pharmacogenetic prediction of a continuous trait using machine learning techniques with application to warfarin dose prediction in African Americans

MOTIVATION: With complex traits and diseases having potential genetic contributions of thousands of genetic factors, and with current genotyping arrays consisting of millions of single nucleotide polymorphisms (SNPs), powerful high-dimensional statistical techniques are needed to comprehensively model the genetic variance. Machine learning techniques have many advantages including lack of parametric assumptions, and high power and flexibility. RESULTS: We have applied three machine learning approaches: Random Forest Regression (RFR), Boosted Regression Tree (BRT) and Support Vector Regression (SVR) to the prediction of warfarin maintenance dose in a cohort of African Americans. We have developed a multi-step approach that selects SNPs, builds prediction models with different subsets of selected SNPs along with known associated genetic and environmental variables and tests the discovered models in a cross-validation framework. Preliminary results indicate that our modeling approach gives much higher accuracy than previous models for warfarin dose prediction. A model size of 200 SNPs (in addition to the known genetic and environmental variables) gives the best accuracy. The R(2) between the predicted and actual square root of warfarin dose in this model was on average 66.4% for RFR, 57.8% for SVR and 56.9% for BRT. Thus RFR had the best accuracy, but all three techniques achieved better performance than the current published R(2) of 43% in a sample of mixed ethnicity, and 27% in an African American sample. In summary, machine learning approaches for high-dimensional pharmacogenetic prediction, and for prediction of clinical continuous traits of interest, hold great promise and warrant further research.     

Image analysis of hyperchromatic crowded cell groups in SurePath cervical cytology

Objective: The discrimination of hyperchromatic crowded cell groups (HCCGs) in cervical cytology is a difficult and error‐prone interpretive task. While the classic features of dyskaryosis are of undoubted value, the contribution of size, shape and colour intensity of HCCGs is less certain. This study employed morphometric analysis to determine whether HCCG area, shape and colour intensity are useful in categorising them. Methods: Seventy‐five digital images from each of six categories of HCCG were subjected to image analysis. Ten variables relating to HCCG size, shape and colour intensity were assessed by discriminant function analysis. A further 28 cases were employed as a test set to determine the classification accuracy of the discriminant model. All samples were SurePath liquid‐based cytology preparations. Results: Nine of the 10 variables contributed significantly to the model (P < 0.001) but no single variable had sufficient discriminative ability. Classification accuracy was highest for abnormal endocervical HCCGs and lowest for squamous metaplastic cells (64.0 vs. 17.3% correct classification rate). The accuracy of the model for distinguishing normal and abnormal HCCGs was 70.0%, which was significantly higher than chance (P < 0.0001), but this reduced to 64.3% for the test cases, which was no better than chance (P > 0.05). Conclusions: The area, shape and colour intensity of HCCGs, either alone or in combination, have little discriminative value. Practitioners and trainers should focus on the well‐established features of dyskaryosis, such as chromatin pattern, nuclear membrane irregularities and group architecture. In terms of morphometric analysis, DNA ploidy and chromatin texture analysis may be more fruitful avenues of investigation.