Quantitative computerized image analysis of Tn and T (Thomsen-Friedenreich) epitopes in prognostication of human breast carcinoma

The precursors of the blood group N and M-immunodominant structures, Tn and T (Thomsen-Friedenreich) epitopes (EPs) occur in approximately 90% of carcinomas (CAs) but are masked in benign-diseased and healthy tissues. We determined quantitatively on 55 primary invasive ductal breast CAs, stages I to IV, the prognostic value of extent of Tn and T EP expression over an observation period exceeding 5 years postoperatively. Classical, established pathological and histological prognostic characteristic indicators associated with survival were subdivided by standard criteria into favorable and unfavorable categories. Tissue sections were reacted with monoclonal anti-Tn and -T antibodies, followed by the streptavidin-biotin-peroxidase-DAB procedure; counterstain was methyl green. Tn and T EPs were then quantitated by computerized image analysis. Of the 55 CAs, 51 clearly expressed Tn and T, and four had traces. Strong Tn EP expression was statistically significantly associated with shortened 5-year disease-free interval, increasing pTNM stages, positive lymph node status, and increasing combined histological grades. T EPs were usually well expressed but showed no significant association with prognostic factors. Our results suggest that quantitative immunohistochemistry-image analysis of Tn EPs of primary breast CAs may add new parameters to prognostication.     

Quantitative image sequence analysis of fundus fluorescein angiography

Interpretation of retinal angiographic studies has heretofore been largely qualitative. The temporal properties associated with fluorescein fluorescence of normal and pathologic fundus features are quantified to potentiate pixel assignment and fundus feature quantitation for clinical studies where precise image metrology is vital. Fluorescein angiography studies were digitized, and temporally sequential images were spatially registered with polynomial warping algorithms, allowing for the construction of a three-dimensional angiogram vector. Temporal profiles through spatially registered, temporally sequential pixels were computed. Fundus feature fluorescence behavior was quantified. Fundus features may be discriminated on the basis of spatio-temporal fluorescein fluorescence properties. Pixel assignment based on spatio-temporal relationships will facilitate fundus feature quantitation.     

Lipid analysis by matrix-assisted laser desorption and ionization mass spectrometry: A methodological approach

It has been hypothesized that protein factors may protect CpG islands from methyltransferase during development and that demethylation may involve protein-DNA interactions at demethylated sites. However, direct evidence has been lacking. In this study, demethylation at the EBNA-1 binding sites of the Epstein-Barr virus latent replication origin, oriP, was investigated by using human cells. Several novel findings are discussed. First, there are specific preferential demethylation sites within the oriP region. Second, the DNA sequence of oriP alone is not the target of an active demethylation process. Third, EBNA-1 binding is required for the site-specific demethylation in oriP. Interestingly, CpG sites adjacent to and between the EBNA-1 sites do not become demethylated. Fourth, demethylation of the first DNA strand in oriP at the EBNA-1 binding sites involves a passive (replication-dependent) mechanism. The second-strand demethylation appears to occur through an active mechanism. That is, EBNA-1 protein binding prevents the EBNA-1 binding sites from being remethylated after one round of DNA replication, and it appears that an active demethylase then demethylates these hemimethylated sites. This study provides clear evidence that protein binding specifies sites of DNA demethylation and provides insights into the sequence of steps and the mechanism of demethylation.     

A methodological approach for estimating turbidity in a river

During the operations of purging and disposal of sediments of a reservoir it is necessary to know the values of turbidity in the river downstream in natural condition, in the absence of dams or river training works. The paper shows that under these conditions the ratio of the average values of sediment discharge to the annual maximum value of water discharge is a function of the average annual turbidity. Turbidity can be considered as representative synthetic index of the climatic conditions, the lithological features and the land cover of the basin, and the geometric characteristics of the river network. The proposed relationship of sediment discharge as a function of water discharge were validated on the basis of data collected from different Italian regions that have very different morphological, geo-lithological and rainfall features and that are characterised by a basin area changing between a few dozen and thousands of square kilometres. The results can be considered satisfying.     

Does music induce emotion? A theoretical and methodological analysis.

Is music ubiquitous in part because it is causally linked to emotion? In this article, a comprehensive theoretical and methodological reevaluation is presented of a classical problem: The direct induction of emotion by music (M→E). The author's Prototypical Emotion-Episode Model (PEEM) is used in the conceptual critique. A close scrutiny of the major published studies, and the author's new data regarding some substantive and methodological issues in several of these, reveal weak support for the M→E model. The conclusion seems justified that music may induce low-grade basic emotions through mediators, such as dance and cognitive associations to real-world events. However, it is suggested--on the basis of the recently developed Aesthetic Trinity Theory (ATT; Kone?ni, 2005) and its further development in the present article--that being moved and aesthetic awe, often accompanied by thrills, may be the most genuine and profound music-related emotional states. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Interpersonal dynamics in a simulated prison: A methodological analysis.

Analyzes the Stanford Prison experiment of P. G. Zimbardo et al (1973) and questions, on methodological grounds, various of their inferences. Empirical evidence is presented to elucidate and buttress these criticisms, and an alternative interpretation of the outcome of the Stanford experiment is proposed. (28 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Role of mechanics in composing of elementary school students: A new methodological approach.

The authors used multiple-group structural equation modeling to analyze structural relationships between latent factors underlying separate measures of handwriting, spelling, and composing in Grades 1–6. For compositional fluency, the paths from both handwriting and spelling were significant in the primary grades, but only the path from handwriting was significant in the intermediate grades. For compositional quality, only the path from handwriting was significant at the primary and intermediate grades. The contribution of spelling to compositional quality was indirect through its correlation with handwriting. Handwriting and spelling accounted for a sizable proportion of the variance in compositional fluency (41% to 66%) and compositional quality (25% to 42%). These findings show that the mechanical skills of writing may exert constraints on amount and quality of composing. Theoretical and educational implications of the findings are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Quantitative analysis of gel electrophoretograms by image analysis and least squares modeling

A computer-aided quantitative method for a complex analysis of gel electrophoretograms is presented. The analysis consists of several steps: (i) determination of the background image by methods of mathematical morphology and its subtraction from the gel image, (ii) selection of an appropriate part of the gel lane including curved lanes and lanes with a nonuniform width, (iii) computation of the lane densitogram by averaging several lane-parallel scans, (iv) decomposition of the lane densitogram into component bands using a data selecting algorithm and Marquardt's minimizer. Several different functions for component bands are utilized. It is shown that the densitogram can be decomposed into component bands with reasonable accuracy only if an appropriate model function is chosen. The algorithms are tested on several different gel electrophoretograms which show typical features as a nonuniform background, curved lanes, an asymmetrical band shape and a superposition of small bands on the shoulders of big ones. It is shown that overlapped bands are best approximated by an asymmetrical Gausian curve and an asymmetrical Gauss-Cauchy function. Linear response to the serial dilution of the protein sample is tested.     

Identification of early apoptosis in feulgen-stained cultured cells in situ by computerized image analysis

A method is presented in which Feulgen-stained apoptotic cells are identified among cultured cells in situ using computerized image analysis of their nuclei. Images of either control (untreated) human lymphoblastoid cell nuclei or of similar cells treated with 3mM methyl methanesulfonate for 1 h, which induces apoptosis in 100% of the cells, were converted to a standard size (80 x 80 pixels) and Fourier transforms and boundary images based on 21 proportional mean gray-level thresholds obtained. The perimeter and the mean fractal dimension of the latter and 39 selected coefficients of the former were then obtained from which data were chosen heuristically and subjected to multivariate linear discrimination analysis. Eighty-two percent of a teaching set of 50 nuclei and 69% of a test set of 29 nuclei were correctly identified as apoptotic versus nonapoptotic by the computer, compared with 57% identified correctly by a panel of 7 pathologists. This study shows the feasibility of using this type of analysis to directly identify apoptotic cells in culture, and probably also in tissues, by direct observation using computerized imaging technology.     

A methodological analysis of developmental studies of identity conservation and equivalence conservation.

Reviews the discrepant findings which have been reported during recent years on the order of emergence of identity conservation and equivalence conservation. An analysis of the procedural details of the conflicting studies revealed that the discrepant findings are probably the result of a measurement error (judgments-plus-explanations response criteria) and a sampling error (older S samples) routinely committed in studies reporting that identity and equivalence do not emerge in a fixed order. Some new data from preschool, kindergarten, and 3rd-grade Ss in an experiment in which these 2 errors were controlled provide support for this conclusion. The general consequences of measurement and sampling errors for concept development studies are discussed. (37 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A. Weismann's germ-plasma theory: a new methodological approach to the problems of general biology

A. Weismann's theory of germ plasm is of special importance in the history of theoretical biology. Its meaning was not confined by presenting of neoperformistic ideas on the new level of science. In fact it predicted reduction division, the continuing of germ plasm and the significance of chromosomes in heredity. For the first time it brought a new methodology to the experimental genetics and the idea of interdisciplinary synthesis.     

Response productivity: A methodological problem in content analysis studies in psychotherapy.

Contends that most content analysts of psychotherapy materials have failed to consider the possibility that the frequency of units coded to the categories of the content analysis system might be correlated with the total number of units produced. The existence of such relationships may confound interpretation of the association between content analysis variables and other external variables. When investigators have attempted to control for response productivity, they have usually divided the frequency of units in each category by the total number of units. This procedure does not control for response productivity and is often uninterpretable. The issues involved are discussed and demonstrated, and appropriate techniques of controlling for productivity are described. (43 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Implementing computerized technology: An organizational analysis.

Why do some organizations succeed and others fail in implementing the innovations they adopt? To begin to answer this question, the authors studied the implementation of manufacturing resource, planning, an advanced computerized manufacturing technology, in 39 manufacturing plants (number of individual respondents?=?1,219). The results of the plant-level analyses suggest that financial resource availability and management support for technology implementation engender high-quality implementation policies and practices and a strong climate for implementation, which in turn foster implementation effectiveness—that is, consistent and skilled technology use. Further research is needed to replicate and extend the findings. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A versatile image analysis approach for simultaneous chromosome identification and localization of FISH probes

Modern cytogenetic techniques, such as comparative genomic hybridization (CGH) and the multi-color fluorescence in situ hybridization (FISH) techniques of multiplex fluorescence in situ hybridization (M-FISH) and spectral karyotyping (SKY), require a coordinated banding analysis to maximize their usefulness. All of the methods currently used, including Giemsa (G-) banding, Alu banding, and 4',6-diamidino-2-phenyl-indole (DAPI) banding, have serious drawbacks. A simple and effective method to band chromosomes concurrently with FISH is needed. To address this problem, we stained chromosomes with DAPI and chromomycin A3, and then used an image analysis program to generate banding by dividing the image taken with a DAPI excitation filter by the image taken with a chromomycin A3 excitation filter. The result was a metaphase spread in which the chromosomes possessed a banding pattern characteristic of R-banding. The image analysis program was then used to generate linescans of pixel intensity versus relative position along the length of chromosomes that were banded using this technique, which we have called D/C R-banding. Each chromosome in a genome was represented by a characteristic scan profile, which was unaffected by FISH signals. Reference linescans were prepared by karyotyping D/C R-banded chromosomes for a given species, and then drawing lines along the length of the known chromosomes. The linescans were combined into a spreadsheet database, which was linked by dynamic data exchange to the image analysis program and normalized for length and intensity. The linescan of an unknown chromosome was then transferred to the spreadsheet, where it was normalized for length and intensity and overlaid on the linescans of each chromosome in the genome. Unknown chromosomes were identified by comparison of their graphs with graphs in the standardized reference genome. We have used this approach to create reference linescan karyotypes of several species, and to identify chromosomes on which FISH was performed.     

A new approach for utility analysis.

A new utility analysis approach is presented. It is demonstrated that the new approach does not require the direct estimation of the most problematic component of current utility analysis equations, the standard deviation of Y. The parsimony of the new approach provides the potential for more directly linking decision-theoretic utility analysis with economic and accounting concepts. The development of the new approach highlights the many necessary and untested assumptions of current utility models. It also points to a need for reassessing the psychometric validity of correcting for criterion unreliability in utility analysis. Furthermore, the CREPID and 40% and 70% rules for estimating the standard deviation of Y are shown to be special cases of the new approach. Research on the efficacy of the assumptions and applicability of the new approach is advocated. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A methodological study of cigarette brand discrimination.

To test the comparative discriminability of the recognition judgment method and an affective (like-dislike) judgment method of brand discrimination, 246 regular cigarette smokers were divided into two groups, and each group member was given one of the 'Big Three' cigarettes with brand name obscured. Members of one group made a recognition judgment; members of the other made a 'like-dislike' judgment. Analysis of variance showed that (1) both types of judgment were made with better than chance accuracy, (2) the like-dislike judgment was slightly but not significantly more sensitive than the recognition judgment, (3) the distribution of responses for each type of judgment was radically different. "It was suggested that… the use of affective judgment… merits further study." (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Measurement of identification: A methodological note.

Each of 16 children (age 5-8 yr.) watched his same-sex parent and a stranger of the same sex compete in a perceptual recognition task. Stranger and parent were prerehearsed to pass and fail specific items during the competition, and each was praised or censured following success or failure. The child's overt behavior and heart rate were recorded during the session. The children smiled more after the parent succeeded and the stranger failed than after parent failure and stranger success. Degree of cardiac acceleration following parent success and stranger failure was larger than under the opposite conditions. The data suggest the feasibility of assessing vicarious involvement with the model as an index of identification. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A general approach to causal mediation analysis.

Traditionally in the social sciences, causal mediation analysis has been formulated, understood, and implemented within the framework of linear structural equation models. We argue and demonstrate that this is problematic for 3 reasons: the lack of a general definition of causal mediation effects independent of a particular statistical model, the inability to specify the key identification assumption, and the difficulty of extending the framework to nonlinear models. In this article, we propose an alternative approach that overcomes these limitations. Our approach is general because it offers the definition, identification, estimation, and sensitivity analysis of causal mediation effects without reference to any specific statistical model. Further, our approach explicitly links these 4 elements closely together within a single framework. As a result, the proposed framework can accommodate linear and nonlinear relationships, parametric and nonparametric models, continuous and discrete mediators, and various types of outcome variables. The general definition and identification result also allow us to develop sensitivity analysis in the context of commonly used models, which enables applied researchers to formally assess the robustness of their empirical conclusions to violations of the key assumption. We illustrate our approach by applying it to the Job Search Intervention Study. We also offer easy-to-use software that implements all our proposed methods. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Negotiating teams: A levels of analysis approach.

In light of the increasing presence of teams and work groups in organizations and their role in negotiations, the authors outline a framework for understanding the dynamics of negotiating teams. The traditional context of dyadic negotiations (i.e., one-on-one) is used as a point of departure for the analysis. The authors bring together research on negotiation, small group dynamics, and individual social cognition into a coherent framework to analyze negotiating teams. At the heart of the framework are 3 categories of psychological processes, corresponding to different levels of analysis, which highlight the contributions of individual, intragroup, and intergroup processes. These processes are discussed in terms of traditional negotiation concepts, such as integrative and distributive bargaining. Finally, guidance for future research is provided. (PsycINFO Database Record (c) 2010 APA, all rights reserved)