Expression of p53 protein has no independent prognostic value in breast cancer

A series of 392 female breast carcinomas was analysed immunohistochemically for expression of p53 protein with special emphasis on the role of p53 as an independent prognostic factor. Altogether, 54.8 per cent of the carcinomas expressed p53 protein, with the mean [standard error (SE)] fraction of positive nuclei being 17.1 per cent (1.2 per cent). Expression of p53 protein was independent of tumour metastasis at diagnosis, axillary lymph node status, tumour diameter, histological type, tubule formation, proportion of intraductal growth, margin formation, necrosis, DNA ploidy, and S-phase fraction. A high fraction of p53-positive nuclei was significantly related to patient age under 70 years, high grade, severe nuclear pleomorphism, dense infiltration of tumour by lymphocytes, high mitotic index, and high apoptotic index (for all, P < 0.05). Impaired survival probability in the entire cohort (P = 0.05) and in the axillary lymph node-positive (ANP) tumours (P = 0.015) was associated with a fraction of p53-positive nuclei less than 25 per cent, while in the axillary lymph node-negative (ANN) tumours, expression of p53 had no prognostic value. In multivariate analysis, independent prognostic predictors included axillary lymph node status, tumour diameter, and mitotic index. In the ANN tumours, tumour diameter, fraction of p53-positive nuclei, and tumour grade were independent prognostic factors, whereas in the ANP tumours, diameter and mitotic index were the two independent prognostic factors. The results suggest that abnormal expression of p53 protein is only a weak independent prognostic factor in female breast cancer.     

Model-based process optimization in the presence of parameter uncertainty

In model-based process optimization one uses a mathematical model to optimize a certain criterion, for example the product yield of a chemical process. Models often contain parameters that have to be estimated from data. Typically, a point estimate (e.g. the least squares estimate) is used to fix the model for the optimization stage. However, parameter estimates are uncertain due to incomplete and noisy data. In this article, it is shown how parameter uncertainty can be taken into account in process optimization. To quantify the uncertainty, Markov Chain Monte Carlo (MCMC) sampling, an emerging standard approach in Bayesian estimation, is used. In the Bayesian approach, the solution to the parameter estimation problem is given as a distribution, and the optimization criteria are functions of that distribution. The formulation and implementation of the optimization is studied, and numerical examples are used to show that parameter uncertainty can have a large effect in optimization results.     

Computational framework for simulating fluorescence microscope images with cell populations

Fluorescence microscopy combined with digital imaging constructs a basic platform for numerous biomedical studies in the field of cellular imaging. As the studies relying on analysis of digital images have become popular, the validation of image processing methods used in automated image cytometry has become an important topic. Especially, the need for efficient validation has arisen from emerging high-throughput microscopy systems where manual validation is impractical. We present a simulation platform for generating synthetic images of fluorescence-stained cell populations with realistic properties. Moreover, we show that the synthetic images enable the validation of analysis methods for automated image cytometry and comparison of their performance. Finally, we suggest additional usage scenarios for the simulator. The presented simulation framework, with several user-controllable parameters, forms a versatile tool for many kinds of validation tasks, and is freely available at http://www.cs.tut.fi/sgn/csb/simcep.     

Preliminary study of ultrasonic structural quality control of Swiss-type cheese

There is demand for a new nondestructive cheese-structure analysis method for Swiss-type cheese. Such a method would provide the cheese-making industry the means to enhance process control and quality assurance. This paper presents a feasibility study on ultrasonic monitoring of the structural quality of Swiss cheese by using a single-transducer 2 MHz longitudinal mode pulse-echo setup. A volumetric ultrasonic image of a cheese sample featuring gas holes (cheese-eyes) and defects (cracks) in the scan area is presented. The image is compared with an optical reference image constructed from dissection images of the same sample. The results show that the ultrasonic method is capable of monitoring the gas-solid structure of the cheese during the ripening process. Moreover, the method can be used to detect and to characterize cheese-eyes and cracks in ripened cheese. Industrial application demands were taken into account when conducting the measurements.     

ESTERASES OF BAKER'S YEAST. III. THE ESTER/ACID RATIO IN MODEL SOLUTIONS

Ester/acid equilibria were studied in reaction mixtures containing ethyl alcohol, ethyl caprylate or caprylic acid, and baker's yeast or an esterase purified from baker's yeast in buffer. The equilibrium concentration of ethyl caprylate after an incubation of yeast or a yeast esterase preparation with caprylic acid was the same as in the case where yeast or esterase preparation was incubated with the ethyl caprylate. The equilibrium attained depends not only on the concentration of the ester and the alcohol but also on the pH, the final ester concentration remaining higher at low pH. It could be shown that yeast esterase is responsible for the hydrolysis or synthesis of the ester. At equilibrium the molar ratio of ethyl caprylate/caprylic acid is about the same as that found in fermentation solutions under the same conditions.     

Effect of nitrapyrin on nitrapyrin residues and nitrate content in red beet roots fertilised with urea

The effect of nitrapyrin [2-chloro-6-(trichloromethyl)pyridine] application on nitrapyrin residues and nitrate content in red beet (Beta vulgaris L. var. conditiva) roots and in soil fertilised with urea was studied during the 1977 growing season. The nitrapyrin residues in roots were on 15 August between 0.00–1.19 μg g^?1 and on 1 October between 0.00–0.45 μg g^?1 (dry weight basis) correlating significantly r = 0.99, P<0.01) to the rates of nitrapyrin applied on 8 June (0–34 kg ha^?1). The content of nitrapyrin in roots decreased in autumn having in August-September a ‘biological half-life’ of 3 weeks. In soil the same parameter was in July-September more than 4 months. The ratio of nitrapyrin to its main breakdown product varied in soil between 3.5–24.8 and in red beets between 0.6–1.4. Neither of these compounds were found in processed canned red beets. Nitrapyrin treatment decreased the nitrate content in both soil and beets. The inhibitor application of 18 kg ha^?1 caused the highest reduction of the NO₃-nitrogen content in beets, the average values on dry weight basis being 0.51–0.34 mg g^?1 for 0–18 kg ha^?1 nitrapyrin application, respectively. The reduction of NO₃-nitrogen in beets from its level of 15 August to its September level was 44%. After 5 September the reduction of the nitrate level in beets was not significant.     

Margarines,butter and vegetable oils as sources of polycyclic aromatic hydrocarbons

Concentrations of polycyclic aromatic hydrocarbons (PAH) were determined in Finnish butter, margarines and vegetable oils and their raw materials. In all the samples some degree of PAH contamination was found. The average per capita intake was estimated at 0.6 μg per day. The plant raw materials are supposed to be contaminated by combustion-derived atmospheric particles during the growing period. Inappropriate drying processes can substantially increase the contamination level. Deodorization processes used by food industry seem to decrease the total PAH levels significantly.     

Improving the bit-parallel NFA of Baeza-Yates and Navarro for approximate string matching

We propose a new variant of the bit-parallel NFA of Baeza-Yates and Navarro (BPD) for approximate string matching [R. Baeza-Yates, G. Navarro, Faster approximate string matching, Algorithmica 23 (1999) 127-158]. BPD is one of the most practical approximate string matching algorithms under moderate pattern lengths and error levels [G. Myers, A fast bit-vector algorithm for approximate string matching based on dynamic programming, J. ACM 46 (3) 1989 395-415; G. Navarro, M. Raffinot, Flexible Pattern Matching in Strings—Practical On-line Search Algorithms for Texts and Biological Sequences, Cambridge University Press, Cambridge, UK, 2002]. Given a length-m pattern and an error threshold k, the original BPD requires (m−k)(k+2) bits of space to represent an NFA with (m−k)(k+1) states. In this paper we remove redundancy from the original NFA representation. Our variant requires (m−k)(k+1) bits of space, which is optimal in the sense that exactly one bit per state is used. The space efficiency is achieved by using an alternative, but equally or even more efficient, simulation algorithm for the bit-parallel NFA. We also present experimental results to compare our modified NFA against the original BPD and its main competitors. Our new variant is more efficient than the original BPD, and it hence takes over/extends the role of the original BPD as one of the most practical approximate string matching algorithms under moderate values of k and m.