SOMEnv: An R package for mining environmental monitoring datasets by Self-Organizing Map and k-means algorithms with a graphical user interface

The Self-Organizing Map (SOM) algorithm belongs to the family of artificial neural networks. It is an unsupervised method that requires no a priori knowledge regarding experimental data classification. Further, it can deal with large datasets and non-linear problems, providing powerful visualization features for outcome exploration on 2D maps. For environmental pollution assessments other unsupervised techniques are widely used, such as principal component and hierarchical cluster analyses, but their application for mining large datasets and properly visualizing the results is limited, making them difficult to use for handling of large datasets obtained by high frequency environmental monitoring. This study presents an R package (SOMEnv) that allows non-expert users to elaborate by SOM algorithm environmental variables (pollutants and/or chemical physical properties) recorded with high frequency for a long monitoring period. Additionally, SOMEnv can also be used for elaborating small datasets derived from uneven sampling. All the calculations and outcome visualizations can be done using a graphical user interface (GUI), meaning that experience in R software coding is not necessary, and only a basic knowledge regarding the employed algorithm is needed to interpret the results. The benefits of the SOMEnv package are that (i) both the software environment and tool are freely available; (ii) it is able to handle large datasets; (iii) it provides heuristic rules for SOM initialization; (iv) it has a built-in GUI for performing calculations and visualizing the results. Moreover, it comes with a wide range of visualizations, several of which are dedicated to high frequency data monitoring. An example of application is presented. The package is freely available on the Comprehensive R Archive Network (CRAN) repository

Psychosocial factors and breast cancer: A 6-year Italian follow-up study

Background. Over the last 20 years contradictory results were obtained as regards to the role of psychosocial factors in favouring the onset of breast cancer and/or in influencing disease progression. Methods. The present study prospectively investigated the association between psychosocial variables and breast cancer in ninety-five out-patients. Within three months from the diagnosis the patients completed a series of questionnaires to evaluate psychological disturbances, emotional repression, adjustment to cancer, social support and occurrence of life events in the previous five years. At a distance of six years from the first assessment, the patients’ charts were re-analyzed in order to evaluate the course of cancer. Results. A higher volume of primary tumour at surgery was shown in patients who had had stressful events in the six months preceding cancer diagnosis. At follow-up, no relationship was found between psychosocial variables and the course of disease. The analysis of the frequency of relapses and deaths, and the survival analysis indicated that positivity of loco-regional lymph nodes, infiltrating histotype of the tumor and tumour stage were the only significant predictors of the time of death. Conclusions. The study suggests that clinical and biological, rather than psychsocial factors exert a major role in breast cancer progression

Metastasis and neuroendocrine system in stressed mice

The effects of experimental stressors have been examined for their differential effects on primary tumor growth and spontaneous lung metastasis in syngeneic mice bearing the weakly immunogenic tumor Lewis lung carcinoma. The effects caused by the early weaning, physical restraint and foot-shock are in general small, and affected by a high variability. On the contrary, spatial disorientation reproducibly causes a specific increase in tumor metastases. The effects of spatial disorientation are sensitive to the inhibition by treatment with bromocryptine and guanethidine, and particularly by a central and peripheral adrenergic neuron blocking agent reserpine. The use of different lighting conditions and assay of urinary melatonin excretion reveal an association between pineal gland function and effects of spatial disorientation on metastasis