Identification of multivariable Boolean patterns in microbiome and microbial gene composition data

Virtually every biological system is governed by complex relations among its components. Identifying such relations requires a rigorous or heuristics-based search for patterns among variables/features of a system. Various algorithms have been developed to identify two-dimensional (involving two variables) patterns employing correlation, covariation, mutual information, etc. It seems obvious, however, that comprehensive descriptions of complex biological systems need also to include more complicated multivariable relations, which can only be described using patterns that simultaneously embrace 3, 4, and more variables. The goal of this manuscript is to (a) introduce a novel type of associations (multivariable Boolean patterns) that can be manifested between features of complex systems but cannot be identified (described) by traditional pair-vise metrics; (b) propose patterns classification method, and (c) provide a novel definition of the pattern's strength (pattern's score) able to accommodate heterogeneous multi-omics data. To demonstrate the presence of such patterns, we performed a search for all possible 2-, 3-, and 4-dimensional patterns in historical data from the Human Microbiome Project (15 body sites) and collection of H. pylori genomes associated with gastric ulcers, gastritis, and duodenal ulcers. In all datasets under consideration, we were able to identify hundreds of statistically significant multivariable patterns. These results suggest that such patterns can be common in microbial genomics/microbiomics systems.

[The pain-emotion: Advocating pain as an emotion]

OBJECTIVES

Pain is a common experience, both physical and emotional. However we often feel powerless with our patients suffering pain. This paper aims to give a new heuristic and psychological understanding of pain.

METHODOLOGY

According to new theories, recent researches as well as different points of view, we form an analogy between pain and emotion. Throughout historical considerations pain has always been perceived through theories and beliefs, changing its definition. This is also the case for emotion. Could they be two ways of expressing a single phenomenon?

RESULTS

First, we must clarify the definition of emotion. In past, emotion was considered as a multiple-conditioned notion. To be considered as an emotion the pain had to fill numerous features, which differ according to the scientific opinions. The emotion may be considered as a physical expression or perceived only as the consequences of a real emotion, i.e., the subjective feeling. We propose as a way of thinking that emotion brings together these two concepts. We support a flexible vision of emotion. To investigate the field of the emotion different mental steps may be thought of: we should conceive of the emotion as a stimulus, as an emotional evaluation and as a tendency to action, which becomes an emotional response. These steps are colored by subjective feelings. It can be summarized in three levels: the situation decoding (1), the response organization (2) and the effectiveness of the response (3). Second pain can be considered as a complex notion involving personal and subjective feelings. We can use multidimensional patterns and consider emotion with its multiple features: the generating mechanisms, the pain perception, the pain behavior and the environment. Each stage can be divided in different ways. Hence pain treatment could be approached as an emotional treatment. Indeed, we can make a link between generating mechanisms and emotion situation decoding, between pain perception and emotion situation decoding and response organization, between pain behavior and environment and emotion response effectiveness and consequences. A heuristic analogy can be formed enriching therapeutic possibilities. First, emotion and pain could be considered as a unique phenomenon that can be expressed in different ways. We can let aside the opposition between psychological and physiological: these are two different levels of a same phenomenon. This point of view can be helpful to treat pain disorders because the skills to manage emotion disorders are well known.