Concrete Metrics Research Articles

Climate change, connectivity and conservation decision making: back to basics

Summary 1. The challenge of climate change forces us to re‐examine the assumptions underlying conservation planning. 2. Increasing ‘connectivity’ has emerged as the most favoured option for conservation in the face of climate change. 3. We argue that the importance of connectivity is being overemphasized: quantifying the benefits of connectivity per se is plagued with uncertainty, and connectivity can be co‐incidentally improved by targeting more concrete metrics: habitat area and habitat quality. 4. Synthesis and applications. Before investing in connectivity projects, conservation practitioners should analyse the benefits expected to arise from increasing connectivity and compare them with alternative investments, to ensure as much biodiversity conservation and resilience to climate change as possible within their budget. Strategies that we expect to remain robust in the face of climate change include maintaining and increasing the area of high quality habitats, prioritizing areas that have high environmental heterogeneity and controlling other anthropogenic threatening processes.

Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications

Many classifications of protein function such as Gene Ontology (GO) are organized in directed acyclic graph (DAG) structures. In these classifications, the proteins are terminal leaf nodes; the categories 'above' them are functional annotations at various levels of specialization and the computation of a numerical measure of relatedness between two arbitrary proteins is an important proteomics problem. Moreover, analogous problems are important in other contexts in large-scale information organization--e.g. the Wikipedia online encyclopedia and the Yahoo and DMOZ web page classification schemes. Here we develop a simple probabilistic approach for computing this relatedness quantity, which we call the total ancestry method. Our measure is based on counting the number of leaf nodes that share exactly the same set of 'higher up' category nodes in comparison to the total number of classified pairs (i.e. the chance for the same total ancestry). We show such a measure is associated with a power-law distribution, allowing for the quick assessment of the statistical significance of shared functional annotations. We formally compare it with other quantitative functional similarity measures (such as, shortest path within a DAG, lowest common ancestor shared and Azuaje's information-theoretic similarity) and provide concrete metrics to assess differences. Finally, we provide a practical implementation for our total ancestry measure for GO and the MIPS functional catalog and give two applications of it in specific functional genomics contexts. The implementations and results are available through our supplementary website at: http://gersteinlab.org/proj/funcsim. Supplementary data are available at Bioinformatics online.

Two-component neutrino in gravitational field

The problem of the exact solutions of the Weyl equation in the presence of the gravitational field is investigated by means of an algebraic method of separation of variables. Only the diagonal metrics are taken into account here. Our approach allows to find all the configurations of the gravitational fields when the complete separation of variables is possible. Some exact solutions of the Weyl equation for the concrete gravitational metrics (namely Kassner metric, Petrov space-time, de Sitter and Friedmann cosmological models) are found.