SLIDER: Mining correlated motifs in protein-protein interaction networks

Abstract—Correlated motif mining (CMM) is the problem to find overrepresented pairs of patterns, called motif pairs, in interacting protein sequences. Algorithmic solutions for CMM thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that CMM is an NP-hard problem for a large class of support measures (including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the method SLIDER which uses local search with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that SLIDER outperforms existing motif-driven CMM methods and scales to large protein-protein interaction networks

A unified approach to nonlinearity, structural change and outliers

This paper demonstrates that the class of conditionally linear and Gaussianstate-space models offers a general and convenient framework for simultaneouslyhandling nonlinearity, structural change and outliers in time series. Manypopular nonlinear time series models, including threshold, smooth transitionand Markov-Switching models, can be written in state-space form. It is thenstraightforward to add components that capture parameter instability andintervention effects. We advocate a Bayesian approach to estimation andinference, using an efficient implementation of Markov Chain Monte Carlosampling schemes for such linear dynamic mixture models. The general modellingframework and the Bayesian methodology are illustrated by means of severalexamples. An application to quarterly industrial production growth rates forthe G7 countries demonstrates the empirical usefulness of the approach.Bayesian inference;threshold models;Markov-switching models;business cycle asymmetry;state-space models

Assessment of the development of aquifer management councils (COTAS) for sustainable groundwater management in Guanajuato, Mexico

Collective groundwater management by water users—self-regulation—is increasingly advocated as a complement to state regulation. This article analyzes the attempts by the Guanajuato State Water Commission (CEAG) in central Mexico to promote user self-regulation through the establishment and development of 14 Consejos Técnicos de Aguas (COTAS; Technical Water Councils). Based on a joint assessment by a former senior CEAG policy-maker and two researchers, Guanajuato’s groundwater-management policy is reviewed to understand why user self-regulation was less successful than expected. It concludes that increasing awareness and improving the knowledge base on groundwater is not enough to trigger self-regulation by groundwater users. A wider delegation of responsibilities to the COTAS is necessary, combined with: (1) functioning mechanisms for enforcing groundwater legislation, especially concerning well permits and pumped volumes, and (2) mechanisms that ensure the legitimacy and accountability of users’ representatives to both users and state agencie

Corporate Governance and the Value of Excess Cash Holdings of Large European Firms

We examine the relation between the quality of corporate governance and the value of excess cash for large European firms (FTSEurofirst 300 Index). We use Deminor ratings for Shareholder rights, Takeover defences, Disclosure and Board as proxies for the quality of corporate governance. We find that the value of excess cash is positively related to the Takeover defences score only. It seems that governance mechanisms—except the market for corporate control—are not strong enough to prevent managers from wasting excess cash. For non-UK firms we find that the value of €1 of excess cash in a poorly governed firm is valued at only €0.89 while the value is €1.45 for a good governed firm. We show that poorly governed firms dissipate excess cash relatively quickly with a negative impact on their operating performance as a result.corporate governance;excess cash;take-over defences

Platial geo-temporal demographics using family names

We introduce platial geo-temporal demographics as a novel way to describe places using family names as markers of migration and change at sub-national scales. By identifying the likely origins of 59,218 surnames in Great Britain, we create platial profiles of surname mixes in terms of the distance their forbears have likely migrated between 1881 and 1998/2016. By combining individual-level data derived from historic censuses of population with near-complete contemporary population registers of enfranchised adults, we demonstrate how locally and regionally distinctive surname mixes can be used in characterizing places in terms of demographic change and stasis. The results suggest that a hierarchy of places arises in Great Britain, with larger conurbations (e.g., London and Birmingham) having more surnames that can be traced back to other parts of Great Britain and beyond, as opposed to places that are characterized by the presence of a larger share of surnames that have a more local origin. These regional differences are likely linked to processes of social mobility and economic activity