Dependence Logic with Generalized Quantifiers: Axiomatizations

We prove two completeness results, one for the extension of dependence logic by a monotone generalized quantifier Q with weak interpretation, weak in the meaning that the interpretation of Q varies with the structures. The second result considers the extension of dependence logic where Q is interpreted as "there exists uncountable many." Both of the axiomatizations are shown to be sound and complete for FO(Q) consequences.Comment: 17 page

Hybrid Algorithms Based on Integer Programming for the Search of Prioritized Test Data in Software Product Lines

In Software Product Lines (SPLs) it is not possible, in general, to test all products of the family. The number of products denoted by a SPL is very high due to the combinatorial explosion of features. For this reason, some coverage criteria have been proposed which try to test at least all feature interactions without the necessity to test all products, e.g., all pairs of features (pairwise coverage). In addition, it is desirable to first test products composed by a set of priority features. This problem is known as the Prioritized Pairwise Test Data Generation Problem. In this work we propose two hybrid algorithms using Integer Programming (IP) to generate a prioritized test suite. The first one is based on an integer linear formulation and the second one is based on a integer quadratic (nonlinear) formulation. We compare these techniques with two state-of-the-art algorithms, the Parallel Prioritized Genetic Solver (PPGS) and a greedy algorithm called prioritized-ICPL. Our study reveals that our hybrid nonlinear approach is clearly the best in both, solution quality and computation time. Moreover, the nonlinear variant (the fastest one) is 27 and 42 times faster than PPGS in the two groups of instances analyzed in this work.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. Partially funded by the Spanish Ministry of Economy and Competitiveness and FEDER under contract TIN2014-57341-R, the University of Málaga, Andalucía Tech and the Spanish Network TIN2015-71841-REDT (SEBASENet)

Sequence-specific long range networks in PSD-95/discs large/ZO-1 (PDZ) domains tune their binding selectivity.

Protein-protein interactions mediated by modular protein domains are critical for cell scaffolding, differentiation, signaling, and ultimately, evolution. Given the vast number of ligands competing for binding to a limited number of domain families, it is often puzzling how specificity can be achieved. Selectivity may be modulated by intradomain allostery, whereby a remote residue is energetically connected to the functional binding site via side chain or backbone interactions. Whereas several energetic pathways, which could mediate intradomain allostery, have been predicted in modular protein domains, there is a paucity of experimental data to validate their existence and roles. Here, we have identified such functional energetic networks in one of the most common protein-protein interaction modules, the PDZ domain. We used double mutant cycles involving site-directed mutagenesis of both the PDZ domain and the peptide ligand, in conjunction with kinetics to capture the fine energetic details of the networks involved in peptide recognition. We performed the analysis on two homologous PDZ-ligand complexes and found that the energetically coupled residues differ for these two complexes. This result demonstrates that amino acid sequence rather than topology dictates the allosteric pathways. Furthermore, our data support a mechanism whereby the whole domain and not only the binding pocket is optimized for a specific ligand. Such cross-talk between binding sites and remote residues may be used to fine tune target selectivity

Systematic evaluation of spliced alignment programs for RNA-seq data

High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions

Charge-Fluctuation-Induced Non-analytic Bending Rigidity

In this Letter, we consider a neutral system of mobile positive and negative charges confined on the surface of curved films. This may be an appropriate model for: i) a highly charged membrane whose counterions are confined to a sheath near its surface; ii) a membrane composed of an equimolar mixture of anionic and cationic surfactants in aqueous solution. We find that the charge fluctuations contribute a non-analytic term to the bending rigidity that varies logarithmically with the radius of curvature. This may lead to spontaneous vesicle formation, which is indeed observed in similar systems.Comment: Revtex, 9 pages, no figures, submitted to PR

Toward Computational Simulations of Behavior During Automated Driving Takeovers: A Review of the Empirical and Modeling Literatures

Objective: This article provides a review of empirical studies of automated vehicle takeovers and driver modeling to identify influential factors and their impacts on takeover performance and suggest driver models that can capture them. Background: Significant safety issues remain in automated-to-manual transitions of vehicle control. Developing models and computer simulations of automated vehicle control transitions may help designers mitigate these issues, but only if accurate models are used. Selecting accurate models requires estimating the impact of factors that influence takeovers. Method: Articles describing automated vehicle takeovers or driver modeling research were identified through a systematic approach. Inclusion criteria were used to identify relevant studies and models of braking, steering, and the complete takeover process for further review. Results: The reviewed studies on automated vehicle takeovers identified several factors that significantly influence takeover time and post-takeover control. Drivers were found to respond similarly between manual emergencies and automated takeovers, albeit with a delay. The findings suggest that existing braking and steering models for manual driving may be applicable to modeling automated vehicle takeovers. Conclusion: Time budget, repeated exposure to takeovers, silent failures, and handheld secondary tasks significantly influence takeover time. These factors in addition to takeover request modality, driving environment, non-handheld secondary tasks, level of automation, trust, fatigue, and alcohol significantly impact post-takeover control. Models that capture these effects through evidence accumulation were identified as promising directions for future work. Application: Stakeholders interested in driver behavior during automated vehicle takeovers may use this article to identify starting points for their work

What do coaches orchestrate? Unravelling the 'quiddity' of practice

The general purpose of this article is threefold. Firstly, it is to further the notion of coaching as orchestration through developing insight into precisely how and what coaches orchestrate. Secondly, it is to firmly position coaching as a relational practice, whilst thirdly it is to better define coaching’s complex nature and how it can be somewhat ordered. Following an introduction where the purpose and value of the paper are outlined, we present the reflective method of critical companionship through which we explored and addressed the aforementioned purposes. The case for the quiddity, or the 'just whatness' (i.e., the inherent nature or essence) of coaching as involving complex, relational acts which can be somewhat explained through recourse to the developing theory of orchestration is subsequently made. In doing so, two precise examples of how we as coaches orchestrate sporting practice are presented. The paper concludes with both a summary of the principal argument(s) made, and some reflective considerations for future directions