Background: G-protein coupled receptors (GPCRs) are involved in many different physiological processes and their function can be modulated by small molecules which bind in the transmembrane (TM) domain. Because of their structural and sequence conservation, the TM domains are often used in bioinformatics approaches to first create a multiple sequence alignment (MSA) and subsequently identify ligand binding positions. So far methods have been developed to predict the common ligand binding residue positions for class A GPCRs.Results: Here we present 1) ss-TEA, a method to identify specific ligand binding residue positions for any receptor, predicated on high quality sequence information. 2) The largest MSA of class A non olfactory GPCRs in the public domain consisting of 13324 sequences covering most of the species homologues of the human set of GPCRs. A set of ligand binding residue positions extracted from literature of 10 different receptors shows that our method has the best ligand binding residue prediction for 9 of these 10 receptors compared to another state-of-the-art method.Conclusions: The combination of the large multi species alignment and the newly introduced residue selection method ss-TEA can be used to rapidly identify subfamily specific ligand binding residues. This approach can aid the design of site directed mutagenesis experiments, explain receptor function and improve modelling. The method is also available online via GPCRDB at http://www.gpcr.org/7tm/. © 2011 Sanders et al; licensee BioMed Central Ltd.
In foul decision-making by football referees, visual search is important for gathering task-specific information to determine whether a foul has occurred. Yet, little is known about the visual search behaviours underpinning excellent on-field decisions. The aim of this study was to examine the on-field visual search behaviour of elite and sub-elite football referees when calling a foul during a match. In doing so, we have also compared the accuracy and gaze behaviour for correct and incorrect calls. Elite and sub-elite referees (elite: N = 5, Mage ± SD = 29.8 ± 4.7yrs, Mexperience ± SD = 14.8 ± 3.7yrs; sub-elite: N = 9, Mage ± SD = 23.1 ± 1.6yrs, Mexperience ± SD = 8.4 ± 1.8yrs) officiated an actual football game while wearing a mobile eye-tracker, with on-field visual search behaviour compared between skill levels when calling a foul (Nelite = 66; Nsub−elite = 92). Results revealed that elite referees relied on a higher search rate (more fixations of shorter duration) compared to sub-elites, but with no differences in where they allocated their gaze, indicating that elites searched faster but did not necessarily direct gaze towards different locations. Correct decisions were associated with higher gaze entropy (i.e. less structure). In relying on more structured gaze patterns when making incorrect decisions, referees may fail to pick-up information specific to the foul situation. Referee development programmes might benefit by challenging the speed of information pickup but by avoiding pre-determined gaze patterns to improve the interpretation of fouls and increase the decision-making performance of referees.
Many studies have shown that experts possess better perceptual-cognitive skills than novices (e.g., in anticipation, decision making, pattern recall), but it remains unclear whether a relationship exists between performance on those tests of perceptual-cognitive skill and actual on-field performance. In this study, we assessed the in situ performance of skilled soccer players and related the outcomes to measures of anticipation, decision making, and pattern recall. In addition, we examined gaze behaviour when performing the perceptual-cognitive tests to better understand whether the underlying processes were related when those perceptual-cognitive tasks were performed. The results revealed that on-field performance could not be predicted on the basis of performance on the perceptual-cognitive tests. Moreover, there were no strong correlations between the level of performance on the different tests. The analysis of gaze behaviour revealed differences in search rate, fixation duration, fixation order, gaze entropy, and percentage viewing time when performing the test of pattern recall, suggesting that it is driven by different processes to those used for anticipation and decision making. Altogether, the results suggest that the perceptual-cognitive tests may not be as strong determinants of actual performance as may have previously been assumed.
Despite the benefits of the widespread deployment of diverse Internet-enabled devices such as IP cameras and smart home appliances - the so-called Internet of Things (IoT) has amplified the attack surface that is being leveraged by cyber criminals. While manufacturers and vendors keep deploying new products, infected devices can be counted in the millions and spreading at an alarming rate all over consumer and business networks. The objective of this project is twofold: (i) to explain the causes behind these infections and the inherent insecurity of the IoT paradigm by exploring innovative data analytics as applied to raw cyber security data; and (ii) to promote effective remediation mechanisms that mitigate the threat of the currently vulnerable and infected IoT devices. By performing large-scale passive and active measurements, this project will allow the characterization and attribution of compromise IoT devices. Understanding the type of devices that are getting compromised and the reasons behind the attacker’s intention is essential to design effective countermeasures. This project will build on the state of the art in information theoretic data mining (e.g., using the minimum description length and maximum entropy principles), statistical pattern mining, and interactive data exploration and analytics to create a casual model that allows explaining the attacker’s tactics and techniques. The project will research formal correlation methods rooted in stochastic data assemblies between IoT-relevant measurements and IoT malware binaries as captured by an IoT-specific honeypot to aid in the attribution and thus the remediation objective. Research outcomes of this project will benefit society in addressing important IoT security problems before manufacturers saturate the market with ostensibly useful and innovative gadgets that lack sufficient security features, thus being vulnerable to attacks and malware infestations, which can turn them into rogue agents. However, the insights gained will not be limited to the attacker behavior and attribution, but also to the remediation of the infected devices. Based on a casual model and output of the correlation analyses, this project will follow an innovative approach to understand the remediation impact of malware notifications by conducting a longitudinal quasi-experimental analysis. The quasi-experimental analyses will examine remediation rates of infected/vulnerable IoT devices in order to make better inferences about the impact of the characteristics of the notification and infected user’s reaction. The research will provide new perspectives, information, insights, and approaches to vulnerability and malware notifications that differ from the previous reliance on models calibrated with cross-sectional analysis. This project will enable more robust use of longitudinal estimates based on documented remediation change. Project results and methods will enhance the capacity of Internet intermediaries (e.g., ISPs and hosting providers) to better handle abuse/vulnerability reporting which in turn will serve as a preemptive countermeasure. The data and methods will allow to investigate the behavior of infected individuals and firms at a microscopic scale and reveal the causal relations among infections, human factor and remediation.
