Protein sectors: statistical coupling analysis versus conservation

Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed "sectors". The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation. It has been asserted that the protein sectors identified by SCA are functionally significant, with different sectors controlling different biochemical properties of the protein. Here we reconsider the available experimental data and note that it involves almost exclusively proteins with a single sector. We show that in this case sequence conservation is the dominating factor in SCA, and can alone be used to make statistically equivalent functional predictions. Therefore, we suggest shifting the experimental focus to proteins for which SCA identifies several sectors. Correlations in protein alignments, which have been shown to be informative in a number of independent studies, would then be less dominated by sequence conservation.Comment: 36 pages, 17 figure

The precision of experienced action video-game players: Line bisection reveals reduced leftward response bias

Twenty-two experienced action video-game players (AVGPs) and 18 non-VGPs were tested on a pen-and-paper line bisection task that was untimed. Typically, right-handers bisect lines 2 % to the left of true centre, a bias thought to reflect the dominance of the right-hemisphere for visuospatial attention. Expertise may affect this bias, with expert musicians showing no bias in line bisection performance. Our results show that experienced-AVGPs also bisect lines with no bias with their right hand and a significantly reduced bias with their left hand compared to non-AVGPs. Bisections by experienced-AVGPs were also more precise than those of non-AVGPs. These findings show the cognitive proficiencies of experienced-AVGPs can generalize beyond computer based tasks, which resemble their training environment

Just how expert are “expert” video-game players? Assessing the experience and expertise of video-game players across “action” video-game genres

Video-game play (particularly “action” video-games) holds exciting promise as an activity that may provide generalized enhancement to a wide range of perceptual and cognitive abilities (for review see Latham et al., 2013a). However, in this article we make the case that to assess accurately the effects of video-game play researchers must better characterize video-game experience and expertise. This requires a more precise and objective assessment of an individual's video-game history and skill level, and making finer distinctions between video-games that fall under the umbrella of “action” games. Failure to consider these factors may partly be responsible for mixed findings (see Boot et al., 2011)

Elephant cognition in primate perspective

On many of the staple measures of comparative psychology, elephants show no obvious differences from other mammals, such as primates: discrimination learning, memory, spontaneous tool use, etc. However, a range of more naturalistic measures have recently suggested that elephant cognition may be rather different. Wild elephants sub-categorize humans into groups, independently making this classification on the basis of scent or colour. In number discrimination, elephants show no effects of absolute magnitude or relative size disparity in making number judgements. In the social realm, elephants show empathy into the problems faced by others, and give hints of special abilities in cooperation, vocal imitation and perhaps teaching. Field data suggest that the elephant’s vaunted reputation for memory may have a factual basis, in two ways. Elephants’ ability to remember large-scale space over long periods suggests good cognitive mapping skills. Elephants’ skill in keeping track of the current locations of many family members implies that working memory may be unusually developed, consistent with the laboratory finding that their quantity judgements do not show the usual magnitude effects.Publisher PDFPeer reviewe

Territorial rights and open borders

Territorial rights consist of the right to jurisdiction, the right to resources and the right to exclude immigrants and are assumed to be essential to state sovereignty. Scholars who have discussed the justification of these rights have mostly focused on the right to jurisdiction. Few engage with the implications of such justification for the right to exclude immigrants. This paper argues that the justification for territorial rights cannot justify the right of states to exclude immigrants. Allowing immigrants to settle within the territory does not undermine any of the interests territorial rights are meant to protect. In addition, the interests of current inhabitants do not provide sufficient reasons to grant the state the right to exclude immigrants from the territory that everyone has equal right to in an original situation. State sovereignty is therefore seen as compatible with open borders

What was a mortarium used for? Organic residues and cultural change in Iron Age and Roman Britain.

The Romans brought the mortarium to Britain in the first century AD, and there has long been speculation on its actual purpose. Using analysis of the residues trapped in the walls of these ‘kitchen blenders’ and comparing them with Iron Age and Roman cooking pots, the authors show that it wasn't the diet that changed — just the method of preparing certain products: plants were being ground in the mortarium as well as cooked in the pot. As well as plants, the mortars contained animal fats, including dairy products. The question that remains, however, is why these natural products were being mixed together in mortaria. Were they for food, pharmaceuticals or face creams?</jats:p

Well rounded Postdoctoral Researchers with initiative, who are not always “tied to the bench” are more successful academically

This article reports the development, application and results of a baseline investigation of contract research staff in 2007 in the Medical School at the University of Sheffield which was carried out in order to develop a specifically tailored training and career development programme and allow for future impact evaluation of the scheme. Postdoctoral researchers reported on their perceived skill levels, academic achievements, career motivations and the current research environment. Results indicated that transferable skills related to communication and awareness of the process of research (i.e. the process of acquisition of funding, commercialisation of research outputs) were lacking. Furthermore, these skills were associated with higher publication outputs, and improved with mobility between institutions at postdoctoral level. This paper also describes how the findings from the baseline evaluation were used to develop a programme to address the lower ranking skills and evaluate the impact of the programme

Bacterial fitness shapes the population dynamics of antibiotic-resistant and -susceptible bacteria in a model of combined antibiotic and anti-virulence treatment

Bacterial resistance to antibiotic treatment is a huge concern: introduction of any new antibiotic is shortly followed by the emergence of resistant bacterial isolates in the clinic. This issue is compounded by a severe lack of new antibiotics reaching the market. The significant rise in clinical resistance to antibiotics is especially problematic in nosocomial infections, where already vulnerable patients may fail to respond to treatment, causing even greater health concern. A recent focus has been on the development of anti-virulence drugs as a second line of defence in the treatment of antibiotic-resistant infections. This treatment, which weakens bacteria by reducing their virulence rather than killing them, should allow infections to be cleared through the body's natural defence mechanisms. In this way there should be little to no selective pressure exerted on the organism and, as such, a predominantly resistant population would be unlikely to emerge. However, much controversy surrounds this approach with many believing it would not be powerful enough to clear existing infections, restricting its potential application to prophylaxis. We have developed a mathematical model that provides a theoretical framework to reveal the circumstances under which anti-virulence drugs may or may not be successful. We demonstrate that by harnessing and combining the advantages of antibiotics with those provided by anti-virulence drugs, given infection-specific parameters, it is possible to identify treatment strategies that would efficiently clear bacterial infections, while preventing the emergence of resistant subpopulations. Our findings strongly support the continuation of research into anti-virulence drugs and demonstrate that their applicability may reach beyond infection prevention.Comment: Pre-review manuscript. Submitted to Journal of Theoretical Biology, July 21st 201

Precision CW laser automatic tracking system investigated

Precision laser tracker capable of tracking a low acceleration target to an accuracy of about 20 microradians rms is being constructed and tested. This laser tracking has the advantage of discriminating against other optical sources and the capability of simultaneously measuring range

Survival of the selfish: contrasting self-referential and survival-based encoding

Processing information in the context of personal survival scenarios elicits a memory advantage, relative to other rich encoding conditions such as self-referencing. However, previous research is unable to distinguish between the influence of survival and self-reference because personal survival is a self-referent encoding context. To resolve this issue, participants in the current study processed items in the context of their own survival and a familiar other person’s survival, as well as in a semantic context. Recognition memory for the items revealed that personal survival elicited a memory advantage relative to semantic encoding, whereas other-survival did not. These findings reinforce suggestions that the survival effect is closely tied with self-referential encoding, ensuring that fitness information of potential importance to self is successfully retained in memory