VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

Background: Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each phase of these analyses can represent significant challenges, particularly when working with entire proteomes (all protein coding sequences in a genome) from a large number of species. Methods: We present VESPA, software capable of automating a selective pressure analysis using codeML in addition to the preparatory analyses and summary statistics. VESPA is written in python and Perl and is designed to run within a UNIX environment. Results: We have benchmarked VESPA and our results show that the method is consistent, performs well on both large scale and smaller scale datasets, and produces results in line with previously published datasets. Discussion: Large-scale gene family identification, sequence alignment, and phylogeny reconstruction are all important aspects of large-scale molecular evolutionary analyses. VESPA provides flexible software for simplifying these processes along with downstream selective pressure variation analyses. The software automatically interprets results from codeML and produces simplified summary files to assist the user in better understanding the results

Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response

It has been proposed that positive selection may be associated with protein functional change. For example, human and macaque have different outcomes to HIV infection and it has been shown that residues under positive selection in the macaque TRIM5α receptor locate to the region known to influence species-specific response to HIV. In general, however, the relationship between sequence and function has proven difficult to fully elucidate, and it is the role of large-scale studies to help bridge this gap in our understanding by revealing major patterns in the data that correlate genotype with function or phenotype. In this study, we investigate the level of species-specific positive selection in innate immune genes from human and mouse. In total, we analyzed 456 innate immune genes using codon-based models of evolution, comparing human, mouse, and 19 other vertebrate species to identify putative species-specific positive selection. Then we used population genomic data from the recently completed Neanderthal genome project, the 1000 human genomes project, and the 17 laboratory mouse genomes project to determine whether the residues that were putatively positively selected are fixed or variable in these populations. We find evidence of species-specific positive selection on both the human and the mouse branches and we show that the classes of genes under positive selection cluster by function and by interaction. Data from this study provide us with targets to test the relationship between positive selection and protein function and ultimately to test the relationship between positive selection and discordant phenotypes

Erratum to: Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response

“Upon publication of the original article [1], it was noticed that there was an error in the author name. The author’s name should be "Micheál Mac Aogáin" instead of Micheál MacAogain.

Carefully supporting autonomy – learning coaching lessons and advancing theory from women’s netball in England.

Back to Netball (B2N) is an initiative that encourages women, whose engagement has lapsed, to return to regular Netball participation. This study explores what aspects of coaching practice within B2N are perceived to be effective. A thematic analysis of semi-structured interviews with 28 B2N participants and 6 coaches was undertaken. Analysis identified four pertinent themes; 1) participants personalising sporting experiences through choice, 2) coaches facilitating and / or directing participants to relevant opportunities, 3) critical considerations of autonomy; a need for balance, 4) caring as a coaching ethic. The subsequent discussion considers autonomy and care as two relevant theoretical explanations. Within the discussion, it is posited that autonomy supportive behaviours and caring relationships may be symbiotic features of successful coaching. A novel interdisciplinary theoretical contribution is therefore made by connecting Self Determination Theory with the burgeoning recognition of coaching as a caring practice

Varieties of linguistic complexity in a standardized assessment of language performance

This study examined the comprehension of linguistically complex sentences among unimpaired adults and adults with aphasia. Participants completed a self-paced reading version of the Computerized Revised Token Test (CRTT-R) containing passive sentences, sentences with adverbial clauses, and sentences with discontinuous adjective-noun dependencies. Off-line measures revealed clear effects of linguistic complexity for passive and discontinuous-dependency sentences, with more complex sentences eliciting lower scores for impaired and aphasic groups, but not for sentences with adverbial clauses. In contrast, on-line measures revealed the opposite pattern: less complex sentences elicited slower reading times. Off-line measures appear more sensitive to linguistic complexity in this task

Back to Netball: Motivations for participation in a female focused Netball sport program.

Background: Back to Netball (B2N) is a UK female national sports program that has been found to engage large number of females in the sport netball. This study sought to understand the participant motives for engaging in this program. Methods: Qualitative methods were used following an initial quantitative survey, which was part of a wider project (outside of this manuscript). Survey participants comprised of 374 females aged 16-68. Participants completed an online survey to capture demographic data. Interviews were conducted with 28 participants either still engaged or no longer engaged in B2N. Analysis involved both inductive and deductive thematic analysis to explore participant perceptions of their coach. Results: Initial motives for engagement were focussed on physical health motives and social motives. The coach was also found to be important in providing opportunities for competence development. Therefore, competence development was found to be an important factor for engagement. Participant motivations moved from an extrinsic concern with losing weight to a more intrinsic foci including socialising opportunities and feelings of competence. Conclusions: As a team sport B2N stimulates social engagement, competence, and other motives. Coaching is also a key facilitator for engagement in B2N. This research has implications for future practitioners and policy makers aiming to engage women in sport and physical activity

Remission in psoriatic arthritis: is it possible and how can it be predicted?

10.1186/ar3021Arthritis Research and Therapy123R9

Rhinocerebral mucormycosis treated with 32 gram liposomal amphotericin B and incomplete surgery: a case report

BACKGROUND: Mucormycosis (or zygomycosis) is the term for infection caused by fungi of the order Mucorales. Mucoraceae may produce severe disease in susceptible individuals, notably patients with diabetes and leukemia. Rhinocerebral mucormycosis most commonly manifests itself in the setting of poorly controlled diabetes, especially with ketoacidosis. CASE PRESENTATION: A 31-year-old diabetic man presented to the outpatient clinic with the following signs and symptoms: headache, periorbital pain, swelling and loss of vision in the right eye. On physical examination his right eye was red and swollen. There was periorbital cellulitis and the conjunctiva was edematous. KOH preparation of purulent discharge showed broad, ribbonlike, aseptate hyphae when examined under a fluorescence microscope. Cranial MRI showed involvement of the right orbit, thrombosis in cavernous sinus and infiltrates at ethmoid and maxillary sinuses. Mucormycosis was diagnosed based on these findings. Amphotericin B (AmBisome(®); 2 mg/kg.d) was initiated after the test doses. Right orbitectomy and right partial maxillectomy were performed; the lesions in ethmoid and maxillary sinuses were removed. The duration of the liposomal amphotericin B therapy was approximately 6 months and the total dose of liposomal amphotericin B used was 32 grams. Liposomal amphotericin B therapy was stopped six months later and oral fluconazole was started. CONCLUSIONS: Although a total surgical debridement of the lesions could not be performed, it is remarkable that regression of the disease could be achieved with medical therapy alone

An Over-Massive Black Hole in the Compact Lenticular Galaxy NGC1277

All massive galaxies likely have supermassive black holes at their centers, and the masses of the black holes are known to correlate with properties of the host galaxy bulge component. Several explanations have been proposed for the existence of these locally-established empirical relationships; they include the non-causal, statistical process of galaxy-galaxy merging, direct feedback between the black hole and its host galaxy, or galaxy-galaxy merging and the subsequent violent relaxation and dissipation. The empirical scaling relations are thus important for distinguishing between various theoretical models of galaxy evolution, and they further form the basis for all black hole mass measurements at large distances. In particular, observations have shown that the mass of the black hole is typically 0.1% of the stellar bulge mass of the galaxy. The small galaxy NGC4486B currently has the largest published fraction of its mass in a black hole at 11%. Here we report observations of the stellar kinematics of NGC 1277, which is a compact, disky galaxy with a mass of 1.2 x 10^11 Msun. From the data, we determine that the mass of the central black hole is 1.7 x 10^10 Msun, or 59% its bulge mass. Five other compact galaxies have properties similar to NGC 1277 and therefore may also contain over-sized black holes. It is not yet known if these galaxies represent a tail of a distribution, or if disk-dominated galaxies fail to follow the normal black hole mass scaling relations.Comment: 7 pages. 6 figures. Nature. Animation at http://www.mpia.de/~bosch/blackholes.htm