nIFTy galaxy cluster simulations II: radiative models

We have simulated the formation of a massive galaxy cluster (M$_{200}^{\rm crit}$ = 1.1$\times$10$^{15}h^{-1}M_{\odot}$) in a $\Lambda$CDM universe using 10 different codes (RAMSES, 2 incarnations of AREPO and 7 of GADGET), modeling hydrodynamics with full radiative subgrid physics. These codes include Smoothed-Particle Hydrodynamics (SPH), spanning traditional and advanced SPH schemes, adaptive mesh and moving mesh codes. Our goal is to study the consistency between simulated clusters modeled with different radiative physical implementations - such as cooling, star formation and AGN feedback. We compare images of the cluster at $z=0$, global properties such as mass, and radial profiles of various dynamical and thermodynamical quantities. We find that, with respect to non-radiative simulations, dark matter is more centrally concentrated, the extent not simply depending on the presence/absence of AGN feedback. The scatter in global quantities is substantially higher than for non-radiative runs. Intriguingly, adding radiative physics seems to have washed away the marked code-based differences present in the entropy profile seen for non-radiative simulations in Sembolini et al. (2015): radiative physics + classic SPH can produce entropy cores. Furthermore, the inclusion/absence of AGN feedback is not the dividing line -as in the case of describing the stellar content- for whether a code produces an unrealistic temperature inversion and a falling central entropy profile. However, AGN feedback does strongly affect the overall stellar distribution, limiting the effect of overcooling and reducing sensibly the stellar fraction

nIFTy galaxy cluster simulations I: dark matter & non-radiative models

We have simulated the formation of a galaxy cluster in a $\Lambda$CDM universe using twelve different codes modeling only gravity and non-radiative hydrodynamics (\art, \arepo, \hydra\ and 9 incarnations of GADGET). This range of codes includes particle based, moving and fixed mesh codes as well as both Eulerian and Lagrangian fluid schemes. The various GADGET implementations span traditional and advanced smoothed-particle hydrodynamics (SPH) schemes. The goal of this comparison is to assess the reliability of cosmological hydrodynamical simulations of clusters in the simplest astrophysically relevant case, that in which the gas is assumed to be non-radiative. We compare images of the cluster at $z=0$, global properties such as mass, and radial profiles of various dynamical and thermodynamical quantities. The underlying gravitational framework can be aligned very accurately for all the codes allowing a detailed investigation of the differences that develop due to the various gas physics implementations employed. As expected, the mesh-based codes ART and AREPO form extended entropy cores in the gas with rising central gas temperatures. Those codes employing traditional SPH schemes show falling entropy profiles all the way into the very centre with correspondingly rising density profiles and central temperature inversions. We show that methods with modern SPH schemes that allow entropy mixing span the range between these two extremes and the latest SPH variants produce gas entropy profiles that are essentially indistinguishable from those obtained with grid based methods

Older and wiser? First year BDS graduate entry students and their views on using social media and professional practice

Introduction The use of social media sites (SMS) has increased exponentially since their creation and introduction in the early 2000s. The number of regular users of SMS is estimated at over two billion people worldwide. Ethical and legal guidelines exert an additional responsibility on the behaviour of both graduate and undergraduate dentists when compared to members of the general public with some assumption that life experience can offer some insight into attitudes about online use of social media in relation to professional practice. Aim We set out to explore the views of the first year graduate entry programme students at the University of Central Lancashire and their use of SMS together with their opinions on what they consider to be professional online behaviour. Methods A mixed-methods approach was adopted with a questionnaire and semi-structured interviews which were designed to elicit the students' opinions. Results For this group of students, 100% were using social media sites and some were aware of some of their limitations and possible impact on their careers. There was some rather superficial knowledge of what is and is not professional to post via social media, however, students were not fully aware about the legal and ethical guidelines in place in relation to the topic. Conclusion Results from this study present an opportunity and a challenge for educators to incorporate additional details not only about professionalism and ethical and legal aspects within the undergraduate curriculum but more specific emphasis on the use of social media as part of the undergraduate BDS course

Similar dispersal patterns between two closely related birds with contrasting migration strategies

Studying dispersal is crucial to understand metapopulation and sink-source dynamics and invasion processes. The capability to disperse is especially important for species living in fragmented habitats like wetlands. We investigated the distribution of natal and breeding dispersal distances and philopatry in Spanish populations of two closely related reedbed-nesting birds, the Moustached Warbler Acrocephalus melanopogon and the Eurasian Reed Warbler Acrocephalus scirpaceus. These warblers are morphologically very similar, but differ in migration strategy and, in our study area, in population size. Our aims were to find the best model for dispersal distances and to assess the occurrence of intra- or interspecific differences in dispersal patterns. We used ringing data from the Spanish marking scheme and selected recaptures to avoid including migrating individuals. In both species, most individuals were philopatric but dispersing birds were able to cross large distances (up to more than 100 km), suggesting the capability to compensate for habitat fragmentation. We found the heavy-tailed Cauchy distribution to be the best conceptual description for our data, in all cases but natal dispersal of Moustached Warblers. Among Eurasian Reed Warblers, natal philopatry was lower than breeding philopatry. We found no significant interspecific differences. This does not confirm the hypothesis of higher dispersal ability in long distance migrants (like Eurasian Reed Warblers) than in resident/short distance migrant bird species (like Moustached Warblers). The similarity in dispersal patterns among the two warblers may be explained by their close phylogenetic relatedness, similar constraints imposed on both species by a patchy habitat or similar evolutionary pressures.We are grateful to the many ringers who collected the data during years of fieldwork in Spain. Francesco Ceresa is supported by an "Atraent talent'' grant from the University of Valencia.Ceresa, F.; Belda, E.; Monrós González, JS. (2016). Similar dispersal patterns between two closely related birds with contrasting migration strategies. Population Ecology. 58(3):421-427. doi:10.1007/s10144-016-0547-0S421427583Banco de datos de anillamiento del remite ICONA – Ministerio de Medio Ambiente (2015) Datos de anillamiento y recuperaciones en España. Ministerio de Agricultura, Alimentación y Medio Ambiente, SEO/BirdLife, ICO, EBD-CSIC y GOB. Madrid (in Spanish)Begon M, Townsend CR, Harper JL (2006) Ecology: from individual to ecosystems, 4th edn. Blackwell Publishing, OxfordBlomqvist D, Fessl B, Hoi H, Kleindorfer S (2005) High frequency of extra-pair fertilisation in the moustached warbler, a songbird with a variable breeding system. Behaviour 142:1133–1148Bohonak AJ (1999) Dispersal, gene flow, and population structure. Q Rev Biol 74:21–45Burnham KP, Anderson DR (2002) Model selection and multi-model inference: a practical information-theoretic approach. Springer Verlag, New YorkCantos FJ, Tellería JL (1994) Stopover site fidelity of four migrant warblers in the Iberian Peninsula. J Avian Biol 25:131–134Carrascal LM, Palomino D (2008) Las aves comunes reproductoras en España. Población en 2004–2006. SEO/BirdLife, Madrid (in Spanish with English abstract)Carrascal LM, Weykam S, Palomino D, Lobo JM, Díaz L (2005) Atlas Virtual de las Aves Terrestres de España. http://www.vertebradosibericos.org/atlasaves.html . Accessed 16 Feb 2016Castany J (2003) El carricerín real (Acrocephalus melanopogon) en el P. N. del Prat de Cabanes-Torreblanca. Doctoral thesis. University of Valencia, Valencia (in Spanish)Castany J, López G (2006) El carricerín real en España. I Censo Nacional (2005). SEO/BirdLife, Madrid (in Spanish with English abstract)Ceresa F, Belda EJ, Kvist L, Rguibi-Idrissi H, Monrós JS (2015) Does fragmentation of wetlands affect gene flow in sympatric Acrocephalus warblers with different migration strategies? J Avian Biol 46:577–588Cooper NW, Murphy MT, Redmond LJ, Dolan AC (2009) Density-dependent age at first reproduction in the eastern kingbird. Oikos 118:413–419Delignette-Muller ML, Dutang C (2015) fitdistrplus: An R Package for fitting distributions. J Stat Softw 64:1–34. http://www.jstatsoft.org/v64/i04/ . Accessed 2 Sep 2015Frankham R, Ballou JD, Briscoe DA (2010) Introduction to conservation genetics, 2nd edn. Cambridge University Press, CambridgeHengeveld R (1994) Small step invasion research. Trends Ecol Evol 9:339–342Hodges MF Jr, Krementz DG (1996) Neotropical migratory breeding bird communities in riparian forests of different widths along the Altamaha River, Georgia. Wilson Bulletin 108:496–506Ibrahim KM, Nichols RA, Hewitt GM (1996) Spatial patterns of genetic variation generated by different forms of dispersal during range expansion. Heredity 77:282–291Kennerley P, Pearson D (2010) Reed and bush warblers. Christopher Helm Publishers Ltd., LondonKoenig WD, Van Vuren D, Hooge PN (1996) Detectability, philopatry, and the distribution of dispersal distances in vertebrates. Trends Ecol Evol 11:514–517Kralj J, Procházka P, Fainová D, Patzenhauerová H, Tutiš V (2010) Intraspecific variation in the wing shape and genetic differentiation of reed warblers Acrocephalus scirpaceus in Croatia. Acta Ornithologica 45:51–58Lambrechts MM, Blondel J, Caizergues A, Dias PC, Pradol R, Thomas DW (1999) Will estimates of lifetime recruitment of breeding offspring on small-scale study plots help us to quantify processes underlying adaptation? Oikos 86:147–151Machtans CS, Villard MA, Hannon SJ (1996) Use of riparian buffer strips as movement corridors by forest birds. Conserv Biol 10:1366–1379Nathan R, Perry G, Cronin JT, Strand AE, Cain ML (2003) Methods for estimating long-distance dispersal. Oikos 103:261–273Newton I (1992) Experiments on the limitation of bird numbers by territorial behaviour. Biol Rev 67:129–173Norberg UM (1990) Vertebrate flight, mechanics, physiology, morphology, ecology and evolution. Springer Verlag, BerlinParacuellos M, Tellería JL (2004) Factors affecting the distribution of a waterbird community: the role of habitat configuration and bird abundance. Waterbirds 27:446–453Paradis E, Baillie SR, Sutherland WJ, Gregory RD (1998) Patterns of natal and breeding dispersal in birds. J Anim Ecol 67:518–536Paradis E, Baillie SR, Sutherland WJ (2002) Modeling large-scale dispersal distances. Ecol Model 151:279–292Peirò IG (2003) Intraspecific variation in the wing shape of the long-distance migrant Reed Warbler Acrocephalus scirpaceus: effects of age and distance of migration. Ardeola 50:31–37Plissner JH, Gowaty PA (1996) Patterns of natal dispersal, turnover, and dispersal costs in eastern bluebirds. Anim Behav 51:1307–1322Procházka P, Stokke BG, Jensen H, Fainová D, Bellinvia E, Fossøy F, Vikan JR, Bryja J, Soler M (2011) Low genetic differentiation among reed warbler Acrocephalus scirpaceus populations across Europe. J Avian Biol 42:103–113R Core Team (2014) R: A language and environment for statistical computing. R foundation for statistical computing, ViennaRobinson WD (1999) Long-term changes in the avifauna of Barro Colorado Island, Panama, a tropical forest isolate. Conserv Biol 13:85–97SEO/BirdLife (2016a) Acrocephalus melanopogon. Anillamientos por década. http://www.anillamientoseo.org/ . Accessed 19 Feb 2016 (in Spanish)SEO/BirdLife (2016b) Acrocephalus scirpaceus. Anillamientos por década. http://www.anillamientoseo.org/ . Accessed 19 Feb 2016 (in Spanish)Shigesada N, Kawasaki K, Takeda Y (1995) Modeling stratified diffusion in biological invasions. Am Nat 146:229–251Silva JP, Phillips L, Jones W, Eldridge J, O’Hara E (2007) Life and Europe’s wetlands, restoring a vital ecosystem. Office for Official Publications of the European Communities, LuxembourgSutherland GD, Harestad AS, Price K, Lertzman KP (2000) Scaling of natal dispersal distances in terrestrial birds and mammals. Conservation ecology 4:16. http://www.consecol.org/vol4/iss1/art16 . Accessed 23 Oct 2015Vadász C, Német Á, Karcza Z, Loránt M, Biró C, Csörgő T (2008) Study on breeding site fidelity of Acrocephalus Warblers in Central Hungary. Acta Zool Acad Sci H 54(Suppl. 1):167–175Van Houtan KS, Pimm SL, Halley JM, Bierregaard RO Jr, Lovejoy TE (2007) Dispersal of Amazonian birds in continuous and fragmented forest. Ecol Lett 10:219–229Van Houtan KS, Bass OL Jr, Lockwood J, Pimm SL (2010) Importance of estimating dispersal for endangered bird management. Conservation Letters 3:260–266Van Vessem J, Hecker N, Tucker GM (1997) Inland wetlands. In: Tucker GM, Evans MI (eds) Habitats for birds in Europe: A conservation strategy for the wider environment. BirdLife Conservation Series 6. BirdLife International, Cambridge, pp 125–158Waser PM, Creel SR, Lucas JR (1994) Death and disappearance: estimating mortality risk associated with philopatry and dispersal. Behav Ecol 5:135–141Willis EO (1974) Populations and local extinctions of birds on Barro Colorado Island, Panama. Ecol Monogr 44:153–169Winkler DW, Wrege PH, Allen PE, Kast TL, Senesac P, Wasson MF, Llambías PE, Ferretti V, Sullivan PJ (2004) Breeding dispersal and philopatry in the tree swallow. Condor 106:768–776Winkler DW, Wrege PH, Allen PE, Kast TL, Senesac P, Wasson MF, Sullivan PJ (2005) The natal dispersal of tree swallows in a continuous mainland environment. J Anim Ecol 74:1080–109

COMPASS identifies T-cell subsets correlated with clinical outcomes.

Advances in flow cytometry and other single-cell technologies have enabled high-dimensional, high-throughput measurements of individual cells as well as the interrogation of cell population heterogeneity. However, in many instances, computational tools to analyze the wealth of data generated by these technologies are lacking. Here, we present a computational framework for unbiased combinatorial polyfunctionality analysis of antigen-specific T-cell subsets (COMPASS). COMPASS uses a Bayesian hierarchical framework to model all observed cell subsets and select those most likely to have antigen-specific responses. Cell-subset responses are quantified by posterior probabilities, and human subject-level responses are quantified by two summary statistics that describe the quality of an individual's polyfunctional response and can be correlated directly with clinical outcome. Using three clinical data sets of cytokine production, we demonstrate how COMPASS improves characterization of antigen-specific T cells and reveals cellular 'correlates of protection/immunity' in the RV144 HIV vaccine efficacy trial that are missed by other methods. COMPASS is available as open-source software

Total ankle prostheses in rheumatoid arthropathy: Outcome in 52 patients followed for 1–9 years

Background and purpose The first generations of total ankle replacements (TARs) showed a high rate of early failure. In the last decades, much progress has been made in the development of TARs, with the newer generation showing better results. We evaluated TARs implanted with rheumatoid arthritis (RA) or juvenile inflammatory arthritis (JIA) as indication

ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci

<p>Abstract</p> <p>Background</p> <p>Growing interest and burgeoning technology for discovering genetic mechanisms that influence disease processes have ushered in a flood of genetic association studies over the last decade, yet little heritability in highly studied complex traits has been explained by genetic variation. Non-additive gene-gene interactions, which are not often explored, are thought to be one source of this "missing" heritability.</p> <p>Methods</p> <p>Stochastic methods employing evolutionary algorithms have demonstrated promise in being able to detect and model gene-gene and gene-environment interactions that influence human traits. Here we demonstrate modifications to a neural network algorithm in ATHENA (the Analysis Tool for Heritable and Environmental Network Associations) resulting in clear performance improvements for discovering gene-gene interactions that influence human traits. We employed an alternative tree-based crossover, backpropagation for locally fitting neural network weights, and incorporation of domain knowledge obtainable from publicly accessible biological databases for initializing the search for gene-gene interactions. We tested these modifications <it>in silico </it>using simulated datasets.</p> <p>Results</p> <p>We show that the alternative tree-based crossover modification resulted in a modest increase in the sensitivity of the ATHENA algorithm for discovering gene-gene interactions. The performance increase was highly statistically significant when backpropagation was used to locally fit NN weights. We also demonstrate that using domain knowledge to initialize the search for gene-gene interactions results in a large performance increase, especially when the search space is larger than the search coverage.</p> <p>Conclusions</p> <p>We show that a hybrid optimization procedure, alternative crossover strategies, and incorporation of domain knowledge from publicly available biological databases can result in marked increases in sensitivity and performance of the ATHENA algorithm for detecting and modelling gene-gene interactions that influence a complex human trait.</p

Impact of early applied upper limb stimulation: The EXPLICIT-stroke programme design

Main claims of the literature are that functional recovery of the paretic upper limb is mainly defined within the first month post stroke and that rehabilitation services should preferably be applied intensively and in a task-oriented way within this particular time window. EXplaining PLastICITy after stroke (acronym EXPLICIT-stroke) aims to explore the underlying mechanisms of post stroke upper limb recovery. Two randomized single blinded trials form the core of the programme, investigating the effects of early modified Constraint-Induced Movement Therapy (modified CIMT) and EMG-triggered Neuro-Muscular Stimulation (EMG-NMS) in patients with respectively a favourable or poor probability for recovery of dexterity.BioMechanical EngineeringMechanical, Maritime and Materials Engineerin

PI3Kinase signaling in glioblastoma

Glioblastoma (GBM) is the most common primary tumor of the CNS in the adult. It is characterized by exponential growth and diffuse invasiveness. Among many different genetic alterations in GBM, e.g., mutations of PTEN, EGFR, p16/p19 and p53 and their impact on aberrant signaling have been thoroughly characterized. A major barrier to develop a common therapeutic strategy is founded on the fact that each tumor has its individual genetic fingerprint. Nonetheless, the PI3K pathway may represent a common therapeutic target to most GBM due to its central position in the signaling cascade affecting proliferation, apoptosis and migration. The read-out of blocking PI3K alone or in combination with other cancer pathways should mainly focus, besides the cytostatic effect, on cell death induction since sublethal damage may induce selection of more malignant clones. Targeting more than one pathway instead of a single agent approach may be more promising to kill GBM cells