The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviourKaiser-Bunbury, C N; Muff, S; Memmott, J; Müller, C B; Caflisch, A Kaiser-Bunbury, C N; Muff, S; Müller, C B; Caflisch, A (2010). Anthropogenic disturbance, however, that promote the extinction of the strongest interactors might induce a sudden collapse of pollination networks.2

1. Popular frameworks for studying habitat selection include resource-selection functions (RSFs) and step-selection functions (SSFs), estimated using logistic and conditional logistic regression, respectively. Both frameworks compare environmental covariates associated with locations animals visit with environmental covariates at a set of locations assumed available to the animals. Conceptually, slopes that vary by individual, that is, random coefficient models, could be used to accommodate inter-individual heterogeneity with either approach. While fitting such models for RSFs is possible with standard software for generalized linear mixed-effects models (GLMMs), straightforward and efficient one-step procedures for fitting SSFs with random coefficients are currently lacking. 2. To close this gap, we take advantage of the fact that the conditional logistic regression model (i.e. the SSF) is likelihood-equivalent to a Poisson model with stratum-specific fixed intercepts. By interpreting the intercepts as a random effect with a large (fixed) variance, inference for random-slope models becomes feasible with standard Bayesian techniques, or with frequentist methods that allow one to fix the variance of a random effect. We compare this approach to other commonly applied alternatives, including models without random slopes and mixed conditional regression models fit using a two-step algorithm. 3. Using data from mountain goats (Oreamnos americanus) and Eurasian otters (Lutra lutra), we illustrate that our models lead to valid and feasible inference. In addition, we conduct a simulation study to compare different estimation approaches for SSFs and to demonstrate the importance of including individual-specific slopes when estimating individual-and population-level habitat-selection parameters. 4. By providing coded examples using integrated nested Laplace approximations (INLA) and Template Model Builder (TMB) for Bayesian and frequentist analysis via the R packages R-INLA and glmmTMB, we hope to make efficient estimation of RSFs and SSFs with random effects accessible to anyone in the field. SSFs with individual-specific coefficients are particularly attractive since they can provide | 81

BackgroundIdentifying ways to promote physical activity and decrease sedentary time during childhood is a key public health issue. Research on the putative influences on preschool children’s physical activity (PA) and sedentary behavior (SB) is limited and has yielded inconsistent results. Our aim was to identify correlates of PA and SB in preschool children.MethodsCross-sectional data were drawn from the Swiss Preschoolers’ Health Study (SPLASHY), a Swiss population-based cohort study. Of 476 two to six year old children, 394 (54% boys) had valid PA data assessed by accelerometry. Information on exposure data was directly measured or extracted from parental questionnaires. Multilevel linear regression modeling was used to separately assess associations between 35 potential correlates and total PA (TPA), moderate-to-vigorous PA (MVPA) and SB.ResultsIn total, 12 correlates from different domains were identified. TPA and MVPA were greater in boys than girls, increased with age and were positively associated with gross motor skills. Children from single parent families had a higher level of TPA and spent less time sedentary than those living with two parents. Time spent outdoors was positively associated with TPA and negatively with SB. The child’s activity temperament was related all three outcomes, whereas parental sports club membership, living area per person and neighborhood safety were associated with SB only. Fixed and random factors in the final models accounted for 28%, 32% and 22% of the total variance in TPA, MVPA and SB, respectively. Variance decomposition revealed that age, sex and activity temperament were the most influential correlates of both, TPA and MVPA, whereas the child’s activity temperament, time outdoors and neighborhood safety were identified as the most important correlates of SB.ConclusionsA multidimensional set of correlates of young children’s activity behavior has been identified. Personal factors had the greatest influence on PA, whereas environmental-level factors had the greatest influence on SB. Moreover, we identified a number of previously unreported, potentially modifiable correlates of young children’s PA and SB. These factors could serve to define target groups or become valuable targets for change in future interventions.Trial registrationCurrent Controlled Trials ISRCTN41045021 (date of registration: 21.03.14).Electronic supplementary materialThe online version of this article (doi:10.1186/s12966-016-0456-9) contains supplementary material, which is available to authorized users.

The conformational space of a 20-residue three-stranded antiparallel β-sheet peptide (double hairpin) was sampled by equilibrium folding/unfolding molecular dynamics simulations for a total of 20 µs. The resulting one-dimensional free-energy profiles (FEPs) provide a detailed description of the free-energy basins and barriers for the folding reaction. The similarity of the FEPs obtained using the probability of folding before unfolding (p fold) or the mean first passage time supports the robustness of the procedure. The folded state and the most populated free-energy basins in the denatured state are described by the one-dimensional FEPs, which avoid the overlap of states present in the usual one- or two-dimensional projections. Within the denatured state, a basin with fluctuating helical conformations and a heterogeneous entropic state are populated near the melting temperature at about 11% and 33%, respectively. Folding pathways from the helical basin or enthalpic traps (with only one of the two hairpins formed) reach the native state through the entropic state, which is on-pathway and is separated by a low barrier from the folded state. A simplified equilibrium kinetic network based on the FEPs shows the complexity of the folding reaction and indicates, as augmented by additional analyses, that the basins in the denatured state are connected primarily by the native state. The overall folding kinetics shows single-exponential behavior because barriers between the non-native basins and the folded state have similar heights.

Topological Kondo insulators have been proposed as a new class of topological insulators in which non-trivial surface states reside in the bulk Kondo band gap at low temperature due to strong spin-orbit coupling. In contrast to other three-dimensional topological insulators, a topological Kondo insulator is truly bulk insulating. Furthermore, strong electron correlations are present in the system, which may interact with the novel topological phase. By applying spin-and angle-resolved photoemission spectroscopy, here we show that the surface states of SmB 6 are spin polarized. The spin is locked to the crystal momentum, fulfilling time reversal and crystal symmetries. Our results provide strong evidence that SmB 6 can host topological surface states in a bulk insulating gap stemming from the Kondo effect, which can serve as an ideal platform for investigating of the interplay between novel topological quantum states with emergent effects and competing orders induced by strongly correlated electrons.

Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have been added since the publication of the original Wordom paper in 2007: assignment of secondary structure, calculation of solvent accessible surfaces, elastic network model, motion cross correlations, protein structure network, shortest intra-molecular and inter-molecular communication paths, kinetic grouping analysis, and calculation of mincut-based free energy profiles. In addition, an interface with the Python scripting language has been built and the overall performance and user accessibility enhanced. The source code of Wordom (in the C programming language) as well as documentation for usage and further development are available as an open source package under the GNU General Purpose License from http://wordom.sf.net. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

The effects of a single-point mutation on folding thermodynamics and kinetics are usually interpreted by focusing on the native structure and the transition state. Here, the entire conformational spaces of a 20-residue three-stranded antiparallel beta-sheet peptide (double hairpin) and of its single-point mutant W10V are sampled close to the melting temperature by equilibrium folding-unfolding molecular dynamics simulations for a total of 40 micros. The folded state as well as the most populated free energy basins in the denatured state are isolated by grouping conformations according to fast relaxation at equilibrium. Such kinetic analysis provides more detailed and useful information than a simple projection of the free energy. The W10V mutant has the same native structure as the wild type peptide, and similar folding rate and stability. In the denatured state, the N-terminal hairpin is about 20% more structured in W10V than the wild type mainly because of van der Waals interactions. Notably, the W10V mutation influences also the van der Waals energy at the transition state ensemble causing a shift in the ratio of fluxes between two different transition state regions on parallel folding pathways corresponding to nucleation at either of the two beta-hairpins. Previous experimental studies have focused on the effects of denaturant-dependent or temperature-dependent changes in the structure of the denatured state. The atomistic simulations show that a single-point mutation in the central strand of a beta-sheet peptide results in remarkable changes in the topography of the denatured state ensemble. These changes modulate the relative accessibility of parallel folding pathways because of kinetic partitioning of the denatured state. Therefore, the observed dependence of the folding process on the starting ensemble raises questions on the biological significance of in vitro folding studies under strongly denaturing conditions.

BiTeI has a layered and noncentrosymmetric structure where strong spin-orbit interaction leads to a giant Rashba spin splitting in the bulk bands. We present direct measurements of the bulk band structure obtained with soft x-ray angle-resolved photoemission (ARPES), revealing the three-dimensional Fermi surface. The observed spindle torus shape bears the potential for a topological transition in the bulk by hole doping. Moreover, the bulk electronic structure is clearly disentangled from the two-dimensional surface electronic structure by means of high-resolution and spin-resolved ARPES measurements in the ultraviolet regime. All findings are supported by ab initio calculations.