SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Model theory

169

[Background] Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. [Results] To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. [Conclusion] The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

Concepts: Protein structure, Enzyme, Mathematics, Protein folding, Model theory, Graph theory, Problem solving, Titin

147

Educational interventions to reduce Lyme disease (LD) among at-risk school children have had little study. The purpose of this study was to evaluate whether a short in-class LD education program based on social learning theory and the Health Belief Model (HBM) impacted a child’s knowledge, attitude, and preventive behavior.

Concepts: Psychology, Truth, Education, Educational psychology, Model theory, Learning, School, History of education

144

More than 35 years and 11 000 publications after the discovery of quasicrystals by Dan Shechtman, quite a bit is known about their occurrence, formation, stability, structures and physical properties. It has also been discovered that quasiperiodic self-assembly is not restricted to intermetallics, but can take place in systems on the meso- and macroscales. However, there are some blank areas, even in the centre of the big picture. For instance, it has still not been fully clarified whether quasicrystals are just entropy-stabilized high-temperature phases or whether they can be thermodynamically stable at 0 K as well. More studies are needed for developing a generally accepted model of quasicrystal growth. The state of the art of quasicrystal research is briefly reviewed and the main as-yet unanswered questions are addressed, as well as the experimental limitations to finding answers to them. The focus of this discussion is on quasicrystal structure analysis as well as on quasicrystal stability and growth mechanisms.

Concepts: Structure, Model theory, System, Need, Centrifugation, Quasicrystal, Quasiperiodicity, Dan Shechtman

54

The relative contribution of increasing incidence and declining mortality to increasing prevalence of type 2 diabetes in Scotland is unclear. Trends in incidence and mortality rates are described for type 2 diabetes in Scotland between 2004 and 2013 by age, sex and socioeconomic deprivation.

Concepts: Epidemiology, Mortality rate, Diabetes mellitus type 2, Medical statistics, Model theory

38

Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form tubules that conserve structural/functional homology with tail sheaths of contractile bacteriophages and pyocins. Here, we used cryoelectron microscopy to solve the structure of the H1-T6SS P. aeruginosa TssB1C1 sheath at 3.3 Å resolution. Our structure allowed us to resolve some features of the T6SS sheath that were not resolved in the Vibrio cholerae VipAB and Francisella tularensis IglAB structures. Comparison with sheath structures from other contractile machines, including T4 phage and R-type pyocins, provides a better understanding of how these systems have conserved similar functions/mechanisms despite evolution. We used the P. aeruginosa R2 pyocin as a structural template to build an atomic model of the TssB1C1 sheath in its extended conformation, allowing us to propose a coiled-spring-like mechanism for T6SS sheath contraction.

Concepts: Bacteria, Microbiology, Secretion, Structure, Pseudomonas aeruginosa, Model theory, System, Cholera

32

Interactions between catalytically active metal particles and reactant gases depend strongly on the particle size, particularly in the subnanometer regime where the addition of just one atom can induce substantial changes in stability, morphology, and reactivity. Here, time-lapse scanning tunneling microscopy (STM) and density functional theory (DFT)-based calculations are used to study how CO exposure affects the stability of Pt adatoms and subnano clusters at the Fe3O4(001) surface, a model CO oxidation catalyst. The results reveal that CO plays a dual role: first, it induces mobility among otherwise stable Pt adatoms through the formation of Pt carbonyls (Pt1-CO), leading to agglomeration into subnano clusters. Second, the presence of the CO stabilizes the smallest clusters against decay at room temperature, significantly modifying the growth kinetics. At elevated temperatures, CO desorption results in a partial redispersion and recovery of the Pt adatom phase.

Concepts: Electron, Fundamental physics concepts, Temperature, Density functional theory, Model theory, Microscopy, Scanning tunneling microscope, Ideal gas

31

Overexploitation and persecution of large carnivores resulting from conflict with humans comprise major causes of declines worldwide. Although little is known about the interplay between these mortality types, hunting of predators remains a common management strategy aimed at reducing predator-human conflict. Emerging theory and data, however, caution that such policy can alter the age structure of populations, triggering increased conflict in which conflict-prone juveniles are involved.

Concepts: Demography, Population, Predation, Model theory, Hunting, Plan, League Against Cruel Sports, Big-game hunter

28

We investigated links between persuasive behavior and theory of mind (ToM) understanding using a novel naturalistic peer persuasion task in which children were invited to convince an interactive puppet to eat raw broccoli or brush his teeth. Sixty-three 3- to 8-year-olds (M age = 6 years, 6 months) took part in the persuasion task and were also given a battery of first-order and advanced false belief tests. As predicted, the number of independent persuasive arguments children produced was significantly associated with false belief scores, even after controlling for age and verbal ability. (PsycINFO Database Record © 2013 APA, all rights reserved).

Concepts: Truth, Philosophy of mind, Model theory, Behaviorism, All rights reserved, Theory of mind, Quantification, Rhetoric

28

Intransitivity is a property of connected, oriented graphs representing species interactions that may drive their coexistence even in the presence of competition, the standard example being the three species Rock-Paper-Scissors game. We consider here a generalization with four species, the minimum number of species allowing other interactions beyond the single loop (one predator, one prey). We show that, contrary to the mean field prediction, on a square lattice the model presents a transition, as the parameter setting the rate at which one species invades another changes, from a coexistence to a state in which one species gets extinct. Such a dependence on the invasion rates shows that the interaction graph structure alone is not enough to predict the outcome of such models. In addition, different invasion rates permit to tune the level of transitiveness, indicating that for the coexistence of all species to persist, there must be a minimum amount of intransitivity.

Concepts: Game theory, Algebraic structure, Model theory, Arithmetic mean, Real number, Graph theory, Graph, Biological interaction

28

Endovascular abdominal aortic aneurysm repair (EVAR) in patients with unfavorable proximal seal zones remains challenging. The purpose of this study was to identify the incidence of proximal extension cuff usage for type I endoleaks in patients with abdominal aortic aneurysms and unfavorable necks treated with the C3 Excluder repositionable endoprosthesis compared with the traditional Excluder stent-graft.

Concepts: Aortic aneurysm, Model theory, Aneurysm, Cerebral aneurysm, Aortic dissection, Aorta, Abdominal aortic aneurysm, Aneurysm of sinus of Valsalva