Dry and wet interfaces: Influence of solvent particles on molecular recognition

We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our basic model showing that the selectivity of the recognition process can be enhanced by considering the explicit influence of single solvent particles. When the number of cavities at the interface of a protein-protein complex is fixed as an intrinsic geometric constraint, there typically exists a characteristic fraction that should be filled with water molecules such that the selectivity exhibits a maximum. In addition the optimum fraction depends on the hydrophobicity of the interface so that one has to distinguish between dry and wet interfaces.Comment: 11 pages, 7 figure

Failure to meet aerobic fitness standards among urban elementary students

The aim of this study was to explore the relationship of aerobic fitness with the elementary school environment and student characteristics among 4th and 5th grade children attending urban public schools in St. Louis, MO, USA. This cross-sectional study was conducted during 2012–2015 and included 2381 children (mean age 10.5 y) who completed the FITNESSGRAM® 20-m Progressive Aerobic Cardiovascular Endurance Run. Healthy Fitness Zone (HFZ) was defined according to FITNESSGRAM® aerobic capacity criteria. Other student-level variables included age, race, National School Lunch Program eligibility, BMI z-score, weight status, and daily pedometer steps. School environment variables included playground features and playground safety, physical education and recess practices, and school census tract data on vacant houses and median household income. Bivariate analyses with sex stratification were used to identify student-level and school-level predictors of failure to achieve the aerobic HFZ; predictors were then included in a multivariable logistic regression model. Failure to meet the aerobic HFZ was observed among 33% of boys and 57% of girls. School environment was not predictive, but higher age and fewer daily steps were: each additional year of age was associated with 41% higher odds of failing to meet the aerobic HFZ among boys and 100% higher odds among girls. Conversely, each additional 1000 daily steps was associated with 15% (boys) and 13% (girls) lower odds of failure. Obesity posed a 60% higher risk of failure to meet HFZ among girls. These results highlight the importance of childhood physical activity opportunities, especially for girls residing in low-resource areas. Keywords: Aerobic fitness, School, Environment, Student, Child, Urban, Low-resourc

Analysing the Security of Google's implementation of OpenID Connect

Many millions of users routinely use their Google accounts to log in to relying party (RP) websites supporting the Google OpenID Connect service. OpenID Connect, a newly standardised single-sign-on protocol, builds an identity layer on top of the OAuth 2.0 protocol, which has itself been widely adopted to support identity management services. It adds identity management functionality to the OAuth 2.0 system and allows an RP to obtain assurances regarding the authenticity of an end user. A number of authors have analysed the security of the OAuth 2.0 protocol, but whether OpenID Connect is secure in practice remains an open question. We report on a large-scale practical study of Google's implementation of OpenID Connect, involving forensic examination of 103 RP websites which support its use for sign-in. Our study reveals serious vulnerabilities of a number of types, all of which allow an attacker to log in to an RP website as a victim user. Further examination suggests that these vulnerabilities are caused by a combination of Google's design of its OpenID Connect service and RP developers making design decisions which sacrifice security for simplicity of implementation. We also give practical recommendations for both RPs and OPs to help improve the security of real world OpenID Connect systems

Highly Designable Protein Structures and Inter Monomer Interactions

By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the interaction potential becomes larger than a critical value, the degree of designability of structures will depend on the parameters of potential. We also show that the existence of a unique ground state is highly sensitive to mutation in certain sites.Comment: 14 pages, Latex file, 3 latex and 6 eps figures are include

A test generation framework for quiescent real-time systems

We present an extension of Tretmans theory and algorithm for test generation for input-output transition systems to real-time systems. Our treatment is based on an operational interpretation of the notion of quiescence in the context of real-time behaviour. This gives rise to a family of implementation relations parameterized by observation durations for quiescence. We define a nondeterministic (parameterized) test generation algorithm that generates test cases that are sound with respect to the corresponding implementation relation. Also, the test generation is exhaustive in the sense that for each non-conforming implementation a test case can be generated that detects the non-conformance

Teachers developing assessment for learning: impact on student achievement

While it is generally acknowledged that increased use of formative assessment (or assessment for learning) leads to higher quality learning, it is often claimed that the pressure in schools to improve the results achieved by students in externally-set tests and examinations precludes its use. This paper reports on the achievement of secondary school students who worked in classrooms where teachers made time to develop formative assessment strategies. A total of 24 teachers (2 science and 2 mathematics teachers, in each of six schools in two LEAs) were supported over a six-month period in exploring and planning their approach to formative assessment, and then, beginning in September 1999, the teachers put these plans into action with selected classes. In order to compute effect sizes, a measure of prior attainment and at least one comparison group was established for each class (typically either an equivalent class taught in the previous year by the same teacher, or a parallel class taught by another teacher). The mean effect size was 0.32

Theta-point universality of polyampholytes with screened interactions

By an efficient algorithm we evaluate exactly the disorder-averaged statistics of globally neutral self-avoiding chains with quenched random charge $q_i=\pm 1$ in monomer i and nearest neighbor interactions $\propto q_i q_j$ on square (22 monomers) and cubic (16 monomers) lattices. At the theta transition in 2D, radius of gyration, entropic and crossover exponents are well compatible with the universality class of the corresponding transition of homopolymers. Further strong indication of such class comes from direct comparison with the corresponding annealed problem. In 3D classical exponents are recovered. The percentage of charge sequences leading to folding in a unique ground state approaches zero exponentially with the chain length.Comment: 15 REVTEX pages. 4 eps-figures . 1 tabl

Geometrically Reduced Number of Protein Ground State Candidates

Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small: For the case of a two-parameter Hydrophobic-Polar lattice model for $L$-mers, the number of these candidates grows only as $L^2$. Moreover, the space of the interaction parameters of the model breaks up into well-defined domains, each corresponding to one ground state candidate, which are separated by sharp boundaries. In addition, by exact enumeration, we show there are some sequences which have one absolute unique native state. These absolute ground states have perfect stability against change of inter-monomer interaction potential.Comment: 9 page, 4 ps figures are include

Viscosity Dependence of the Folding Rates of Proteins

The viscosity dependence of the folding rates for four sequences (the native state of three sequences is a beta-sheet, while the fourth forms an alpha-helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is given by the Langevin equation we show that the folding rates increase linearly at low viscosities \eta, decrease as 1/\eta at large \eta and have a maximum at intermediate values. The Kramers theory of barrier crossing provides a quantitative fit of the numerical results. By mapping the simulation results to real proteins we estimate that for optimized sequences the time scale for forming a four turn \alpha-helix topology is about 500 nanoseconds, whereas the time scale for forming a beta-sheet topology is about 10 microseconds.Comment: 14 pages, Latex, 3 figures. One figure is also available at http://www.glue.umd.edu/~klimov/seq_I_H.html, to be published in Physical Review Letter

Influence of physical education on moderate-to-vigorous physical activity of urban public school children in St. Louis, Missouri, 2011–2014

We quantified the moderate-to-vigorous physical activity (MVPA, heart rate ≥140 bpm) of urban public elementary school children on school days with and school days without physical education (PE) class by using continuous heart rate monitoring. The heart rate of 81 students (93.8% black) in grades 3 and 5 was recorded in 15-second intervals. On the basis of 575 school-day observations (mean 7.1 days/student), students accumulated 44.4 (standard deviation [SD], 34.4) minutes of MVPA on days with PE and 30.6 (SD, 29.9) MVPA minutes on days without PE (P < .001). School policies should promote daily PE to help children in under-resourced areas achieve the recommended 60 minutes per day of MVPA