SANA NetGO: A combinatorial approach to using Gene Ontology (GO) terms to score network alignments

Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure the GO similarity between two proteins in isolation, but pairs of proteins in a network alignment are not isolated: each pairing is implicitly dependent upon every other pairing via the alignment itself. Current methods fail to take into account the frequency of GO terms across the networks, and attempt to account for common GO terms in an ad hoc fashion by imposing arbitrary rules on when to "allow" GO terms based on their location in the GO hierarchy, rather than using readily available frequency information in the PPI networks themselves. Here we develop a new measure, NetGO, that naturally weighs infrequent, informative GO terms more heavily than frequent, less informative GO terms, without requiring arbitrary cutoffs. In particular, NetGO down-weights the score of frequent GO terms according to their frequency in the networks being aligned. This is a global measure applicable only to alignments, independent of pairwise GO measures, in the same sense that the edge-based EC or S3 scores are global measures of topological similarity independent of pairwise topological similarities. We demonstrate the superiority of NetGO by creating alignments of predetermined quality based on homologous pairs of nodes and show that NetGO correlates with alignment quality much better than any existing GO-based alignment measures. We also demonstrate that NetGO provides a measure of taxonomic similarity between species, consistent with existing taxonomic measures--a feature not shared with existing GO-based network alignment measures. Finally, we re-score alignments produced by almost a dozen aligners from a previous study and show that NetGO does a better job than existing measures at separating good alignments from bad ones

Shadowing-based reliability decay in softened n-body simulations

A shadow of a numerical solution to a chaotic system is an_exact_ solution to the equations of motion that remains close to the numerical solution for a long time. In a collisionless n-body system, we know that particle motion is governed by the global potential rather than by inter-particle interactions. As a result, the trajectory of each individual particle in the system is independently shadowable. It is thus meaningful to measure the number of particles that have shadowable trajectories as a function of time. We find that the number of shadowable particles decays exponentially with time as exp(-mu t), and that for eps in [~0.2,1] (in units of the local mean inter-particle separation $\bar n$), there is an explicit relationship between the decay constant mu, the timestep h of the leapfrog integrator, the softening eps, and the number of particles N in the simulation. Thus, given N and eps, it is possible to pre-compute the timestep h necessary to acheive a desired fraction of shadowable particles after a given length of simulation time. We demonstrate that a large fraction of particles remain shadowable over ~100 crossing times even if particles travel up to about 1/3 of the softening length per timestep. However, a sharp decrease in the number of shadowable particles occurs if the timestep increases to allow particles to travel further than 1/3 the softening length in one timestep, or if the softening is decreased below ~0.2$\bar n$.Comment: 4 pages, 5 figure

Deriving real-time action systems with multiple time bands using algebraic reasoning

The verify-while-develop paradigm allows one to incrementally develop programs from their specifications using a series of calculations against the remaining proof obligations. This paper presents a derivation method for real-time systems with realistic constraints on their behaviour. We develop a high-level interval-based logic that provides flexibility in an implementation, yet allows algebraic reasoning over multiple granularities and sampling multiple sensors with delay. The semantics of an action system is given in terms of interval predicates and algebraic operators to unify the logics for an action system and its properties, which in turn simplifies the calculations and derivations

An investigation in to different factors related to problematic smartphone use

Smartphone use is increasing, and problematic smartphone use (PSU) has frequently been labelled a public health concern. Building upon the vast number of studies exploring the relationship between different correlates and PSU, many reviews exist exploring how PSU relates to a range of psychological factors. Previously no succinct review existed to help guide researchers/clinicians to make sense of this area or aid theory/intervention development. A meta-review was undertaken that synthesised reviews exploring correlates of PSU between the years of 2019 – 2022. Sixteen reviews were synthesised into five main themes, sleep, emotional and mental health factors, trait factors, ways of coping and physical activity. There was a consistent positive relationship between PSU and increased emotional and mental health difficulties, poorer sleep, trait factors (such as insecure attachment), unhelpful ways of coping and reduced levels of physical activity. However, differentmethodological limitations mean some associations should be interpreted cautiously and not generalised to other samples (physical activity or ways of coping). This meta-review supports the view that different correlates are related to PSU across different themes, countries and, to some extent, populations. Studies sampling older populations that also utilise models used in psychological therapy are recommended for areas of future research

Effect of a simulated engine jet blowing above an arrow wing at Mach 2.0

The effects of a gas jet simulating a turbojet engine exhaust blowing above a cambered and twisted arrow wing were investigated. Tests were conducted in the Langley 4-foot supersonic pressure tunnel at a Mach number of 2.0. Nozzle pressure ratios from 1 to 64 were tested with both helium and air used as jet gases. The tests were conducted at angles of attack from -2 deg to 8 deg at a Reynolds number of 9,840,000 per meter. Only the forces and moments on the wing were measured. Results of the investigation indicated that the jet blowing over the wing caused reductions in maximum lift-drag ratio of about 4 percent for helium and 6 percent for air at their respective design nozzle pressure ratios, relative to jet-off data. Moderate changes in the longitudinal, vertical, or angular positions of the jet relative to the wing had little effect on the wing aerodynamic characteristics