Efflux Pumps Represent Possible Evolutionary Convergence onto the Beta Barrel Fold

Preprint now published in Structure doi: 10.1016/j.str.2018.06.007There are around 100 types of integral outer membrane proteins in each Gram negative bacteria. All of these proteins have the same fold—an up-down β-barrel. It has been suggested that all membrane β-barrels other than lysins are homologous. Here we suggest that β-barrels of efflux pumps have converged on this fold as well. By grouping structurally-solved outer membrane β-barrels (OMBBs) by sequence we find evidence that the membrane environment may have led to convergent evolution of the barrel fold. Specifically, the lack of sequence linkage to other barrels coupled with distinctive structural differences, such as differences in strand tilt and barrel radius, suggest that efflux pumps have evolutionarily converged on the barrel. Finally, we find a possible ancestor for the OMBB efflux pumps as they are related to periplasmic components of the same pumps

Wall effects on the transportation of a cylindrical particle in power-law fluids

The present work deals with the numerical calculation of the Stokes-type drag undergone by a cylindrical particle perpendicularly to its axis in a power-law fluid. In unbounded medium, as all data are not available yet, we provide a numerical solution for the pseudoplastic fluid. Indeed, the Stokes-type solution exists because the Stokes’ paradox does not take place anymore. We show a high sensitivity of the solution to the confinement, and the appearance of the inertia in the proximity of the Newtonian case, where the Stokes’ paradox takes place. For unbounded medium, avoiding these traps, we show that the drag is zero for Newtonian and dilatant fluids. But in the bounded one, the Stokes-type regime is recovered for Newtonian and dilatant fluids. We give also a physical explanation of this effect which is due to the reduction of the hydrodynamic screen length, for pseudoplastic fluids. Once the solution of the unbounded medium has been obtained, we give a solution for the confined medium numerically and asymptotically. We also highlight the consequence of the confinement and the backflow on the settling velocity of a fiber perpendicularly to its axis in a slit. Using the dynamic mesh technique, we give the actual transportation velocity in a power-law “Poiseuille flow”, versus the confinement parameter and the fluidity index, induced by the hydrodynamic interactions

Diagonal splittings of toric varieties and unimodularity

We use a polyhedral criterion for the existence of diagonal splittings to investigate which toric varieties X are diagonally split. Our results are stated in terms of the vector configuration given by primitive generators of the 1-dimensional cones in the fan defining X. We show, in particular, that X is diagonally split at all q if and only if this configuration is unimodular, and X is not diagonally split at any q if this configuration is not 2-regular. We also study implications for the possibilities for the set of q at which a toric variety X is diagonally split.Comment: 11 pages v2: minor revisions, to appear in Proc. Amer. Math. So

MGARD+: Optimizing Multilevel Methods for Error-Bounded Scientific Data Reduction

Nowadays, data reduction is becoming increasingly important in dealing with the large amounts of scientific data. Existing multilevel compression algorithms offer a promising way to manage scientific data at scale but may suffer from relatively low performance and reduction quality. In this paper, we propose MGARD+, a multilevel data reduction and refactoring framework drawing on previous multilevel methods, to achieve high-performance data decomposition and high-quality error-bounded lossy compression. Our contributions are four-fold: 1) We propose to leverage a level-wise coefficient quantization method, which uses different error tolerances to quantize the multilevel coefficients. 2) We propose an adaptive decomposition method which treats the multilevel decomposition as a preconditioner and terminates the decomposition process at an appropriate level. 3) We leverage a set of algorithmic optimization strategies to significantly improve the performance of multilevel decomposition/recompositing. 4) We evaluate our proposed method using four real-world scientific datasets and compare with several state-of-the-art lossy compressors. Experiments demonstrate that our optimizations improve the decomposition/recompositing performance of the existing multilevel method by up to $70 \times$70x, and the proposed compression method can improve compression ratio by up to $2 \times$2x compared with other state-of-the-art error-bounded lossy compressors under the same level of data distortion

Respiratory pandemics, urban planning and design: a multidisciplinary rapid review of the literature.

COVID-19 is the most recent respiratory pandemic to necessitate better knowledge about city planning and design. The complex connections between cities and pandemics, however challenge traditional approaches to reviewing literature. In this article we adopted a rapid review methodology. We review the historical literature on respiratory pandemics and their documented connections to urban planning and design (both broadly defined as being concerned with cities as complex systems). Our systematic search across multidisciplinary databases returned a total of 1323 sources, with 92 articles included in the final review. Findings showed that the literature represents the multi-scalar nature of cities and pandemics – pandemics are global phenomena spread through an interconnected world, but require regional, city, local and individual responses. We characterise the literature under ten themes: scale (global to local); built environment; governance; modelling; non-pharmaceutical interventions; socioeconomic factors; system preparedness; system responses; underserved and vulnerable populations; and future-proofing urban planning and design. We conclude that the historical literature captures how city planning and design intersects with a public health response to respiratory pandemics. Our thematic framework provides parameters for future research and policy responses to the varied connections between cities and respiratory pandemics