Effect of specific non-pharmaceutical intervention policies on SARS-CoV-2 transmission in the counties of the United States.

Non-pharmaceutical interventions (NPIs) remain the only widely available tool for controlling the ongoing SARS-CoV-2 pandemic. We estimated weekly values of the effective basic reproductive number (R) using a mechanistic metapopulation model and associated these with county-level characteristics and NPIs in the United States (US). Interventions that included school and leisure activities closure and nursing home visiting bans were all associated with a median R below 1 when combined with either stay at home orders (median R 0.

Nucleophilic Cleavage of Lignin Model Compounds under Acidic Conditions in an Ionic Liquid: A Mechanistic Study.

A range of lignin model compounds were examined for their reactivity with hydrogen bromide in the ionic liquid N-butylpyridinium triflate. It was found that the ionic liquid enabled rapid reaction at both the hydroxy and methyl ether sites of the model compounds at room temperature. Reactions at the phenyl ether moieties were more complex; rather than facilitating cleavage at these sites, alternate breakdown products that had not been seen in previous studies were observed; these products are consistent with functionalisation of the aromatic components of the model compounds.

Cleavage of ethers in an ionic liquid. Enhancement, selectivity and potential application.

The cleavage of a series of ethers was examined in an ionic liquid containing hydrogen bromide. Reactions that did not proceed in either water or DMSO were found to proceed readily in this system, with notable selectivity between the cleavage of the different ether types examined herein. Increasing the proportion of water in the reaction mixture dramatically decreased the rate constant of ether cleavage; this could, in part, be attributed to a decrease in the solvent stabilisation of the transition state.

Facile, room-temperature pre-treatment of rice husks with tetrabutylphosphonium hydroxide: Enhanced enzymatic and acid hydrolysis yields.

Aqueous solutions of tetrabutylphosphonium hydroxide have been evaluated as pretreatment media for rice husks, prior to sulphuric acid hydrolysis or cellulase enzymatic hydrolysis. Varying the water:tetrabutylphosphonium hydroxide ratio varied the rate of delignification, as well as silica, lignin and cellulose solubility. Pre-treatment with 60wt% hydroxide dissolved the rice husk and the regenerated material was thus heavily disrupted.

The abilities of selenium dioxide and selenite ion to coordinate DNA-bound metal ions and decrease oxidative DNA damage.

Several transition metals react with H2O2 and produce reactive oxygen species (ROS) responsible for oxidative damage linked to many diseases and disorders, and species that form coordination complexes with these metal ions show promise as antioxidants. The present study demonstrates that metal-mediated radical and non-radical oxidative DNA damage decreases when selenium dioxide (SeO2) and sodium selenite (Na2SeO3) are present. Radical-induced damage is associated with production of 8-hydroxy-2'-deoxyguanosine (8-OH-dG), which arises from ROS generated at or near the guanine base, and the selenium compounds reduce Fe(II)-, Cr(III)- and Cu(II)-mediated radical damage to differing degrees based on the identity of the metal ion and the order in which the metals, selenium compounds and DNA are combined.

A filter-based evolutionary algorithm for constrained optimization.

We introduce a filter-based evolutionary algorithm (FEA) for constrained optimization. The filter used by an FEA explicitly imposes the concept of dominance on a partially ordered solution set. We show that the algorithm is provably robust for both linear and nonlinear problems and constraints.

Locally-adaptive and memetic evolutionary pattern search algorithms.

Recent convergence analyses of evolutionary pattern search algorithms (EPSAs) have shown that these methods have a weak stationary point convergence theory for a broad class of unconstrained and linearly constrained problems. This paper describes how the convergence theory for EPSAs can be adapted to allow each individual in a population to have its own mutation step length (similar to the design of evolutionary programing and evolution strategies algorithms). These are called locally-adaptive EPSAs (LA-EPSAs) since each individual's mutation step length is independently adapted in different local neighborhoods.

Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling.

The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program.

A convergence analysis of unconstrained and bound constrained evolutionary pattern search.

We present and analyze a class of evolutionary algorithms for unconstrained and bound constrained optimization on R(n): evolutionary pattern search algorithms (EPSAs). EPSAs adaptively modify the step size of the mutation operator in response to the success of previous optimization steps. The design of EPSAs is inspired by recent analyses of pattern search methods.

Measurement and classification of retinal vascular tortuosity.

Automatic measurement of blood vessel tortuosity is a useful capability for automatic ophthalmological diagnostic tools. We describe a suite of automated tortuosity measures for blood vessel segments extracted from RGB retinal images. The tortuosity measures were evaluated in two classification tasks: (1) classifying the tortuosity of blood vessel segments and (2) classifying the tortuosity of blood vessel networks.

Learning foraging thresholds for lizards: an analysis of a simple learning algorithm.

This paper gives proof of convergence for a learning algorithm that describes how anoles (lizards found in the Caribbean) learn foraging threshold distance. An anole will pursue a prey if and only if it is within this threshold of the anole's perch. The learning algorithm was proposed by Roughgarden and his colleagues.

Lattice and off-lattice side chain models of protein folding: linear time structure prediction better than 86% of optimal.

This paper considers the protein energy minimization problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models.

Robust proofs of NP-hardness for protein folding: general lattices and energy potentials.

This paper addresses the robustness of intractability arguments for simplified models of protein folding that use lattices to discretize the space of conformations that a protein can assume. We present two generalized NP-hardness results. The first concerns the intractability of protein folding independent of the lattice used to define the discrete protein-folding model.

Automated measurement of retinal vascular tortuosity.

Automatic measurement of blood vessel tortuosity is a useful capability for automatic ophthalmological diagnostic tools. We describe a suite of automated tortuosity measures for blood vessel segments extracted from RGB retinal images. The tortuosity measures were evaluated in two classification tasks: (1) classifying the tortuosity of blood vessel segments and (2) classifying the tortuosity of blood vessel networks.

Fast protein folding in the hydrophobic-hydrophilic model within three-eighths of optimal.

We present performance-guaranteed approximation algorithms for the protein folding problem in the hydrophobic-hydrophilic model (Dill, 1985). Our algorithms are the first approximation algorithms in the literature with guaranteed performance for this model (Dill, 1994). The hydrophobic-hydrophilic model abstracts the dominant force of protein folding: the hydrophobic interaction.

Nemaline (rod) myopathy: a possible cause of rapidly fatal infantile hypotonia.

Two infant siblings (male and female) manifested extreme hypotonia and flaccidity at birth and had a rapidly fatal course. In each, rod-like structures were demonstrated within a variety of skeletal muscles, and accumulations of thin filaments were seen in numerous muscle fibers. The possibility exists that this represents a severe and rapidly fatal form of nemaline myopathy that should be included in the differential diagnosis of infantile hypotonias.