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. Sulphuric acid hydrolysis of 60wt%-treated samples yielded the highest amount of glucose per gram of rice husk. Solutions with good lignin and silica solubility but only moderate to negligible cellulose solubility (10-40wt% hydroxide) were equally effective as pre-treatment media for both acid and enzymatic hydrolysis. However, pre-treatment with 60wt% hydroxide solutions was incompatible with downstream enzymatic hydrolysis. This was due to significant incorporation of phosphonium species in the regenerated biomass, which significantly inhibited the activity of the cellulase enzymes.

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. We show that EPSAs can be cast as stochastic pattern search methods, and we use this observation to prove that EPSAs have a probabilistic, weak stationary point convergence theory. This convergence theory is distinguished by the fact that the analysis does not approximate the stochastic process of EPSAs, and hence it exactly characterizes their convergence properties.

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. These tortuosity measures were able to achieve a classification rate of 91% for the first problem and 95% on the second problem, which confirms that they capture much of the ophthalmologists' notion of tortuosity. Finally, we discuss how the accuracy of these measures can be influence by the method used to extract the blood vessel segments.

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. We consider two side chain models: a lattice model that generalizes the HP model (Dill, 1985) to explicitly represent side chains on the cubic lattice and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. We describe algorithms with mathematically guaranteed error bounds for both of these models. In particular, we describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 86% of optimal in a face-centered cubic lattice, and we demonstrate how this provides a better than 70% performance guarantee for the HP-TSSC model. Our analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Ngo et al. (1994) concerning the complexity of protein folding models that include side chains.

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. We consider a previously studied model and prove that for any reasonable lattice the protein-structure prediction problem is NP-hard. The second hardness result concerns the intractability of protein folding for a class of energy formulas that contains a broad range of mean force potentials whose form is similar to commonly used pair potentials (e.g., the Lennard-Jones potential). We prove that protein-structure prediction is NP-hard for any energy formula in this class. These are the first robust intractability results that identify sources of computational complexity of protein-structure prediction that transcend particular problem formulations.

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. These tortuosity measures were able to achieve a classification rate of 91% for the first problem and 95% on the second problem, which confirms that they capture much of the ophthalmologists' notion of tortuosity.

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. The protein is modeled as a chain of amino acids of length n that are of two types; H (hydrophobic, i.e., nonpolar) and P (hydrophilic, i.e., polar). Although this model is a simplification of more complex protein folding models, the protein folding structure prediction problem is notoriously difficult for this model. Our algorithms have linear (3n) or quadratic time and achieve a three-dimensional protein conformation that has a guaranteed free energy no worse than three-eighths of optimal. This result answers the open problem of Ngo et al. (1994) about the possible existence of an efficient approximation algorithm with guaranteed performance for protein structure prediction in any well-studied model of protein folding. By achieving speed and near-optimality simultaneously, our algorithms rigorously capture salient features of the recently proposed framework of protein folding by Sali et al. (1994). Equally important, the final conformations of our algorithms have significant secondary structure (antiparallel sheets, beta-sheets, compact hydrophobic core). Furthermore, hypothetical folding pathways can be described for our algorithms that fit within the framework of diffusion-collision protein folding proposed by Karplus and Weaver (1979). Computational limitations of algorithms that compute the optimal conformation have restricted their applicability to short sequences (length < or = 90). Because our algorithms trade computational accuracy for speed, they can construct near-optimal conformations in linear time for sequences of any size.

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.