Zero-One Designs Produce Small Hard SAT Instances

Some basics of combinatorial block design are combined with certain constraint satisfaction problems of interest to the satisfiability community. The paper shows how such combinations lead to satisfiability problems, and shows empirically that these are some of the smallest very hard satisfiability problems ever constructed. Partially balanced (0,1) designs (PB01Ds) are introduced as an extension of balanced incomplete block designs (BIBDs) and (0,1) designs. Also, (0,1) difference sets are introduced as an extension of certain cyclical difference sets. Constructions based on (0,1) difference sets enable generation of PB01Ds over a much wider range of parameters than is possible for BIBDs. Building upon previous work of Spence, it is shown how PB01Ds lead to small, very hard, unsatisfiable formulas. A new three-dimensional form of combinatorial block design is introduced, and leads to small, very hard, satisfiable formulas. The methods are validated on solvers that performed well in the SAT 2009 and earlier competitions.

Optimal diet choice for large herbivores: an extended contingency model

1. A more general contingency model of optimal diet choice is developed, allowing for simultaneous searching and handling, which extends the theory to include grazing and browsing by large herbivores.</p><p>2. Foraging resolves into three modes: purely encounter-limited, purely handling-limited and mixed-process, in which either a handling-limited prey type is added to an encounter-limited diet, or the diet becomes handling-limited as it expands.</p><p>3. The purely encounter-limited diet is, in general, broader than that predicted by the conventional contingency model,</p><p>4. As the degree of simultaneity of searching and handling increases, the optimal diet expands to the point where it is handling-limited, at which point all inferior prey types are rejected,</p><p>5. Inclusion of a less profitable prey species is not necessarily independent of its encounter rate and the zero-one rule does not necessarily hold: some of the less profitable prey may be included in the optimal diet. This gives an optimal foraging explanation for herbivores' mixed diets.</p><p>6. Rules are shown for calculating the boundary between encounter-limited and handling-limited diets and for predicting the proportion of inferior prey to be included in a two-species diet,</p><p>7. The digestive rate model is modified to include simultaneous searching and handling, showing that the more they overlap, the more the predicted diet-breadth is likely to be reduced.</p>

Averaged Extended Tree Augmented Naive Classifier

This work presents a new general purpose classifier named Averaged Extended Tree Augmented Naive Bayes (AETAN), which is based on combining the advantageous characteristics of Extended Tree Augmented Naive Bayes (ETAN) and Averaged One-Dependence Estimator (AODE) classifiers. We describe the main properties of the approach and algorithms for learning it, along with an analysis of its computational time complexity. Empirical results with numerous data sets indicate that the new approach is superior to ETAN and AODE in terms of both zero-one classification accuracy and log loss. It also compares favourably against weighted AODE and hidden Naive Bayes. The learning phase of the new approach is slower than that of its competitors, while the time complexity for the testing phase is similar. Such characteristics suggest that the new classifier is ideal in scenarios where online learning is not required.

The conjugacy problem for two-by-two matrices over polynomial rings

We give an effective solution of the conjugacy problem for two-by-two matrices over the polynomial ring in one variable over a finite field.

Ionic liquid-reconstituted cellulose composites as solid support matrices for biocatalyst immobilization

Preparation of cellulose-polyamine composite films and beads, which provide high loading of primary amines on the surface allowing direct one-step bioconjugation of active species, is reported using an ionic liquid (IL) dissolution and regeneration process. Films and bead architectures were prepared and used as immobilization supports for laccase as a model system demonstrating the applicability of this approach. Performance of these materials, compared to commercially available products, has been assessed using millimeter-sized beads of the composites and the lipase-catalyzed transesterification of ethyl butyrate.

Dynamics of nonlinearly coupled magnetic-field-aligned electromagnetic electron-cyclotron waves near the zero-group-dispersion point in magnetized plasmas

The nonlinear coupling between two magnetic-field-aligned electromagnetic electron-cyclotron (EMEC) waves in plasmas is considered. Evaluating the ponderomotive coupling between the EMEC waves and quasistationary plasma density perturbations, a pair of coupled nonlinear Schrodinger equations (CNLSEs) is obtained. The CNLSEs are then used to investigate the occurrence of modulational instability in magnetized plasmas. Waves in the vicinity of the zero-group-dispersion point are considered, so that the group dispersion terms may either bear the same or different signs. It is found that a stable EMEC wave can be destabilized due to its nonlinear interactions with an unstable one, while a pair of unstable EMEC waves yields an increased instability growth rate. Individually stable waves remain stable while interacting with one another. Stationary nonlinear solutions of the coupled equations are presented. The relevance of our investigation to nonlinear phenomena in space plasmas is discussed. (c) 2005 American Institute of Physics.

Boson pairs in a one-dimensional split trap

We describe the properties of a pair of ultracold bosonic atoms in a one-dimensional harmonic trapping potential with a tunable zero-ranged barrier at the trap center. The full characterization of the ground state is done by calculating the reduced single-particle density, the momentum distribution, and the two-particle entanglement. We derive several analytical expressions in the limit of infinite repulsion (Tonks-Girardeau limit) and extend the treatment to finite interparticle interactions by numerical solution. As pair interactions in double wells form a fundamental building block for many-body systems in periodic potentials, our results have implications for a wide range of problems.

Pharmacokinetics of UC781-loaded intravaginal ring segments in rabbits: a comparison of polymer matrices

UC781 is a potent and poorly water-soluble nonnucleoside reverse transcriptase inhibitor being investi- gated as a potential microbicide for preventing sexual transmission of HIV-1. This study was designed to evaluate the in vivo release and pharmacokinetics of UC781 delivered from matrix-type intravaginal ring segments in rabbits. Three polymer matrices (polyurethane, ethylene vinyl acetate copolymer, and silicone elastomer) and two drug loadings (5 and 15 mg/segment) were evaluated in at least one of two independent studies for up to 28 days in vivo. Inter-study comparison of in vivo release, vaginal tissue, and plasma concentrations for similar formulations demonstrated good reproducibility of the animal model. Mean estimates for a 28-day in vivo release ranged from 0.35 to 3.17 mg UC781 per segment. Mean proximal vaginal tissue levels (adjacent to the IVR segment) were 8– 410 ng/g and did not change significantly with time for most formulations. Distal vaginal tissue levels of UC781 were 6- to 49-fold lower than proximal tissue levels. Mean UC781 plasma levels were low for all formulations, at 0.09–0.58 ng/mL. All formulations resulted in similar UC781 concentrations in vaginal tissue and plasma, except the low loading polyurethane group which provided significantly lower levels. Loading dependent release and pharmacokinetics were only clearly observed for the polyurethane matrix. Based on these results, intravaginal ring segments loaded with UC781 led to vaginal tissue concen- trations ranging from below to approximately two orders of magnitude higher than UC781’s EC50 under in vitro conditions (2.8 ng/mL), with little influence by polymer matrix or UC781 loading. Moreover, these findings support the use of rabbit vaginal pharmacokinetic studies in preclinical testing of microbicide intravaginal rings.

Discovering subgroups of patients from DNA copy number data using NMF on compacted matrices

In the study of complex genetic diseases, the identification of subgroups of patients sharing similar genetic characteristics represents a challenging task, for example, to improve treatment decision. One type of genetic lesion, frequently investigated in such disorders, is the change of the DNA copy number (CN) at specific genomic traits. Non-negative Matrix Factorization (NMF) is a standard technique to reduce the dimensionality of a data set and to cluster data samples, while keeping its most relevant information in meaningful components. Thus, it can be used to discover subgroups of patients from CN profiles. It is however computationally impractical for very high dimensional data, such as CN microarray data. Deciding the most suitable number of subgroups is also a challenging problem. The aim of this work is to derive a procedure to compact high dimensional data, in order to improve NMF applicability without compromising the quality of the clustering. This is particularly important for analyzing high-resolution microarray data. Many commonly used quality measures, as well as our own measures, are employed to decide the number of subgroups and to assess the quality of the results. Our measures are based on the idea of identifying robust subgroups, inspired by biologically/clinically relevance instead of simply aiming at well-separated clusters. We evaluate our procedure using four real independent data sets. In these data sets, our method was able to find accurate subgroups with individual molecular and clinical features and outperformed the standard NMF in terms of accuracy in the factorization fitness function. Hence, it can be useful for the discovery of subgroups of patients with similar CN profiles in the study of heterogeneous diseases.

Constructing random matrices to represent real ecosystems

Models of complex systems with n components typically have order n² parameters because each component can potentially interact with every other. When it is impractical to measure these parameters, one may choose random parameter values and study the emergent statistical properties at the system level. Many influential results in theoretical ecology have been derived from two key assumptions: that species interact with random partners at random intensities and that intraspecific competition is comparable between species. Under these assumptions, community dynamics can be described by a community matrix that is often amenable to mathematical analysis. We combine empirical data with mathematical theory to show that both of these assumptions lead to results that must be interpreted with caution. We examine 21 empirically derived community matrices constructed using three established, independent methods. The empirically derived systems are more stable by orders of magnitude than results from random matrices. This consistent disparity is not explained by existing results on predator-prey interactions. We investigate the key properties of empirical community matrices that distinguish them from random matrices. We show that network topology is less important than the relationship between a species’ trophic position within the food web and its interaction strengths. We identify key features of empirical networks that must be preserved if random matrix models are to capture the features of real ecosystems.