Two loop detection mechanisms: a comparison

In order to compare two loop detection mechanisms we describe two calculi for theorem proving in intuitionistic propositional logic. We call them both MJ Hist, and distinguish between them by description as `Swiss' or `Scottish'. These calculi combine in different ways the ideas on focused proof search of Herbelin and Dyckhoff & Pinto with the work of Heuerding emphet al on loop detection. The Scottish calculus detects loops earlier than the Swiss calculus but at the expense of modest extra storage in the history. A comparison of the two approaches is then given, both on a theoretic and on an implementational level

Tessellations and Pattern Formation in Plant Growth and Development

The shoot apical meristem (SAM) is a dome-shaped collection of cells at the apex of growing plants from which all above-ground tissue ultimately derives. In Arabidopsis thaliana (thale cress), a small flowering weed of the Brassicaceae family (related to mustard and cabbage), the SAM typically contains some three to five hundred cells that range from five to ten microns in diameter. These cells are organized into several distinct zones that maintain their topological and functional relationships throughout the life of the plant. As the plant grows, organs (primordia) form on its surface flanks in a phyllotactic pattern that develop into new shoots, leaves, and flowers. Cross-sections through the meristem reveal a pattern of polygonal tessellation that is suggestive of Voronoi diagrams derived from the centroids of cellular nuclei. In this chapter we explore some of the properties of these patterns within the meristem and explore the applicability of simple, standard mathematical models of their geometry.Comment: Originally presented at: "The World is a Jigsaw: Tessellations in the Sciences," Lorentz Center, Leiden, The Netherlands, March 200

On the dependence of the leak-rate of seals on the skewness of the surface height probability distribution

Seals are extremely useful devices to prevent fluid leakage. We present experimental result which show that the leak-rate of seals depend sensitively on the skewness in the height probability distribution. The experimental data are analyzed using the critical-junction theory. We show that using the top-power spectrum result in good agreement between theory and experiment.Comment: 5 pages, 9 figure

Detecting Determinacy in Prolog Programs: 22nd International Conference, ICLP 2006, Seattle, WA, USA, August 17-20, 2006. Proceedings

In program development it is useful to know that a call to a Prolog program will not inadvertently leave a choice-point on the stack. Determinacy inference has been proposed for solving this problem yet the analysis was found to be wanting in that it could not infer determinacy conditions for programs that contained cuts or applied certain tests to select a clause. This paper shows how to remedy these serious deficiencies. It also addresses the problem of identifying those predicates which can be rewritten in a more deterministic fashion. To this end, a radically new form of determinacy inference is introduced, which is founded on ideas in ccp, that is capable of reasoning about the way bindings imposed by a rightmost goal can make a leftmost goal deterministic

Myogenin Regulates Exercise Capacity and Skeletal Muscle Metabolism in the Adult Mouse

Although skeletal muscle metabolism is a well-studied physiological process, little is known about how it is regulated at the transcriptional level. The myogenic transcription factor myogenin is required for skeletal muscle development during embryonic and fetal life, but myogenin's role in adult skeletal muscle is unclear. We sought to determine myogenin's function in adult muscle metabolism. A Myog conditional allele and Cre-ER transgene were used to delete Myog in adult mice. Mice were analyzed for exercise capacity by involuntary treadmill running. To assess oxidative and glycolytic metabolism, we performed indirect calorimetry, monitored blood glucose and lactate levels, and performed histochemical analyses on muscle fibers. Surprisingly, we found that Myog-deleted mice performed significantly better than controls in high- and low-intensity treadmill running. This enhanced exercise capacity was due to more efficient oxidative metabolism during low- and high-intensity exercise and more efficient glycolytic metabolism during high-intensity exercise. Furthermore, Myog-deleted mice had an enhanced response to long-term voluntary exercise training on running wheels. We identified several candidate genes whose expression was altered in exercise-stressed muscle of mice lacking myogenin. The results suggest that myogenin plays a critical role as a high-level transcriptional regulator to control the energy balance between aerobic and anaerobic metabolism in adult skeletal muscle

Homeomorphic Embedding for Online Termination of Symbolic Methods

Well-quasi orders in general, and homeomorphic embedding in particular, have gained popularity to ensure the termination of techniques for program analysis, specialisation, transformation, and verification. In this paper we survey and discuss this use of homeomorphic embedding and clarify the advantages of such an approach over one using well-founded orders. We also discuss various extensions of the homeomorphic embedding relation. We conclude with a study of homeomorphic embedding in the context of metaprogramming, presenting some new (positive and negative) results and open problems

Safe and complete contig assembly via omnitigs

Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be safely reported from $G$ as contigs? In this paper we finally answer this question, and also give a polynomial time algorithm to find them. Our experiments show that these strings, which we call omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201

Specializing Interpreters using Offline Partial Deduction

We present the latest version of the Logen partial evaluation system for logic programs. In particular we present new binding-types, and show how they can be used to effectively specialise a wide variety of interpreters.We show how to achieve Jones-optimality in a systematic way for several interpreters. Finally, we present and specialise a non-trivial interpreter for a small functional programming language. Experimental results are also presented, highlighting that the Logen system can be a good basis for generating compilers for high-level languages

Alignment between PIN1 Polarity and Microtubule Orientation in the Shoot Apical Meristem Reveals a Tight Coupling between Morphogenesis and Auxin Transport

Morphogenesis during multicellular development is regulated by intercellular signaling molecules as well as by the mechanical properties of individual cells. In particular, normal patterns of organogenesis in plants require coordination between growth direction and growth magnitude. How this is achieved remains unclear. Here we show that in Arabidopsis thaliana, auxin patterning and cellular growth are linked through a correlated pattern of auxin efflux carrier localization and cortical microtubule orientation. Our experiments reveal that both PIN1 localization and microtubule array orientation are likely to respond to a shared upstream regulator that appears to be biomechanical in nature. Lastly, through mathematical modeling we show that such a biophysical coupling could mediate the feedback loop between auxin and its transport that underlies plant phyllotaxis

Effects of acute fatigue on the volitional and magnetically-evoked electromechanical delay of the knee flexors in males and females

Neuromuscular performance capabilities, including those measured by evoked responses, may be adversely affected by fatigue; however, the capability of the neuromuscular system to initiate muscle force rapidly under these circumstances is yet to be established. Sex-differences in the acute responses of neuromuscular performance to exercise stress may be linked to evidence that females are much more vulnerable to ACL injury than males. Optimal functioning of the knee flexors is paramount to the dynamic stabilisation of the knee joint, therefore the aim of this investigation was to examine the effects of acute maximal intensity fatiguing exercise on the voluntary and magnetically-evoked electromechanical delay in the knee flexors of males and females. Knee flexor volitional and magnetically-evoked neuromuscular performance was assessed in seven male and nine females prior to and immediately after: (i) an intervention condition comprising a fatigue trial of 30-seconds maximal static exercise of the knee flexors, (ii) a control condition consisting of no exercise. The results showed that the fatigue intervention was associated with a substantive reduction in volitional peak force (PFV) that was greater in males compared to females (15.0%, 10.2%, respectively, p < 0.01) and impairment to volitional electromechanical delay (EMDV) in females exclusively (19.3%, p < 0.05). Similar improvements in magnetically-evoked electromechanical delay in males and females following fatigue (21%, p < 0.001), however, may suggest a vital facilitatory mechanism to overcome the effects of impaired voluntary capabilities, and a faster neuromuscular response that can be deployed during critical times to protect the joint system