On the Disambiguation of Weighted Automata

We present a disambiguation algorithm for weighted automata. The algorithm admits two main stages: a pre-disambiguation stage followed by a transition removal stage. We give a detailed description of the algorithm and the proof of its correctness. The algorithm is not applicable to all weighted automata but we prove sufficient conditions for its applicability in the case of the tropical semiring by introducing the *weak twins property*. In particular, the algorithm can be used with all acyclic weighted automata, relevant to applications. While disambiguation can sometimes be achieved using determinization, our disambiguation algorithm in some cases can return a result that is exponentially smaller than any equivalent deterministic automaton. We also present some empirical evidence of the space benefits of disambiguation over determinization in speech recognition and machine translation applications

Off-diagonal impedance in amorphous wires and application to linear magnetic sensors

The magnetic-field behaviour of the off-diagonal impedance in Co-based amorphous wires is investigated under the condition of sinusoidal (50 MHz) and pulsed (5 ns rising time) current excitations. For comparison, the field characteristics of the diagonal impedance are measured as well. In general, when an alternating current is applied to a magnetic wire the voltage signal is generated not only across the wire but also in the coil mounted on it. These voltages are related with the diagonal and off-diagonal impedances, respectively. It is demonstrated that these impedances have a different behaviour as a function of axial magnetic field: the former is symmetrical and the latter is antisymmetrical with a near linear portion within a certain field interval. In the case of the off-diagonal response, the dc bias current eliminating circular domains is necessary. The pulsed excitation that combines both high and low frequency harmonics produces the off-diagonal voltage response without additional bias current or field. This suits ideal for a practical sensor circuit design. The principles of operation of a linear magnetic sensor based on C-MOS transistor circuit are discussed.Comment: Accepted to IEEE Trans. Magn. (2004

Containment and equivalence of weighted automata: Probabilistic and max-plus cases

This paper surveys some results regarding decision problems for probabilistic and max-plus automata, such as containment and equivalence. Probabilistic and max-plus automata are part of the general family of weighted automata, whose semantics are maps from words to real values. Given two weighted automata, the equivalence problem asks whether their semantics are the same, and the containment problem whether one is point-wise smaller than the other one. These problems have been studied intensively and this paper will review some techniques used to show (un)decidability and state a list of open questions that still remain

Vibration and buckling of thin-walled composite I-beams with arbitrary lay-ups under axial loads and end moments

A finite element model with seven degrees of freedom per node is developed to study vibration and buckling of thin-walled composite I-beams with arbitrary lay-ups under constant axial loads and equal end moments. This model is based on the classical lamination theory, and accounts for all the structural coupling coming from material anisotropy. The governing differential equations are derived from the Hamilton’s principle. Numerical results are obtained for thin-walled composite I-beams to investigate the effects of axial force, bending moment and fiber orientation on the buckling moments, natural frequencies, and corresponding vibration mode shapes as well as axial-moment-frequency interaction curves

Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

Non-simply-laced Lie algebras via F theory strings

In order to describe the appearance in F theory of the non--simply--laced Lie algebras, we use the representation of symmetry enhancements by means of string junctions. After an introduction to the techniques used to describe symmetry enhancement, that is algebraic geometry, BPS states analysis and string junctions, we concentrate on the latter. We give an explicit description of the folding of D_{2n} to B_n of the folding of E_6 to F_4 and that of D_4 to G_2 in terms of junctions and Jordan strings. We also discuss the case of C_n, but we are unable in this case to provide a string interpretation.Comment: 24 pages, 3 figure

Weak ferromagnetism with very large canting in a chiral lattice: (pyrimidine)2FeCl2

The transition metal coordination compound (pyrimidine)2FeCl2 crystallizes in a chiral lattice, space group I 4_1 2 2 (or I4_3 2 2). Combined magnetization, Mossbauer spectroscopy and powder neutron diffraction studies reveal that it is a canted antiferromagnet below T_N = 6.4 K with an unusually large canting of the magnetic moments of 14 deg. from their general antiferromagnetic alignment, one of the largest reported to date. This results in weak ferromagnetism with a ferromagnetic component of 1 mu_B. The large canting is due to the interplay between the antiferromagnetic exchange interaction and the local single-ion anisotropy in the chiral lattice. The magnetically ordered structure of (pyrimidine)2FeCl2, however, is not chiral. The implications of these findings for the search of molecule based materials exhibiting chiral magnetic ordering is discussed.Comment: 6 pages, 5 figure

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with arXiv:1103.434

Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation

Background Social amoebae are lower eukaryotes that inhabit the soil. They are characterized by the construction of a starvation-induced multicellular fruiting body with a spore ball and supportive stalk. In most species, the stalk is filled with motile stalk cells, as represented by the model organism Dictyostelium discoideum, whose developmental mechanisms have been well characterized. However, in the genus Acytostelium, the stalk is acellular and all aggregated cells become spores. Phylogenetic analyses have shown that it is not an ancestral genus but has lost the ability to undergo cell differentiation. Results We performed genome and transcriptome analyses of Acytostelium subglobosum and compared our findings to other available dictyostelid genome data. Although A. subglobosum adopts a qualitatively different developmental program from other dictyostelids, its gene repertoire was largely conserved. Yet, families of polyketide synthase and extracellular matrix proteins have not expanded and a serine protease and ABC transporter B family gene, tagA, and a few other developmental genes are missing in the A. subglobosum lineage. Temporal gene expression patterns are astonishingly dissimilar from those of D. discoideum, and only a limited fraction of the ortholog pairs shared the same expression patterns, so that some signaling cascades for development seem to be disabled in A. subglobosum. Conclusions The absence of the ability to undergo cell differentiation in Acytostelium is accompanied by a small change in coding potential and extensive alterations in gene expression patterns

Pregnane X receptor (PXR) activation: A mechanism for neuroprotection in a mouse model of Niemann-Pick C disease

Niemann–Pick type C1 (NPC1) disease is a fatal neurodegenerative disease characterized by neuronal lipid storage and progressive Purkinje cell loss in the cerebellum. We investigated whether therapeutic approaches to bypass the cholesterol trafficking defect in NPC1 disease might delay disease progression in the npc1−/− mouse model. We show that the neurosteroid allopregnanolone (ALLO) and T0901317, a synthetic oxysterol ligand, act in concert to delay onset of neurological symptoms and prolong the lifespan of npc1−/− mice. ALLO and T0901317 therapy preserved Purkinje cells, suppressed cerebellar expression of microglial-associated genes and inflammatory mediators, and reduced infiltration of activated microglia in the cerebellar tissue. To establish whether the mechanism of neuroprotection in npc1−/− mice involves GABAA receptor activation, we compared treatment of natural ALLO and ent-ALLO, a stereoisomer that has identical physical properties of natural ALLO but is not a GABAA receptor agonist. ent-ALLO provided identical functional and survival benefits as natural ALLO in npc1−/− mice, strongly supporting a GABAA receptor-independent mechanism for ALLO action. On the other hand, the efficacy of ALLO, ent-ALLO, and T0901317 therapy correlated with the ability of these compounds to activate pregnane X receptor-dependent pathways in vivo. These findings suggest that treatment with pregnane X receptor ligands may be useful clinically in delaying the progressive neurodegeneration in human NPC disease