A cause for consilience: Utilizing multiple genomic data types to resolve problematic nodes within Arthropoda and Ecdysozoa

A major turning point in the study of metazoan evolution was the recognition of the existence of the Ecdysozoa in 1997. This is a group of eight animal phyla (Nematoda, Nematomorpha, Loricifera, Kinorhyncha, Priapulida, Tardigrada, Onychophora and Arthropoda). Ecdysozoa is the most specious clade of animals to ever exist and the relationships among its eight phyla are still heatedly debated. Similarly also the relationships among the three sub-phyla (Chelicerata, Pancrustacea and Myriapoda) within the most important ecdysozoan phylum (the Arthropoda) are still debated. Indeed, the two major problems in ecdysozoan phylogeny refer to the relationships of Myriapoda within Arthropoda, and of Tardigrada within Ecdysozoa. Difficulties in ecdysozoan relationships resides in lineages characterized by rapid, deep divergences and subsequently long periods of divergent evolution. Phylogenetic signal to resolve the relationships of these lineages is diluted, increasing the likelihood of recovery of phylogenetic artifacts. In an attempt to resolve the relationships within Ecdysozoa, consilience of three independent phylogenetic data sets was investigated. EST and rRNA and microRNA (miRNA) data were sampled across all major ecdysozoan phyla. In particular, a major contribution of this thesis is the first time sequencing of miRNAs for all the panarthropod phyla. MicroRNAs are genome regulatory elements that recently emerged as a source of useful phylogenetic data (Sempere et al. 2006) because of their low homoplasy levels. The considered data sets were analysed under phylogenetic methods and models, implemented to minimize the occurrence of phylogenetic reconstruction artifacts to understand the evolution of Ecdysozoa. Analyses of independent data types recovered well supported and corroborating evidence for the monophyly of Panarthropoda (Arthropoda, Onychophora and Tardigrada), a sister group relationships between Myriapoda and Pancrustacea within Arthropoda, and the paraphyly of Cycloneuralia (Nematoda, Nematomorpha, Loricifera, Kinorhyncha and Priapulida).

A cause for consilience: Utilizing multiple genomic data types to resolve problematic nodes within Arthropoda and Ecdysozoa

A major turning point in the study of metazoan evolution was the recognition of the existence of the Ecdysozoa in 1997. This is a group of eight animal phyla (Nematoda, Nematomorpha, Loricifera, Kinorhyncha, Priapulida, Tardigrada, Onychophora and Arthropoda). Ecdysozoa is the most specious clade of animals to ever exist and the relationships among its eight phyla are still heatedly debated. Similarly also the relationships among the three sub-phyla (Chelicerata, Pancrustacea and Myriapoda) within the most important ecdysozoan phylum (the Arthropoda) are still debated. Indeed, the two major problems in ecdysozoan phylogeny refer to the relationships of Myriapoda within Arthropoda, and of Tardigrada within Ecdysozoa. Difficulties in ecdysozoan relationships resides in lineages characterized by rapid, deep divergences and subsequently long periods of divergent evolution. Phylogenetic signal to resolve the relationships of these lineages is diluted, increasing the likelihood of recovery of phylogenetic artifacts. In an attempt to resolve the relationships within Ecdysozoa, consilience of three independent phylogenetic data sets was investigated. EST and rRNA and microRNA (miRNA) data were sampled across all major ecdysozoan phyla. In particular, a major contribution of this thesis is the first time sequencing of miRNAs for all the panarthropod phyla. MicroRNAs are genome regulatory elements that recently emerged as a source of useful phylogenetic data (Sempere et al. 2006) because of their low homoplasy levels. The considered data sets were analysed under phylogenetic methods and models, implemented to minimize the occurrence of phylogenetic reconstruction artifacts to understand the evolution of Ecdysozoa. Analyses of independent data types recovered well supported and corroborating evidence for the monophyly of Panarthropoda (Arthropoda, Onychophora and Tardigrada), a sister group relationships between Myriapoda and Pancrustacea within Arthropoda, and the paraphyly of Cycloneuralia (Nematoda, Nematomorpha, Loricifera, Kinorhyncha and Priapulida).

On metric regularity of Reed-Muller codes

In this work we study metric properties of the well-known family of binary Reed-Muller codes. Let $A$ be an arbitrary subset of the Boolean cube, and $\widehat{A}$ be the metric complement of $A$ -- the set of all vectors of the Boolean cube at the maximal possible distance from $A$. If the metric complement of $\widehat{A}$ coincides with $A$, then the set $A$ is called a {\it metrically regular set}. The problem of investigating metrically regular sets appeared when studying {\it bent functions}, which have important applications in cryptography and coding theory and are also one of the earliest examples of a metrically regular set. In this work we describe metric complements and establish the metric regularity of the codes $\mathcal{RM}(0,m)$ and $\mathcal{RM}(k,m)$ for $k \geqslant m-3$. Additionally, the metric regularity of the codes $\mathcal{RM}(1,5)$ and $\mathcal{RM}(2,6)$ is proved. Combined with previous results by Tokareva N. (2012) concerning duality of affine and bent functions, this establishes the metric regularity of most Reed-Muller codes with known covering radius. It is conjectured that all Reed-Muller codes are metrically regular.Comment: 29 page

On the Sizes of DPDAs, PDAs, LBAs

Abstract There are languages A such that there is a Pushdown Automata (PDA) that recognizes A which is much smaller than any Deterministic Pushdown Automata (DPDA) that recognizes A. There are languages A such that there is a Linear Bounded Automata (Linear Space Turing Machine, henceforth LBA) that recognizes A which is much smaller than any PDA that recognizes A. There are languages A such that both A and A are recognizable by a PDA, but the PDA for A is much smaller than the PDA for A. There are languages A 1 , A 2 such that A 1 , A 2 , A 1 ∩ A 2 are recognizable by a PDA, but the PDA for A 1 and A 2 are much smaller than the PDA for A 1 ∩ A 2 . We investigate these phenomema and show that, in all these cases, the size difference is captured by a function whose Turing degree is on the second level of the arithmetic hierarchy. Our theorems lead to infinitely-often results. For example: for infinitely many n there exists a language A n such that there is a small PDA for A n , but any DPDA for A n is large. We look at cases where we can get almost-all results, though with much smaller size differences

On the Sizes of DPDAs, PDAs, LBAs

Abstract There are languages A such that there is a Pushdown Automata (PDA) that recognizes A which is much smaller than any Deterministic Pushdown Automata (DPDA) that recognizes A. There are languages A such that there is a Linear Bounded Automata (Linear Space Turing Machine, henceforth LBA) that recognizes A which is much smaller than any PDA that recognizes A. There are languages A such that both A and A are recognizable by a PDA, but the PDA for A is much smaller than the PDA for A. There are languages A 1 , A 2 such that A 1 , A 2 , A 1 ∩ A 2 are recognizable by a PDA, but the PDA for A 1 and A 2 are much smaller than the PDA for A 1 ∩ A 2 . We investigate these phenenoma and show that, in all these cases, the size difference is captured by a function whose Turing degree is on the second level of the arithmetic hierarchy. Our theorems lead to infinitely-often results. For example: for infinitely many n there exists a language A n such that there is a small PDA for A n , but any DPDA for A n is large. We look at cases where we can get almost-all results, though with much smaller size differences

VLT/VIMOS integral field spectroscopy of luminous and ultraluminous infrared galaxies: 2D kinematic properties

We present and discuss the 2D kinematic properties of the ionized gas (Halpha) in a sample of 38 local (ultra) luminous infrared galaxies [(U)LIRGs] (31 LIRGs and 7 ULIRGs) observed with VIMOS at the VLT using integral field spectroscopy. This sample covers well the less studied LIRG luminosity range and includes isolated disks, interacting systems, and mergers. The majority of the galaxies have two main kinematically distinct components. One component (i.e., narrow or systemic) extends over the whole line-emitting region and is characterized by small to intermediate velocity dispersions (i.e., sigma from 30 to 160 km s^-1). It traces the overall velocity field. The second component (broad) has in general a larger velocity dispersion (up to 320 km s^-1), mainly found in the inner regions and generally blueshifted with respect to the systemic component. Most of the objects (76%) are dominated by rotation, more relevant in LIRGs than in ULIRGs. Isolated disks, interacting galaxies, and merging systems define a sequence of increasing mean velocity dispersion, and decreasing velocity field amplitude.The LIRGs classified as isolated disks have similar velocity amplitudes but larger mean velocity dispersions (44 vs. 24 km s^-1) than local spirals, implying a larger turbulence and thicker disks. Interacting systems and mergers have values closer to those of low velocity dispersion ellipticals/lenticular galaxies (E/SOs). The (U)LIRGs classified as mergers have kinematic properties similar to those shown by the Lyman break analogs (LBAs). The dynamical masses range from \sim 0.04 m* to 1.4 m* (i.e., m* = 1.4x10^{11} Msun), with ULIRGs (M{dyn} sim 0.5 +/- 0.2 m*) being more massive than LIRGs by, on average, a factor of about 2. The mass ratio of individual pre-coalescence galaxies is <2.5 for most of the systems, confirming that most (U)LIRG mergers involve sub-m* galaxies of similar mass.Comment: 66 pages, 5 figures plus 45 figures in App. A; accepted for publication in A&

Cryptanalysis of protocols using (Simultaneous) Conjugacy Search Problem in certain Metabelian Platform Groups

There are many group-based cryptosystems in which the security relies on the difficulty of solving Conjugacy Search Problem (CSP) and Simultaneous Conjugacy Search Problem (SCSP) in their underlying platform groups. In this paper we give a cryptanalysis of these systems which use certain semidirect product of abelian groups