Leaf anatomical and molecular studies in Bulbophyllum section Micranthae (Orchidaceae) and their implications for systematics

Bulbophyllum section Micranthae comprises 12 species of rupicolous or epiphytic orchids occurring in forests or in open rocky fields in Cerrado/Atlantic Forest ecotones throughout South America. We examined the leaf anatomy of 14 species and compared them with molecular data (nrITS) in phylogenetic analyses. The leaves of Bulbophyllum section Micranthae are characterised by uniseriate epidermis, with periclinal external cell wall thicker than the internal, presence of epicuticular wax, stomata present only on the abaxial surface with suprastomatic chambers, and collateral vascular bundles associated with sclerenchyma fibres. Some of these characters are shared with other rupicolous Orchidaceae species, demonstrating adaptive convergence in xeromorphic habitats. We found some anatomical characteristics with phylogenetic value. Bulbophyllum section Micranthae can be separated into two lineages: those with needle-like leaves, or flat leaves. The analyses show that anatomical characters as well as molecular data may contribute to the development of phylogenetic hypotheses. © 2013 Botanical Society of Sao Paulo.

Algebraic Techniques in Coding Theory: Entropy Vectors, Frames, and Constrained Coding

The study of codes, classically motivated by the need to communicate information reliably in the presence of error, has found new life in fields as diverse as network communication, distributed storage of data, and even has connections to the design of linear measurements used in compressive sensing. But in all contexts, a code typically involves exploiting the algebraic or geometric structure underlying an application. In this thesis, we examine several problems in coding theory, and try to gain some insight into the algebraic structure behind them.

The first is the study of the entropy region - the space of all possible vectors of joint entropies which can arise from a set of discrete random variables. Understanding this region is essentially the key to optimizing network codes for a given network. To this end, we employ a group-theoretic method of constructing random variables producing so-called "group-characterizable" entropy vectors, which are capable of approximating any point in the entropy region. We show how small groups can be used to produce entropy vectors which violate the Ingleton inequality, a fundamental bound on entropy vectors arising from the random variables involved in linear network codes. We discuss the suitability of these groups to design codes for networks which could potentially outperform linear coding.

The second topic we discuss is the design of frames with low coherence, closely related to finding spherical codes in which the codewords are unit vectors spaced out around the unit sphere so as to minimize the magnitudes of their mutual inner products. We show how to build frames by selecting a cleverly chosen set of representations of a finite group to produce a "group code" as described by Slepian decades ago. We go on to reinterpret our method as selecting a subset of rows of a group Fourier matrix, allowing us to study and bound our frames' coherences using character theory. We discuss the usefulness of our frames in sparse signal recovery using linear measurements.

The final problem we investigate is that of coding with constraints, most recently motivated by the demand for ways to encode large amounts of data using error-correcting codes so that any small loss can be recovered from a small set of surviving data. Most often, this involves using a systematic linear error-correcting code in which each parity symbol is constrained to be a function of some subset of the message symbols. We derive bounds on the minimum distance of such a code based on its constraints, and characterize when these bounds can be achieved using subcodes of Reed-Solomon codes.

The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda

The complete mitochondrial (mt) genome sequence of Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda) was determined; a circular molecule of 15,783 bp in length. The gene content and arrangement are consistent with the pancrustacean ground pattern. The mt control region of O. oratoria is characterized by no GA-block near the 3' end and different position of [TA(A)]n-blocks compared with other reported Stomatopoda species. The sequence of the second hairpin structure is relative conserved which suggests this region may be a synapomorphic character for the Stomatopoda. In addition, a relative large intergenic spacer (101 bp) with higher A + T content than that in control region was identified between the tRNA(Glu) and tRNA(Phe) genes. Phylogenetic analyses based on the current dataset of complete mt genomes strongly support the Stomatopoda is closely related to Euphausiacea. They in turn cluster with Penaeoidea and Caridea clades while other decapods form a separate group, which rejects the monophyly of Decapoda. This challenges the suitability of Stomatopoda as an outgroup of Decapoda in phylogenetic analyses. The basal position of Stomatopoda within Eumalacostraca according to the morphological characters is also questioned. (C) 2010 Elsevier Inc. All rights reserved.

A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data

Mark Pagel, Andrew Meade (2004). A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Systematic Biology, 53(4), 571-581. RAE2008

Gröbner basis techniques for certain problems in coding and systems theory

There is much common ground between the areas of coding theory and systems theory. Fitzpatrick has shown that a Göbner basis approach leads to efficient algorithms in the decoding of Reed-Solomon codes and in scalar interpolation and partial realization. This thesis simultaneously generalizes and simplifies that approach and presents applications to discrete-time modeling, multivariable interpolation and list decoding. Gröbner basis theory has come into its own in the context of software and algorithm development. By generalizing the concept of polynomial degree, term orders are provided for multivariable polynomial rings and free modules over polynomial rings. The orders are not, in general, unique and this adds, in no small way, to the power and flexibility of the technique. As well as being generating sets for ideals or modules, Gröbner bases always contain a element which is minimal with respect tot the corresponding term order. Central to this thesis is a general algorithm, valid for any term order, that produces a Gröbner basis for the solution module (or ideal) of elements satisfying a sequence of generalized congruences. These congruences, based on shifts and homomorphisms, are applicable to a wide variety of problems, including key equations and interpolations. At the core of the algorithm is an incremental step. Iterating this step lends a recursive/iterative character to the algorithm. As a consequence, not all of the input to the algorithm need be available from the start and different "paths" can be taken to reach the final solution. The existence of a suitable chain of modules satisfying the criteria of the incremental step is a prerequisite for applying the algorithm.

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites "pattern-heterogeneity" to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate- variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program.

Coding behavioural data for cladistic analysis: using dynamic homology without parsimony

Many of the controversies around the concept of homology rest on the subjectivity inherent to primary homology propositions. Dynamic homology partially solves this problem, but there has been up to now scant application of it outside of the molecular domain. This is probably because morphological and behavioural characters are rich in properties, connections and qualities, so that there is less space for conflicting character delimitations. Here we present a new method for the direct optimization of behavioural data, a method that relies on the richness of this database to delimit the characters, and on dynamic procedures to establish character state identity. We use between-species congruence in the data matrix and topological stability to choose the best cladogram. We test the methodology using sequences of predatory behaviour in a group of spiders that evolved the highly modified predatory technique of spitting glue onto prey. The cladogram recovered is fully compatible with previous analyses in the literature, and thus the method seems consistent. Besides the advantage of enhanced objectivity in character proposition, the new procedure allows the use of complex, context-dependent behavioural characters in an evolutionary framework, an important step towards the practical integration of the evolutionary and ecological perspectives on diversity. (C) The Willi Hennig Society 2010.

Goma curriculum, a character education paradigm: Composing a text for shaping classroom character culture

The written text, and approaches to reading it, serves well as an analogy for the classroom space as a "text" that teachers are able to compose; and students are able to read, interpret meaning(s) of, and make responses to and about (Rosenblatt, 1988). Researchers point to ways in which the classroom can be conceptualized as a text to be evoked, experienced, and read (Freire & Macedo, 1987; Powell, 2009; Rosenblatt, 1988; Spears-Bunton & Powell, 2009).^ The present study analyzed secondary data including: 10 transcripts of teacher talks and six self-reports retrieved from the program evaluation archives of DOR Foundation. The data described six teachers' classroom experiences subsequent to professional development centered on Goma character education curriculum that was used during a summer youth program located in South Georgia. Goma, an acronym that stands for Goal, Objective, Method, and Attitude, is a character education paradigm derived from The Inclusive Community Building Ellison Model, the theoretical framework used for this study. The Model identifies conflict resolution as one of its five foci (Hunt, Howard, & Rice, 1998). Hunt (2006) conceived Goma as part of a 7-Step unitary process, also named the 7-Step pathway, to demonstrate how conflict resolution is accomplished within a variety of contexts.^ Analysis of the data involved: (a) a priori coding of teacher talks transcripts using the components of the Goma 7-Step pathway as coding categories, (b) emergent coding of teacher talks transcripts for the types of experiences teachers evidenced, and (c) emergent coding of teachers' self-reports for categories of teachers' instructional activities. Results of the study showed positive influence of Goma curriculum on participating teachers and their instructional practices. Teachers were shown to have had cognitive, instructional, emotional, and social experiences that were most evident when they reported changes in their attitudes toward their students, themselves, and their instructional practices. The present study provided implications for classroom teachers wherein all aspects of teachers' instructional practices can be guided by principles of positive character; and can be used to help compose the kinds of "texts" that may likely contribute to a classroom character culture.^

Goma Curriculum, A Character Education Paradigm: Composing a Text for Shaping Classroom Character Culture

The written text, and approaches to reading it, serves well as an analogy for the classroom space as a “text” that teachers are able to compose; and students are able to read, interpret meaning(s) of, and make responses to and about (Rosenblatt, 1988). Researchers point to ways in which the classroom can be conceptualized as a text to be evoked, experienced, and read (Freire & Macedo, 1987; Powell, 2009; Rosenblatt, 1988; Spears-Bunton & Powell, 2009). The present study analyzed secondary data including: 10 transcripts of teacher talks and six self-reports retrieved from the program evaluation archives of DOR Foundation. The data described six teachers’ classroom experiences subsequent to professional development centered on Goma character education curriculum that was used during a summer youth program located in South Georgia. Goma, an acronym that stands for Goal, Objective, Method, and Attitude, is a character education paradigm derived from The Inclusive Community Building Ellison Model, the theoretical framework used for this study. The Model identifies conflict resolution as one of its five foci (Hunt, Howard, & Rice, 1998). Hunt (2006) conceived Goma as part of a 7-Step unitary process, also named the 7-Step pathway, to demonstrate how conflict resolution is accomplished within a variety of contexts. Analysis of the data involved: (a) a priori coding of teacher talks transcripts using the components of the Goma 7-Step pathway as coding categories, (b) emergent coding of teacher talks transcripts for the types of experiences teachers evidenced, and (c) emergent coding of teachers’ self-reports for categories of teachers’ instructional activities. Results of the study showed positive influence of Goma curriculum on participating teachers and their instructional practices. Teachers were shown to have had cognitive, instructional, emotional, and social experiences that were most evident when they reported changes in their attitudes toward their students, themselves, and their instructional practices. The present study provided implications for classroom teachers wherein all aspects of teachers’ instructional practices can be guided by principles of positive character; and can be used to help compose the kinds of “texts” that may likely contribute to a classroom character culture.