Metalevel algorithms for variant satisfiability

Variant satisfiability is a theory-generic algorithm to decide quantifier-free satisfiability in an initial algebra when its corresponding theory has the finite variant property and its constructors satisfy a compactness condition. This paper: (i) gives a precise definition of several meta-level sub-algorithms needed for variant satisfiability; (ii) proves them correct; and (iii) presents a reflective implementation in Maude 2.7 of variant satisfiability using these sub-algorithms.NSF CNS 13-19109Ope

From Parent to Gamete: Vertical Transmission of Symbiodinium (Dinophyceae) ITS2 Sequence Assemblages in the Reef Building Coral Montipora capitata

Parental effects are ubiquitous in nature and in many organisms play a particularly critical role in the transfer of symbionts across generations; however, their influence and relative importance in the marine environment has rarely been considered. Coral reefs are biologically diverse and productive marine ecosystems, whose success is framed by symbiosis between reef-building corals and unicellular dinoflagellates in the genus Symbiodinium. Many corals produce aposymbiotic larvae that are infected by Symbiodinium from the environment (horizontal transmission), which allows for the acquisition of new endosymbionts (different from their parents) each generation. In the remaining species, Symbiodinium are transmitted directly from parent to offspring via eggs (vertical transmission), a mechanism that perpetuates the relationship between some or all of the Symbiodinium diversity found in the parent through multiple generations. Here we examine vertical transmission in the Hawaiian coral Montipora capitata by comparing the Symbiodinium ITS2 sequence assemblages in parent colonies and the eggs they produce. Parental effects on sequence assemblages in eggs are explored in the context of the coral genotype, colony morphology, and the environment of parent colonies. Our results indicate that ITS2 sequence assemblages in eggs are generally similar to their parents, and patterns in parental assemblages are different, and reflect environmental conditions, but not colony morphology or coral genotype. We conclude that eggs released by parent colonies during mass spawning events are seeded with different ITS2 sequence assemblages, which encompass phylogenetic variability that may have profound implications for the development, settlement and survival of coral offspring

Schemas for Unordered XML on a DIME

We investigate schema languages for unordered XML having no relative order among siblings. First, we propose unordered regular expressions (UREs), essentially regular expressions with unordered concatenation instead of standard concatenation, that define languages of unordered words to model the allowed content of a node (i.e., collections of the labels of children). However, unrestricted UREs are computationally too expensive as we show the intractability of two fundamental decision problems for UREs: membership of an unordered word to the language of a URE and containment of two UREs. Consequently, we propose a practical and tractable restriction of UREs, disjunctive interval multiplicity expressions (DIMEs). Next, we employ DIMEs to define languages of unordered trees and propose two schema languages: disjunctive interval multiplicity schema (DIMS), and its restriction, disjunction-free interval multiplicity schema (IMS). We study the complexity of the following static analysis problems: schema satisfiability, membership of a tree to the language of a schema, schema containment, as well as twig query satisfiability, implication, and containment in the presence of schema. Finally, we study the expressive power of the proposed schema languages and compare them with yardstick languages of unordered trees (FO, MSO, and Presburger constraints) and DTDs under commutative closure. Our results show that the proposed schema languages are capable of expressing many practical languages of unordered trees and enjoy desirable computational properties.Comment: Theory of Computing System

Unification modulo Lists with Reverse, Relation with Certain Word Equations

International audienceDecision procedures for various list theories have been investigated in the literature with applications to automated verification. Here we show that the unifiability problem for some list theories with a \emph{reverse} operator is NP-complete. We also give a unifiability algorithm for the case where the theories are extended with a \emph{length} operator on lists

Improved Resolution of Reef-Coral Endosymbiont (Symbiodinium) Species Diversity, Ecology, and Evolution through psbA Non-Coding Region Genotyping

Ribosomal DNA sequence data abounds from numerous studies on the dinoflagellate endosymbionts of corals, and yet the multi-copy nature and intragenomic variability of rRNA genes and spacers confound interpretations of symbiont diversity and ecology. Making consistent sense of extensive sequence variation in a meaningful ecological and evolutionary context would benefit from the application of additional genetic markers. Sequences of the non-coding region of the plastid psbA minicircle (psbAncr) were used to independently examine symbiont genotypic and species diversity found within and between colonies of Hawaiian reef corals in the genus Montipora. A single psbAncr haplotype was recovered in most samples through direct sequencing (∼80–90%) and members of the same internal transcribed spacer region 2 (ITS2) type were phylogenetically differentiated from other ITS2 types by substantial psbAncr sequence divergence. The repeated sequencing of bacterially-cloned fragments of psbAncr from samples and clonal cultures often recovered a single numerically common haplotype accompanied by rare, highly-similar, sequence variants. When sequence artifacts of cloning and intragenomic variation are factored out, these data indicate that most colonies harbored one dominant Symbiodinium genotype. The cloning and sequencing of ITS2 DNA amplified from these same samples recovered numerically abundant variants (that are diagnostic of distinct Symbiodinium lineages), but also generated a large amount of sequences comprising PCR/cloning artifacts combined with ancestral and/or rare variants that, if incorporated into phylogenetic reconstructions, confound how small sequence differences are interpreted. Finally, psbAncr sequence data from a broad sampling of Symbiodinium diversity obtained from various corals throughout the Indo-Pacific were concordant with ITS lineage membership (defined by denaturing gradient gel electrophoresis screening), yet exhibited substantially greater sequence divergence and revealed strong phylogeographic structure corresponding to major biogeographic provinces. The detailed genetic resolution provided by psbAncr data brings further clarity to the ecology, evolution, and systematics of symbiotic dinoflagellates

Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis

<p>Abstract</p> <p>Background</p> <p>Motivated by the precarious state of the world's coral reefs, there is currently a keen interest in coral transcriptomics. By identifying changes in coral gene expression that are triggered by particular environmental stressors, we can begin to characterize coral stress responses at the molecular level, which should lead to the development of more powerful diagnostic tools for evaluating the health of corals in the field. Furthermore, the identification of genetic variants that are more or less resilient in the face of particular stressors will help us to develop more reliable prognoses for particular coral populations. Toward this end, we performed deep mRNA sequencing of the cauliflower coral, <it>Pocillopora damicornis</it>, a geographically widespread Indo-Pacific species that exhibits a great diversity of colony forms and is able to thrive in habitats subject to a wide range of human impacts. Importantly, <it>P. damicornis </it>is particularly amenable to laboratory culture. We collected specimens from three geographically isolated Hawaiian populations subjected to qualitatively different levels of human impact. We isolated RNA from colony fragments ("nubbins") exposed to four environmental stressors (heat, desiccation, peroxide, and hypo-saline conditions) or control conditions. The RNA was pooled and sequenced using the 454 platform.</p> <p>Description</p> <p>Both the raw reads (n = 1, 116, 551) and the assembled contigs (n = 70, 786; mean length = 836 nucleotides) were deposited in a new publicly available relational database called PocilloporaBase <url>http://www.PocilloporaBase.org</url>. Using BLASTX, 47.2% of the contigs were found to match a sequence in the NCBI database at an E-value threshold of ≤.001; 93.6% of those contigs with matches in the NCBI database appear to be of metazoan origin and 2.3% bacterial origin, while most of the remaining 4.1% match to other eukaryotes, including algae and amoebae.</p> <p>Conclusions</p> <p><it>P. damicornis </it>now joins the handful of coral species for which extensive transcriptomic data are publicly available. Through PocilloporaBase <url>http://www.PocilloporaBase.org</url>, one can obtain assembled contigs and raw reads and query the data according to a wide assortment of attributes including taxonomic origin, PFAM motif, KEGG pathway, and GO annotation.</p

Chimerism in Wild Adult Populations of the Broadcast Spawning Coral Acropora millepora on the Great Barrier Reef

Chimeras are organisms containing tissues or cells of two or more genetically distinct individuals, and are known to exist in at least nine phyla of protists, plants, and animals. Although widespread and common in marine invertebrates, the extent of chimerism in wild populations of reef corals is unknown.The extent of chimerism was explored within two populations of a common coral, Acropora millepora, on the Great Barrier Reef, Australia, by using up to 12 polymorphic DNA microsatellite loci. At least 2% and 5% of Magnetic Island and Pelorus Island populations of A. millepora, respectively, were found to be chimeras (3% overall), based on conservative estimates. A slightly less conservative estimate indicated that 5% of colonies in each population were chimeras. These values are likely to be vast underestimates of the true extent of chimerism, as our sampling protocol was restricted to a maximum of eight branches per colony, while most colonies consist of hundreds of branches. Genotypes within chimeric corals showed high relatedness, indicating that genetic similarity is a prerequisite for long-term acceptance of non-self genotypes within coral colonies.While some brooding corals have been shown to form genetic chimeras in their early life history stages under experimental conditions, this study provides the first genetic evidence of the occurrence of coral chimeras in the wild and of chimerism in a broadcast spawning species. We hypothesize that chimerism is more widespread in corals than previously thought, and suggest that this has important implications for their resilience, potentially enhancing their capacity to compete for space and respond to stressors such as pathogen infection

Internet-based self-help treatment for depression in multiple sclerosis: study protocol of a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Depression in MS patients is frequent but often not treated adequately. An important underlying factor may be physical limitations that preclude face-to-face contact. Internet-based treatment showed to be effective for depressive symptoms in general and could thus be a promising tool for treatment in MS.</p> <p>Methods/design</p> <p>Here, we present a study protocol to investigate the effectiveness of a 5 week Internet-based self-help problem solving treatment (PST) for depressive symptoms in MS patients in a randomized controlled trial. We aim to include 166 MS patients with moderate to severe depressive symptoms who will be randomly assigned to an Internet-based intervention (with or without supportive text-messages) or waiting list control group. The primary outcome is the change in depressive symptoms defined by a change in the sum score on the Beck Depression Inventory (BDI-II). Secondary outcomes will include measures of anxiety, fatigue, cognitive functioning, physical and psychological impact of MS, quality of life, problem solving skills, social support, mastery, satisfaction and compliance rate. Assessments will take place at baseline (T0), within a week after the intervention (T1), at four months (T2) and at ten months follow-up (T3: only the intervention group). The control group will be measured at the same moments in time. Analysis will be based on the intention-to-treat principle.</p> <p>Discussion</p> <p>If shown to be effective, Internet-based PST will offer new possibilities to reach and treat MS patients with depressive symptoms and to improve the quality of care.</p> <p>Trial Registration</p> <p>The Dutch Cochrane Center, NTR2772</p

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente