An Institution of Modal Logics for Coalgebras

This paper presents a modular framework for the specification of certain inductively-defined coalgebraic types. Modal logics for coalgebras of polynomial endofunctors on the category of sets have been studied in [M. Rößiger, Coalgebras and modal logic, in: H. Reichel (Ed.), Coalgebraic Methods in Computer Science, Electronic Notes in Theoretical Computer Science, vol. 33, Elsevier Science, 2000, pp. 299–320; B. Jacobs, Many-sorted coalgebraic modal logic: a model-theoretic study, Theoretical Informatics and Applications 35(1) (2001) 31–59]. These logics are here generalised to endofunctors on categories of sorted sets, in order to allow collections of inter-related types to be specified simultaneously. The inductive nature of the coalgebraic types considered is then used to formalise semantic relationships between different types, and to define translations between the associated logics. The resulting logical framework is shown to be an institution, whose specifications and specification morphisms admit final and respectively cofree models

Generalized Macdonald-Ruijsenaars systems

We consider the polynomial representation of Double Affine Hecke Algebras (DAHAs) and construct its submodules as ideals of functions vanishing on the special collections of affine planes. This generalizes certain results of Kasatani in types A_n, (C_n^\vee,C_n). We obtain commutative algebras of difference operators given by the action of invariant combinations of Cherednik-Dunkl operators in the corresponding quotient modules of the polynomial representation. This gives known and new generalized Macdonald-Ruijsenaars systems. Thus in the cases of DAHAs of types A_n and (C_n^\vee,C_n) we derive Chalykh-Sergeev-Veselov operators and a generalization of the Koornwinder operator respectively, together with complete sets of quantum integrals in the explicit form

Assembling and enriching digital library collections

People who create digital libraries need to gather together the raw material, add metadata as necessary, and design and build new collections. This paper sets out the requirements for these tasks and describes a new tool that supports them interactively, making it easy for users to create their own collections from electronic files of all types. The process involves selecting documents for inclusion, coming up with a suitable metadata set, assigning metadata to each document or group of documents, designing the form of the collection in terms of document formats, searchable indexes, and browsing facilities, building the necessary indexes and data structures, and putting the collection in place for others to use. Moreover, different situations require different workflows, and the system must be flexible enough to cope with these demands. Although the tool is specific to the Greenstone digital library software, the underlying ideas should prove useful in more general contexts

Interfacing the Collection

The digital age has led to the advent of electronic collections with millions or even billions of items. This paper examines the types of interfaces that are emerging for large-scale collections, specifically addressing what a large collection looks like online and how it can be managed by users.  In examining these questions, we propose some features that we feel are universally desirable in interfaces to collections.  Overall, there appear to be two sets of features that help users effectively use and sort online content: tools to view, organize and navigate collections; and tools to customize and manage user-created sub-collections

SPPADBASE: the first on-line searchable database of PCR primers for phytopathogenic fungi

The fast and unambiguous identification of microbial pathogens affecting plants or plant products is an essential prerequisite for obtaining high-quality and safe production. Ecologically friendly practice of the modern agriculture requires the adoption of diagnostic techniques able to detect minimum inoculum levels of pathogens in soil, seeds, transplants or crops, to limit the raise of epidemics and to address the adoption of rational and efficient control means. Moreover, there is an increasing public and official awareness of the potential threat of bio-terrorism directed against food and agriculture (Monke, 2004). Rapid detection techniques for bioweapon agents are a critical need for the first-responder community. Among the nucleic acid-based diagnostic techniques, those involving the Polymerase Chain Reaction (PCR; Mullis and Faloona, 1987) are the most suited for early detection of phytopathogenic agents, due to their high sensitivity and the potential for automation. Many sequence source types could be selected and used as target for specific primer design. These may include, for instance, Random Amplified Polymorphic DNAs (Williams et al., 1990; Welsh and McClelland, 1990), internal transcribed spacer (ITS) regions of the ribosomal RNA genes (White et al., 1990) or other specific gene sequences. Primer sets can be designed to target specificity at the genus, species, or physiological race level, to distinguish a particular pathogen from closely related organisms. A common and tedious task for researchers and technicians is to search for and retrieve bibliographic references of published and validated specific primer sets for a given pathogen querying the Internet, abstract collections and monthly journals’ tables of contents. Very few examples of specific primer set collections for phytopathogenic agents have been released: a summary of primers for the diagnostic characterization of phytopathogenic bacteria seems to be the only one printed so far (Louws et al., 1999). Moreover, among 719 molecular biology databases publicly available recorded by Galperin (2006) or among the 2470 BMC biomedical databases catalog available at http://databases.biomedcentral.com/, no online repository of primer sets of this kind is accessible. To overcome this lack of information, we released the first online searchable database of primer sets useful for the detection and identification of plant pathogenic fungi

Using Kinds to Represent Heterogeneous Collections in a Static Type System (Extended Abstract)

We consider the problem of representing heterogeneous collections of objects in a typed polymorphic programming language in such a way that common properties of members of a collection, such as having commonly named field with a common type can be expressed in the type system. The use of such collections is widespread in object-oriented and database programming and has so far been achieved in statically typed systems only through the use of a single dynamic type, which effectively hides all the structure of a value. In this paper we exploit a system of types and kinds (sets of types) to represent dynamic values with some known properties. The type system is shown to be sound and to have a complete type inference algorithm

Seriation, Superposition, and Interdigitation: a History of Americanist Graphic Depictions of Culture Change

Histories of Americanist archaeology regularly confuse frequency seriation with a technique for measuring the passage of time based on superposition - percentage stratigraphy - and fail to mention interdigitation as an important component of some percentage-stratigraphic studies. Frequency seriation involves the arrangement of collections so that each artifact type displays a unimodal frequency distribution, but the direction of time\u27s flow must be determined from independent evidence. Percentage stratigraphy plots the fluctuating frequencies of types, but the order of collections is based on their superposition, which in turn illustrates the direction of time\u27s flow. Interdigitation involves the integration of sets of percentage-stratigraphy data from different horizontal proveniences under the rules that (1) the order of superposed collections cannot be reversed and (2) each type must display a unimodal frequency distribution. Ceramic stratigraphy is similar to occurrence seriation, as both focus on the presence-absence of types with limited temporal distributions - index fossils - but the former uses the superposed positions of types to indicate the direction of time\u27s flow, whereas occurrence seriation does not