Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

BACKGROUND: In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. DEVELOPMENT AND TESTING OF THE ONTOLOGY: Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. RESULTS AND SIGNIFICANCE: Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.

A reified temporal logic

This paper presents a reified temporal logic for representing and reasoning about temporal and non-temporal relationships between non-temporal assertions. A clear syntax and semantics for the logic is formally provided. Three types of predicates, temporal predicates, non-temporal predicates and meta-predicates, are introduced. Terms of the proposed language are partitioned into three types, temporal terms, non-temporal terms and propositional terms. Reified propositions consist of formulae with each predicate being either a temporal predicate or a meta-predicate. Meta-predicates may take both temporal terms and propositional terms together as arguments or take propositional terms alone. A standard formula of the classical first-order language with each predicate being a non-temporal predicate taking only non-temporal terms as arguments is reified as just a propositional term. A general time ontology has been provided which can be specialized to a variety of existing temporal systems. The new logic allows one to predicate and quantify over propositional terms while according a special status of time; for example, assertions such as ‘effects cannot precede their causes’ is ensured in the logic, and some problematic temporal aspects including the delay time between events and their effects can be conveniently expressed. Applications of the logic are presented including the characterization of the negation of properties and their contextual sentences, and the expression of temporal relations between actions and effects.

Guest Editorial. Special Issue: Temporal logic in engineering

Logic-based models are thriving within artificial intelligence. A great number of new logics have been defined, and their theory investigated. Epistemic logics introduce modal operators for knowledge or belief; deontic logics are about norms, and introduce operators of deontic necessity and possibility (i.e., obligation or prohibition). And then we have a much investigated class—temporal logics—to whose application to engineering this special issue is devoted. This kind of formalism deserves increased widespread recognition and application in engineering, a domain where other kinds of temporal models (e.g., Petri nets) are by now a fairly standard part of the modelling toolbox.

[Book Review] Vardah Shiloh, Millon 'Ivri-'Arami-'Aššuri bs-Lahag Yihude Zaxo (A New Neo-Aramaic Dictionary: Jewish Dialect of Zakho). Volume I: 'alef—nun\ Volume II: samex-tav. V. Shilo (16 Ben-Gamla Street), Jerusalem 1995. Pp. xiv + 488 (Vol. I); 489-963 (Vol. II). (Modern Hebrew, Zakho Jewish Neo-Aramaic).

Review of: Vardah Shiloh, Millon 'Ivri-'Arami-'Aššuri bs-Lahag Yihude Zaxo (A New Neo-Aramaic Dictionary: Jewish Dialect of Zakho). Volume I: 'alef—nun\ Volume II: samex-tav. V. Shilo (16 Ben-Gamla Street), Jerusalem 1995. Pp. xiv + 488 (Vol. I); 489-963 (Vol. II). (Modern Hebrew, Zakho Jewish Neo-Aramaic). Hbk.

A sound and complete reified temporal logic

There are mainly two known approaches to the representation of temporal information in Computer Science: modal logic approaches (including tense logics and hybrid temporal logics) and predicate logic approaches (including temporal argument methods and reified temporal logics). On one hand, while tense logics, hybrid temporal logics and temporal argument methods enjoy formal theoretical foundations, their expressiveness has been criticised as not power enough for representing general temporal knowledge; on the other hand, although current reified temporal logics provide greater expressive power, most of them lack of complete and sound axiomatic theories. In this paper, we propose a new reified temporal logic with a clear syntax and semantics in terms of a sound and complete axiomatic formalism which retains all the expressive power of the approach of temporal reification.

[BSHM meetings] Topics in the history of financial mathematics: early commerce to chaos in modern stock markets

This account provides an overview of the study day, entitled 'Topics in the History of Financial Mathematics: Early commerce to chaos in modern stock markets,' held by the British Society for the History of Mathematics jointly with Gresham College, at Gresham College, London on 25th April 2008. The series of talks explored the development of mathematics and mathematical techniques in a commercial and financial context.

Narrating the archive and archiving narrative: the electronic book and the logic of the index

The creation of my hypermedia work Index of Love, which narrates a love story as an archive of moments, images and objects recollected, also articulated for me the potential of the book as electronic text. The book has always existed as both narrative and archive. Tables of contents and indexes allow the book to function simultaneously as linear narrative and non-linear, searchable database. The book therefore has more in common with the so-called 'new media' of the 21st century than it does with the dominant 20th century media of film, video and audiotape, whose logic and mode of distribution are resolutely linear. My thesis is that the non-linear logic of new media brings to the fore an aspect of the book - the index - whose potential for the production of narrative is only just beginning to be explored. When a reader/user accesses an electronic work, such as a website, via its menu, they simultaneously experience it as narrative and archive. The narrative journey taken is created through the menu choices made. Within the electronic book, therefore, the index (or menu) has the potential to function as more than just an analytical or navigational tool. It has the potential to become a creative, structuring device. This opens up new possibilities for the book, particularly as, in its paper based form, the book indexes factual work, but not fiction. In the electronic book, however, the index offers as rich a potential for fictional narratives as it does for factual volumes. [ABSTRACT FROM AUTHOR]

Reality-experiential history documentaries: the Trench (BBC, 2002) and Britain's modern memory of the First World War

Culloden (BBC, 1964) The Great War (BBC, 1964) 1914-18 (BBC/KCET, 1996) Haig: the Unknown Soldier (BBC, 1996) Veterans: the Last Survivors of the Great War (BBC, 1998) 1900s House (Channel 4, 1999) The Western Front (BBC, 1999) History of Britain (BBC, 2000) 1940s House (Channel 4, 2001) The Ship (BBC, 2002) Surviving the Iron Age (BBC, 2001) The Trench (BBC, 2002) Frontier House (Channel 4, 2002) Lad's Army (BBC, 2002) Edwardian Country House (Channel 4, 2002) Spitfire Ace (Channel 4, 2003) World War One in Colour (Channel 5, 2003) 1914: the War Revolution (BBC, 2003) The First World War (Channel 4, 2003) Dunkirk (BBC, 2004) Dunkirk: The Soldier's Story (BBC, 2004) D-Day to Berlin (BBC, 2004) Bad Lad's Army (ITV, 2004) Destination D-Day: Raw Recruits (BBC, 2004) Bomber Crew (Channel 4, 2004) Battlefield Britain (BBC, 2004) The Last Battle (ARTE/ZDF, 2005) Who Do You Think You Are? (BBC, 2004, 2006) The Somme (Channel 4, 2005) [From the Publisher]

Creating a modern database from archive material - The Norman Holme archive: Interpretation of marine field research notebooks in the historical context of the MBA, 1958-83

This document provides details of the transfer of the Norman Holme archive data held in the National Marine Biological Library onto a modern database, specifically Marine Recorder. A key part in the creation of the database was the retrieval of a large amount of information recorded in field notebooks and on loosely-bound sheets of paper. As this work involved amending, interpreting and updating the available information, it was felt that an accurate record of this process should exist to allow scientists of the future to be able to clearly link the modern database to the archive material. This document also provides details of external information sources that were used to enhance and qualify the historical interpretation, such as estimating volumes and species abundances.