Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. METHODOLOGY/PRINCIPAL FINDINGS: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. CONCLUSIONS/SIGNIFICANCE: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

REVOLUTIONARY VIOLIN LITERATURE IN THE TRANSFORMATIVE PERIOD OF THE 20TH CENTURY, 1900-1970

In satisfaction of requirements for a Doctor of Musical Arts degree at the University of Maryland, College Park, three recitals were given consisting of works of the early 21st Century European composers. The works performed on these recitals showcase a variety of compositional styles that explore different qualities of the violin. The purpose of this project was to demonstrate how the war and conflict in Europe and attendant radical cultural and social developments affected these composers. The first recital program includes: Sonata for Violin and Cello and Piece en Forme de Habanera by Maurice Ravel; Op. 30 Mythesfor Violin and Piano by Karol Szymanowski; Concertina for Violin and Piano and Sonata No.2 for Violin Solo by Grazyna Bacewicz. The second recital program consists of: Sonata for Violin and Piano by Leos Janacek; Quartet for the End of Time: movement VIII "Louange a l'Immortalite de Jesus" by Oliver Messiaen; Sonata for Solo Violin by Erwin Schulhoff; and Passacaglia & Fuga for String Trio by Hans Krasa. The third recital highlights the works of Russian composers: Sonata for Violin and Piano Op.134 by Dmitri Shostakovich; and Violin Sonata No.2 in D major Op. 94 by Sergei Prokofiev. These composers represent individual, distinct and fascinating adaptation to events beyond their control as well as their power of transformation. The first recital was performed in collaboration with Hsiang-Ling Hsiao on piano and Gozde Yasar on cello. The second recital was given with Hsiang-Ling Hsiao on piano, Gozde Yasar on cello, and Asli Gultekin Ozek on viola. The third recital was performed with David Ballena on piano. The recitals were recorded on compact discs and are archived within the Digital Repository at the University of Maryland (DRUM).

CANCIONES ARGENTINAS (SONGS OFARGENTINA): A RECORDING PROJECT

This Dissertation Project comprises recordings of Argentine art songs. The discs are approximately 40-60 minutes in length and consist of songs from the traditional art-song repertoire for voice and piano. This project is particularly appropriate because of the very limited number of recordings of Argentine songs, which are notable both not only for their high quality but for their accessibility of performance for voice teachers, students, and professional singers alike. Art songs in the Spanish language are a welcome resource, and the poetry included in this project is of an outstanding quality. Some of the poets set to music are Gabriela Mistral (a poet laureate of Chile and the first Latin American woman to win the Nobel Prize for Literature), Pablo Neruda (also a Nobel laureate), Luis Cernuda, and Leon Benar6s. The lyrics of some songs are based on traditional sources, and the melodies and rhythms of all are representative of South American-indigenous and European­ immigrant cultures. The composers represented here will be familiar to some listeners but more than likely unfamiliar to most. Yet Alberto Ginastera (1916-1983) is considered to be the greatest of all Argentine composers. Alberto Williams (1862-1952) is known as the father of the Nationalist School of composition in Argentina, and Carlos Lopez Buchardo (1881-1963) is a most influential composer and pedagogue after whom the national Conservatory of Music in Buenos Aries is named. Two composers who remain relatively unknown outside of South America, Abraham Jurafsky (1906- 1993) and Julio Perceval (1903-1963) are also represented in this project. A complete compact disc is devoted to the works of Carlos Guastavino. Known as the "Argentine Schubert", Guastavino has over 250 songs to his credit. Chiefly a composer for piano and voice, his recent death (October 2000) makes a recording of his works especially appropriate. This project also includes a written component, a supportive dissertation briefly describing the history of the Argentine art song and the lives and influences of the composers and poets represented in the studio recordings. The CD recordings are held in the Michelle Smith Performing Arts Library at the University of Maryland.

Post-1945 Danish Piano Trio Literature: A Recording Dissertation

This recording dissertation surveys post-1945 literature written for piano trio (violin, violoncello and piano) by ten Danish composers. The literature was first considered for inclusion by searching a database provided by the Danish Music Information Center (www.mic.dk). Scores were rented from the publisher Edition Wilhelm Hansen AS, or purchased from the publisher Samfundet til Udgivelse af Dansk Musik. An additional score published by Viking Musikforlag was used as well. The music was then studied and evaluated for selection. During the selection process, the following criteria were considered: 1) quality of the compositions; 2) recognition of the composers at the national or international level; 3) whether the compositions had been previously recorded; and 4) variety of compositional styles. The selected works are written by Niels Viggo Bentzon, Vagn Holmboe, Anders Koppel, Herman D. Koppel, Bent Lorentzen, Anders Nordentoft, Per Norgard, Michael Nyvang, Karl Aage Rasmussen, and Poul Rovsing Olsen. The selected compositions were practiced, rehearsed, and performed under direct supervision of the composers and other expert musicians. In order to better understand the compositional style of each composer, relevant books, articles, and recordings were researched and studied. This recording dissertation is supported by a written document. A subjective preference for program balance was exercised to determine the order of recorded works. The written document is divided into chapters defined by composer, following the order of the recorded document, which include the composers' biographies and notes referring to the recorded compositions. The recording took place at the Manzius Gaarden, Birkerod, Denmark during three sessions: July 31-August 2, 2002, March 2 and 3, 2003, and June 2-4, 2003. The music for this dissertation was recorded by the members of the Jalina Trio; Line Fredens, violin, Janne Fredens, cello and Natsuki Fukasawa, piano. Aksel Trige, a well-respected recording engineer, was engaged for the recording and editing. Additionally, a Hamburg Steinway concert grand piano was rented and a Joseph Guarnerius filius Andreas Cremona violin (1706) was provided by the Augustinus Fonden, Denmark. The cellist used her own instrument, Vuillaume of Paris (c. 1850). The expense of this recording was partially paid by generous grants from the Augustinus Fonden, the Solist Foreningen af 1921, and the Dansk Musikerforbunds Kollective Rettighedsmidler. The compositions selected for this recording dissertation are assumed to be previously unrecorded, with the exception of Poul Rovsing Olsen's Trio II.

Road Traffic Injury Prevention Initiatives: A Systematic Review and Metasummary of Effectiveness in Low and Middle Income Countries.

BACKGROUND: Road traffic injuries (RTIs) are a growing but neglected global health crisis, requiring effective prevention to promote sustainable safety. Low- and middle-income countries (LMICs) share a disproportionately high burden with 90% of the world's road traffic deaths, and where RTIs are escalating due to rapid urbanization and motorization. Although several studies have assessed the effectiveness of a specific intervention, no systematic reviews have been conducted summarizing the effectiveness of RTI prevention initiatives specifically performed in LMIC settings; this study will help fill this gap. METHODS: In accordance with PRISMA guidelines we searched the electronic databases MEDLINE, EMBASE, Scopus, Web of Science, TRID, Lilacs, Scielo and Global Health. Articles were eligible if they considered RTI prevention in LMICs by evaluating a prevention-related intervention with outcome measures of crash, RTI, or death. In addition, a reference and citation analysis was conducted as well as a data quality assessment. A qualitative metasummary approach was used for data analysis and effect sizes were calculated to quantify the magnitude of emerging themes. RESULTS: Of the 8560 articles from the literature search, 18 articles from 11 LMICs fit the eligibility and inclusion criteria. Of these studies, four were from Sub-Saharan Africa, ten from Latin America and the Caribbean, one from the Middle East, and three from Asia. Half of the studies focused specifically on legislation, while the others focused on speed control measures, educational interventions, enforcement, road improvement, community programs, or a multifaceted intervention. CONCLUSION: Legislation was the most common intervention evaluated with the best outcomes when combined with strong enforcement initiatives or as part of a multifaceted approach. Because speed control is crucial to crash and injury prevention, road improvement interventions in LMIC settings should carefully consider how the impact of improvements will affect speed and traffic flow. Further road traffic injury prevention interventions should be performed in LMICs with patient-centered outcomes in order to guide injury prevention in these complex settings.

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.

Developing Quantitative Methodologies for the Digital Humanities: A Case Study of 20th Century American Commentary on Russian Literature

Using scientific methods in the humanities is at the forefront of objective literary analysis. However, processing big data is particularly complex when the subject matter is qualitative rather than numerical. Large volumes of text require specialized tools to produce quantifiable data from ideas and sentiments. Our team researched the extent to which tools such as Weka and MALLET can test hypotheses about qualitative information. We examined the claim that literary commentary exists within political environments and used US periodical articles concerning Russian literature in the early twentieth century as a case study. These tools generated useful quantitative data that allowed us to run stepwise binary logistic regressions. These statistical tests allowed for time series experiments using sea change and emergency models of history, as well as classification experiments with regard to author characteristics, social issues, and sentiment expressed. Both types of experiments supported our claim with varying degrees, but more importantly served as a definitive demonstration that digitally enhanced quantitative forms of analysis can apply to qualitative data. Our findings set the foundation for further experiments in the emerging field of digital humanities.

Film and literature in the legal classroom

The way in which law and lawyers are portrayed in popular film and literature is a fascinating subject not only for the social scientist but, more importantly, the lawyer and law student. Increasingly in law schools, films and classic literature with a legal theme are being used to identify various aspects of legal activity ranging from legal practice (i.e. intrinsic lawyer skills including legal argument, negotiation and advocacy) to various aspects of the legal process (e.g. the function of the judge and jury) as well as important elements of legal and ethical theory. This article focuses on the Law Through Film and Literature option which is offered to law students in the final year of their LLB (Hons) degree at Greenwich. The aim is to show how law-related film and literature can be a useful tool in the legal classroom, as well as providing some insights into how students have responded and developed as a result of their experiences on the course.

Postcolonial futures: postcolonial literature and the Obama moment

In an analysis of President Obama's Acceptance Speech, this article argues that postcolonial theory is now being re-formulated for a global, transnational sensibility.

Nursing resources and patient outcomes in intensive care: a systematic review of the literature

Objectives: To evaluate the empirical evidence linking nursing resources to patient outcomes in intensive care settings as a framework for future research in this area. Background: Concerns about patient safely and the quality of care are driving research on the clinical and cost-effectiveness of health care interventions, including the deployment of human resources. This is particularly important in intensive care where a large proportion of the health care budget is consumed and where nursing staff is the main item of expenditure. Recommendations about staffing levels have been trade but may not be evidence based and may not always be achieved in practice. Methods: We searched systematically for studies of the impact of nursing resources (e.g. nurse-patient ratios, nurses' level of education, training and experience) on patient Outcomes, including mortality and adverse events, in adult intensive care. Abstracts of articles were reviewed and retrieved if they investigated the relationship between nursing resources and patient Outcomes. Characteristics of the studies were tabulated and the quality of the Studies assessed. Results: Of the 15 studies included in this review, two reported it statistical relationship between nursing resources and both mortality and adverse events, one reported ail association to mortality only, seven studies reported that they Could not reject the null hypothesis of no relationship to mortality and 10 studies (out of 10 that tested the hypothesis) reported a relationship to adverse events. The main explanatory mechanisms were the lack of time for nurses to perform preventative measures, or for patient surveillance. The nurses' role in pain control was noted by One author. Studies were mainly observational and retrospective and varied in scope from 1 to 52 units. Recommendations for future research include developing the mechanisms linking nursing resources to patient Outcomes, and designing large multi-centre prospective Studies that link patient's exposure to nursing care oil a shift-by-shift basis over time. (C) 2007 Elsevier Ltd. All rights reserved.