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).

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.

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.

Efecto de la aplicación de abonos orgánicos sobre las características físico-químicas y microbiológicas de suelos bajo cultivo de vid de la provincia de Mendoza

El efecto de los abonos orgánicos sobre las características químicas y microbiológicas del suelo depende del cultivo, tipo de abono, dosis, frecuencia y forma de aplicación. En el caso de la vid, algunos estudios sobre la aplicación de abonos orgánicos (AAO) han reportado incrementos en los nutrientes del suelo y planta. Considerando la escasa información sobre el manejo de compost y vermicompost en suelos de viñedos de Mendoza, el objetivo de esta tesis fue evaluar el efecto de abonos orgánicos en algunas características del suelo y del cultivo. Para ello, en un viñedo ubicado en Mendoza se evaluaron los efectos de una y dos aplicaciones, superficial y enterrada, de compost y vermicompost sobre las características químicas y microbiológicas del suelo, crecimiento y rendimiento de la vid. La duración del ensayo fue de 2 años y la dosis anual fue 8 Mg ha-1. Luego de 360 días, todos los microorganismos evaluados fueron afectados por la AAO. El número de microorganismos celulolíticos fue mayor en las parcelas que recibieron compost (3,08 log10UFC g-1) que en aquellas que recibieron vermicompost (2,66 log10UFC g-1). También fue mayor cuando la aplicación fue superficial (3,07 log10UFC g-1) que cuando fue enterrada (2,67 log10UFC g-1), independientemente del tipo de abono. La AAO no afectó la salinidad del suelo. El fósforo disponible y potasio intercambiable incrementaron 237 por ciento y 28 por ciento en suelos abonados respecto de suelos al inicio del ensayo. El contenido de potasio total en pecíolo incrementó 15 por ciento en parcelas que recibieron abono orgánico respecto de las que no recibieron. La AAO en suelos de regadío de la zona árida de Mendoza se considera una alternativa promisoria por su impacto en algunas poblaciones microbianas, su efecto sobre el contenido de nutrientes en suelo y propiedades que hacen a la salinidad edáfica.

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.

A grey literature review of the Cultural Olympiad

This article considers the development of the UK Cultural Olympiad supporting London's successful bid to stage the Olympic Games in 2012. It suggests that the Cultural Olympiad is a complex event itself and needs to be better understood if any impacts are to be felt in a meaningful sense. The event is thus considered through review of over 50 documents relating to its management, in the context of a number of identified themes: cultural development, developing institutional frameworks, social benefit, educational benefit and promotional benefit.

Jung’s cultural writing: spiral essays and performing symbols (in literature)

Performance is a key ingredient of Jung’s writings on culture and of the function of the Jungian symbol in literature. This paper will compare and contrast Jung’s performance of cultural analysis and healing in his essays with the way his notion of the symbol works in literature to knit the individual psyche into the collective. It will explore Jung’s unique essay form of the spiral as a literary innovation, and look at the way a Jungian reading of literary reveals a significant contribution to cultural studies. [From the Author]

Psyche and the arts: Jungian approaches to music, architecture, literature, painting and film

Does art connect the individual psyche to history and culture? Psyche and the Arts challenges existing ideas about the relationship between Jung and art, and offers exciting new dimensions to key issues such as the role of image in popular culture, and the division of psyche and matter in art form. Divided into three sections - Getting into Art, Challenging the Critical Space and Interpreting Art in the World - the text shows how Jungian ideas can work with the arts to illuminate both psychological theory and aesthetic response. Psyche and the Arts offers new critical visions of literature, film, music, architecture and painting, as something alive in the experience of creators and audiences challenging previous Jungian criticism. This approach demonstrates Jung’s own belief that art is a healing response to collective cultural norms. This diverse yet focused collection from international contributors invites the reader to seek personal and cultural value in the arts, and will be essential reading for Jungian analysts, trainees and those more generally interested in the arts. [From the Publisher]