A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

Abstract Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. Results This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. Conclusions This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.

Panorama atual dos repositórios institucionais das instituições de ensino superior no Brasil

O cenário atual de repositórios digitais mundialmente distribuídos estimula estudos diversificados com os quais esse trabalho visa contribuir, objetivando um levantamento dos repositórios de instituições de ensino superior no Brasil, verificando a eficácia de uma ferramenta experimental no tratamento e análise dos dados e usando como fontes os diretórios Registry of Open Access Repositories (ROAR), Directory of Open Access Repositories (OpenDOAR), Diretório Luso-Brasileiro de Periódicos e Repositórios de Acesso Livre e a lista L_repositories. A ferramenta experimental Google Fusion Tables foi aplicada nos dados dos repositórios institucionais pesquisados, categorizando suas principais características: Instituição mantenedora, Natureza da instituição, Local, Região geográfica, Software adotado e sua versão, adoção do padrão Dublin Core e quantidade de trabalhos disponibilizados na data do estudo. Foram identificados 49 repositórios que em agosto de 2013 disponibilizavam 396.881 itens, sendo as instituições federais as com maior povoamento e o repositório LUME o primeiro em volume de itens; a região Sudeste com o maior número de repositórios e volume de itens disponibilizados; o DSpace o software predominante, com maior utilização da versão 1.6.2 e o padrão de metadados Dublin Core em todas as aplicações desse software. Este estudo comprovou a eficácia e utilidade do FusionTables, permitindo caracterizar o panorama atual de repositórios de instituições de ensino superior no Brasil. Os resultados foram disponibilizados em um Catálogo de Repositórios de Instituições de Ensino Superior no Brasil e um Mapa interativo dos Repositórios de Instituições de Ensino Superior no Brasil.

BDPI Digital Library of USP in intellectual production

USP INFORMATION MANDATE – Resolution 6444 – Oct. 22th, 2012 Make public and accessible the knowledge generated by research developed at USP, encouraging the sharing, the use and generation of new content; •Preserve institutional memory by storing the full text of Intellectual Production (scientific, academic, artistic and technical); •Increase the impact of the knowledge generated in the university within the scientific community and the general public; •It is suggested to all members of the USP community to publish the results of their research, preferably, in open-access publication outlets and/or repositories and to include the permission to deposit their production in the BDPI system in their publication agreements. •Institutional Repository for Intellectual Production; •Official Source USP Statistical Yearbook.

Cultura "Open" e nuovi modelli normativi per la gestione della conoscenza

L'obiettivo della ricerca è di compiere un'analisi dell'impatto della cosiddetta cultura "open" alla luce dell'attuale condizione del World Wide Web. Si prenderà in considerazione, in particolare, la genesi del movimento a partire dalle basi di cultura hacker e la relativa evoluzione nella filosofia del software libero, con il fine ultimo di identificare il ruolo attuale del modello open source nello scenario esistente. L'introduzione al concetto di Open Access completerà la ricerca anche considerando la recente riaffermazione della conoscenza come bene comune all'interno della Società dell'Informazione

Bucknell Shares Its Research With the World

Bucknell University recently passed an open access publishing initiative and established Bucknell Digital Commons, its institutional repository.

Making business in the open: coping with economic and institutional risk and insecurity in the Kafue flats, Zambia

This paper deals with the difference between risk and insecurity from an anthropological perspective using a critical New Institutionalist approach. Risk refers to the ability to reduce undesirable outcomes, based on a range of information actors have on possible outcomes; insecurity refers to the lack of this information. With regard to the neo-liberal setting of a resource rich area in Zambia, Central Africa, local actors – men and women – face risk and insecurity in market constellations between rural and urban areas. They attempt to cope with risk using technical means and diversification of livelihood strategies. But as common-pool resources have been transformed from common property institutions to open access, also leading to unpredictability of competitors and partners in “free” markets, actors rely on magic options to reduce insecurity and transform it into risk-assessing strategies as an adaptation to modern times. Keywords: Risk, insecurity, institutional change, neo-liberal market, common pool resources, livelihood strategies, magic, Zambia.

UNDERSTANDING NURSE CREATED COGNITIVE ARTIFACTS: PERSONALLY-CREATED-COGNITIVE-ARTIFACTS AS EXTERNAL REPRESENTATIONS OF DISTRIBUTED COGNITION

Manuscript 1: “Conceptual Analysis: Externalizing Nursing Knowledge” We use concept analysis to establish that the report tool nurses prepare, carry, reference, amend, and use as a temporary data repository are examples of cognitive artifacts. This tool, integrally woven throughout the work and practice of nurses, is important to cognition and clinical decision-making. Establishing the tool as a cognitive artifact will support new dimensions of study. Such studies can characterize how this report tool supports cognition, internal representation of knowledge and skills, and external representation of knowledge of the nurse. Manuscript 2: “Research Methods: Exploring Cognitive Work” The purpose of this paper is to describe a complex, cross-sectional, multi-method approach to study of personal cognitive artifacts in the clinical environment. The complex data arrays present in these cognitive artifacts warrant the use of multiple methods of data collection. Use of a less robust research design may result in an incomplete understanding of the meaning, value, content, and relationships between personal cognitive artifacts in the clinical environment and the cognitive work of the user. Manuscript 3: “Making the Cognitive Work of Registered Nurses Visible” Purpose: Knowledge representations and structures are created and used by registered nurses to guide patient care. Understanding is limited regarding how these knowledge representations, or cognitive artifacts, contribute to working memory, prioritization, organization, cognition, and decision-making. The purpose of this study was to identify and characterize the role a specific cognitive artifact knowledge representation and structure as it contributed to the cognitive work of the registered nurse. Methods: Data collection was completed, using qualitative research methods, by shadowing and interviewing 25 registered nurses. Data analysis employed triangulation and iterative analytic processes. Results: Nurse cognitive artifacts support recall, data evaluation, decision-making, organization, and prioritization. These cognitive artifacts demonstrated spatial, longitudinal, chronologic, visual, and personal cues to support the cognitive work of nurses. Conclusions: Nurse cognitive artifacts are an important adjunct to the cognitive work of nurses, and directly support patient care. Nurses need to be able to configure their cognitive artifact in ways that are meaningful and support their internal knowledge representations.

Acceso abierto real y potencial a la producción científica de un país. El caso argentino

Se aporta una metodología para estimar la disponibilidad real y potencial de la producción científica de un país, según el modelo de acceso de las revistas elegidas por los investigadores para publicar sus artículos. Se estudia el caso de la producción científica argentina del período 2008-2010 en medicina, física y astronomía, agricultura y ciencias biológicas, y ciencias sociales y humanidades. La producción fue recogida de la base de datos Scopus y los modelos de acceso de las revistas, determinados a partir de la consulta a DOAJ, e-revist@s, SciELO, RedALyC, PubMed, Romeo-Sherpa y Dulcinea. Se concluye que Argentina presenta condiciones muy favorables para liberar un alto porcentaje de la literatura científica generada en el país bajo la modalidad de acceso abierto a través de repositorios; y que la metodología es reproducible para realizar comparaciones con otros países y campos temáticos. Los resultados aportan conocimiento útil a los gestores de repositorios de las instituciones académicas y de investigación de cara a promocionar su desarrollo y justificar su sostenimiento

Acceso abierto real y potencial a la producción científica de un país. El caso argentino

Se aporta una metodología para estimar la disponibilidad real y potencial de la producción científica de un país, según el modelo de acceso de las revistas elegidas por los investigadores para publicar sus artículos. Se estudia el caso de la producción científica argentina del período 2008-2010 en medicina, física y astronomía, agricultura y ciencias biológicas, y ciencias sociales y humanidades. La producción fue recogida de la base de datos Scopus y los modelos de acceso de las revistas, determinados a partir de la consulta a DOAJ, e-revist@s, SciELO, RedALyC, PubMed, Romeo-Sherpa y Dulcinea. Se concluye que Argentina presenta condiciones muy favorables para liberar un alto porcentaje de la literatura científica generada en el país bajo la modalidad de acceso abierto a través de repositorios; y que la metodología es reproducible para realizar comparaciones con otros países y campos temáticos. Los resultados aportan conocimiento útil a los gestores de repositorios de las instituciones académicas y de investigación de cara a promocionar su desarrollo y justificar su sostenimiento

Acceso abierto real y potencial a la producción científica de un país. El caso argentino

Se aporta una metodología para estimar la disponibilidad real y potencial de la producción científica de un país, según el modelo de acceso de las revistas elegidas por los investigadores para publicar sus artículos. Se estudia el caso de la producción científica argentina del período 2008-2010 en medicina, física y astronomía, agricultura y ciencias biológicas, y ciencias sociales y humanidades. La producción fue recogida de la base de datos Scopus y los modelos de acceso de las revistas, determinados a partir de la consulta a DOAJ, e-revist@s, SciELO, RedALyC, PubMed, Romeo-Sherpa y Dulcinea. Se concluye que Argentina presenta condiciones muy favorables para liberar un alto porcentaje de la literatura científica generada en el país bajo la modalidad de acceso abierto a través de repositorios; y que la metodología es reproducible para realizar comparaciones con otros países y campos temáticos. Los resultados aportan conocimiento útil a los gestores de repositorios de las instituciones académicas y de investigación de cara a promocionar su desarrollo y justificar su sostenimiento

Echolocation detections and digital video surveys provide reliable estimates of the relative density of harbour porpoises

Acknowledgements We would like to thank Erik Rexstad and Rob Williams for useful reviews of this manuscript. The collection of visual and acoustic data was funded by the UK Department of Energy & Climate Change, the Scottish Government, Collaborative Offshore Wind Research into the Environment (COWRIE) and Oil & Gas UK. Digital aerial surveys were funded by Moray Offshore Renewables Ltd and additional funding for analysis of the combined datasets was provided by Marine Scotland. Collaboration between the University of Aberdeen and Marine Scotland was supported by MarCRF. We thank colleagues at the University of Aberdeen, Moray First Marine, NERI, Hi-Def Aerial Surveying Ltd and Ravenair for essential support in the field, particularly Tim Barton, Bill Ruck, Rasmus Nielson and Dave Rutter. Thanks also to Andy Webb, David Borchers, Len Thomas, Kelly McLeod, David L. Miller, Dinara Sadykova and Thomas Cornulier for advice on survey design and statistical approache. Data Accessibility Data are available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.cf04g

Changes in Access to Health Services of the Immigrant and Native-Born Population in Spain in the Context of Economic Crisis

Aim: To analyze changes in access to health care and its determinants in the immigrant and native-born populations in Spain, before and during the economic crisis. Methods: Comparative analysis of two iterations of the Spanish National Health Survey (2006 and 2012). Outcome variables were: unmet need and use of different healthcare levels; explanatory variables: need, predisposing and enabling factors. Multivariate models were performed (1) to compare outcome variables in each group between years, (2) to compare outcome variables between both groups within each year, and (3) to determine the factors associated with health service use for each group and year. Results: unmet healthcare needs decreased in 2012 compared to 2006; the use of health services remained constant, with some changes worth highlighting, such as the decline in general practitioner visits among autochthons and a narrowed gap in specialist visits between the two populations. The factors associated with health service use in 2006 remained constant in 2012. Conclusion: Access to healthcare did not worsen, possibly due to the fact that, until 2012, the national health system may have cushioned the deterioration of social determinants as a consequence of the financial crisis. Further studies are necessary to evaluate the effects of health policy responses to the crisis after 2012.

Interlibrary loan trends : making access a reality /

"May 1992."

OpenAIREplus

Directions the outcomes of the OpenAIRE project, which implements the EC Open Access (OA) pilot. Capitalizing on the OpenAIRE infrastructure, built for managing FP7 and ERC funded articles, and the associated supporting mechanism of the European Helpdesk System, OpenAIREplus will “develop an open access, participatory infrastructure for scientific information”. It will significantly expand its base of harvested publications to also include all OA publications indexed by the DRIVER infrastructure (more than 270 validated institutional repositories) and any other repository containing “peer-reviewed literature” that complies with certain standards. It will also generically harvest and index the metadata of scientific datasets in selected diverse OA thematic data repositories. It will support the concept of linked publications by deploying novel services for “linking peer- reviewed literature and associated data sets and collections”, from link discovery based on diverse forms of mining (textual, usage, etc.), to storage, visual representation, and on-line exploration. It will offer both user-level services to experts and “non-scientists” alike as well as programming interfaces for “providers of value-added services” to build applications on its content. Deposited articles and data will be openly accessible through an enhanced version of the OpenAIRE portal, together with any available relevant information on associated project funding and usage statistics. OpenAIREplus will retain its European footprint, engaging people and scientific repositories in almost all 27 EU member states and beyond. The technical work will be complemented by a suite of studies and associated research efforts that will partly proceed in collaboration with “different European initiatives” and investigate issues of “intellectual property rights, efficient financing models, and standards”.