bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catastrophe Finance: An Emerging Discipline
Authors: Elsner James B. , Burch R. King , Jagger Thomas H. 
Published: August 2009

While the recent disasters in the world's financial markets demonstrate that finance theory remains far from perfected, science also faces steep challenges in the quest to predict and manage the effects of natural disasters. Worldwide, as many as half a million people have died in disasters such as earthquakes, tsunamis, and tropical cyclones since the turn of the 21st century [Wirtz, 2008]. Further, natural disasters can lead to extreme financial losses, and independent financial collapses can be exacerbated by natural disasters.In financial cost, 2008 was the second most expensive year on record for such catastrophes and for financial market declines. These extreme events in the natural and financial realms push the issue of risk management to the fore, expose the deficiencies of existing knowledge and practice, and suggest that progress requires further research and training at the graduate level.
Development of Incentives for Data Sharing in Ecology, Evolution, and Organismal Biology
Authors: Duke Clifford 
Published: August 2009

AbstractReady access to data is a key concern in both basic research and problem-solving in the biological sciences, as the scale and scope of the questions that researchers ask expand, and as global problems demand data collected from around the world. With a grant from the National Science Foundation, from 2004 through 2009, the Ecological Society of America (ESA) has led a series of five workshops on data sharing, to help the ecology, evolution, and organismal biology communities find common ground on how to make data more readily discoverable and accessible in their own disciplines. The most recent of these focused in the development of incentives for data sharing, both at the individual and organizational level. This presentation will summarize the workshop recommendations, with a focus on preservation, curation, and access to data; access to analytical and visualization tools; and the need to make data archiving simple and routine. The roles of funders and publishers of research are also key and will be highlighted.
Background/Question/Methods
Ready access to data is a key concern in both basic research and problem-solving in the biological sciences, as the scale and scope of the questions that researchers ask expand, and as global problems demand data collected from around the world. With a grant from the National Science Foundation, from 2004 through 2009, the Ecological Society of America (ESA) has led a series of five workshops on data sharing, to help the ecology, evolution, and organismal biology communities find common ground on how to make data more readily discoverable and accessible in their own disciplines. The most recent of these focused in the development of incentives for data sharing, both at the individual and organizational level.

Results/Conclusions
This presentation will summarize the workshop recommendations, with a focus on preservation, curation, and access to data; access to analytical and visualization tools; and the need to make data archiving simple and routine. The roles of funders and publishers of research are also key and will be highlighted.
Status and habitat requirements of Physaria thamnophila, an endangered species of Tamaulipan thornscrub
Authors: Fowler Norma , Price Dana , Best Christopher , Hempel Alice 
Published: August 2009

Abstract	Physaria (Lesquerella) thamnophila (Brassicaceae; henceforth Physaria) is an endangered herbaceous perennial plant of remnant patches of Tamaulipan thornscrub near the southern Texas border. Six years of censuses of four populations of Physaria were analyzed. Quantitative data were collected to describe the plant community in the four sites. There was no overall trend in population size, but fluctuations in observed numbers of plants among years were extremely large: a single census cannot provide a reliable assessment of a population of this species. Seedling numbers were positively related with shrub canopy cover. However, there were many more Physaria plants in the brush-cleared portion of one site than in its uncleared portion. Seedling survival may be facilitated by anything that reduces movement of the highly erodible soils of these sites.
Binding of cyclic nucleotides to phosphodiesterase 10A and 11A GAF domains does not stimulate catalytic activity
Authors: Matthiesen Karina , Nielsen Jacob 
Published: August 2009

To date eleven human PDE (3′,5′-cyclic nucleotide phosphodiesterase) families have been identified. Of these, five families contain non-catalytic tandem GAF (cGMP-specific and -stimulated phosphodiesterases, Anabaenaadenylate cyclases and Escherichia coliFhlA) domains, GAFa and GAFb, in the N-terminal part of the enzyme. For PDE2A, PDE5A and PDE6 the GAF domains have been shown to bind cGMP with high affinity. For PDE2A and PDE5A this ligand binding has been shown to stimulate the catalytic activity of the enzyme. PDE10A and PDE11A are the two most recently described PDEs and it has been suggested that their GAF domains bind to cAMP and cGMP respectively. We have developed a scintillation proximity-based assay to directly measure cyclic nucleotide binding to the PDE2A, PDE10A and PDE11A GAF domains, and in the present study we demonstrate binding of cyclic nucleotides to the PDE10A and PDE11A GAF domains. We show that these non-catalytic sites bind cAMP and cGMP respectively with much higher affinity than has previously been suggested using indirect assessment of the interaction. The GAFb domain of PDE10A binds cAMP with a Kd of 48 nM and the GAFa domain of PDE11A binds cGMP with a Kd of 110 nM. The effect of cyclic nucleotides binding to the GAF domains on the enzyme activity was investigated through the use of modified cyclic nucleotides. In contrast with other GAF domain-containing PDEs, and with what has previously been predicted, ligand binding to the GAF domains of PDE10A and PDE11A does not stimulate catalytic activity.
A comparison of frameworks and objectives for implementation of marine protected areas in Northern Europe and in Southeast Asia
Authors: Sørensen Thomas Kirk , Thomsen Linda Nguyen 
Published: August 2009

A proliferation of marine protected areas around the world, including Europe and Southeast Asia, is evidence of a growing global concern for the marine environment and its living resources. While marine protected areas in Europe on a wider scale have generally been considered a tool for either nature conservation or a technical measure in management of fisheries, overall management objectives of marine protected areas in Southeast Asian countries have varied more significantly between countries and sites due to differences in societal needs and opportunities, spatial scales, environmental conditions and varying threats. These differences have resulted in different approaches to marine protected area development and management.
Management of the Northern European marine environment and its living resources is highly sectoral and largely determined by central directives and policies stemming from the European Union, such as the Habitats Directive and the Common Fisheries Policy. This paper however, will touch upon an ongoing evolution within the European Union from a strictly sectoral approach to marine protected areas and marine management, towards a more integrated, ecosystem approach to management of fisheries and the marine environment.
In Southeast Asia, marine protected area development is usually determined by individual governments, municipalities and coastal communities, based upon specific needs and settings. Examples of such marine protected areas in Vietnam and the Philippines will be described, including their underlying institutional frameworks and objectives such as tourism, management of artisanal fisheries, etc.
Examples of differences and similarities between Northern European and Southeast Asian marine protected areas will be presented and areas in which regions might learn from one another identified. For instance, where Southeast Asian protected areas have addressed the inevitable interdependency between healthy ecosystems and sustainable coastal fisheries for decades, marine protected areas in Northern Europe usually address either large scale management of stocks of individual fish species or nature conservation. Tourism has long been an overarching driving force in marine protected area implementation in SE Asia, while in Northern Europe especially this has only had little influence on overall objectives pertaining to the marine environment.
The Young Person's CORE: Development of a brief outcome measure for young people
Authors: Twigg Elspeth , Barkham Michael , Bewick Bridgette M. , Mulhern Brendan , Connell Janice , Cooper Mick 
Published: August 2009

AbstractBackground: There is a need for a user‐friendly measure of change for use in school and youth counselling services which is easy for practitioners to administer and score, and which is appropriate for brief interventions. Aims: To develop such a measure and to present psychometric data on reliability, validity and sensitivity to change for the measure. Method: We employed a three‐stage approach: first, creating a pool of potential items; second, developing an 18‐item version; and third, refining to a final version comprising 10 items. We called the measure the Young Person's CORE (YP‐CORE). Results: The measure comprised eight negative and two positive items and included a single (negatively‐framed) risk‐to‐self item. Psychometric properties were all acceptable. Sensitivity to change was good and yielded an average improvement of 10 points on the YP‐CORE in a clinical group, broadly equivalent to changes in adult versions (e.g. Clinical Outcomes in Routine Evaluation – Outcome Measure (CORE‐OM)). Conclusion: Initial validation work showed the measure to be well designed and sensitive to change. Analysis showed considerable variability as a function of age and gender suggesting the need for the collection of a large and diverse data set in order to produce gender and age‐specific norms.
School counsellors' and teachers' perceptions of their students' problems: Shared and divergent views
Authors: Tatar Moshe , Bekerman Zvi 
Published: August 2009

AbstractPrimary objective: This study investigates how school counsellors and teachers perceive their adolescent students’ problems and identifies the professional practices that allow them to understand and deal with these problems. Methods and procedures: An open‐ended questionnaire was administered to 38 Israeli senior‐high school counsellors and to 38 homeroom teachers working in educational institutions representing a variety of Jewish Israeli student populations. Results: Learning problems were identified by the counsellors and teachers as the main challenges for the students. The majority of the counsellors attribute students’ problems to the individuals themselves relying mainly on teachers’ reports. Teachers base their perceptions and assessments on direct observation of their students’ behaviours. Conversational techniques are the most preferred professional practices for tackling students’ problems. Conclusions: The importance of collaboration and team work between school counsellors and teachers and the parameters relevant for developing and promoting this collaboration more effectively are proposed and discussed.
Secondary school students’ preferences for school counsellors to be of the same ethnic origin as themselves
Authors: Chan Stephanie , Quinn Philip 
Published: August 2009

AbstractAims: This study looked at whether secondary school students would rather see a counsellor of the same ethnic origin as themselves, and whether this varied by ethnicity and gender. Method: A questionnaire survey was conducted with 761 students participating from two Glasgow secondary schools and four Belfast secondary/grammar schools. The study investigated participants’ responses to the question ‘Do you prefer speaking to a counsellor who is of the same ethnic origin as you?’ Results: Overall, the study found that 26.6% of students would rather see a counsellor of similar ethnic origin, 5.5% would rather not, 14.8% were not sure, and 53.1% did not mind. Students of white, Black and Minority Ethnic (BME) and non‐specific ethnic origins did not differ significantly in how much they would rather see a counsellor from their own ethnic background; but students of a BME background were approximately three times more likely to express a preference for a counsellor not of their ethnic origin as compared with white students. It was also found that twice as many male students would prefer not to see a counsellor of the same ethnic origin as themselves, as compared with female students. Implications of these findings are discussed in relation to other research and methodological limitations of this study are considered.
Secondary school students' preferences for location, format of counselling and gender of counsellor: A replication study based in Northern Ireland
Authors: Quinn Philip , Chan Stephanie 
Published: August 2009

AbstractAims: This study replicates a research investigation conducted by Cooper (2006), examining three factors that may affect students’ willingness to attend a school‐based counselling service: location of the service (school‐based or external); format (individual or group); and gender of counsellor. Method: The views of 589 students from four Northern Ireland secondary and grammar schools were surveyed and analysed using descriptive and inferential statistics. Results: As found by Cooper (2006), more than two thirds (68.2%) of students expressed a preference for seeing a counsellor in their school; over 80% of students expressed a preference for seeing a counsellor on their own; and a marked preference for female counsellors existed, particularly amongst female students.
‘Extra appendage’ or integrated service? School counsellors' reflections on their professional identity in an era of education reform
Authors: Harris Belinda 
Published: August 2009

AbstractAims: Since 2003, Government policies have located increasing responsibility for children's well‐being on schools working in partnership with other agencies. This study sought to investigate how these policies affect the working lives and professional identities of counsellors in schools in challenging circumstances in England. Method: In‐depth interviews with six school counsellors (4 primary and 2 secondary). Transcripts were analysed using Interpretive Phenomenological Analysis to reveal five master themes, one of which is the focus of this paper. Findings: School counsellors derive most reward from their therapeutic work with children. Their sense of professional identity however, is affected by their positioning within schools. Counsellors with dual roles perceive themselves as ‘insiders’ with the capacity to influence and contribute meaningfully to the school's well‐being agenda. Counsellors engaged on part‐time contracts either independently or via an agency feel like ‘outsiders’, situated on the margins of school life and vulnerable to neglectful and oppressive practices from school leadership. Some implications for practice are considered.
Practitioners’ views and experiences of participating in a school counselling evaluation study
Authors: Tracey Anne , McElearney Aisling , Adamson Gary , Shevlin Mark 
Published: August 2009

AbstractIntroduction: This study documents and describes practitioners’ views and experiences of the process of implementing an ‘impact evaluation’ of the independent school counselling service provided by the National Society for the Prevention of Cruelty to Children (NSPCC) in Northern Ireland. Method: Data was gathered from practitioners (n=18) across the duration of the evaluation process; at the pre, mid and post implementation stages of the evaluation process. Data‐gathering methods included consultation focus groups, records of training meetings, minutes of strategic advisory group meetings, a practitioner internet based discussion board and a structured questionnaire. A thematic analysis was carried out using Nvivo software. Results: Practitioner reflections confirmed the evaluation process as challenging yet with considerable benefits for recognition, self‐reflection and practice development. Discussion: Recommendations for integrating outcome evaluation within school counselling practice are presented.
School counselling in Wales: Recommendations for good practice
Authors: Pattison Sue , Rowland Nancy , Richards Kaye , Cromarty Karen , Jenkins Peter , Polat Filiz 
Published: August 2009

AbstractAims: This paper presents the context, methodologies and findings of a research project commissioned by the Welsh Assembly Government to evaluate school counselling and services available to children and young people in the UK and to make recommendations for future service development in Wales. Method: The study adopted three research methods: desk research (a literature review), a quantitative survey, and qualitative fieldwork. The survey included a sample of primary and secondary schools in Wales, as well as local authorities. Fieldwork included interviews with teachers, counsellors, parents, and children. Findings: Evidence‐based recommendations for counselling service provision in schools in Wales were developed, which now inform the Welsh Assembly Government's (WAG) National Strategy for counselling in schools in Wales (2008).
CEAS: cis-regulatory element annotation system
Authors: Shin Hyunjin , Liu Tao , Manrai Arjun K. , Liu X. Shirley 
Published: August 2009

Abstract
Summary: We present a tool designed to characterize genome-wide protein–DNA interaction patterns from ChIP-chip and ChIP-Seq data. This stand-alone extension of our web application CEAS (cis-regulatory element annotation system) provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene bodies or exons, and infers the genes most likely to be regulated by the binding factor under study. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic regions, particularly allowing observation of continuous and broad ChIP enrichment that might be too subtle to detect from ChIP peaks alone.
Availability: The CEAS Python package is publicly available at http://liulab.dfci.harvard.edu/CEAS.
Contact: shin@jimmy.harvard.edu; xsliu@jimmy.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Correlating multiple SNPs and multiple disease phenotypes: penalized non-linear canonical correlation analysis
Authors: Waaijenborg Sandra , Zwinderman Aeilko H. 
Published: August 2009

AbstractMotivation: Canonical correlation analysis (CCA) can be used to capture the underlying genetic background of a complex disease, by associating two datasets containing information about a patient's phenotypical and genetic details. Often the genetic information is measured on a qualitative scale, consequently ordinary CCA cannot be applied to such data. Moreover, the size of the data in genetic studies can be enormous, thereby making the results difficult to interpret.Results: We developed a penalized non-linear CCA approach that can deal with qualitative data by transforming each qualitative variable into a continuous variable through optimal scaling. Additionally, sparse results were obtained by adapting soft-thresholding to this non-linear version of the CCA. By means of simulation studies, we show that our method is capable of extracting relevant variables out of high-dimensional sets. We applied our method to a genetic dataset containing 144 patients with glial cancer.Contact: s.waaijenborg@amc.uva.nl
Mobyle: a new full web bioinformatics framework
Authors: Néron Bertrand , Ménager Hervé , Maufrais Corinne , Joly Nicolas , Maupetit Julien , Letort Sébastien , Carrere Sébastien , Tuffery Pierre , Letondal Catherine 
Published: August 2009

Abstract
Motivation: For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally, given that scientific tools can be difficult to install, it is particularly helpful for biologists to be able to use these tools through a web user interface. However, providing a web interface for a set of tools raises the problem that a single web portal cannot offer all the existing and possible services: it is the user, again, who has to cope with data copy among a number of different services. A framework enabling portal administrators to build a network of cooperating services would therefore clearly be beneficial.
Results: We have designed a system, Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software. While being focused on the end user, the Mobyle system also addresses the need, for the bioinfomatician, to automate remote services execution: PlayMOBY is a companion tool that automates the publication of BioMOBY web services, using Mobyle program definitions.
Availability: The Mobyle system is distributed under the terms of the GNU GPLv2 on the project web site (http://bioweb2.pasteur.fr/projects/mobyle/). It is already deployed on three servers: http://mobyle.pasteur.fr, http://mobyle.rpbs.univ-paris-diderot.fr and http://lipm-bioinfo.toulouse.inra.fr/Mobyle. The PlayMOBY companion is distributed under the terms of the CeCILL license, and is available at http://lipm-bioinfo.toulouse.inra.fr/biomoby/PlayMOBY/.
Contact: mobyle-support@pasteur.fr; mobyle-support@rpbs.univ-paris-diderot.fr; letondal@pasteur.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach
Authors: Kashima Hisashi , Yamanishi Yoshihiro , Kato Tsuyoshi , Sugiyama Masashi , Tsuda Koji 
Published: August 2009

AbstractMotivation: The existing supervised methods for biological network inference work on each of the networks individually based only on intra-species information such as gene expression data. We believe that it will be more effective to use genomic data and cross-species evolutionary information from different species simultaneously, rather than to use the genomic data alone.Results: We created a new semi-supervised learning method called Link Propagation for inferring biological networks of multiple species based on genome-wide data and evolutionary information. The new method was applied to simultaneous reconstruction of three metabolic networks of Caenorhabditis elegans, Helicobacter pylori and Saccharomyces cerevisiae, based on gene expression similarities and amino acid sequence similarities. The experimental results proved that the new simultaneous network inference method consistently improves the predictive performance over the individual network inferences, and it also outperforms in accuracy and speed other established methods such as the pairwise support vector machine.Availability: The software and data are available at http://cbio.ensmp.fr/∼yyamanishi/LinkPropagation/.Contact: kashima@mist.i.u-tokyo.ac.jpSupplementary information: Supplementary data are available at Bioinformatics online.