bluuebunny/crossref_metadata_2025 huggingface dataset:
Off the Mark?
Authors: McCarthy Linda
Published: February 2009

Targeting public redevelopment funding toward the most marketable brownfields is viewed as an economically efficient use of scarce resources because it may guarantee the greatest likelihood of success. But to what extent does this policy result in spatial and social inequities by neglecting contaminated sites in distressed neighborhoods containing minority and low-income populations? This case study of Milwaukee, Wisconsin, identified that tracts with above-average percentages of African Americans and Hispanics, although containing above-average numbers of brownfields per square mile and higher percentages of brownfields compared to percentage of the city's area, had below-average city-assisted redevelopments as a percentage of all brownfields. A policy implication is that despite difficulties promoting brownfield redevelopment in distressed neighborhoods, in addition to economic efficiencies, more emphasis is needed on the social benefits of public assistance for brownfield redevelopment, including potential spillover benefits, such as crime reduction and health improvements for surrounding neighborhoods.
Using GIS and Individual-Level Data for Whole Communities
Authors: DeBats Donald A.
Published: February 2009

Geographic Information Systems (GIS) can assist the reintegration of the estranged fields of American political and social history when focused on individual-level political and social information for whole communities of moderate size. This article illustrates these integrative possibilities through an exploration of political and social life in four 19th-century North American communities. Place of residence has been determined for approximately 80% of past inhabitants in each case study and spatial data serve as the link for all information. GIS provides a new variable—spatial relationships—of interest to both political and social historians. GIS employed in this type of ``total history'' adds value for its analytic capacities as well as its more familiar strengths in visualization. GIS in this way is returned to the narrative and placed at the center of the interests of both political and social history.
Standard of Living Effects Due to Infrastructure Improvements in the 19th Century
Authors: Groote Peter D. , Elhorst J. Paul , Tassenaar P.G.
Published: February 2009

We use Geographic Information Systems (GIS) to analyze the relationship between the biological standard of living and the development of the transport network in 90 municipalities located in the rural provinces of Groningen and Drenthe, the Netherlands, in the historical context of the 19th century. By running advanced spatiotemporal models, we find empirical evidence in favor of the so-called antebellum puzzle. This puzzle states that although the 19th-century infrastructure improvements had a positive effect on the standard of living in the long term, the short-term effect is negative.
Metropolitan Telecommunication
Authors: Wenzlhuemer Roland
Published: February 2009

Although the United Kingdom has long lost its position at the heart of a practically global empire, the British capital London still continues to stand at the very center of a global telecommunication and information network. Yet, global connectivity is not evenly distributed throughout the metropolis. As recent studies show, information-dependent businesses tend to concentrate in particular quarters in and around the City of London and the West End despite the spatial flexibility that modern telecommunication technology allows for. This study seeks to demonstrate how the modern ``digital divide'' that rips through London continuously evolved from similarly uneven connectivity patterns in the telegraphic network of late 19th-century London. With the help of historical Geographic Information Systems (GIS), these patterns will be visualized. This examination will show how important a role continuity played in the evolution of modern informational patterns and how this sheds new light on issues of technological dynamism and agency.
Cultural Future Matters
Authors: Adam Barbara
Published: February 2009

This article argues that human futurity is central to cultural being in general and contemporary social life in particular. It suggests that the social sciences have difficulty engaging with this important subject matter; that it poses problems at the level of theory and methodology. In his methodological writings, Max Weber addressed social futurity implicitly through the concepts of rationality and progress, ethics and values, purposes and motives, options and choices, calculation and the means-end schema, responsibility and vocation. This article uses Max Weber's methodological writings to focus discussion on some of the central tensions and difficulties that arise when sociologists seek explicitly to encompass in their work the temporal domain of the `not yet'. The overall aim of the article is to open up futurity and contemporary social extension into the long-term future as issues for social science consideration and debate.
Conflicting Temporalities
Authors: Hope Wayne
Published: February 2009

The information and communication technology (ICT) driven, real-time tendencies of global capitalism are predominant, but they are not universal. Fast, short-term profits undermine long-term strategies of capital accumulation. In this respect, the structures and activities of global capitalism are riven by temporal contradictions. Such is evident between and within different fractions of capital. Fast and long-term imperatives also conflict within transnational corporations and business administration. On a global scale, the clash between different cultural traditions of corporate capitalism reflects opposing temporal logics of profit maximization. How then do these temporal contradictions play out empirically? My response to this question explores the general idea that spatio-temporal fixes enable the cohesion and reproduction of capitalist systems. To this end, I will point out that under global capitalism spatio-temporal fixes cannot be guaranteed. There are no built-in congruities interlinking state, nation, economy and society. Global networks of finance, production and corporate governance may weaken the conjunctures between nation, state, economy and society and exacerbate temporal disjunctures within them. From these observations, I will argue that state-centred constructions of time and temporality are weakening against the general, real-time tendencies of global capitalism. This sharpens temporal conflicts within the nationally constituted economy and the nationally circumscribed state. As upper reaches of the nation state conform to the temporal urgency of institutionalized supranational decision making, the marginalized national polity is answerable to the slower temporal rhythms of representative assembly, the election cycle, public policy formation and civil society. Against this background, worldwide coalitions opposed to ruling global interests are also riven by conflicting temporalities. Such conflicts reflect the temporal contradictions of global capitalism and the associated temporal conflicts within states, nations and economies.
Social Change and the Timing of Family Transitions in West Germany
Authors: Scherger Simone
Published: February 2009

This article addresses the timing of family transitions in early adulthood. Theoretical and empirical analyses are used to investigate the appropriateness of the notions of destandardization, differentiation and individualization for characterizing recent changes in West German life courses. Data from the German Socio-Economic Panel (GSOEP) are used for a comparison of (West German) birth cohorts and the respective timing of moving out of the parental home, first marriage and first parenthood. These transitions have, in fact, undergone a certain temporal destandardization. However, the results suggest that this destandardization is limited to certain dimensions, is clearly socially structured and is in part brought about by changing structural conditions. Furthermore, these changes in timing can be partly explained by differentiation according to education. Individualization, too, is only applicable to a certain degree and in particular to women's life courses.
Time at R&D Work
Authors: Yli-Kauhaluoma Sari
Published: February 2009

This article seeks to increase understanding of the temporal aspects in technological innovation processes. Based on an empirical case, the aim is first to identify various types of time and then to study how R&D professionals in chemistry interact with time as they collaborate in developing and applying technological inventions. The article suggests that the distribution of work to collaborators can be seen as an attempt to extend the time resources in a project. Furthermore, participation of R&D professionals in short-term projects can be seen as an attempt to build long-term collaborative relationships. The study participates in a debate on how people in an R&D context approach collaboration from the time perspective.
The Screen of the Crime: Judging the Affect of Cinematic Violence
Authors: Young Alison
Published: February 2009

Discussions of screen violence polarize around the question of whether images can cause people to behave differently. Proponents of this position point to the influence of images in other contexts; its critics reject the implication that individuals can be so simplistically motivated. Such debate is intensified by events such as the Columbine or Virginia Tech shootings, where cultural products are named as the causes of lethal violence. This article engages with the assumption that the violence in violent imagery is a relatively homogeneous category. It explores paradigms of cinematic violence through the analysis of exemplary scenes from four representative films ( The Matrix, Reservoir Dogs , Natural Born Killers and Elephant), each of which has been linked to violence flowing in and from the image. Each shows multiple killings in highly graphic ways, yet each deploys different representational techniques to produce a range of affective responses in the spectator. As such, the article seeks to answer the question of how to judge the affect of cinematic violence and to investigate the implication of the spectator in the affects and aesthetics of screen violence.
Beyond the Dislocation(s) of Human Rights
Authors: Tie Warwick
Published: February 2009

Approaches that analyse disruptions to the cogency of human rights discourse in terms of `the exception', rather than in terms that are internal to that field, are vulnerable to accusations of nihilism. Three such analyses of dislocation are reviewed here: a betrayal of individual liberty that exceptional political circumstance requires for the securing of a universal right to liberty (Ignatieff, 2004); the complicity of human rights discourse in the strengthening of political powers capable of systematically violating human freedoms (Douzinas, 2000); and the insufficiency of knowledge about human rights abuses to counter people's denials of rights-abuse (Cohen, 2001). In the course of interpreting their respective instances of dislocation, each of the approaches inhabits in a performative manner the same space held by the exception to the discourse. Various challenges arise as a consequence of doing so for those who look to performative engagement with dislocation as a source of progressive socio-legal pulsion. Rather than being nihilistic in form, however, these challenges are political. Moreover, the political issues that emerge differ starkly from one another, reflecting divergences in perspective regarding the nature of performativity. They include a closure of debate that can occur around the political commitments which motivate performative analyses of dislocation and, conversely, the emergence of an undetermined space of political struggle as a consequence of new practices that transpire from performative responses to dislocation.
Unknowable Bodies, Unthinkable Sexualities: Lesbian and Transgender Legal Invisibility in the Toronto Women's Bathhouse Raid
Authors: Lamble Sarah
Published: February 2009

Although litigation involving sexual orientation and gender identity discrimination claims has generated considerable public attention in recent years, lesbian and transgender bodies and sexualities still remain largely invisible in Anglo-American courts. While such invisibility is generally attributed to social norms that fail to recognize lesbian and transgender experiences, the capacity to `not see' or `not know' queer bodies and sexualities also involves wilful acts of ignorance. Drawing from R. v Hornick (2002) a Canadian case involving the police raid of a women's bathhouse, this article explores how lesbian and transgender bodies and sexualities are actively rendered invisible via legal knowledge practices, norms and rationalities. It argues that limited knowledge and limited thinking not only regulate the borders of visibility and belonging, but play an active part in shaping identities, governing conduct and producing subjectivity.
Development and Initial Validation of the Disinhibition Inventory
Authors: Dindo Lilian , McDade-Montez Elizabeth , Sharma Leigh , Watson David , Clark Lee Anna
Published: February 2009

The broad personality trait of disinhibition reflects the tendency to behave in an underconstrained versus overconstrained manner and is associated with externalizing psychopathology and risk-taking behaviors. This article describes the development and initial validation of the Disinhibition Inventory (DIS-I), a multifaceted measure of disinhibition that helps explicate the nature of this important higher-order dimension more fully. Factor analyses of an initial item pool resulted in five content-distinct, yet correlated scales measuring both high (Manipulativeness, Distractibility, Risk Taking) and low (Prosociality, Orderliness) levels of disinhibition that cross-validated in an independent sample. Evidence for the construct validity of the DIS-I is presented, including convergent and discriminant relations with Big-Three and Big-Five/five-factor model measures of personality. Results indicate that the DIS-I scales are associated most strongly with other measures of disinhibition, but that the DIS-I additionally contains content absent in extant adult measures of disinhibition that may prove useful in the assessment of externalizing psychopathology.
Literature as Qualitative Inquiry
Authors: Brinkmann Svend
Published: February 2009

In recent years, there has been a literary turn in parts of the social sciences. Attention has been given to social science writings as literature. In this article, the author approaches the issue from the opposite direction by engaging with literature as qualitative social inquiry. He does so through a reading of the French novelist Michel Houellebecq. Houellebecq’s style represents a form of “lyrical sociology,” depicting human experience in a consumer society. The author argues that we can learn as much from Houellebecq about contemporary human lives, experiences, and sufferings as we can from traditional forms of empirical qualitative research. He concludes with a more general proposal of how to think about fact and fiction in social science writings.
Who Participates and Why: Building a Process Model of Citizen Participation
Authors: Foster-Fishman Pennie G. , Pierce Steven J. , Van Egeren Laurie A.
Published: February 2009

Initiating and sustaining sufficient levels of participation among residents in low-income and urban neighborhoods have become significant focuses of many initiatives that strive to develop healthy communities. This study examines the factors associated with citizen participation levels in resident leaders and followers in seven low-income neighborhoods in one community. Overall, the findings suggest that different factors facilitate participation in leaders and followers. Leaders are more likely to actively participate in neighborhood and community affairs if they perceive themselves as having the skills needed to organize others and make change happen. Whereas perceived skill levels also matter for followers, these residents are strongly influenced by the norms for activism within their neighborhood. These norms mediate the impact of neighborhood readiness and capacity for change on citizen participation levels. Implications for funders and practitioners interested in promoting healthy communities are discussed.
Do Self-Assessments Work to Detect Workshop Success?
Authors: Lam Tony C. M.
Published: February 2009

D'Eon et al. concluded that change in performance self-assessment means from before to after a workshop can detect workshop success in their and other situations. In this commentary, their recommendation is refuted by showing that (a) self-assessments with balanced over- and underestimations are still biased and should not be used to evaluate workshops, even though the means of self-assessments and criterion measures are artificially equal; (b) participants' performance should not be attributed directly to training, even if the self-assessments are psychometrically valid and obtained prior to the workshop as well; (c) self-assessment findings should not be generalized to other situations without further analysis and caution, even if the participants' performance can be attributed to training. For clarifying the recommendation by D'Eon et al. to use ``aggregated self-assessments'' to evaluate workshops, analysis of multilevel data is explained and discussed. Finally, nine rules of thumb in using self-assessments for evaluating training are provided.
Treatment Fidelity in Multisite Evaluation
Authors: Zvoch Keith
Published: February 2009

Program implementation data obtained from the repeated observation of teachers delivering one of two early childhood literacy programs to economically disadvantaged students in a large southwestern school district were analyzed to estimate protocol adherence levels at the onset of the intervention as well as the change in adherence over the intervention period. Application of multilevel growth models to the classroom observation data revealed that fidelity to program protocol varied within and between treatment sites during the initial observation and over time. An exploratory examination of select teacher, classroom, and site characteristics indicated that the background characteristics of teachers and contextual factors in the treatment environment were associated with the fidelity outcomes. These results provide some insight into the range of factors that are associated with protocol adherence and highlight the challenge of achieving and maintaining fidelity to a treatment intervention that is delivered by multiple providers over multiple treatment sites.
Paradoxes in schooling gender — a messy story
Authors: Rudberg Monica
Published: February 2009

The fact that girls on the average seem to do better than boys at all levels of schooling has triggered off a debate on ‘feminization of schools’ as a problem in many Western countries. In this article, a competing hypothesis is proposed, namely the ‘new girl hypothesis’, relating the academic success to the change of cultural as well as psychological positions among young girls of today. The story of schooling gender is told on the basis of data from a three-generational study of girls and their mothers and grandmothers in Norway, interviewed in 1991–92, and with a follow up for the girls ten years later. This story proves to be a rather ‘messy’ one, showing both ruptures and continuities between the generations. To understand this ‘messy story’ the article explores some paradoxes in schooling gender: Firstly, the paradoxes of pedagogy wavering between gender neutrality and gender reproduction, secondly the paradox of the welfare state wavering between individualizing policy and reproductive family orientation, and finally the paradoxes of knowledge-seeking itself, which can be seen as both gendered as well as transgressing gender boundaries.
Young people's education to work transitions and inter-generational social mobility in post-soviet central Asia
Authors: Roberts Ken , Kamruzzaman Palash , Tholen Jochen
Published: February 2009

This paper is based on evidence gathered in 20 firms, matched by size and business sector, in each of three Central Asia cities — Almaty in Kazakhstan, Bishkek in Kyrgyzstan, and Samarkand in Uzbekistan. In each firm the owner(s) and/or senior managers supplied information about the business, focusing on methods of recruitment, training, and employee career development. Parallel questionnaire surveys gathered information about the family and educational backgrounds, and labour market and employment biographies, of all the young (up to age 30) employees in each of the 20 companies. A total of 1,402 young employees completed questionnaires, and from these, eight per city, with equal numbers of males and females, with and without higher education, were subsequently interviewed in depth. The evidence is used to identify how families that were advantaged under the old (communist) system were continuing to reproduce their advantages inter-generationally. It is shown that this was mainly, though not entirely, via their children's superior chances of progressing through higher education. The evidence is also used to argue that cultural capital was playing a stronger role than social capital in the inter-generational transmission of advantages, that the critical events in the potentially life-long status attainment process were concentrated within a relatively short time frame, and that the multiple strategies to which families with economic and cultural assets could resort were liable to neutralise all efforts to diminish their ability to pass their advantages down the generations.
Cultural Norms Informing Other-Conscious Selfhood in Chinese Relational Worlds
Authors: Wang Mao-jin , Dai Jing-jing
Published: February 2009

This research adopts methodological relationalism as its conceptual framework. The Collection of Sages' Maxims (CSM) is used as the basic data to derive the cultural norms. Based on these norms, eight parameters (prs) are derived with 24 metaperception components of filial piety and fraternal submission(FPFS)-based interpersonal loyalty. These FPFS loyalty (FPFSL) metaperception components as third-eye party are seen to be highly sensitive and vigilant with regard to transgressions of the cultural maxim-based norms. Then these metaperception components are supposed to help prompt the transgressor to generate emotions of guilt and shame in his/her reflection.
Commentary: Accessing the Experience of a Dialogical Self: Some Needs and Concerns
Authors: Cunha Carla , Gonçalves Miguel M.
Published: February 2009

This commentary focuses on König's (2009) work as an opportunity to elaborate on selfhood as a dynamic and dialogical phenomenon. We depart from Bakhtinian dialogism and dialogical self theory to focus on the dynamics of selfhood processes and draw a more explicit theoretical link between the dialogical self and phenomenological experience. The interconnected dimensions of discontinuity and continuity in a multiple, multipositioned self are also elaborated. We defend that the construction of similitude in the self is permitted by self-regulation and self-organization processes that create recurring patterns in a moving self. Finally, the role that the introduction of difference and alterity can play in the promotion of change and development is also discussed.
Patterns of Party Integration, Influence and Autonomy in Seven Federations
Authors: Thorlakson Lori
Published: February 2009

In this article, I develop three measures of party organization in multi-level systems: vertical integration, influence and autonomy. I assess these in 27 parties in Canada, Australia, Germany, Austria, Switzerland, the United States and Spain and investigate how parties respond to the incentives and opportunities created by their institutional environment. Clear patterns emerge between the form of federal state design and the predominant form of party organization: in decentralized federations with low coordination requirements between federal and state-level governments, a tendency can be found towards highly autonomous state parties. Where resources are centralized and intergovernmental coordination requirements are high, integrated parties with low autonomy can be found. However, neither aspect of institutional design has a significant relationship with `upward' influence of state-level parties in the governance structure of federal parties.
The Saliency of Regionalization in Party Systems
Authors: Mazzoleni Martino
Published: February 2009

The article centres on the saliency that regional decentralization has had for British, Italian and French political parties in the past 60 years. A longitudinal analysis of the emphasis that parties have assigned to this issue in their manifestos confirms the hypothesis that certain environmental factors influence the changes of attention of parties on regionalization in their electoral discourse. Electoral threats and institutional reforms have a relevant impact and are mediated by the nature of party goals (policy-, vote- or office-seeking).
The untenable boundaries of biomedical knowledge: epistemologies and rhetoric strategies in the debate over evaluating complementary and alternative medicine
Authors: Keshet Yael
Published: February 2009

The article addresses contemporary epistemologies in examining struggles between the proponents of diverse medical approaches — some accepted as scientific and others that have not gained this status. It is based on research that investigated one of the central questions raised as a result of the growing popularity of complementary and alternative medicine (CAM) in western countries during the past three decades, namely: How can we know if CAM treatments are effective and beneficial? Discourse analysis was conducted on publications written by medical knowledge producers — experts participating in different professional groups addressing controversies over questions such as the desirability of researching CAM treatment effects, the appropriate methodology to be employed and the appropriate criteria for evaluating these effects. Some central debates are presented in the article. Examination of these controversies indicates that diverse kinds of knowledge are held by different groups of medical professionals. The ways in which they justify their knowledge and the rhetoric strategies they use for legitimizing it are specified. The great variety found among the different kinds of medical knowledge and rhetoric strategies and their dispersal along a `scientific'—'nonscientific' continuum, highlight the untenable and ambiguous boundaries of orthodox institutionalized biomedical knowledge.
Organizing allergy and being a `good' parent: parents' narratives about their children's emerging problems
Authors: Gunnarsson Nina , Hydén Lars-Christer
Published: February 2009

The article focuses on the early and problem-solving phases of the child's illness trajectory and on how child allergies are constructed and organized by the parents in a moral everyday context. The parents' narratives were reconstructed as narratives, describing the pathways parents take before they decide to seek professional medical aid as well as showing how they construct themselves as responsible parents. Before consulting health professionals the parents have often tried a range of different ways to define, control and manage their children's various problems. Allergy problems were interpreted and responded to differently, depending on the way they emerged in everyday life. Acute reactions quickly led to an illness definition and a diagnosis. Gradual and diffuse problems were not so easily defined. They were at first interpreted and responded to as normal infant problems, but, through the parents' readiness and various situational and temporal clues, they were organized as symptoms of illness . Parents seek medical aid when their own strategies fail or do not fully work, but their decisions are also formed within a pre-problem context of their moral accountability as parents.
`Automatically you become a polygamist': `culture' and `norms' as resources for normalization and managing accountability in talk about responses to infertility
Authors: de Kok B.C.
Published: February 2009

In the developing world, infertility is a serious problem. It leads to both psychological and social hardship, in part because childless marriages often result in divorce, men taking another wife or extramarital relationships. Such responses have been attributed to cultural norms that mandate procreation. However, there are theoretical, methodological and moral issues with treating cultural norms as behavioural determinants. They have been insufficiently acknowledged in health research. Therefore, I demonstrate an alternative discursive approach, which examines how people actively mobilize `culture' or `norms' in interactions, and the interpersonal functions thereby fulfilled (e.g. blaming or justifying). Analysis is presented of interviews on (responses to) infertility in Malawi. I show how respondents construct polygamy and extramarital affairs as culturally and normatively required, `automatic' and normal solutions for fertility problems and play down people's accountability for these practices. These accounts and constructions appear to facilitate engagement in affairs and polygamy when people face fertility problems, which seems problematic from a health and gender perspective. Thus, detailed analysis of how people use `culture' and `norms' in situ is important because it provides insights into its potentially undesirable consequences. Moreover, such analysis provides a starting point for culturally and gender sensitive interventions, since it highlights people's agency, and creates a space to re-construct and change practices.
Little bottles and the promise of probiotics
Authors: Burges Watson Duika , Moreira Tiago , Murtagh Madeleine
Published: February 2009

In this article we explore `regimes of hope' in contemporary bioscience as articulated in spaces of health consumption. We use the case study of probiotic little bottles, highlighting their promissory branding as consumer products, to consider how hope and truth play out across different spaces of health care — the supermarket, media and laboratory. Drawing on work within both sociological and geographic literatures to think about hope, truth and probiotics, this article explores their ambiguous promise through an analysis of their biomedical and popular representation. The seemingly incommensurate promise of probiotics between popular and medical spheres provides the point of departure for an examination of the geographies of hope, truth and selfhood.
The centrality of personal relationships in the creation and amelioration of mental health problems: the current interdisciplinary case
Authors: Pilgrim David , Rogers Anne , Bentall Richard
Published: February 2009

An interdisciplinary case is made for the centrality of personal relationships in the creation and amelioration of mental health problems. Taking the work of John Bowlby as a starting point, the article summarizes accumulating evidence from the past 50 years about the link between childhood adversity and adult mental health problems. Evidence is also reviewed about contemporary interpersonal impacts on adult mental health from natural social settings and in professional therapy. These empirical summaries are then discussed in the context of dominant trends in professional knowledge about bio-determinism within psychiatry and the emphasis upon models and techniques in professional and political advocates of the psychological therapies. It is concluded that the latter trends are diverting us from policies, which properly concede the importance of relationships for improving the mental health of the population.
Be wealthy to stay healthy
Authors: Lixin Cai
Published: February 2009

Using the Household, Income and Labour Dynamics in Australia (HILDA) survey data, this study examines the effect of wealth on health transitions of older Australians. By focusing on health transitions instead of health status itself, the study avoids potential endogeneity of wealth arising from the reverse effect of health on wealth. Two health indicators are used to define health transitions: self-reported general health status and the existence of long-term health conditions. The results show that, for both health indicators, wealthy people are less likely to experience a transition from good to poor health, suggesting that wealth might have a causal effect on health.
A time varying hidden Markov model with latent information
Authors: Otranto Edoardo
Published: February 2009

The time varying hidden Markov models are based on the use of some observable variables, which we suppose to drive the transition probabilities. The estimation of the model is conditional on the availability of this information, which is not obvious. In this paper we propose a time varying hidden Markov model with the transition probabilities driven by a latent variable subject to the same Markovian changes of the dependent variable. The model has a state-space form and the latent variable is estimated using a modified Kim filter, so that this information is always available; furthermore, the estimation of this latent variable is useful to forecast the changes in the state. We show the practical characteristics of this model through an example in which the latent variable is the business cycle.
Modelling general patterns of digit preference
Authors: Camarda Carlo G. , Eilers Paul H.C. , Gampe Jutta
Published: February 2009

In many applications data can be interpreted as indirect observations of a latent distribution. A typical example is the phenomenon known as digit preference, i.e. the tendency to round outcomes to pleasing digits. The composite link model (CLM) is a useful framework to uncover such latent distributions. Moreover, when applied to data showing digit preferences, this approach allows estimation of the proportions of counts that were transferred to neighbouring digits. As the estimating equations generally are singular or severely ill-conditioned, we impose smoothness assumptions on the latent distribution and penalize the likelihood function. To estimate the misreported proportions, we use a weighted least-squares regression with an added L1 penalty. The optimal smoothing parameters are found by minimizing the Akaike’s information Criterion (AIC). The approach is verified by a simulation study and several applications are presented.
Understanding young people's citizenship learning in everyday life
Authors: Biesta Gert , Lawy Robert , Kelly Narcie
Published: February 2009

In this article we present insights from research which has sought to deepen understanding of the ways in which young people (aged 13—21) learn democratic citizenship through their participation in a range of different formal and informal practices and communities. Based on the research, we suggest that such understanding should focus on the interplay between contexts for action, relationships within and across contexts, and the dispositions that young people bring to such contexts and relationships. In the first part of the article we show how and why we have broadened the narrow parameters of the existing citizenship discourse with its focus on political socialization to encompass a more wide-ranging conception of citizenship learning that is not just focused on school or the curriculum. In the second part of the article we describe our research and present two exemplar case studies of young people who formed part of the project. In the third part we present our insights about the nature and character of citizenship learning that we have been able to draw from our research. In the concluding section we highlight those dimensions of citizenship learning that would have remained invisible had we focused exclusively on schools and the curriculum. In this way we demonstrate the potential of the approach to understanding citizenship learning that we have adopted.
Testing citizenship and allegiance
Authors: Osler Audrey
Published: February 2009

This article examines recent UK government policy and proposals relating to immigration and citizenship, and the ways in which these policies are presented as means of securing allegiance and integration. From 1997, the incoming Labour government emphasized the importance of informed, active citizenship and social justice. From 2001, the emphasis shifted to community cohesion, with immigrants identified as a potential threat to cohesion. The article analyses the knowledge required of new settlers through the `citizenship test', introduced in 2005, and the assumptions made about immigrants and about British culture and society in the test. It critiques the concepts of `active citizenship', `earned citizenship' and `probationary citizenship' in the 2008 Green Paper, The Path to Citizenship . These policy proposals, if enacted, threaten migrants' employment opportunities, risk creating barriers to participation and undermining social cohesion. They place unrealistic demands on aspirant citizens, which are not placed on established citizens.
RankAggreg, an R package for weighted rank aggregation
Authors: Pihur Vasyl , Datta Susmita , Datta Somnath
Published: February 2009

Background

Researchers in the field of bioinformatics often face a challenge of combining several ordered lists in a proper and efficient manner. Rank aggregation techniques offer a general and flexible framework that allows one to objectively perform the necessary aggregation. With the rapid growth of high-throughput genomic and proteomic studies, the potential utility of rank aggregation in the context of meta-analysis becomes even more apparent. One of the major strengths of rank-based aggregation is the ability to combine lists coming from different sources and platforms, for example different microarray chips, which may or may not be directly comparable otherwise.

Results

The RankAggreg package provides two methods for combining the ordered lists: the Cross-Entropy method and the Genetic Algorithm. Two examples of rank aggregation using the package are given in the manuscript: one in the context of clustering based on gene expression, and the other one in the context of meta-analysis of prostate cancer microarray experiments.

Conclusion

The two examples described in the manuscript clearly show the utility of the RankAggreg package in the current bioinformatics context where ordered lists are routinely produced as a result of modern high-throughput technologies.
"Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes
Authors: Ren Jianfeng , Liu Xiao , Zhang Guofan , Liu Bin , Guo Ximing
Published: February 2009

Duplications and rearrangements of coding genes are major themes in the evolution of mitochondrial genomes, bearing important consequences in the function of mitochondria and the fitness of organisms. Yu et al. (BMC Genomics 2008, 9:477) reported the complete mt genome sequence of the oyster Crassostrea hongkongensis (16,475 bp) and found that a DNA segment containing four tRNA genes (trnK

1
, trnC, trnQ

1
and trnN), a duplicated (rrnS) and a split rRNA gene (rrnL5') was absent compared with that of two other Crassostrea species. It was suggested that the absence was a novel case of "tandem duplication-random loss" with evolutionary significance. We independently sequenced the complete mt genome of three C. hongkongensis individuals, all of which were 18,622 bp and contained the segment that was missing in Yu et al.'s sequence. Further, we designed primers, verified sequences and demonstrated that the sequence loss in Yu et al.'s study was an artifact caused by placing primers in a duplicated region. The duplication and split of ribosomal RNA genes are unique for Crassostrea oysters and not lost in C. hongkongensis. Our study highlights the need for caution when amplifying and sequencing through duplicated regions of the genome.
Gene Ontology annotation highlights shared and divergent pathogenic strategies of type III effector proteins deployed by the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic Escherichia coli strains
Authors: Lindeberg Magdalen , Biehl Bryan S , Glasner Jeremy D , Perna Nicole T , Collmer Alan , Collmer Candace W
Published: February 2009

Genome-informed identification and characterization of Type III effector repertoires in various bacterial strains and species is revealing important insights into the critical roles that these proteins play in the pathogenic strategies of diverse bacteria. However, non-systematic discipline-specific approaches to their annotation impede analysis of the accumulating wealth of data and inhibit easy communication of findings among researchers working on different experimental systems. The development of Gene Ontology (GO) terms to capture biological processes occurring during the interaction between organisms creates a common language that facilitates cross-genome analyses. The application of these terms to annotate type III effector genes in different bacterial species – the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic strains of Escherichia coli – illustrates how GO can effectively describe fundamental similarities and differences among different gene products deployed as part of diverse pathogenic strategies. In depth descriptions of the GO annotations for P. syringae pv tomato DC3000 effector AvrPtoB and the E. coli effector Tir are described, with special emphasis given to GO capability for capturing information about interacting proteins and taxa. GO-highlighted similarities in biological process and molecular function for effectors from additional pathosystems are also discussed.
Programmed cell death in host-symbiont associations, viewed through the Gene Ontology
Authors: Chibucos Marcus C , Collmer Candace W , Torto-Alalibo Trudy , Gwinn-Giglio Michelle , Lindeberg Magdalen , Li Donghui , Tyler Brett M
Published: February 2009

Manipulation of programmed cell death (PCD) is central to many host microbe interactions. Both plant and animal cells use PCD as a powerful weapon against biotrophic pathogens, including viruses, which draw their nutrition from living tissue. Thus, diverse biotrophic pathogens have evolved many mechanisms to suppress programmed cell death, and mutualistic and commensal microbes may employ similar mechanisms. Necrotrophic pathogens derive their nutrition from dead tissue, and many produce toxins specifically to trigger programmed cell death in their hosts. Hemibiotrophic pathogens manipulate PCD in a most exquisite way, suppressing PCD during the biotrophic phase and stimulating it during the necrotrophic phase. This mini-review will summarize the mechanisms that have evolved in diverse microbes and hosts for controlling PCD and the Gene Ontology terms developed by the Plant-Associated Microbe Gene Ontology (PAMGO) Consortium for describing those mechanisms.
Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae
Authors: Meng Shaowu , Brown Douglas E , Ebbole Daniel J , Torto-Alalibo Trudy , Oh Yeon Yee , Deng Jixin , Mitchell Thomas K , Dean Ralph A
Published: February 2009

Background

Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly.

Methods

A similarity-based (i.e., computational) GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked.

Results

In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO). In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57%) being annotated with 1,957 distinct and specific GO terms. Unannotated proteins were assigned to the 3 root terms. The Version 5 GO annotation is publically queryable via the GO site http://amigo.geneontology.org/cgi-bin/amigo/go.cgi. Additionally, the genome of M. oryzae is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html. The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System.

Conclusion

Our analysis provides comprehensive and robust GO annotations of the M. oryzae genome assemblies that will be solid foundations for further functional interrogation of M. oryzae.