bluuebunny/crossref_metadata_2025 huggingface dataset:
Unemployment Benefits, Unemployment Duration and Subsequent Job Quality
Authors: Pollmann-Schult Matthias , Büchel Felix
Published: February 2005

The high unemployment figures in many European countries are often attributed to overgenerous unemployment benefits. However, proponents of benefit cuts tend not to recognize that unemployment benefits also facilitate longer job searches and, as a result, ultimately improve job matches. In this article, we investigate the effects of unemployment benefits on subsequent job quality by differentiating between transitions from unemployment to correctly allocated jobs and to over-education. Data are drawn from the West German Life History Study (GLHS). Results from Kaplan-Meier estimators and hazard regression models show that non-recipients of unemployment benefits indeed have a shorter unemployment duration, but that they also have significantly higher rates of transition to over-education than recipients of unemployment benefits. On the other hand, the receipt of unemployment benefits does not influence the transition to qualified jobs, which seems to be influenced more by labour demand. It is therefore important to bear in mind that reforming the unemployment compensation system by reducing unemployment benefits will not only shorten the average unemployment duration, but also increase the incidence of over-education and consequently reduce the overall job match quality in the labour market.
Ready... Ready... Drop!
Authors: Clark Andrew M. , Christie Thomas B.
Published: February 2005

This content analysis of coalition leaflets dropped in Iraq during the recent war is viewed through a framework developed to analyze government international communication efforts to affect international public opinion and policy support. Under the framework, such messages have three main functions: survival, countering disinformation and facilitative communication. The study’s hypothesis that most leaflets would have ‘survival’ messages is supported. Such messages have the strongest potential to influence public opinion, based on the positive effects of limiting casualties and ensuring economic survival. Messages countering disinformation address enemy propaganda, and messages used for facilitative communication create a friendly atmosphere. The study also analyzed intended audiences and categorized specific leaflet messages. The study is useful in understanding the nature and effectiveness of government efforts to influence public opinion during times of crisis or war.
Where Freedom Matters
Authors: Dimitrova Daniela V. , Beilock Richard
Published: February 2005

The goal of this study was to explore inter-country differences in Internet connectivity among the formerly socialist countries of Eastern Europe, the former Soviet Union and Mongolia. Of particular interest was investigating if, in a region where per capita income and infrastructure differences are not extreme, other factors would become the dominant determinants. The results of the multivariate analysis show that the openness of society and cultural factors, using religion as a proxy, play critical roles. Countries with higher levels of civil liberties and those with Christian majority populations tend to have higher Internet connectivity.
Torsion of Open and Closed Thin-Walled Laminated Composite Sections
Authors: Salim Hani A. , Davalos Julio F.
Published: February 2005

Vlasov’s theory is expanded to perform the linear analysis of open and closed sections made of general laminated composites. Following the guidelines of Mechanics of Laminated Beams, the transverse shear deformations are included in the formulation. To overcome the overestimation of stiffness by the often assumption of negligible tangential stress, the laminate resultant force and moment are instead set to zero in this paper. The present model accounts for all possible elastic couplings in composite sections, such as extension- and bending-torsion. Applications of the formulation to flanged and box sections are presented and guidelines are provided on how to evaluate the torsional stiffness coefficients of the beam. A general solution for a fixed composite beam under tip torsional loads is derived, and the steps can be used to derive solutions for any other boundary conditions. The effect of warping-torsion on the torsional stiffness of the beam is investigated. Composite beams were tested in torsion and the angle of twist and shear strains were measured for verification of the analytical model predictions, which agree closely with the experimental results and finite element results.
Development and Application of a Model Using Center of Gravity of Hysteresis Loops to Predict Fatigue Damage Accumulation in Fiber-reinforced Plastic Laminates
Authors: Momenkhani Kourosh , Sarkani Shahram , Jones D. L.
Published: February 2005

A new methodology for modeling fatigue damage accumulation in fiber-reinforced plastic (FRP) laminates is introduced. This new model, termed the CG method, or the CG Model, utilizes the center of gravity (CG) of hysteresis loops (HL). It is inspired by previous investigations into damage accumulation models based on HL, such as maximum displacement (the width of the HL), energy dissipation (the area of the HL), plastic strain (the width of the interior part of the HL), and stiffness reduction. The CG method combines all these models, relates them to each other, and presents very consistent results. The CG model is especially helpful in cases where the other models cannot be used. This study shows that using the CG model a set of straight lines is created that present the evolution of the positions of the CG of the HLs during fatigue tests. These ‘curves’ may then be employed to build the complete set of curves that, even for untested specimens at different stress levels, accurately predict fatigue damage accumulation in FRP laminates. Employing this method also provides more insight into the damage condition of the specimen than other models allow.
The Proof of the Pudding: Proverbs and Gender in the Performance Arena
Authors: Fontaine Carole R.
Published: February 2005

Context of use often determines the final, embedded meaning of an aphorism. Use in a ‘performance arena' proceeds through a complex interaction between folklore users and audiences, and a shared set of meanings which is invoked by the saying. Issues of status, gender, and age of proverb users and audiences also influence performance and meaning. Building on the work of folklorist John Miles Foley and others, this study outlines features of the performance arena for the use of aphorisms, usingElihu in Job 32.6-10, and a slave woman's use of a proverbial sayingin the Westcar Papyrus. A visual model of proverb performance based on computer object editing is proposed.
The Relationship Between Leaders’ Personality and Their Reactions to and Use of Multisource Feedback
Authors: Smither James W. , London Manuel , Richmond Kristin Roukema
Published: February 2005

This study examined the extent to which personality predicts leaders’ reactions to multisource feedback and use of the feedback for development. Leaders ( N = 116) in an elite unit of the U.S. military completed the Jackson Personality Inventory 6 months prior to multisource performance measurement. Self-report and psychologists’ ratings of reactions to feedback were collected immediately after feedback was provided ( n = 95). Self-report ratings ( n = 49) of development were collected 6 months later. Breadth of interest was positively related to viewing the feedback as valuable. Leaders high in emotional stability were more likely to be rated by a psychologist as motivated to use the feedback. Leaders high in responsibility felt obligated to use the feedback results. Six months later, leaders high in sociability were more likely to have sought additional feedback, and leaders high in responsibility were more likely to have engaged in developmental behaviors.
A Construct Validity Study of Commitment and Perceived Support Variables
Authors: Bishop James W. , Scott K. Dow , Goldsby Michael G. , Cropanzano Russell
Published: February 2005

Social exchange theory suggests that employees feel commitment toward both their employing organizations and their work teams, while also experiencing varying levels of support from these same entities. Unfortunately, previous work has neither fully explored this possibility nor tested the capacity of currently available instruments to adequately measure the distinctiveness of the associated constructs. To address this need, we collected data from 902 employees in four diverse organizations. As predicted, respondents distinguished among organizational commitment, team commitment, organizational support, and team support. Furthermore, as predicted, perceived support from an entity predicted commitment to that same entity.
The Enduring Place of Hierarchy in World Politics: Tracing the Social Logics of Hierarchy and Political Change
Authors: Hobson John M. , Sharman J. C.
Published: February 2005

Conventional wisdom maintains that since 1648 the international system has comprised states-as-like units endowed with Westphalian sovereignty under anarchy. And while radical globalization theorists certainly dispute the centrality of the state in modern world politics, nevertheless most assume that the state retains its sovereignty under globalization. In contrast we argue that hierarchical sub-systems (and hence unlike units) have been common since 1648, and that the international system continues to be characterized by hierarchical (as well as anarchic) relations. The article goes on to reveal the existence of these multiple hierarchic formations and uncovers the differing social logics connected with identity-formation processes that govern their reproduction. Successive religious, racial, socialist and democratic social logics not only constitute their reproduction, but the emergence of new norms, social ideas and identities have to an important extent accounted for the rise and decay of successive hierarchies.
Screening and treatment for prostate cancer: The evidence and implications for practice
Authors: Steggall Martin J. , Lee Angela
Published: February 2005

Prostate cancer is the second most diagnosed cancer in men, but there is considerable debate over whether or not to screen for the condition. The issues in the debate surrounding screening are clarified in this paper. One of the recommendations of the guidelines for urology from the National Institute for Clinical Excellence (NICE, 2002) is that patients receive balanced information about management options for their condition.

The NICE guidelines also suggest that ‘major improvements' are required in information and support services for patients and carers, and that nurse specialists in the urology cancer team will play a key role in these services. The options for management and treatment are discussed in the light of these recommendations and the relative merits of each are considered.
Future career pathways in nursing and midwifery. A Delphi survey of nurses and midwives in South West England
Authors: Beattie Angela , Hek Gill , Ross Kath , Galvin Kathleen
Published: February 2005

There is growing interest, both nationally and internationally and within healthcare research, regarding future career pathways for nurses and midwives and what these pathways should represent. This paper presents the results of a research project that investigated these issues. A Delphi approach was taken to determine consensus, and consisted of three rounds: round 1 — statementgeneration, rounds 2 and 3 — rating and ranking of statements. The study aimed to discover the extent to which participants agreed about what the key features of a future career pathway should represent. Forty-three nurses and midwives representing a wide range of nurses and midwives participated. Consensus was achieved and 14 key features were identified. The paper concludes by suggesting that these statements will aid and inform stakeholders and decision-makers as to the future direction that career pathways in nursing and midwifery could take.
Meeting research governance requirements by developing a joint research and development strategy between NHS and higher education partners
Authors: Carnwell Ros , Jones Julie A. , Baker Sally-Ann
Published: February 2005

The Research Governance Framework (DoH, 2001) requires health and social care organisations to promote a research culture in their organisation and ensure that staff are supported in, and held accountable for, the professional conduct of research. In Wales, recent policy documents also necessitate the building of research capacity in health and social care in order to develop a high-quality workforce (WAG, 2002: 31) and deal with recruitment and retention problems by supporting initiatives and developments (NAfW, 2001). A literature search revealed that, although such strategies exist, none were reported to use an action research framework.

This paper, therefore, reports on the progress of an action research project to develop, implement and evaluate a Joint Research and Development Strategy between North East Wales NHS Trust and North East Wales Institute of Higher Education. The strategy reported on in this paper used action research as a means of empowering stakeholders to become involved in research, whilst ensuring that the strategy continues to be implemented and evaluated. The paper reports on progress made in the first cycle of this action research process and outlines plans for future cycles.
The Research Governance Framework for Health and Social Care: Implications for developing research in primary care
Authors: Meerabeau Liz , Ruston Annmarie , Clayton Julie
Published: February 2005

The Research Governance Framework for Health and Social Care is a framework of responsibilities and quality checks formulated by the English Department of Health for researchers and others. Primary care trusts were required to comply with the RGF by April 1, 2003. Implementing research governance within primary care trusts includes establishing systems for being notified of any research activity, peer review and scientific support.

This paper discusses findings arising from research commissioned in south London in 2003 by one of the national pilot sites for research governance in primary care. Data were gathered by means of telephone interviews with 23 experienced academics within the four south London higher education institutions included in the project. In particular, the paper explores issues concerning the effects of the research government framework on student projects, and the implications of these for the development of research capacity in primary care.

A key message from this paper is that primary care research is still quite fragile, and that a heavy-handed introduction of research governance may deter neophytes and hamper research capacity-building. In particular, the withdrawal of higher education institutions from requiring primary datagathering for MScs because of the increasing hurdles of bureaucracy could make it more difficult for experienced practitioners to develop research skills.
Research governance issues in the care home sector
Authors: Reed Jan , Cook Glenda , Cook Margaret
Published: February 2005

Research governance in care homes is a complex process, due to the ambiguous status of the care home as a public and a private space. As such, public sector research governance processes may infringe individual's rights to make decisions about participation in research, while treating the processes of informed consent as a purely individual matter may fail to safeguard individuals who may be vulnerable. This paper discusses these dilemmas in the light of existing research governance frameworks, and goes on to outline protocols that the team have developed for their own use.
Clinical and academic perspectives on how to develop and enhance nursing research activities
Authors: Jinks Annette M. , Green Helen E.
Published: February 2005

This paper seeks to outline how clinical and academic colleagues can work together to promote nursing research and development in order to enhance care delivery. The literature shows that problems concerning capacity and capability continue to impede progress in developing further the contribution that nursing research can make to patient care. The settings which are the focus of this collaboration are a large acute teaching hospital NHS Trust and a post-1992 university. In order to develop firm foundations that a collaborative nursing research strategy could rest on, a SWOT analysis was undertaken. The SWOT analysis demonstrates that there is a clear need to increase the number of nurses participating in research and development activities in both settings. This is a fundamental requirement if evidence based nursing practice is to be a reality.
Towards a collaborative learning environment for children’s pain management: leveraging an online discussion forum
Authors: Curran-Smith Janet , Abidi Syed Sibte Raza , Forgeron Paula
Published: February 2005

Effective management of pediatric pain requires proactive and effective collaboration between health practitioners from a variety of health disciplines. This article investigates the merits of a collaborative learning environment to address the knowledge gaps experienced by a community of pediatric pain practitioners. We present a knowledge management solution that leverages an online discussion forum as a collaborative learning environment rooted in team members sharing experiences, offering support to solve problems, guiding members to information/knowledge resources, informing peers about clinical practice guidelines, and simply seeking advice on matters pertaining to pediatric pain management. Team interactions, via the discussion forum, will be captured and represented as a social network to provide useful insights into the dynamics of team collaboration and to identify the patterns of knowledge flow amongst the team members.
Tacit knowledge, rule following and Pierre Bourdieu’s philosophy of social science
Authors: Gerrans Philip
Published: February 2005

Pierre Bourdieu has developed a philosophy of social science, grounded in the phenomenological tradition, which treats knowledge as a practical ability embodied in skilful behaviour, rather than an intellectual capacity for the representation and manipulation of propositional knowledge. He invokes Wittgenstein’s remarks on rule-following as one way of explicating the idea that knowledge is a skill. Bourdieu’s conception of tacit knowledge is a dispositional one, adopted to avoid a perceived dilemma for methodological individualism. That dilemma requires either the explanation of regularities in social behaviour as the result of the tacit representation of procedural rules (‘legalism’) or the self-conscious representation of behavioural goals (‘voluntarism’) by individuals. After explaining the apparent dilemma, I then argue that Wittgenstein’s remarks on rule following actually undermine, rather than support, a dispositional solution. Nonetheless, the philosophy of social science can survive without a dispositional account of knowledge. Such a social science needs, firstly, to embrace one horn of the dilemma, voluntarism, provided that the relevant regularities can be explained as unintended consequences of agents’ self-represented intentions. Secondly, such a social science should treat theorists’ interpretations as unifying generalizations, not hypotheses about the acquisition of tacit knowledge. Finally, where appeal to cognitive psychology can distinguish otherwise equivalent theories in social science, social science should incorporate the data of cognitive psychology concerning tacit mental processes.
Intersubjective openings
Authors: Driver Susan
Published: February 2005

This essay explores notions of maternal desire within feminist psychoanalysis with an interest in challenging heteronormative frameworks of analysis. Providing close critical readings of texts by Jessica Benjamin, Julia Kristeva, Kaja Silverman and Hortense Spillers, I trace conceptual openings through which to interpret maternal sexuality as a mobile process of intersubjectivity that is grounded in changing historical relations of experience. I argue that Spillers’ approach transforms a critical process of reading desire away from the insularities and exclusions of conventional psychoanalytic knowledges towards a democratic and reflexive process of representation and analysis.
‘Who put the “Me” in feminism?’
Authors: Tyler Imogen
Published: February 2005

This article examines what is at stake in the attribution of narcissism to femininity and feminism and the routes through which arguments about ‘feminist narcissism’ became central to the popular abjection of feminism. It emphasizes the central role of narcissistic theories of identity in enabling feminist theory to prise open the mechanisms of feminine identity and thereby expose and critique the sexual politics of identity practices. The article argues that theorizing the politics of narcissism opens up ways of thinking through some of the pressing and complex questions which face women today, questions of self-identity, self-esteem, body image, cultural idealization, normativity, incorporation, consumption and agency.
Exposing the fallacies of anti-porn feminism
Authors: Shrage Laurie
Published: February 2005

This paper examines an issue at the centre of feminist debates about pornography and sex work, and that is whether these practices reduce women to sex objects. I question the assumption that the expression of sexual desire is unique in its power to degrade and dehumanize persons. I show that this assumption underlies Catharine MacKinnon’s attack on pornography by considering MacKinnon’s intellectual debt to the philosopher Immanuel Kant. I then examine recent discussions of sexual objectification in the philosophical literature and argue that MacKinnon’s adaptation of Kant has flaws comparable to Kant’s original account of sexual desire.
Inside Out
Authors: Attwood Feona
Published: February 2005

This article examines the representation of men as domestic experts in the lifestyle genre on British primetime TV. This is contextualized in relation to changing representations of the home as a space for the stylish individual and to changes in British primetime programming, where a movement towards hybrid TV forms appears to rearticulate the mission to ‘inform, educate and entertain’ and to transform private matters into public spectacle. The article aims to examine the ways in which contemporary representations of the male domestic expert struggle to negotiate perceived boundaries between the ‘inside’ of private space and the ‘outside’ of the public sphere and between the categories of femininity and masculinity, a struggle that is evident across the lifestyle genre and within individual programmes, such as BBC2’s Home Front. In Home Front, aestheticism and camp become key strategies for the redefinition of the home and masculinity as matters of lifestyle.
The marketplace, emerging technology and marketing theory
Authors: Zinkhan George M.
Published: February 2005

The marketplace is a human invention that simultaneously delivers a standard of living and serves as a forum for the exchange of ideas. In the 21st century, we see the ‘marketspace’ as an innovation that has potential to enhance human experiences. In this commentary, we explore how emerging technology (e.g. the Internet) is transforming the marketplace, and we discuss how marketing theory might evolve in order to keep pace with this phenomenon.
Concept discovery, process explanation, and theory deepening in e-marketing research: The case of online auctions
Authors: Dholakia Utpal M.
Published: February 2005

By reviewing recent consumer research on online auctions, the commentary distinguishes between three forms of e-marketing research: (1) concept discovery, leveraging advances in technology to identify and describe new concepts or phenomena of significance to marketers; (2) process explanation, seeking to provide insights into the psychological, social, and economic mechanisms underlying the discovered concepts or phenomena through asking and answering ‘when’ and ‘why’ questions; and (3) theory deepening, using the online environment as the setting or context to develop, elaborate on, and test general marketing and consumer behavior theories. It is argued that while there is substantial value in each of these research forms for advancing marketing knowledge, theory deepening has perhaps been the least popular form of research conducted in online environments thus far, but it may yet turn out to be the most significant and enduring form in the long run.
Next stop, unravel: The tangled web of e-consumer research
Authors: Mittal Banwari
Published: February 2005

Current research in e-consumer behavior is examined to recognize gains in our understanding as well as to identify a much needed alteration in our general research strategy. I call this altered strategy unraveling, and illustrate its use with contributions from extant studies. This suggested strategy calls for a more inclusive framework of explanatory factors, kept disentangled, decompounded, and disaggregated, if we are to move beyond the hitherto largely exploratory research phase toward a more generalizable body of knowledge on e-consumer behavior.
Assessing Cross-Cultural Validity of Fear of Crime Measures through Comparisons between Linguistic Communities in Belgium
Authors: Pauwels Lieven , Pleysier Stefaan
Published: February 2005

In order for cross-cultural comparisons of ‘fear of crime’ to be meaningful, the instruments used to measure the constructs—both ‘fear of crime’ itself and other constructs used to explain it—have to exhibit adequate cross-cultural equivalence. Not only does potential cross-cultural bias invalidate ‘fear of crime’ comparisons, it also distorts the true relationships between explanatory variables and ‘fear of crime’ when testing a conceptual model. This paper uses comparisons between the Flemish- and French-speaking populations of Belgium to explore these problems of cross-cultural equivalence. The data are provided by the Belgian Safety Monitor 1998, a large-scale national survey focusing on ‘fear of crime’ and related topics. Cross-cultural equivalence within a theory-driven contextual model was assessed using structural equation modelling (LISREL). A theoretically relevant, exploratory model with ‘fear of crime’ as the dependent variable was tested. Both the dependent and independent constructs in the model were assessed for their cross-cultural equivalence. In principle, this allows a model that is free from cultural bias to be specified. However, in this case there was no evidence of measurement variance between the two cultural groups.
Violent Hypocrisy
Authors: Hobbs Dick , Winlow Simon , Hadfield Philip , Lister Stuart
Published: February 2005

The development of alcohol-based night-time economies as part of government-sponsored post-industrial urban regeneration involves two interconnected political and economic processes. The first is the shift to a consumer economy, and the second is the movement within local governance from the provision of services towards a focus upon nurturing economic growth. The violence and disorder that have resulted from the huge expansion in these night-time economies have produced a crisis for state policing that has led, via licensing, to the expansion of commercially relevant control strategies. This paper, based upon extensive empirical research, discusses the hypocrisy that is inherent in the governance of liminal licence.
The ‘Other’ Lessons from Ireland?
Authors: Mulcahy Aogán
Published: February 2005

In a paper entitled ‘Lessons from Ireland’, Paddy Hillyard argued that Northern Ireland essentially served as a testing ground for the development of repressive policy measures that eventually would transfer elsewhere. In this article, I engage with the important thesis advanced by Hillyard and others, and argue that it stands in need of theoretical refinement and empirical elaboration. First, I highlight some factors that might be considered in any re-evaluation of this approach. Second, I examine the impact of the Northern conflict on policing in Britain and the Republic of Ireland, both to demonstrate the salience of these issues and to highlight ways in which the conflict’s impact was tempered by other factors. Finally, I suggest that a focus on the negative lessons of conflict should be complemented by attention to positive lessons of conflict and its resolution
Intronic splicing of hyaluronan synthase 1 (HAS1): a biologically relevant indicator of poor outcome in multiple myeloma
Authors: Adamia Sophia , Reiman Tony , Crainie Mary , Mant Michael J. , Belch Andrew R. , Pilarski Linda M.
Published: February 2005

In this study, we show that the hyaluronan synthase 1 (HAS1) gene undergoes aberrant intronic splicing in multiple myeloma (MM). In addition to HAS1 full length (HAS1FL), we identify 3 novel splice variants of HAS1, HAS1Va, HAS1Vb, and HAS1Vc, detected in patients with MM or monoclonal gammopathy of undetermined significance (MGUS). HAS1Vb and HAS1Vc undergo intronic splicing with creation of a premature stop codon. MM cells expressing one or more HAS1 variants synthesize extracellular and/or intracellular hyaluronan (HA). Expression of the HAS1Vb splice variant was significantly correlated with reduced survival (P = .001). Together, alternative HAS1 gene splicing, the correlations between HAS1 splicing and HA synthesis, and the correlations between HAS1 splicing and reduced survival of MM patients support the hypothesis that the family of HAS1 protein plays a significant role in disease progression. Further, expression of HAS1Vb, in conjunction with HAS1FL and/or other HAS1 variants, may lead to accumulation of intracellular HA molecules and an impact on receptor for HA-mediated motility (RHAMM)-mediated mitotic abnormalities in MM. This study highlights the potential importance of HAS1 and its alternative splicing in pathophysiology of MGUS and MM. (Blood. 2005;105: 4836-4844)
PSSM-based prediction of DNA binding sites in proteins
Authors: Ahmad Shandar , Sarai Akinori
Published: February 2005

Background

Detection of DNA-binding sites in proteins is of enormous interest for technologies targeting gene regulation and manipulation. We have previously shown that a residue and its sequence neighbor information can be used to predict DNA-binding candidates in a protein sequence. This sequence-based prediction method is applicable even if no sequence homology with a previously known DNA-binding protein is observed. Here we implement a neural network based algorithm to utilize evolutionary information of amino acid sequences in terms of their position specific scoring matrices (PSSMs) for a better prediction of DNA-binding sites.

Results

An average of sensitivity and specificity using PSSMs is up to 8.7% better than the prediction with sequence information only. Much smaller data sets could be used to generate PSSM with minimal loss of prediction accuracy.

Conclusion

One problem in using PSSM-derived prediction is obtaining lengthy and time-consuming alignments against large sequence databases. In order to speed up the process of generating PSSMs, we tried to use different reference data sets (sequence space) against which a target protein is scanned for PSI-BLAST iterations. We find that a very small set of proteins can actually be used as such a reference data without losing much of the prediction value. This makes the process of generating PSSMs very rapid and even amenable to be used at a genome level. A web server has been developed to provide these predictions of DNA-binding sites for any new protein from its amino acid sequence.

Availability

Online predictions based on this method are available at http://www.netasa.org/dbs-pssm/
FlyPNS, a database of the Drosophila embryonic and larval peripheral nervous system
Authors: Orgogozo Virginie , Grueber Wesley B
Published: February 2005

Background

The embryonic and larval peripheral nervous system of Drosophila melanogaster is extensively studied as a very powerful model of developmental biology. One main advantage of this system is the ability to study the origin and development of individual sensory cells. However, there remain several discrepancies regarding the organization of sensory organs in each abdominal segment A1-A7.

Description

We have constructed a web site called FlyPNS (for Fly Peripheral Nervous System) that consolidates a wide range of published and unpublished information about the embryonic and larval sensory organs. It communicates (1) a PNS pattern that solves the discrepancies that have been found in the recent literature, (2) the correspondence between the different nomenclatures that have been used so far, (3) a comprehensive description of each sensory organ, and (4) a list of both published and unpublished markers to reliably identify each PNS cell.

Conclusions

The FlyPNS database integrates disparate data and nomenclature and thus helps understanding the conflicting observations that have been published recently. Furthermore, it is designed to provide assistance in the identification and study of individual sensory cells. We think it will be a useful resource for any researcher with interest in Drosophila sensory organs.
A novel replication-independent histone H2a gene in mouse
Authors: Nishida Hiromi , Suzuki Takahiro , Tomaru Yasuhiro , Hayashizaki Yoshihide
Published: February 2005

Background

An uncharacterized histone H2a-coding transcript (E130307C13) has been cloned from a mouse full-length cDNA library. This transcript is encoded on chromosome 6, approximately 4 kb upstream of a histone H4 gene, Hist4h4. The proteins encoded by this transcript and the human H2afj mRNA isoform-2 have the highest amino acid similarity. In this paper, we characterize it from the expression pattern given by quantitative RT-PCR.

Results

Quantitative RT-PCR indicated that the gene that encodes E130307C13 (E130307C13) is regulated in a replication-independent manner, and therefore it is H2afj. Certainly, H2afj transcript lacks a stem-loop structure at the 3'-UTR but contains a poly (A) signal. In addition, its promoter region has a different structure from those of the replication-dependent histone H2a genes.

Conclusion

The bioinformatics imply that E130307C13 is a replication-independent H2a gene. In addition, quantitative RT-PCR analysis shows that it is replication-independent. Thus, it is H2afj, a novel replication-independent H2a gene in mouse.
Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes
Authors: Maier Lisa M , Smyth Deborah J , Vella Adrian , Payne Felicity , Cooper Jason D , Pask Rebecca , Lowe Christopher , Hulme John , Smink Luc J , Fraser Heather , Moule Carolyn , Hunter Kara M , Chamberlain Giselle , Walker Neil , Nutland Sarah , Undlien Dag E , Rønningen Kjersti S , Guja Cristian , Ionescu-Tîrgovişte Constantin , Savage David A , Strachan David P , Peterson Laurence B , Todd John A , Wicker Linda S , Twells Rebecca C
Published: February 2005

Background

One strategy to help identify susceptibility genes for complex, multifactorial diseases is to map disease loci in a representative animal model of the disorder. The nonobese diabetic (NOD) mouse is a model for human type 1 diabetes. Linkage and congenic strain analyses have identified several NOD mouse Idd (insulin dependent diabetes) loci, which have been mapped to small chromosome intervals, for which the orthologous regions in the human genome can be identified. Here, we have conducted re-sequencing and association analysis of six orthologous genes identified in NOD Idd loci: NRAMP1/SLC11A1 (orthologous to Nramp1/Slc11a1 in Idd5.2), FRAP1 (orthologous to Frap1 in Idd9.2), 4-1BB/CD137/TNFRSF9 (orthologous to 4-1bb/Cd137/Tnrfrsf9 in Idd9.3), CD101/IGSF2 (orthologous to Cd101/Igsf2 in Idd10), B2M (orthologous to B2m in Idd13) and VAV3 (orthologous to Vav3 in Idd18).

Results

Re-sequencing of a total of 110 kb of DNA from 32 or 96 type 1 diabetes cases yielded 220 single nucleotide polymorphisms (SNPs). Sixty-five SNPs, including 54 informative tag SNPs, and a microsatellite were selected and genotyped in up to 1,632 type 1 diabetes families and 1,709 cases and 1,829 controls.

Conclusion

None of the candidate regions showed evidence of association with type 1 diabetes (P values > 0.2), indicating that common variation in these key candidate genes does not play a major role in type 1 diabetes susceptibility in the European ancestry populations studied.
The domain architecture of large guanine nucleotide exchange factors for the small GTP-binding protein Arf
Authors: Mouratou Barbara , Biou Valerie , Joubert Alexandra , Cohen Jean , Shields David J , Geldner Niko , Jürgens Gerd , Melançon Paul , Cherfils Jacqueline
Published: February 2005

Background

Small G proteins, which are essential regulators of multiple cellular functions, are activated by guanine nucleotide exchange factors (GEFs) that stimulate the exchange of the tightly bound GDP nucleotide by GTP. The catalytic domain responsible for nucleotide exchange is in general associated with non-catalytic domains that define the spatio-temporal conditions of activation. In the case of small G proteins of the Arf subfamily, which are major regulators of membrane trafficking, GEFs form a heterogeneous family whose only common characteristic is the well-characterized Sec7 catalytic domain. In contrast, the function of non-catalytic domains and how they regulate/cooperate with the catalytic domain is essentially unknown.

Results

Based on Sec7-containing sequences from fully-annotated eukaryotic genomes, including our annotation of these sequences from Paramecium, we have investigated the domain architecture of large ArfGEFs of the BIG and GBF subfamilies, which are involved in Golgi traffic. Multiple sequence alignments combined with the analysis of predicted secondary structures, non-structured regions and splicing patterns, identifies five novel non-catalytic structural domains which are common to both subfamilies, revealing that they share a conserved modular organization. We also report a novel ArfGEF subfamily with a domain organization so far unique to alveolates, which we name TBS (TB C-S ec7).

Conclusion

Our analysis unifies the BIG and GBF subfamilies into a higher order subfamily, which, together with their being the only subfamilies common to all eukaryotes, suggests that they descend from a common ancestor from which species-specific ArfGEFs have subsequently evolved. Our identification of a conserved modular architecture provides a background for future functional investigation of non-catalytic domains.
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site
Authors: Feder Marcin , Bujnicki Janusz M
Published: February 2005

Background

Prediction of structure and function for uncharacterized protein families by identification of evolutionary links to characterized families and known structures is one of the cornerstones of genomics. Theoretical assignment of three-dimensional folds and prediction of protein function even at a very general level can facilitate the experimental determination of the molecular mechanism of action and the role that members of a given protein family fulfill in the cell. Here, we predict the three-dimensional fold and study the phylogenomic distribution of members of a large family of uncharacterized proteins classified in the Clusters of Orthologous Groups database as COG4636.

Results

Using protein fold-recognition we found that members of COG4636 are remotely related to Holliday junction resolvases and other nucleases from the PD-(D/E)XK superfamily. Structure modeling and sequence analyses suggest that most members of COG4636 exhibit a new, unusual variant of the putative active site, in which the catalytic Lys residue migrated in the sequence, but retained similar spatial position with respect to other functionally important residues. Sequence analyses revealed that members of COG4636 and their homologs are found mainly in Cyanobacteria, but also in other bacterial phyla. They undergo horizontal transfer and extensive proliferation in the colonized genomes; for instance in Gloeobacter violaceus PCC 7421 they comprise over 2% of all protein-encoding genes. Thus, members of COG4636 appear to be a new type of selfish genetic elements, which may fulfill an important role in the genome dynamics of Cyanobacteria and other species they invaded. Our analyses provide a platform for experimental determination of the molecular and cellular function of members of this large protein family.

Conclusion

After submission of this manuscript, a crystal structure of one of the COG4636 members was released in the Protein Data Bank (code 1wdj; Idaka, M., Wada, T., Murayama, K., Terada, T., Kuramitsu, S., Shirouzu, M., Yokoyama, S.: Crystal structure of Tt1808 from Thermus thermophilus Hb8, to be published). Our analysis of the Tt1808 structure reveals that we correctly predicted all functionally important features of the COG4636 family, including the membership in the PD-(D/E)xK superfamily of nucleases, the three-dimensional fold, the putative catalytic residues, and the unusual configuration of the active site.
Using purine skews to predict genes in AT-rich poxviruses
Authors: Da Silva Melissa , Upton Chris
Published: February 2005

Background

Clusters or runs of purines on the mRNA synonymous strand have been found in many different organisms including orthopoxviruses. The purine bias that is exhibited by these clusters can be observed using a purine skew and in the case of poxviruses, these skews can be used to help determine the coding strand of a particular segment of the genome. Combined with previous findings that minor ORFs have lower than average aspartate and glutamate composition and higher than average serine composition, purine content can be used to predict the likelihood of a poxvirus ORF being a "real gene".

Results

Using purine skews and a "quality" measure designed to incorporate previous findings about minor ORFs, we have found that in our training case (vaccinia virus strain Copenhagen), 59 of 65 minor (small and unlikely to be a real genes) ORFs were correctly classified as being minor. Of the 201 major (large and likely to be real genes) vaccinia ORFs, 192 were correctly classified as being major. Performing a similar analysis with the entomopoxvirus amsacta moorei (AMEV), it was found that 4 major ORFs were incorrectly classified as minor and 9 minor ORFs were incorrectly classified as major. The purine abundance observed for major ORFs in vaccinia virus was found to stem primarily from the first codon position with both the second and third codon positions containing roughly equal amounts of purines and pyrimidines.

Conclusion

Purine skews and a "quality" measure can be used to predict functional ORFs and purine skews in particular can be used to determine which of two overlapping ORFs is most likely to be the real gene if neither of the two ORFs has orthologs in other poxviruses.
Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley
Authors: La Rota Mauricio , Kantety Ramesh V , Yu Ju-Kyung , Sorrells Mark E
Published: February 2005

Background

Earlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) were linkage maps based on cDNA-RFLP markers. The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps. Higher density comparative maps using PCR-based anchor markers are necessary to better estimate the conservation of colinearity among cereal genomes. The purposes of this study were to characterize the proportion of transcribed DNA sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags.

Results

The proportions of SSR types (di-, tri-, tetra-, and penta-nucleotide repeats) and motifs varied with the length of the SSRs within and among the three species, with trinucleotide SSRs being the most frequent. Distributions of genomic microsatellites (gSSRs), EST-derived microsatellites (EST-SSRs), and transcribed regions in the contiguous sequence of rice chromosome 1 were highly correlated. More than 13,000 primer pairs were developed for use by the cereal research community as potential markers in wheat, barley and rice.

Conclusion

Trinucleotide SSRs were the most common type in each of the species; however, the relative proportions of SSR types and motifs differed among rice, wheat, and barley. Genomic microsatellites were found to be primarily located in gene-rich regions of the rice genome. Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals.
Selection of reference genes for gene expression studies in human neutrophils by real-time PCR
Authors: Zhang Xiaozhu , Ding Lily , Sandford Andrew J
Published: February 2005

Background

Reference genes, which are often referred to housekeeping genes, are frequently used to normalize mRNA levels between different samples. However the expression level of these genes may vary among tissues or cells, and may change under certain circumstances. Thus the selection of reference gene(s) is critical for gene expression studies. For this purpose, 10 commonly used housekeeping genes were investigated in isolated human neutrophils.

Results

Initial screening of the expression pattern demonstrated that 3 of the 10 genes were expressed at very low levels in neutrophils and were excluded from further analysis. The range of expression stability of the other 7 genes was (from most stable to least stable): GNB2L1 (Guanine nucleotide binding protein, beta polypeptide 2-like 1), HPRT1 (Hypoxanthine phosphoribosyl transferase 1), RPL32 (ribosomal protein L32), ACTB (beta-actin), B2M (beta-2-microglobulin), GAPD (glyceraldehyde-3-phosphate dehydrogenase) and TBP (TATA-binding protein). Relative expression levels of the genes (from high to low) were: B2M, ACTB, GAPD, RPL32, GNB2L1, TBP, and HPRT1.

Conclusion

Our data suggest that GNB2L1, HPRT1, RPL32, ACTB, and B2M may be suitable reference genes in gene expression studies of neutrophils.
Central neuropeptide Y receptors are involved in 3rd ventricular ghrelin induced alteration of colonic transit time in conscious fed rats
Authors: Tebbe Johannes J , Tebbe Clemens G , Mronga Silke , Ritter Michael , Schäfer Martin KH
Published: February 2005

Background

Feeding related peptides have been shown to be additionally involved in the central autonomic control of gastrointestinal functions. Recent studies have shown that ghrelin, a stomach-derived orexigenic peptide, is involved in the autonomic regulation of GI function besides feeding behavior. Pharmacological evidence indicates that ghrelin effects on food intake are mediated by neuropeptide Y in the central nervous system.

Methods

In the present study we examine the role of ghrelin in the central autonomic control of GI motility using intracerobroventricular and IP microinjections in a freely moving conscious rat model. Further the hypothesis that a functional relationship between NPY and ghrelin within the CNS exists was addressed.

Results

ICV injections of ghrelin (0.03 nmol, 0.3 nmol and 3.0 nmol/5 μl and saline controls) decreased the colonic transit time up to 43%. IP injections of ghrelin (0.3 nmol – 3.0 nmol kg-1 BW and saline controls) decreased colonic transit time dose related. Central administration of the NPY1 receptor antagonist, BIBP-3226, prior to centrally or peripherally administration of ghrelin antagonized the ghrelin induced stimulation of colonic transit. On the contrary ICV-pretreatment with the NPY2 receptor antagonist, BIIE-0246, failed to modulate the ghrelin induced stimulation of colonic motility.

Conclusion

The results suggest that ghrelin acts in the central nervous system to modulate gastrointestinal motor function utilizing NPY1 receptor dependent mechanisms.