bluuebunny/crossref_metadata_2025 huggingface dataset:
Ethnic Differences in the Effects of Intergenerational Relations on Adolescent Problem Behavior in U.S. Single-Mother Families
Authors: Pan En-ling , Farrell Michael P.
Published: July 2006

This study examines whether the effects of single-mother families (SMFs) on adolescent problem behavior are buffered by supportive mothering and the involvement of nonresident fathers and whether the effectiveness of these two buffers varies by ethnicity. Based on the data from the National Longitudinal Study of Adolescent Health, the authors find that supportive mothering within SMFs buffers their effects for most groups. Compared to other ethnic groups, Asian American mothers’ supportiveness is less effective in buffering the impact on drug use. For Black adolescents, nonresident father involvement buffers the effects on delinquency and drug use. However, Asian American and Hispanic father involvement in SMFs is associated with increased problem behavior. The findings suggest that ethnic groups with more experience dealing with SMFs may be ahead of those with less experience in developing child-rearing practices that buffer the effects of SMFs on problem behavior.
Participative Case Studies: Integrating Case Writing and a Traditional Case Study Approach in a Marketing Context
Authors: Forman Howard
Published: July 2006

Case-based pedagogy is a valuable tool for applying business concepts and theories to organizational contexts. Traditional case-based pedagogy offers such learning opportunities. What this pedagogy lacks, however, is an element of real-time experiential learning opportunities. This research focuses on the advantages of incorporating a case-writing assignment in an MBA curriculum and integrating it with the traditional case-study methodology in what is termed participative case writing. This research details the integrated case-study methodology and includes specific implementation recommendations.
Why We Don't Really Know What Statistical Significance Means: Implications for Educators
Authors: Hubbard Raymond , Armstrong J. Scott
Published: July 2006

In marketing journals and market research textbooks, two concepts of statistical significance—p values and αlevels—are commonly mixed together. This is unfortunate because they each have completely different interpretations. The upshot is that many investigators are confused over the meaning of statistical significance. We explain how this confusion has arisen and make several suggestions to teachers and researchers about how to overcome it.
Where Does the Time Go? A Diary Approach to Business and Marketing Students’ Time Use
Authors: Nonis Sarath A. , Philhours Melodie J. , Hudson Gail I.
Published: July 2006

What are students doing with their time? Existing research mostly has focused on time used for study and/or work in relation to academic outcomes. This study uses a diary approach to explore business and marketing students’ time use encompassing all student activities, not just study or work. A clustering procedure resulted in two meaningful groups, campus-centered students (CCS) and life-centered students (LCS), that were similar in terms of students’ ability, gender, race, age, and so on but differed in that CCS worked fewer hours and spent more time studying, watching TV, and in entertainment than LCS. Perhaps most importantly, CCS achieved higher semester and cumulative grade point averages and perceived academic performance than LCS. Strategies are offered for faculty and administrators in terms of course and program design and delivery, including online and Web-assisted courses, syllabi that assist students in propitious time-management choices, chunking, personalization, and required time-use diaries.
The Impact of Image Management, Self-Justification, and Escalation of Commitment on Knowledge Development in the Marketing Discipline
Authors: Sharmaa Dheeraj , Albers-Miller Nancy D. , Pelton Lou E. , Straughan Robert D.
Published: July 2006

The paramount role of scholarship in the modern academic environment is manifest across program accreditation, individual evaluation, and institutional reputation processes. At the microlevel, success in this domain positively influences scholars’performance evaluations and institutions’external reputations. At the macrolevel, research expands and deepens the boundaries of the discipline. It is widely accepted that knowledge development is seminal to the advancement of marketing as a discipline. Accordingly, the academic community is increasingly concerned with potential limits and constraints on knowledge development. This article explores the influence of image management, self-justification, and escalation of commitment within the marketing discipline. A two-phase study using both a broad survey of marketing academicians and in-depth interviews of faculty at two universities indicates that these influences may be constraining creative marketing thought and may limit knowledge development.
DenseSLAM: Simultaneous Localization and Dense Mapping
Authors: Nieto Juan , Guivant Jose , Nebot Eduardo
Published: July 2006

This paper addresses the problem of environment representation for Simultaneous Localization and Mapping (SLAM) algorithms.

One of the main problems of SLAM is how to interpret and synthesize the external sensory information into a representation of the environment that can be used by the mobile robot to operate autonomously. Traditionally, SLAM algorithms have relied on sparse environment representations. However, for autonomous navigation, a more detailed representation of the environment is necessary, and the classic feature-based representation fails to provide a robot with sufficient information. While a dense representation is desirable, it has not been possible for SLAM paradigms.

This paper presents DenseSLAM, an algorithm to obtain and maintain detailed environment representations. The algorithm represents different sensory information in dense multi-layered maps. Each layer can represent different properties of the environment, such as occupancy, traversability, elevation or each layer can describe the same environment property using different representations. Implementations of the algorithm with two different representations for the dense maps are shown.

A rich representation has several potential advantages to assist the navigation process, for example to facilitate data association using multi-dimensional maps. This paper presents two particular applications to improve the localization process; the extraction of complex landmarks from the dense maps and the detection of areas with dynamic objects. The paper also presents an analysis of consistency of the maps obtained with DenseSLAM. The position error in the dense maps is analyzed and a method to select the landmarks in order to minimize these errors is explained.

The algorithm was tested with outdoor experimental data taken with a ground vehicle. The experimental results show that the algorithm can obtain dense environment representations and that the detailed representation can be used to improve the vehicle localization process.
Stability of Phase-Based Gain Modulation with Designer-Chosen Switch Functions
Authors: Armstrong Brian S. R. , Gutierrez José A. , Wade Bruce A. , Joseph Ralph
Published: July 2006

Phase-Based Gain-Modulation (PBGM) control is realized by modulating controller gains in response to the phase of the system state or tracking error. PBGM controllers have been applied to robotic hands, parallel manipulators and flexible mechanisms to give increased damping, reduced tracking error and friction compensation.

A novel method is presented to establish Lyapunov stability for PBGM control. Prior PBGM stability results incorporated a constraint which limited the range of provably stable systems. The present result removes this constraint, establishing Lyapunov stability for a substantially broader class of systems. Additionally, the new approach decouples the selection of the Lyapunov function from the controller design, permitting the controls designer to independently specify a switch function which determines the application of gain modulation.

The present results are applied to analyze PBGM control of the Sarcos dextrous manipulator, illuminating the stability properties of control experiments previously reported in the literature. Numerical methods for design calculations are also presented.
Smith Predictor Type Control Architectures for Time Delayed Teleoperation
Authors: Smith Andrew C. , Hashtrudi-Zaad Keyvan
Published: July 2006

An early control methodology for time delayed plants is the Smith predictor, in which the plant model is utilized to predict the non-delayed output of the plant and move the delay out of the control loop. Recent Smith predictor based teleoperation control architectures have used linear or fixed-parameter dynamic approximations of the slave/environment at the master for environment contact prediction. This paper discusses and analyzes the performance of the previous work and proposes new architectures to overcome their shortcomings. The proposed architectures consist of a novel pseudo two-channel nonlinear predictive controller and its variations that use neural networks for online estimation of the slave and environment dynamics to replicate the environment contact force at the master using a similar local network. Intermittent contact experiments are conducted on a teleoperation test-bed consisting of two Planar Twin-Pantograph haptic devices. The experimental results with half a second delay demonstrate significant improvement in stability and performance by the proposed neural network based predictive control architectures over traditional force-position and linear Smith predictor based control architectures.
The Relationship Between Moral Reasoning, Provictim Attitudes, and Interpersonal Aggression Among Imprisoned Young Offenders
Authors: Palmer Emma J. , Begum Asia
Published: July 2006

This study examined the relationship between moral reasoning, provictim attitudes, and interpersonal aggression among imprisoned young offenders. The participants were 60 imprisoned male young offenders from a young offender institution or remand centre. Using the Direct and Indirect Prisoner Behaviour Checklist, the offenders were categorised as one of four groups: perpetrator, victim, perpetrator-victim, or not involved. Participants in the four groups were compared on measures of provictim attitudes and sociomoral reasoning. The results showed that the majority of the participants were involved in victimising behaviours, with 43.3% falling into the perpetrator-victim category. Victims had significantly more empathic attitudes toward victims than did those in the perpetrator-victim group. No significant differences were found among the four groups on the sociomoral reasoning measure, nor was there a significant correlation between sociomoral reasoning and provictim attitudes. The results are discussed in terms of previous research and their implications for practice.
Parricides in the Media
Authors: Boots Denise Paquette , Heide Kathleen M.
Published: July 2006

This article is a content analysis of news reports of parricide cases occurring worldwide. An extensive search of online databases found coverage of more than 200 cases of children killing parents reported in the news media. Data pertaining to incidents, case-related variables (e.g., weapons used, other charges), and the processing of offenders from the initial charge through conviction and sentencing are examined. To the extent possible, media accounts are used to classify cases according to motive and Heide’s three types of parricide offenders. Twelve significant differences are discussed between U.S. and non-U.S. cases of parricide with respect to characteristics of parricide incidents, motives and other areas of clinical interest in reported parricide offenders, and Heide’s typology. The article concludes with a discussion of media representations of the phenomenon versus the actual occurrence, several observations that emerged from these news accounts, and directions for future research.
Validities and Abilities in Criminal Profiling
Authors: Kocsis Richard N.
Published: July 2006

This article discusses misconceptions in Bennell, Jones, Taylor, and Snook’s (2006) critique of Kocsis (2003a) concerning the validities and abilities surrounding criminal profiling. It also, in part, serves to canvass the approach of investigative psychology and what may be viewed as an imperative for some of its proponents to challenge evidence into the validity of criminal profiling, which is not easily reconcilable with that ideology.
Passive Recruitment in the Russian Urban Labor Market
Authors: Yakubovich Valery
Published: July 2006

About half of the hires made in the Russian city of Samara in 1998 were accomplished without an employer's outreach effort to fill the position. Such passive recruitment is supported primarily by hiring managers’ personal ties and the networks of the firm's current and previous employees. The positive effect of a job's attractiveness on the likelihood of passive recruitment is dampened by an increase in the stringency of the job's technical and social requirements. Thus, if necessary, employers actively search for candidates who meet the job requirements, and therefore the cost of search is the primary factor behind passive recruitment.
Beyond Profit? Sectoral Differences in High-Performance Work Practices
Authors: Kalleberg Arne L. , Marsden Peter V. , Reynolds Jeremy , Knoke David
Published: July 2006

Drawing on a recent survey of establishments in the United States, the authors examine how nonprofit, public, and for-profit establishments vary in the use of high-performance work organization (HPWO) practices that offer opportunities for participation in decision making (via self-directed teams and offline committees), enhance the capacity for participation (via multiskilling practices such as job rotation), and provide incentives for participation (via compensation practices). Nonprofit and public organizations are less likely to use performance incentives (gain sharing and bonuses) and some multiskilling practices than are for-profit organizations but more likely to use both self-directed work teams and offline committees. Sectoral differences in the prevalence of incentive compensation and self-directed teams persist after correlates of sector that predict HPWO prevalence—including establishment size, industry, computational requirements, and unionization—are controlled.
Restoring the American Dream
Authors: Marshall Ray
Published: July 2006

Restoring the American Dream requires a new social contract to replace the one revoked by extensive reliance on free-market ideologies. The industrial-era contract was based on the enormous productivity of the mass-production system and supportive policies to counteract some of that system's most serious weaknesses. Restoring the dream of good jobs and opportunities for all requires that highly stressed families demand more flexible high-road policies to unlock the knowledge economy's enormous potential, including stronger worker participation on corporate boards, at work, and in the larger society.
Pathways Out of Poverty
Authors: Rank Mark R.
Published: July 2006

This essay reviews three books that explore the feasibility of different avenues out of poverty. These include working one's way out of poverty through the low-wage labor market, the role of microenterprise programs in assisting individuals into economic prosperity, and the effectiveness of governmental social welfare and employment policies aimed at inequality and poverty reduction. The findings from these books provide strong support for the importance of strategies that address the structural rather than individual dynamics of poverty.
“It's the End of Work as We Know It...But Maybe Not”
Authors: Smith Vicki
Published: July 2006

Jeremy Rifkin's 1995 book, The End of Work, has recently been reissued, “updated for the 21st century.” Rifkin's prediction of how changing technologies will displace workers and lead to massive global unemployment by the mid-21st century has been repeatedly cited by many academics, policy makers, and members of the public. This essay revisits Rifkin's argument, asking, “How well does it stand a decade later?” The author contends that although The End of Work will continue to generate lively debate, it doesn't provide a defensible sociological guide for understanding work trends and, in fact, probably never should have been viewed as one.
Directive and Supportive Behaviors Used by Families of Hospitalized Older Adults to Affect the Process of Hospitalization
Authors: Jacelon Cynthia S.
Published: July 2006

As part of a grounded-theory study exploring the social processes of hospitalized older adults, family members were asked about their roles in relation to their hospitalized relative. Participants included five hospitalized older adults (aged ≥ 75 years), a family member, and a nurse for each older adult. Data saturation determined the number of participants. Data were analyzed using the constant comparative method to develop the substantive theory of managing personal integrity during hospitalization. Personal integrity is a concept encompassing the properties of health, dignity, and autonomy. Siblings, spouses, children, and grandchildren used a combination of supportive and directive behaviors to affect personal integrity and the hospitalization for their older relatives. In prior research, the entire family was viewed as the patient. This research is unique in that the family is viewed as a modifier of hospitalization affecting the older adult's hospital experience and not as the focus of care.
Family Systems Nursing
Authors: Simpson Peggy , Yeung “Frederick” Keung Kin , Kwan “Alan” Tsang Yat , Wah Wu Kam
Published: July 2006

In Hong Kong, mental health care has traditionally focused on the individual and the concept of considering the family as the unit of care is relatively new. The purpose of this article is to describe the process of planning, implementing, and evaluating a family systems nursing project in a psychiatric setting in Hong Kong. Psychiatric nurses ( N = 110) participated in seminars focusing on family systems nursing concepts and individuals and families suffering from mental illness. The Calgary Family Assessment Model and the Calgary Family Intervention Model formed the framework for practice. Significant changes were found both in the nurses' critical appraisal of their clinical practice related to family systems nursing and in their reflections on the reciprocity in their nurse/family relationships. In addition, hospital-wide systems outcomes were noted. This project appears to demonstrate that a family systems nursing approach is relevant for psychiatric nurses caring for Chinese individuals and their families suffering from mental illness.
Exploring the Therapeutic Family Intervention of Commendations
Authors: Limacher Lori Houger , Wright Lorraine M.
Published: July 2006

Offered in this article are interpretations that emerged in a qualitative, interpretive study focused on the family intervention called a “commendation.” The tradition of philosophical hermeneutics informs and shapes the analysis of the data. Research participants include a heterosexual couple and a nurse who engaged in therapeutic conversations focused on difficulties with Internet pornography. Data sources include videotapes of clinical sessions, documentation, and research interviews. Isolated segments of clinical videotape are shared with the couple to prompt their memory of commending practices that emerged in clinical sessions. Commendations are not experienced by this couple as gentle and warm but instead as extremely provocative, albeit constructive. This study illuminates the complex, contextual nature of commending practice and suggests that the noticing of strengths and resources contains much more than the spoken word.
The personal, the political and the popular
Authors: van Zoonen Liesbet
Published: July 2006

This article looks at articulations of gender, politics and citizenship by examining two European female heads of state: Tarja Halonen (Finland) and Angela Merkel (Germany). It discusses their personae in the context of emerging public debate about the merits and shortcomings of what is nowadays called ‘celebrity politics’, constituted by popularization and personalization. The analysis suggests that the increasing presence of popular culture in politics presents a complex and often unfavourable arena to women because of its inbuilt and extreme polarization of femininity and politics. It shows how Tarja Halonen and Angela Merkel have bypassed the personalization of politics and present a thoroughly political and professional persona to the public, rigidly concealing their private lives. As a result, female politicians - at least the two heads of state analysed here - tend to represent a classic ideal of political citizenship with clear boundaries and singular codes and conventions.
The public sphere on the beach
Authors: Hartley John , Green Joshua
Published: July 2006

This article discusses the idea of a ‘cultural public sphere’ together with related notions of ‘the’ public sphere, ‘counterpublics’ and ‘discourse publics’. It argues that the cultural public sphere emerges from cultural sources (e.g. ethnic identity) rather than political ones and is organized through private pursuits such as music, domestic life and leisure or entertainment venues. The article investigates the formation of a cultural public sphere by using the December 2005 ‘race riots’ on Australian beaches as a case study. It argues that culture interacts with politics as ‘new’ media interact with mainstream news; and that counterpublic spheres interact with the cultural public sphere as ‘internal’ communication coexists with ‘external’. The role of mainstream media in reporting and commenting on extreme displays is in part to stage conflict so that the general public can think through cultural-political issues via the theatrics.
United States of Europe or Free Trade Zone? No Thanks!
Authors: Vighi Fabio , Feldner Heiko
Published: July 2006

This article seeks to unravel the theoretical implications of Slavoj Žižek’s plea for a leftist Eurocentrism, focusing specifically on his defence of the ‘No’ vote in the French and Dutch referenda on the European Constitution (29 May and 1 June 2005, respectively). While most liberal commentators have read these results as a blow to the hopes of a United Europe against the overwhelming geopolitical power of the United States, Žižek argues that the French and Dutch ‘No’ votes express a deep-seated desire for a radically changed idea of Europe - a desire disclosing the need to move beyond the very notion of liberal democracy in order to ‘reinvent that which is to be defended’: democracy itself. While exploring the theoretical background to Žižek’s argument on Europe through an in-depth analysis of its psychoanalytic foundations (Lacan), the article also contextualizes it within the Marxist tradition, looking particularly at Lenin’s 1915 pamphlet, ‘On the Slogan for a United States of Europe’.
Feminist Reflections on Habermas’s Communicative Action
Authors: Pajnik Mojca
Published: July 2006

This article explores critiques and reformulations of Habermas’s concept of communicative action as presented by feminist authors. Numerous articles considering communicative action as developed by Habermas from a feminist perspective have been published, but no systematic analysis of these arguments exists. This article aims to fill the gap by providing an examination of various readings of communicative action from a feminist standpoint. If, on one hand, the article collects the dispersed feminist critique of communicative action and offers insight into feminist argumentation, its aim is, on the other hand, to reflect the critique itself. Therefore, attention is devoted both to feminist readings of communicative action, as well as to the potential shortcomings of these readings that are detected by a closer examination of Habermas’s own works. The article’s aim is also to show how feminist critics, in their interpretations and reformulations of communicative action, focus on an explication of the inclusive elements of communicative action.
Action of chelators in iron-loaded cardiac cells: accessibility to intracellular labile iron and functional consequences
Authors: Glickstein Hava , El Rinat Ben , Link Gabi , Breuer William , Konijn Abraham M. , Hershko Chaim , Nick Hanspeter , Cabantchik Z. Ioav
Published: July 2006

Labile iron in hemosiderotic plasma and tissue are sources of iron toxicity. We compared the iron chelators deferoxamine, deferiprone, and deferasirox as scavengers of labile iron in plasma and cardiomyocytes at therapeutic concentrations. This comprised chelation of labile plasma iron (LPI) in samples from thalassemia patients; extraction of total cellular iron; accessing labile iron accumulated in organelles and preventing formation of reactive-oxidant species; and restoring impaired cardiac contractility. Neonatal rat cardiomyocytes were used for monitoring chelator extraction of LCI (labile cell iron) as 59Fe; assessing in situ cell iron chelation by epifluorescence microscope imaging using novel fluorescent sensors for iron and reactive oxygen species (ROS) selectively targeted to organelles, and monitoring contractility by time-lapse microscopy. At plasma concentrations attained therapeutically, all 3 chelators eliminated LPI but the orally active chelators rapidly gained access to the LCI pools of cardiomyocytes, bound labile iron, attenuated ROS formation, extracted accumulated iron, and restored contractility impaired by iron overload. The effect of deferoxamine at therapeutically relevant concentrations was primarily by elimination of LPI. The rapid accessibility of the oral chelators deferasirox and deferiprone to intracellular labile iron compartments renders them potentially efficacious for protection from and possibly reversal of cardiac damage induced by iron overload.
STAT5 acts as a repressor to regulate early embryonic erythropoiesis
Authors: Schmerer Matthew , Torregroza Ingrid , Pascal Aude , Umbhauer Muriel , Evans Todd
Published: July 2006

STAT5 regulates definitive (adult stage) erythropoiesis through its ability to transduce signals from the erythropoietin receptor. A function for STAT-dependent signaling during primitive (embryonic) erythropoiesis has not been analyzed. We tested this in the Xenopus system, because STAT5 is expressed at the right time and place to regulate development of the embryonic primitive ventral blood island. Depletion of STAT5 activity results in delayed accumulation of the first globinexpressing cells, indicating that the gene does regulate primitive erythropoiesis. Our results suggest that in this context STAT5 functions as a repressor, since forced expression of an activator isoform blocks erythropoiesis, while embryos expressing a repressor isoform develop normally. The erythroid phenotype caused by the activator isoform of STAT5 resembles that caused by overexpression of fibroblast growth factor (FGF). We show that STAT5 isoforms can function epistatic to FGF and can be phosphorylated in response to hyperactivated FGF signaling in Xenopus embryos. Therefore, our data indicate that STAT5 functions in both primitive and definitive erythropoiesis, but by different mechanisms.
Blockade of αvβ3 and αvβ5 integrins by RGD mimetics induces anoikis and not integrin-mediated death in human endothelial cells
Authors: Maubant Sylvie , Saint-Dizier Dominique , Boutillon Morgane , Perron-Sierra Francoise , Casara Patrick J. , Hickman John A. , Tucker Gordon C. , Van Obberghen-Schilling Ellen
Published: July 2006

αv integrins are thought to play an important role in tumor angiogenesis. However, discrepancies between findings with Arg-Gly-Asp (RGD) mimetics, which block angiogenesis in animal models, and knockout mice, in which loss of some αv integrins enhances tumor angiogenesis, raise questions concerning the function of these integrins and the precise role of αv substrate mimetics in antiangiogenic therapies. We have examined the effects of a novel non–peptide RGD mimetic, S 36578-2, on human endothelial cells to elucidate its antagonist activity and to identify possible agonist functions. S 36578-2 is highly selective for αvβ3 and αvβ5 integrins and induces detachment, caspase-8 activation, and apoptosis in human umbilical endothelial cells (HUVECs) plated on vitronectin. Importantly, the compound has no effect on the morphology or survival of cells plated on interstitial matrix components such as fibronectin, and it does not potentiate the apoptotic process in suspended cells. Identical results were obtained with a cyclic RGD peptide with similar target specificity. In microvascular endothelial cells, S 36578-2–induced death was also linked to its antiadhesive effect, with established lines markedly more resistant than primary cultures to the antiadhesive and proapoptotic effects. Altogether, these findings have important implications for the development of this class of antiangiogenics.
Interleukin-6 induces hepcidin expression through STAT3
Authors: Wrighting Diedra M. , Andrews Nancy C.
Published: July 2006

Iron homeostasis is maintained through meticulous regulation of circulating hepcidin levels. Hepcidin levels that are inappropriately low or high result in iron overload or iron deficiency, respectively. Although hypoxia, erythroid demand, iron, and inflammation are all known to influence hepcidin expression, the mechanisms responsible are not well defined. In this report we show that the inflammatory cytokine interleukin-6 (IL-6) directly regulates hepcidin through induction and subsequent promoter binding of signal transducer and activator of transcription 3 (STAT3). STAT3 is necessary and sufficient for the IL-6 responsiveness of the hepcidin promoter. Our findings provide a mechanism by which hepcidin can be regulated by inflammation or, in the absence of inflammatory stimuli, by alternative mechanisms leading to STAT3 activation.
Tools for integrated sequence-structure analysis with UCSF Chimera
Authors: Meng Elaine C , Pettersen Eric F , Couch Gregory S , Huang Conrad C , Ferrin Thomas E
Published: July 2006

Background

Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a) provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b) facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit); (c) can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d) interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals.

Results

The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided.

Conclusion

The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is available for Microsoft Windows, Apple Mac OS X, Linux, and other platforms from http://www.cgl.ucsf.edu/chimera.
Similarities and differences of polyadenylation signals in human and fly
Authors: Retelska Dorota , Iseli Christian , Bucher Philipp , Jongeneel C Victor , Naef Felix
Published: July 2006

Background

Cleavage of messenger RNA (mRNA) precursors is an essential step in mRNA maturation. The signal recognized by the cleavage enzyme complex has been characterized as an A rich region upstream of the cleavage site containing a motif with consensus AAUAAA, followed by a U or UG rich region downstream of the cleavage site.

Results

We studied these signals using exhaustive databases of cleavage sites obtained from aligning raw expressed sequence tags (EST) sequences to genomic sequences in Homo sapiens and Drosophila melanogaster. These data show that the polyadenylation signal is highly conserved in human and fly. In addition, de novo motif searches generated a refined description of the U-rich downstream sequence (DSE) element, which shows more divergence between the two species. These refined motifs are applied, within a Hidden Markov Model (HMM) framework, to predict mRNA cleavage sites.

Conclusion

We demonstrate that the DSE is a specific motif in both human and Drosophila. These findings shed light on the sequence correlates of a highly conserved biological process, and improve in silico prediction of 3' mRNA cleavage and polyadenylation sites.
A novel flow cytometric assay for measurement of In Vivo pulmonary neutrophil phagocytosis
Authors: Vander Top Elizabeth A , Perry Greg A , Gentry-Nielsen Martha J
Published: July 2006

Background

Phagocytosis assays are traditionally performed in vitro using polymorphonuclear leukocytes (PMNs) isolated from peripheral blood or the peritoneum and heat-killed, pre-opsonized organisms. These assays may not adequately mimic the environment within the infected lung. Our laboratory therefore has developed a flow cytometric in vivo phagocytosis assay that enables quantification of PMN phagocytosis of viable bacteria within the lungs of rats. In these studies, rats are injected transtracheally with lipopolysaccharide (LPS) to recruit PMNs to their lungs. They are then infected with live 5(-and 6) carboxyfluorescein diacetate succinimidyl ester (CFDA/SE) labeled type 3 Streptococcus pneumoniae. Bronchoalveolar lavage is performed and resident alveolar macrophages and recruited PMNs are labeled with monoclonal antibodies specific for surface epitopes on each cell type. Three color flow cytometry is utilized to identify the cell types, quantify recruitment, and determine uptake of the labeled bacteria.

Results

The viability of the alveolar macrophages and PMNs isolated from the lavage fluid was >95%. The values of the percentage of PMNs in the lavage fluid as well as the percentage of PMNs associated with CFSE-labeled S. pneumoniae as measured through flow cytometry showed a high degree of correlation with the results from manual counting of cytospin slides.

Conclusion

This assay is suitable for measuring bacterial uptake within the infected lung. It can be adapted for use with other organisms and/or animal model systems.
Immunochemical characterization of polysaccharide antigens from six clinical strains of Enterococci
Authors: Hsu Carolyn T , Ganong Amanda L , Reinap Barbara , Mourelatos Zafiria , Huebner Johannes , Wang Julia Y
Published: July 2006

Background

Enterococci have become major nosocomial pathogens due to their intrinsic and acquired resistance to a broad spectrum of antibiotics. Their increasing drug resistance prompts us to search for prominent antigens to develop vaccines against enterococci. Given the success of polysaccharide-based vaccines against various bacterial pathogens, we isolated and characterized the immunochemical properties of polysaccharide antigens from five strains of Enterococcus faecalis and one strain of vancomycin-resistant E. faecium.

Results

We cultured large batches of each strain, isolated sufficient quantities of polysaccharides, analyzed their chemical structures, and compared their antigenic specificity. Three classes of polysaccharides were isolated from each strain, including a polyglucan, a teichoic acid, and a heteroglycan composed of rhamnose, glucose, galactose, mannosamine, and glucosamine. The polyglucans from all six strains are identical and appear to be dextran. Yields of the teichoic acids were generally low. The most abundant polysaccharides are the heteroglycans. The six heteroglycans are structurally different as evidenced by NMR spectroscopy. They also differ in their antigenic specificities as revealed by competitive ELISA. The heteroglycans are not immunogenic by themselves but conjugation to protein carriers significantly enhanced their ability to induce antibodies.

Conclusion

The six clinical strains of enterococci express abundant, strain-specific cell-surface heteroglycans. These polysaccharides may provide a molecular basis for serological typing of enterococcal strains and antigens for the development of vaccines against multi-drug resistant enterococci.
Carcinosarcoma of the colon: report of a case with morphological, ultrastructural and molecular analysis
Authors: Ambrosini-Spaltro Andrea , Vaira Valentina , Braidotti Paola , Rovati Marco PL , Ferrero Stefano , Bosari Silvano
Published: July 2006

Background

Carcinosarcoma of the colon is a rare histopathological entity with uncertain histogenesis, that shows both epithelial and mesenchymal malignant differentiation. Carcinosarcoma rarely affects the gastrointestinal tract and only few cases are reported in the colon. Herein we describe a carcinosarcoma of the ascending colon, with morphological, ultrastructural and molecular analysis.

Case presentation

An 81-year-old man was hospitalised for asthenia, weight loss and iron-deficiency anaemia. The patient underwent colonoscopy and adenocarcinoma was diagnosed by endoscopic biopsy. A right hemicolectomy was performed and, during surgical operation, liver metastases were detected. Histological examination of the surgical specimen revealed areas of both carcinomatous and sarcomatous differentiation, completely separated by fibrous septae. The sarcomatous component exhibited areas of smooth muscle and osteoblastic differentiation, with focal osteoid material deposition. Molecular analysis conducted separately on the epithelial and mesenchymal components revealed the same p53 gene mutation (R282W in exon 8) and identical polymorphisms in p53 exon 4, in EGFR exons 20 and 21, and in c-kit exon 17. Microsatellite markers analysis revealed a common loss of heterozygosis on 18q. Overall, the data are consistent with a common origin of the two tumor components. The patient was treated with 8 cycles of oral capecitabine (1250 mg/m2 twice a day for 14 days repeated every 28 days) and two years after surgery is alive with liver metastases.

Conclusion

Carcinosarcoma of the colon is a rare tumour with both epithelial and sarcomatous components. Molecular analysis of the current case suggests the histogenesis from a common cell progenitor.
Defining a common set of indicators to monitor road accidents in the European Union
Authors: Farchi Sara , Molino Nunzio , Giorgi Rossi Paolo , Borgia Piero , Krzyzanowski Michael , Dalbokova Dafina , Kim Rokho ,   the European Road Accident Indicator Working Group
Published: July 2006

Background

currently road accidents are mostly monitored through mortality and injury rates. This paper reports the methodology and the results of a project set forth by the European Union (EU) and coordinated by the WHO aimed at identifying and evaluating a core set of indicators to monitor the causal chain of road accident health effects. The project is part of the ECOEHIS (Development of Environment and Health Indicators for European Union Countries).

Methods

a group of experts (WG), identified 14 indicators after a review of the information collected at the EU level, each of them representing a specific aspect of the DPSEEA (Driving, Pressure, State, Exposure, Effect, Action) model applied and adapted to the road accidents.

Each indicator was scored according to a list of 16 criteria chosen by the WG. Those found to have a high score were analysed to determine if they were compatible with EU legislation and then tested in the feasibility study.

Results

11 of the 14 indicators found to be relevant and compatible with the criteria of selection were proposed for the feasibility study. Mortality, injury, road accident rate, age of vehicle fleet, and distance travelled are the indicators recommended for immediate implementation.

Conclusion

after overcoming the limitations that emerged (absence of a common definition of death by road accident and injury severity, underestimation of injuries, differences in information quality) this core set of indicators will allow Member States to carry out effective internal/external comparisons over time.
The glucocorticoid RU24858 does not distinguish between transrepression and transactivation in primary human eosinophils
Authors: Janka-Junttila Mirkka , Moilanen Eeva , Hasala Hannele , Zhang Xianzhi , Adcock Ian , Kankaanranta Hannu
Published: July 2006

Background

Glucocorticoids are used to treat chronic inflammatory diseases such as asthma. Induction of eosinophil apoptosis is considered to be one of the main mechanisms behind the anti-asthmatic effect of glucocorticoids. Glucocorticoid binding to its receptor (GR) can have a dual effect on gene transcription. Activated GR can activate transcription (transactivation), or by interacting with other transcription factors such as NF-κB suppress transcription (transrepression). RU24858 has been reported to transrepress but to have little or no transactivation capability in other cell types. The dissociated properties of RU24858 have not been previously studied in non-malignant human cells. As the eosinophils have a very short lifetime and many of the modern molecular biological methods cannot be used, a "dissociated steroid" would be a valuable tool to evaluate the mechanism of action of glucocorticoids in human eosinophils. The aim of this study was to elucidate the ability of RU24858 to activate and repress gene expression in human eosinophils in order to see whether it is a dissociated steroid in human eosinophils.

Methods

Human peripheral blood eosinophils were isolated under sterile conditions and cultured in the presence and/or absence RU24858. For comparison, dexamethasone and mometasone were used. We measured chemokine receptor-4 (CXCR4) and Annexin 1 expression by flow cytometry and cytokine production by ELISA. Apoptosis was measured by DNA fragmentation and confirmed by morphological analysis.

Results

RU24858 (1 μM) increased CXCR4 and Annexin 1 expression on eosinophils to a similar extent as mometasone (1 μM) and dexamethasone (1 μM). Like dexamethasone and mometasone, RU24858 did suppress IL-8 and MCP-1 production in eosinophils. RU24858 also increased spontaneous eosinophil apoptosis to a similar degree as dexamethasone and mometasone, but unlike dexamethasone and mometasone it did not reverse IL-5- or GM-CSF-induced eosinophil survival.

Conclusion

Our results suggest that in human eosinophils RU24858 acts as transactivator and transrepressor like classical glucocorticoids. Thus, RU24858 seems not to be a "dissociated steroid" in primary human eosinophils in contrast to that reported in animal cells. In addition, functionally RU24858 seems to be a less potent glucocorticoid as it did not reverse IL-5- and GM-CSF-afforded eosinophil survival similarly to dexamethasone and mometasone.
Electrophoresis of proteins and DNA on horizontal sodium dodecyl sulfate polyacrylamide gels
Authors: Izzo Vincenzo , Costa Maria A , Di Fiore Renata , Duro Giovanni , Bellavia Daniele , Cascone Eleonora , Colombo Paolo , Gioviale Maria C , Barbieri Rainer
Published: July 2006

An inexpensive Plexiglas apparatus which allows a simple and rapid preparation of horizontal polyacrylamide gels of different dimensions for different purposes, is described. Preparation of such gels is as easy and rapid as agarose gel preparation, and polymerized polyacrylamide gels are used to fractionate proteins or small DNA fragments using a common horizontal electrophoretic tank. This apparatus was used to electrophoretically fractionate proteins or DNA for immuno-blot analyses, particularirly in the study of the allergenic response to Parietaria judaica pollen in senescence, for Southern-blot hybridizations and in the study of DNA polymorphisms.
Effect of a lung recruitment maneuver by high-frequency oscillatory ventilation in experimental acute lung injury on organ blood flow in pigs
Authors: David Matthias , Gervais Hendrik W , Karmrodt Jens , Depta Arno L , Kempski Oliver , Markstaller Klaus
Published: July 2006

Introduction

The objective was to study the effects of a lung recruitment procedure by stepwise increases of mean airway pressure upon organ blood flow and hemodynamics during high-frequency oscillatory ventilation (HFOV) versus pressure-controlled ventilation (PCV) in experimental lung injury.

Methods

Lung damage was induced by repeated lung lavages in seven anesthetized pigs (23–26 kg). In randomized order, HFOV and PCV were performed with a fixed sequence of mean airway pressure increases (20, 25, and 30 mbar every 30 minutes). The transpulmonary pressure, systemic hemodynamics, intracranial pressure, cerebral perfusion pressure, organ blood flow (fluorescent microspheres), arterial and mixed venous blood gases, and calculated pulmonary shunt were determined at each mean airway pressure setting.

Results

The transpulmonary pressure increased during lung recruitment (HFOV, from 15 ± 3 mbar to 22 ± 2 mbar, P < 0.05; PCV, from 15 ± 3 mbar to 23 ± 2 mbar, P < 0.05), and high airway pressures resulted in elevated left ventricular end-diastolic pressure (HFOV, from 3 ± 1 mmHg to 6 ± 3 mmHg, P < 0.05; PCV, from 2 ± 1 mmHg to 7 ± 3 mmHg, P < 0.05), pulmonary artery occlusion pressure (HFOV, from 12 ± 2 mmHg to 16 ± 2 mmHg, P < 0.05; PCV, from 13 ± 2 mmHg to 15 ± 2 mmHg, P < 0.05), and intracranial pressure (HFOV, from 14 ± 2 mmHg to 16 ± 2 mmHg, P < 0.05; PCV, from 15 ± 3 mmHg to 17 ± 2 mmHg, P < 0.05). Simultaneously, the mean arterial pressure (HFOV, from 89 ± 7 mmHg to 79 ± 9 mmHg, P < 0.05; PCV, from 91 ± 8 mmHg to 81 ± 8 mmHg, P < 0.05), cardiac output (HFOV, from 3.9 ± 0.4 l/minute to 3.5 ± 0.3 l/minute, P < 0.05; PCV, from 3.8 ± 0.6 l/minute to 3.4 ± 0.3 l/minute, P < 0.05), and stroke volume (HFOV, from 32 ± 7 ml to 28 ± 5 ml, P < 0.05; PCV, from 31 ± 2 ml to 26 ± 4 ml, P < 0.05) decreased. Blood flows to the heart, brain, kidneys and jejunum were maintained. Oxygenation improved and the pulmonary shunt fraction decreased below 10% (HFOV, P < 0.05; PCV, P < 0.05). We detected no differences between HFOV and PCV at comparable transpulmonary pressures.

Conclusion

A typical recruitment procedure at the initiation of HFOV improved oxygenation but also decreased systemic hemodynamics at high transpulmonary pressures when no changes of vasoactive drugs and fluid management were performed. Blood flow to the organs was not affected during lung recruitment. These effects were independent of the ventilator mode applied.