bluuebunny/crossref_metadata_2025 huggingface dataset:
Syndesmotic Ankle Sprains in Athletes
Authors: Williams Glenn N. , Jones Morgan H. , Amendola Annunziato
Published: May 2007

Ankle sprains are among the most common athletic injuries and represent a significant source of persistent pain and disability. Despite the high incidence of ankle sprains in athletes, syndesmosis injuries have historically been underdiagnosed, and assessment in terms of severity and optimal treatment has not been determined. More recently, a heightened awareness in sports medicine has resulted in more frequent diagnoses of syndesmosis injuries. However, there is a low level of evidence and a paucity of literature on this topic compared with lateral ankle sprains. As a result, no clear guidelines are available to help the clinician assess the severity of injury, choose an imaging modality to visualize the injury, make a decision in terms of operative versus nonoperative treatment, or decide when the athlete may return to play. Increased knowledge and understanding of these injuries by clinicians and researchers are essential to improve the prevention, diagnosis, and treatment of this significant condition. This review will discuss the anatomy, mechanism of injury, diagnosis, and treatment of syndesmosis sprains of the ankle while identifying controversies in management and topics for future research.
Aqueous Degradation of MATER BI Y—Sisal Fibers Biocomposites
Authors: Alvarez V.A. , Ruseckaite R.A. , Vázquez A.
Published: May 2007

The effect of biotic and sterile aqueous environment (phosphate buffer pH 7.2, 25°C) on the water sorption, degradation behavior, and residual mechanical properties of short sisal fibers—Mater bi Y biocomposites is evaluated. The composite shows a higher water resistance in both media probably due to the presence of fiber—fiber and/or fiber—matrix interactions which are absent in the unfilled matrix. The presence of fibers seems to favor the microbial attack and the preferential loss of starch and hemicelluloses. The higher drop in dynamical-mechanical properties and creep behavior showed by the composite is not only associated with the loss of components but also with the detriment of fiber—matrix interface.
Studies on Melamine Formaldehyde (MF) Loaded Polyvinyl Acetate—Polyester Nonwoven Fabric Composites
Authors: Satheesh Kumar M.N. , Siddaramaiah
Published: May 2007

A series of composites is fabricated by impregnating the needled polyester nonwoven fabric in polyvinyl acetate (PVAc) latex. The effects of loading different amounts of melamine formaldehyde (MF) into PVAc on the physicomechanical properties of the composites have been studied. Percentage water absorption of composites have been determined both at room temperature for 24 h and in boiling water for 2 h. Heat aging studies conducted at 150 and 200 °C reveal that the composites have better dimensional stability at 150°C. The effect of salt water soaking at different temperatures viz., 30, 50, and 70°C on the mechanical properties, such as tensile strength, percentage elongation, and stitch tear strength has been studied. Vertical flammability test shows that the increase in the MF content has enhanced the flame resistance of the composites. The cyclic water-soaking test of the composites exhibits a reduction in thickness swelling with increase in the MF content in the system.
International Expert Organizations and Policy Adoption
Authors: Dalgic Umud K.
Published: May 2007

Microfinance as a development policy tool has enjoyed an increasing popularity in the last few years. The United Nations declared 2005 as the international year of microcredit. Since Muhammad Yunus and his Grameen Bank shared the Nobel Peace Prize in 2006, microfinance is once more under the spotlight. The prominence of development programs is mainly promoted by powerful international organizations like the World Bank. This article examines the World Bank's World Development Reports over time to demonstrate how the Bank became interested in, interpreted, and framed microfinance in accordance with its general background assumptions on poverty and development. The neoliberal interpretation by the Bank in the 1990s of notions such as social capital and gender is crucial for understanding its adoption of microfinance.
Alternative careers for graduates of LIS schools
Authors: Weech Terry L. , Konieczny Alison M.
Published: May 2007

Schools of Library and Information Science (LIS) have often promoted alternative careers as a marketing tool and some students enrol in LIS schools specifically to explore alternative careers. The literature on LIS career patterns continues to suggest that those non-traditional careers are desirable and viable alternatives. Yet the survey research based literature indicates that very few LIS graduates report finding employment outside traditional libraries in the US and Canada. This paper reviews the challenges of obtaining more accurate information on the career patterns of LIS graduates and discusses the international implications for analysing career patterns for LIS school graduates.
OFSTED and libraries in first and primary schools
Authors: Shenton Andrew K.
Published: May 2007

Little research has investigated the treatment of school libraries in OFSTED reports. This paper is devoted to a recent study that has examined the conclusions reached by inspectors visiting first and primary schools in a metropolitan borough in northern England. Forty-four reports relating to schools of these types were subjected to rigorous content analysis. Libraries were not given great prominence in the reports. Indeed, in 41 percent of them the school library was not referred to at all. Where the library was mentioned, inspectors typically emphasized the need for the organization to make a significant contribution to pupils' wider educational achievement.
The Sociocultural Needs of International Students in Higher Education: A Comparison of Staff and Student Views
Authors: Bartram Brendan
Published: May 2007

The following article examines the sociocultural needs of higher education students on an international degree programme delivered jointly by a post-1992 university in England and a polytechnic institution in the Netherlands. A brief discussion of relevant literature is followed by a methodological overview, detailing the qualitative research design, sample, and method. Results from the focus-group interviews indicate that the majority of students attach great significance to their sociocultural needs in all years of the programme. A number of specific social support mechanisms were identified by the students, as was a greater need for staff assistance in helping the learners create and maintain their social networks. Student views are subsequently compared to those of teaching staff, who articulate a more general awareness of growing student needs and dependency on staff. The article examines these disparities in understandings and discusses staff perceptions of the ways in which institutions might resolve such tensions.
A Comparative Study of Personal Time Perspective Differences Between Korean and American College Students
Authors: Kim Oi-Sook , Geistfeld Loren V.
Published: May 2007

This article compares the personal time perspectives of Korean and American college students. The results indicate American students have a personal time perspective that is different from their Korean counterparts. Implications for working with Koreans and Americans as foreign students are considered.
Group Argument
Authors: Seibold David R. , Meyers Renee A.
Published: May 2007

This article reviews and assesses the structuration program of research on group argument that has evolved over more than two decades. The authors first position group argument research in relationship to argument studies across many disciplines and especially at the intersection of three research traditions in communication. Acknowledging structuration theory foundations, the authors explicate their conceptualization of argument and explain the theoretical foundations of their approach. They next describe the methods that have been used to analyze group argument, including participants, data collection procedures, coding scheme and process, and contexts that have been employed in past investigations. They also survey the findings of this research program and how they have enhanced understanding of argument processes in groups and group argument—outcome linkages. The authors then offer a critique of the program, including challenges and unanswered questions. They note projects currently under way and conclude by identifying opportunities for interdisciplinary research on group argument.
Do Juries Deliberate? A Study of Deliberation, Individual Difference, and Group Member Satisfaction at a Municipal Courthouse
Authors: Gastil John , Burkhalter Stephanie , Black Laura W.
Published: May 2007

Despite long-standing interest in juries and a growing body of work on public deliberation, we have a limited understanding of how often everyday juries actually engage in meaningful deliberation. This study uses deliberative theory and small group research to develop a set of research questions and hypotheses regarding how juror characteristics promote deliberation as well as how deliberation influences juror satisfaction. Examination of 267 jurors' accounts of their experiences deliberating on municipal criminal juries suggests that juries do, indeed, deliberate at a remarkably high level of competence. Results show complex relationships between juror characteristics and their levels of deliberation as well as a direct link between the quality of deliberation and juror satisfaction.
Multinational and Multicultural Distributed Teams
Authors: Connaughton Stacey L. , Shuffler Marissa
Published: May 2007

Teams that span multiple geographic, temporal, and cultural boundaries have become prevalent in many industries and sectors. Researchers from multiple disciplines have begun to examine these multinational, multicultural (MNMC) distributed teams. The purpose of this article is to provide a review and critique of existing research in this area. To this end, the authors examine the ways scholars have conceptualized culture in this research, discuss the role that distribution is found to play in these teams, and provide a research agenda. The authors argue that scholars should continue to complicate their views of culture and embrace nuanced views of distribution to reflect the complexities of MNMC distributed team characteristics and processes.
How to Improve Decision Making in Small Groups
Authors: Klocke Ulrich
Published: May 2007

Decision-making groups are often biased in favor of shared information (sharedness bias) and in favor of its members' initial preferences (preference bias). The present experiment aimed at analyzing both biases at the group level (communication of information and preferences) and at the individual level (evaluation of information) simultaneously. Two interventions were evaluated, each focusing on one of the two biases and illustrating it with a group exercise. The interventions enhanced the amount of discussed information and reduced the preference bias but had no effects on decision quality. Dissent (diversity in members' initial preferences) enhanced the preference bias in information exchange but reduced both biases in information evaluation and improved decision quality when no intervention was applied. Decision quality correlated with individual-level processes but not with group-level processes.
SHRUB BATTLE: Understanding the making of landscape
Authors: Depigny Sylvain , Michelin Yves
Published: May 2007

Landscape changes in Europe's rural areas seem to generate a more visible impact. This trend raises new questions on rural management and brings about a conflict between farmers' land-use patterns and public expectations, which are often exclusively based on esthetics. The aim of the SHRUB BATTLE board game is to help tutors make future rural planners aware of the complex relationships between landscape dynamics and agricultural practices. It provides a novel illustration of vegetation dynamics. Three players each pilot a plant species. Their pawns are spread across the board to progressively shape the landscape. Opposite them, a fourth player in the role of the animal farmer implements the best grassland-management practices to fulfill a landscape purpose. The interaction between players' strategies combined with random natural or cyclical events serves to illustrate the land-use conflicts occurring in the field. This pedagogical tool can be used to instill the fundamental principles of relationships between landscape dynamics and agricultural activities. This game makes students aware of the fact that rural planning requires multidisciplinary skills and knowledge of collective processes.
Visual problem appraisal—Kerala's Coast: A simulation for social learning about integrated coastal zone management
Authors: Witteveen Loes , Enserink Bert
Published: May 2007

Integrated management of coastal zones is crucial for the sustainable use of scarce and vulnerable natural resources and the economic survival of local and indigenous people. Conflicts of interest in coastal zones are manifold, especially in regions with high population pressure, such as Kerala (in southwest India). The simulation of a consultancy mission to Kerala described in this article was designed for a classroom situation but it can also be applied in settings with local stakeholders as a tool for social learning. Filmed interviews with real stakeholders contributed largely to the realism of the simulation and stimulated learning: Students aligned with local stakeholders and acquired professional skills as future analysts; local people learned about their own situation and the frames of other stakeholders.
The Neurodevelopmental Impact of Prenatal Infections at Different Times of Pregnancy: The Earlier the Worse?
Authors: Meyer Urs , Yee Benjamin K. , Feldon Joram
Published: May 2007

Environmental insults taking place in early brain development may have long-lasting consequences for adult brain functioning. There is a large body of epidemiological data linking maternal infections during pregnancy to a higher incidence of psychiatric disorders with a presumed neurodevelopmental origin in the offspring, including schizophrenia and autism. Although specific gestational windows may be associated with a differing vulnerability to infection-mediated disturbances in normal brain development, it still remains debatable whether and/or why certain gestation periods may confer maximal risk for neurodevelopmental disturbances following the prenatal exposure to infectious events. In this review, the authors integrate both epidemiological and experimental findings supporting the hypothesis that infection-associated immunological events in early fetal life may have a stronger neurodevelopmental impact compared to late pregnancy infections. This is because infections in early gestation may not only interfere with fundamental neurodevelopmental events such as cell proliferation and differentiation, but it may also predispose the developing nervous system to additional failures in subsequent cell migration, target selection, and synapse maturation, eventually leading to multiple brain and behavioral abnormalities in the adult offspring. The temporal dependency of the epidemiological link between maternal infections during pregnancy and a higher risk for brain disorders in the offspring may thus be explained by specific spatiotemporal events in the course of fetal brain development. NEUROSCIENTIST 13(3):241—256, 2007.
Neurotransmitters and Brain Maturation: Early Paracrine Actions of GABA and Glutamate Modulate Neuronal Migration
Authors: Manent Jean-Bernard , Represa Alfonso
Published: May 2007

Migration of neurons from their birthplace to their final destination is an extremely important step in brain maturation, and cortical migration disorders are the most common brain developmental alteration observed in human patients. Among the mechanisms that govern neuronal migration, the neurotransmitters GABA and glutamate deserve particular attention: 1) neurotransmitters and receptors are expressed early in the developing brain, 2) neurotransmitters may act as paracrine signaling molecules in the immature brain, and 3) neurotransmitters regulate intracellular calcium required for many cellular functions, including cytoskeletal dynamic changes. Thus, many reports reviewed here aimed to demonstrate that the activation of specific GABA and glutamate receptors is instrumental in cell migration by acting as motility promoting, acceleratory, or stop signal. Interestingly, the regulation of migration by neurotransmitters and receptors depends on the type of migration (radial, tangential, or chain migration), the type of cells (principal glutamatergic neurons vs. GABAergic interneurons), and the brain area (neocortex, cerebellum, rostral migratory stream). A hypothesis is proposed that these differential actions in different cell types arise from a “homeostatic-like” regulation that controls final position, timing, and number of cells at destination. NEUROSCIENTIST 13(3):268—279, 2007.
Prefrontal Cortex and Long-Term Memory Encoding: An Integrative Review of Findings from Neuropsychology and Neuroimaging
Authors: Blumenfeld Robert S. , Ranganath Charan
Published: May 2007

Recent findings have led to a growing appreciation of the role of the lateral prefrontal cortex (PFC) in episodic long-term memory (LTM). Here, the authors will review results from neuropsychological and neuroimaging studies of humans and present a framework to explain how different regions of the PFC contribute to successful LTM formation. Central to this framework is the idea that different regions within the PFC implement different control processes that augment memory by enhancing or attenuating memory for certain aspects of a particular item or event. Evidence reviewed here suggests that ventrolateral regions of the PFC contribute to the ability to select goal-relevant item information, and that this processing strengthens the representation of goal-relevant features of items during LTM encoding. Dorsolateral regions of the PFC may contribute to the ability to organize multiple pieces of information in working memory, thereby enhancing memory for associations among items in LTM. Thus, dorsolateral and ventrolateral regions of the PFC may implement different control processes that support LTM formation in a complementary fashion. NEUROSCIENTIST 13(3):280—291, 2007.
The Restoration of Nature and Biogeography
Authors: Clark Brett , York Richard
Published: May 2007

Alfred Russel Wallace was one of the most renowned naturalists and scientific explorers of the 19th century. After 4 years exploring the Amazon basin, he spent 8 years traveling in the Malay Archipelago, during which time he discovered the principle of natural selection independently of Darwin. Wallace was a complex and contradictory figure who was an evolutionist and socialist as well as a strong defender of spiritualism. He is widely considered the key founder of biogeography—the field that studies the spatial distribution of species. He had a deep commitment to the natural world. His 1878 essay “Epping Forest” was a forward-looking statement about the need for ecological restoration, which was sufficiently radical for its time to cost him the post as superintendent of Epping Forest, which he was seeking.
Environmental Review as Battleground
Authors: Bonds Eric
Published: May 2007

Environmental reviews are required in the United States to determine in what ways and to what extent a proposed industrial development will affect the natural environment and human health. In this study, the author considers environmental reviews within the context of the treadmill of production and contributes to the empirical literature on the Treadmill of Production Model. The author does so by closely examining how power was exercised within one particular environmental review regarding a proposed tire-burning power plant in rural Minnesota. After documenting the ways power was exercised by the corporate developers of the plant, by state agency officials, and by citizen opponents, the author proposes that environmental reviews are best conceptualized as battlegrounds where contradictions of the treadmill can be fought out in protracted struggles. As such, environmental reviews provide citizens with tools to leverage power against owners and managers of capital that would not otherwise be available. However, achieving such leverage requires an inordinate expenditure of citizen resources, which means that environmental reviews tend overall to favor corporate interests and facilitate the expansion of production. The author ends by proposing changes to environmental review processes to create more favorable conditions for environmental protection.
Site the Mine in Our Backyard! Discursive Strategies of Community Stakeholders in an Environmental Conflict in New Zealand
Authors: Walton Sara
Published: May 2007

This article is centered around a decision to site a mining operation in a conservation area near a small community on the South Island of New Zealand. Two key groups emerged in the dispute over the decision: One was in favor of the mining operation and one was opposed. This intense conflict provided the opportunity to examine the notion of community as stakeholder—a stakeholder group not often considered by researchers. Through interviews and a media analysis, the discursive strategies employed by the various parties to actively support or oppose the decision are identified. In constituting these positions, both groups engage with broader discourses of place and identity and with classic rhetorical themes in business-environmental conflict. However, the identification of an activist community group willing and eager to have the mining operation sited in their local environment is the most unexpected finding in the research.
Landscapes of Risk
Authors: Meyler Deanna , Stimpson Jim P. , Cutchin Malcolm P.
Published: May 2007

Several hurricanes and industrial explosions in 2005 brought increasing public attention to the risk inherent in the location of US petrochemical facilities. The upper Texas Gulf Coast is home to a significant cluster of petrochemical industries including some of the largest refineries in the United States. Residents live, play and work in the shadow of petrochemical towers. While the petrochemical industries have brought jobs and economic development to the area, they have permanently changed the landscape and been linked to increased stress and illness for local residents. Nevertheless, the US demand for their products means that these industries will continue to pose ongoing risks for citizens that live near them. Our photo essay intends to provide insight into these particularly important and complex landscapes of risk—landscapes in which the natural environment and well-being of residents is largely ignored as fuel prices and energy security are debated.
Optical models of complex fenestration systems
Authors: Laouadi A. , Parekh A.
Published: May 2007

The need for energy conservation in buildings has spurred innovations in window technologies. These products include windows combined with shading devices, and windows featuring complex glazing such as switchable glazing, diffuse glazing, translucent and transparent insulation, patterned or decorative glass, etc. Current fenestration simulation tools for energy performance product ratings do not cover complex fenestration products. This paper addresses the development of detailed calculation models to compute the optical characteristics of complex fenestration products made up of a mixture of clear and scattering glazing layers. The models take into account not only the optical properties of the individual glazing layers making up the window product, but also the haze and gloss properties of the glazing layers. Specific optical models are developed to compute the optics of a clear substrate with applied or laminated scattering film, and composite film made up of a number of homogeneous materials with known optical properties. A general optical model was also developed for screen-like glazing panes such as insect/shading screens, roller blinds, drapery sheets, honeycomb transparent insulation and fibreglass translucent glazing.
Complex fenestration systems: towards product ratings for indoor environment quality
Authors: Laouadi A. , Parekh A.
Published: May 2007

Complex fenestration systems (CFS) include windows featuring complex glazing such as translucent and transparent insulation, solar control films, patterned or decorative glass, in-between pane shades, etc. CFS are believed to exhibit superior energy performance, but may have adverse effects on environmental features important for building-occupant satisfaction requirements such as the outdoor view (connection to outside), indoor view (feeling of privacy), luminance (major factor for discomfort glare), and light diffusion quality (relates to uniformity of illuminance on work plane). This article is part of a larger effort to rate complex fenestration systems for energy performance and indoor environment quality (IEQ). In the end, IEQ ratings must be derived from direct studies of how building occupants perceive the indoor environment conditions created by the installed fenestration product. As a first step, this work tackles the theoretical development of new metrics to rate CFS with regards to IEQ, namely the view impairment index, luminance index, and light diffusion quality index. The new indices are applied to some typical CFS, namely a diffuse window, and a clear window combined with an interior shading screen, and integrated perforated Venetian blinds. The results show that the diffuse window may increase the luminance by more than 100% under clear sky conditions when compared with a clear window with a similar light transmittance. White colored Venetian blinds may increase the window luminance by up to 50% and reduce the outdoor view by up to 66% as compared with a clear window with a similar light transmittance.
Phenomenology in practice: towards a methodology for a ‘subjective’ approach
Authors: Hamilton Sue , Whitehouse Ruth , Brown Keri , Combes Pamela , Herring Edward , Thomas Mike Seager
Published: May 2007

The article deals with the practice of phenomenological archaeological fieldwork, which is concerned with sensory experience of landscapes and locales. Phenomenological approaches in archaeology have cast light on aspects of past human experience not addressed by traditional archaeological methods. So far, however, they have neither developed explicit methodologies nor a discussion of methodological practice and have laid themselves open to accusations of being ‘subjective’ and ‘unscientific’. This article describes and explores three experiments in phenomenological archaeology developed in the context of the Tavoliere–Gargano Prehistory Project and carried out on Neolithic settlement sites of the type known asvillaggi trincerati.Our aims are both to develop explicit methods for this type of fieldwork and to combine phenomenology with other more traditional approaches, such as those concerned with technological, economic and environmental aspects of landscapes and sites. Our work also differs from other phenomenological archaeology in its concern with familiar, everyday experience and domestic contexts, rather than exceptional, special experience in ritual contexts. We consider how our particular approach might be used to further understandings of past lives.
High T-cell response to human cytomegalovirus induces chemokine-mediated endothelial cell damage
Authors: Bolovan-Fritts Cynthia A. , Trout Rodney N. , Spector Stephen A.
Published: May 2007

Human cytomegalovirus (CMV) infection has been linked to inflammatory diseases that involve vascular endothelial damage, including vascular disease and chronic transplant rejection. We previously reported that the host CD4+ T-cell response to CMV antigen presented by endothelial cells can produce interferon-γ and tumor necrosis factor-α at levels sufficient to drive induction of fractalkine, a key marker of inflammation, in endothelial cells. In this work, we report that donors with high frequencies of antigen-specific T cells to CMV (high responders) induce higher levels of activation-associated chemokines such as fractalkine, RANTES (regulated on activation, normal T cell expressed and secreted), and macrophage inflammatory protein-1β, together with cell-adhesion markers in endothelial cells compared with donors with low levels of CMV-specific T cells (low responders). High-responder cultures had higher levels of leukocyte recruitment and adherence to the endothelial monolayers associated with progressive damage and loss of the endothelial cells. These processes that led to endothelial destruction only required viral antigen and did not require infectious virus. Our findings further support that CMV may represent one member of a class of persistent pathogens in which a high antigen-specific T-cell response defines an important risk factor for development of chronic inflammation and endothelial cell injury.
Pathobiology of ALK+ anaplastic large-cell lymphoma
Authors: Amin Hesham M. , Lai Raymond
Published: May 2007

Anaplastic large-cell lymphoma (ALCL) was initially recognized on the basis of morphologic features and the consistent expression of CD30. It then became evident that the majority of these tumors are derived from lymphoid cells of T or null immunophenotype. The subsequent finding that t(2;5)(p23;q35) occurs in 40% to 60% of ALCL patients established a distinct clinicopathologic entity. This chromosomal translocation induces the formation of the chimeric protein nucleophosmin–anaplastic lymphoma kinase (NPM-ALK), which possesses significant oncogenic potential resulting from the constitutive activation of the tyrosine kinase ALK. In addition to its specific pathophysiologic events, NPM-ALK–expressing lymphoma presents with consistent clinical manifestations. Only 13 years after the identification of NPM-ALK, tremendous progress has been made in our understanding of this molecule because of the relentless efforts of multiple investigators who have dissected its biologic roles using in vitro and in vivo experimental models. Several upstream modulators, cross-reacting oncogenes, and downstream effectors of NPM-ALK have been identified and characterized. Understanding these interacting oncogenic systems is expected to facilitate the design of new therapeutic strategies and agents. In this review, we briefly discuss ALCL and focus on NPM-ALK.
Robust detection and verification of linear relationships to generate metabolic networks using estimates of technical errors
Authors: Kose Frank , Budczies Jan , Holschneider Matthias , Fiehn Oliver
Published: May 2007

Background

The size and magnitude of the metabolome, the ratio between individual metabolites and the response of metabolic networks is controlled by multiple cellular factors. A tight control over metabolite ratios will be reflected by a linear relationship of pairs of metabolite due to the flexibility of metabolic pathways. Hence, unbiased detection and validation of linear metabolic variance can be interpreted in terms of biological control. For robust analyses, criteria for rejecting or accepting linearities need to be developed despite technical measurement errors. The entirety of all pair wise linear metabolic relationships then yields insights into the network of cellular regulation.

Results

The Bayesian law was applied for detecting linearities that are validated by explaining the residues by the degree of technical measurement errors. Test statistics were developed and the algorithm was tested on simulated data using 3–150 samples and 0–100% technical error. Under the null hypothesis of the existence of a linear relationship, type I errors remained below 5% for data sets consisting of more than four samples, whereas the type II error rate quickly raised with increasing technical errors. Conversely, a filter was developed to balance the error rates in the opposite direction. A minimum of 20 biological replicates is recommended if technical errors remain below 20% relative standard deviation and if thresholds for false error rates are acceptable at less than 5%. The algorithm was proven to be robust against outliers, unlike Pearson's correlations.

Conclusion

The algorithm facilitates finding linear relationships in complex datasets, which is radically different from estimating linearity parameters from given linear relationships. Without filter, it provides high sensitivity and fair specificity. If the filter is activated, high specificity but only fair sensitivity is yielded. Total error rates are more favorable with deactivated filters, and hence, metabolomic networks should be generated without the filter. In addition, Bayesian likelihoods facilitate the detection of multiple linear dependencies between two variables. This property of the algorithm enables its use as a discovery tool and to generate novel hypotheses of the existence of otherwise hidden biological factors.
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
Authors: Grissa Ibtissem , Vergnaud Gilles , Pourcel Christine
Published: May 2007

Background

In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element) are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations.

Description

We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter.

Conclusion

It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the dictionary creator. CRISPRdb is accessible at http://crispr.u-psud.fr/crispr
Clustering protein environments for function prediction: finding PROSITE motifs in 3D
Authors: Yoon Sungroh , Ebert Jessica C , Chung Eui-Young , De Micheli Giovanni , Altman Russ B
Published: May 2007

Background

Structural genomics initiatives are producing increasing numbers of three-dimensional (3D) structures for which there is little functional information. Structure-based annotation of molecular function is therefore becoming critical. We previously presented FEATURE, a method for describing microenvironments around functional sites in proteins. However, FEATURE uses supervised machine learning and so is limited to building models for sites of known importance and location. We hypothesized that there are a large number of sites in proteins that are associated with function that have not yet been recognized. Toward that end, we have developed a method for clustering protein microenvironments in order to evaluate the potential for discovering novel sites that have not been previously identified.

Results

We have prototyped a computational method for rapid clustering of millions of microenvironments in order to discover residues whose surrounding environments are similar and which may therefore share a functional or structural role. We clustered nearly 2,000,000 environments from 9,600 protein chains and defined 4,550 clusters. As a preliminary validation, we asked whether known 3D environments associated with PROSITE motifs were "rediscovered". We found examples of clusters highly enriched for residues that share PROSITE sequence motifs.

Conclusion

Our results demonstrate that we can cluster protein environments successfully using a simplified representation and K-means clustering algorithm. The rediscovery of known 3D motifs allows us to calibrate the size and intercluster distances that characterize useful clusters. This information will then allow us to find new clusters with similar characteristics that represent novel structural or functional sites.
Using indirect protein interactions for the prediction of Gene Ontology functions
Authors: Chua Hon Nian , Sung Wing-Kin , Wong Limsoon
Published: May 2007

Background

Protein-protein interaction has been used to complement traditional sequence homology to elucidate protein function. Most existing approaches only make use of direct interactions to infer function, and some have studied the application of indirect interactions for functional inference but are unable to improve prediction performance. We have previously proposed an approach, FS-Weighted Averaging, which uses topological weighting and level-2 indirect interactions (protein pairs connected via two interactions) for predicting protein function from protein interactions and have found that it yields predictions with superior precision on yeast proteins over existing approaches. Here we study the use of this technique to predict functional annotations from the Gene Ontology for seven genomes:Saccharomyces cerevisiae,Drosophila melanogaster,Caenorhabditis elegans,Arabidopsis thaliana,Rattus norvegicus,Mus musculus, andHomo sapiens.

Results

Our analysis shows that protein-protein interactions provide supplementary coverage over sequence homology in the inference of protein function and is definitely a complement to sequence homology. We also find that FS-Weighted Averaging consistently outperforms two classical approaches, Neighbor Counting and Chi-Square, across the seven genomes for all three categories of the Gene Ontology. By randomly adding and removing interactions from the interactions, we find that Weighted Averaging is also rather robust against noisy interaction data.

Conclusion

We have conducted a comprehensive study over seven genomes. We conclude that FS-Weighted Averaging can effectively make use of indirect interactions to make the inference of protein functions from protein interactions more effective. Furthermore, the technique is general enough to work over a variety of genomes.
The chemokine Sdf-1 and its receptor Cxcr4 are required for formation of muscle in zebrafish
Authors: Chong Shang-Wei , Nguyet Le-Minh , Jiang Yun-Jin , Korzh Vladimir
Published: May 2007

Background

During development cell migration takes place prior to differentiation of many cell types. The chemokine receptor Cxcr4 and its ligand Sdf1 are implicated in migration of several cell lineages, including appendicular muscles.

Results

We dissected the role ofsdf1-cxcr4during skeletal myogenesis. We demonstrated that the receptorcxcr4ais expressed in the medial-anterior part of somites, suggesting that chemokine signaling plays a role in this region of the somite. Previous reports emphasized co-operation of Sdf1a and Cxcr4b. We found that during early myogenesis Sdf1a co-operates with the second Cxcr4 of zebrafish – Cxcr4a resulting in the commitment of myoblast to form fast muscle. Disrupting this chemokine signal caused a reduction inmyoDandmyf5expression and fast fiber formation. In addition, we showed that a dimerization partner of MyoD and Myf5, E12, positively regulates transcription ofcxcr4aandsdf1ain contrast to that of Sonic hedgehog, which inhibited these genes through induction of expression ofid2.

Conclusion

We revealed a regulatory feedback mechanism betweencxcr4a-sdf1aand genes encoding myogenic regulatory factors, which is involved in differentiation of fast myofibers. This demonstrated a role of chemokine signaling during development of skeletal muscles.
The promoter and transcribed regions of the Leishmania tarentolae spliced leader RNA gene array are devoid of nucleosomes
Authors: Hitchcock Robert A , Thomas Sean , Campbell David A , Sturm Nancy R
Published: May 2007

Background

The spliced leader (SL) RNA provides the 5' m7G cap and first 39 nt for all nuclear mRNAs in kinetoplastids. This small nuclear RNA is transcribed by RNA polymerase II from individual promoters. In Leishmania tarentolae the SL RNA genes reside in two multi-copy tandem arrays designated MINA and MINB. The transcript accumulation from the SL promoter on the drug-selected, episomal SL RNA gene cassette pX-tSL is ~10% that of the genomic array in uncloned L. tarentolae transfectants. This disparity is neither sequence- nor copy-number related, and thus may be due to interference of SL promoter function by epigenetic factors. To explore these possibilities we examined the nucleoplasmic localization of the SL RNA genes as well as their nucleosomal architecture.

Results

The genomic SL RNA genes and the episome did not co-localize within the nucleus. Each genomic repeat contains one nucleosome regularly positioned within the non-transcribed intergenic region. The 363-bp MINA array was resistant to micrococcal nuclease digestion between the -258 and -72 positions relative to the transcription start point due to nucleosome association, leaving the promoter elements and the entire transcribed region exposed for protein interactions. A pattern of ~164-bp protected segments was observed, corresponding to the amount of DNA typically bound by a nucleosome. By contrast, nucleosomes on the pX-tSL episome were randomly distributed over the episomal SL cassette, reducing transcription factor access to the episomal promoter by approximately 74%. Cloning of the episome transfectants revealed a range of transcriptional activities, implicating a mechanism of epigenetic heredity.

Conclusion

The disorganized nucleosomes on the pX episome are in a permissive conformation for transcription of the SL RNA cassette approximately 25% of the time within a given parasite. Nucleosome interference is likely the major factor in the apparent transcriptional repression of the SL RNA gene cassette. Coupled with the requirement for run-around transcription that drives expression of the selectable drug marker, transcription of the episomal SL may be reduced even further due to sub-optimal nucleoplasmic localization and initiation complex disruption.
Widespread pyocyanin over-production among isolates of a cystic fibrosis epidemic strain
Authors: Fothergill Joanne L , Panagea Stavroula , Hart Charles A , Walshaw Martin J , Pitt Tyrone L , Winstanley Craig
Published: May 2007

Background

Some isolates of the Liverpool cystic fibrosis epidemic strain of Pseudomonas aeruginosa exhibit an unusual virulence-related phenotype, characterized by over-production of quorum sensing-regulated exoproducts such as pyocyanin and LasA protease. Our aim was to determine the prevalence of this unusual phenotype amongst isolates of the epidemic strain, and to study other intraclonal phenotypic and genotypic variations.

Results

The unusual phenotype was detected in at least one epidemic strain isolate from the majority of cystic fibrosis patients tested, and can be retained for up to seven years during chronic infection. Multiple sequential isolates of the epidemic strain taken from six patients over a period of up to nine years exhibited a wide range of phenotypes, including different antimicrobial susceptibilities. Our data suggest that each sputum sample contains a mixture of phenotypes and genotypes within the epidemic strain population, including within colony morphotypes. Many isolates exhibit premature (during early rather than late exponential growth) and over-production of pyocyanin, which has a number of toxic effects directly relevant to cystic fibrosis.

Conclusion

The widespread occurrence of this unusual phenotype suggests that it may play an important role in the success of the epidemic strain.
Drug susceptibility testing of clinical isolates of streptococci and enterococci by the Phoenix automated microbiology system
Authors: Brigante Gioconda R , Luzzaro Francesco A , Pini Beatrice , Lombardi Gianluigi , Sokeng Gertrude , Toniolo Antonio Q
Published: May 2007

Background

Drug resistance is an emerging problem among streptococcal and enterococcal species. Automated diagnostic systems for species identification and antimicrobial susceptibility testing (AST) have become recently available. We evaluated drug susceptibility of clinical isolates of streptococci and enterococci using the recent Phoenix system (BD, Sparks, MD). Diagnostic tools included the new SMIC/ID-2 panel for streptococci, and the PMIC/ID-14 for enterococci. Two-hundred and fifty isolates have been investigated: β-hemolytic streptococci (n = 65), Streptococcus pneumoniae (n = 50), viridans group streptococci (n = 32), Enterococcus faecium (n = 40), Enterococcus faecalis (n = 43), other catalase-negative cocci (n = 20). When needed, species ID was determined using molecular methods. Test bacterial strains were chosen among those carrying clinically-relevant resistance determinants (penicillin, macrolides, fluoroquinolones, glycopeptides). AST results of the Phoenix system were compared to minimal inhibitory concentration (MIC) values measured by the Etest method (AB Biodisk, Solna, Sweden).

Results

Streptococci: essential agreement (EA) and categorical agreement (CA) were 91.9% and 98.8%, respectively. Major (ME) and minor errors (mE) accounted for 0.1% and 1.1% of isolates, respectively. No very major errors (VME) were produced. Enterococci: EA was 97%, CA 96%. Small numbers of VME (0.9%), ME (1.4%) and mE (2.8%) were obtained. Overall, EA and CA rates for most drugs were above 90% for both genera. A few VME were found: a) teicoplanin and high-level streptomycin for E. faecalis, b) high-level gentamicin for E. faecium. The mean time to results (± SD) was 11.8 ± 0.9 h, with minor differences between streptococci and enterococci.

Conclusion

The Phoenix system emerged as an effective tool for quantitative AST. Panels based on dilution tests provided rapid and accurate MIC values with regard to clinically-relevant streptococcal and enterococcal species.