bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of the interdisciplinary nature of library and information science
Authors: Prebor Gila
Published: October 2010

Library and information science (LIS) is highly interdisciplinary by nature and is affected by the incessant evolution of technologies. A recent study surveying research trends in the years 2002—6 at various information science departments worldwide has found that a clear trend was identified in Masters theses and doctoral dissertations of social aspects of information moving into the spotlight. The study found that only a third of the research that was tagged on the ProQuest Digital Dissertations database under either or both ‘Library Science’ and ‘Information Science’ was actually conducted at LIS departments. The current study aims to examine the remaining two thirds of these papers, conducted in non-LIS departments. This will contribute toward our understanding of the field and its future development. The research findings indicate that there is a relatively clear division of research topics between the studies conducted in various information studies departments and those conducted in other departments that study information. The main difference found is the opposite foci of LIS and non-LIS studies. While LIS scholars focus on the information user, other fields, headed by business administration, computer science, education and communication, focus on the system, on information technology, the information industry and the management of information.
Justification of Effort by Humans and Pigeons
Authors: Zentall Thomas R.
Published: October 2010

Justification of effort by humans is a form of reducing cognitive dissonance by enhancing the value of rewards when they are more difficult to obtain. Presumably, assigning greater value to rewards provides justification for the greater effort needed to obtain them. We have found such effects in adult humans and children with a highly controlled laboratory task. More importantly, under various conditions we have found similar effects in pigeons, animals not typically thought to need to justify their behavior to themselves or others. To account for these results, I propose a simpler mechanism than justification of effort—a mechanism based on contrast between the end of the effort and the reinforcement (or signal for reinforcement) that follows. This model predicts that any relatively aversive event can serve to enhance the value of the reward that follows it simply through the contrast between those two events. In support of this general model, my colleagues and I have found this effect in pigeons when the prior event consists of (a) more rather than less effort (pecking), (b) a long rather than a short delay, and (c) the absence of food rather than food. We have also found that a pigeon’s preference for food at one location can shift toward a different location if acquiring food at the new location requires that the pigeon work harder to obtain the food. Contrast may also play a role in other social psychological phenomena that have been interpreted in terms of cognitive dissonance.
New Approaches to the Study of Childhood Language Disorders
Authors: Nittrouer Susan , Pennington Bruce
Published: October 2010

Not long ago, poor language skills did not necessarily interfere with the quality of a person's life. Many occupations did not require sophisticated language or literacy. Interactions with other people could reasonably be restricted to family members and a few social or business contacts. But in the 21st century, advances in technology and burgeoning population centers have made it necessary for children to acquire high levels of proficiency with at least one language, in both spoken and written form. This situation increases the urgency for us to develop better theoretical accounts of the problems underlying disorders of language, including dyslexia. Empirical investigations of language-learning deficits largely focus on phonological representations and often ask to what extent labeling responses are “categorical.” This article describes the history of this approach and presents some relevant findings regarding the perceptual organization of speech signals—findings that should prompt us to expand our investigations of language disorders.
Computational Models as Aids to Better Reasoning in Psychology
Authors: Farrell Simon , Lewandowsky Stephan
Published: October 2010

Scientists can reason about natural systems, including the mind and brain, in many ways, with each form of reasoning being associated with its own set of limitations. The limitations on human reasoning imply that the process of reasoning about theories and communicating those theories will be error prone; we must therefore be concerned about the reproducibility of theories whose very nature is shaped by constraints on human reasoning. The problem of reproducibility can be alleviated by computational modeling, which maximizes correspondence between the actual behavior of a posited system and its behavior inferred through reasoning and increases the fidelity of communication of our theories to others.
Learning Vicariously From Failure: The Case of Major League Soccer and the Collapse of the North American Soccer League
Authors: Francis John , Congcong Zheng
Published: October 2010

Organizations are often encouraged to learn from the failures of others. However, failures can be extremely complicated and multifaceted, defying clear cause attribution. Learning organizations face challenges in adopting and implementing the lessons of such failures and many times are unable to appropriately correct the root causes. Using a grounded theory approach, the authors present a learning case by Major League Soccer (MLS) from its failed predecessor—the North American Soccer League (NASL), depicting patterns of learning in four aspects: control, foreign players, media relationships, and financial viability. The authors propose a two-stage process model of vicarious learning from failure based on two fundamental processes: cause attribution and lesson implementation.
Policy and Practice: Recursive Learning From Crisis
Authors: Elliott Dominic , Macpherson Allan
Published: October 2010

Data from the 2007 U.K. floods are examined using institutional theory and practice theory lenses. We note that learning from crisis ultimately results in “lessons learned” being institutionalized in new norms, tools, and infrastructure. As the basis of legitimate action for coping in the future, they may provide a measure of resilience, but crisis management and recovery is an active and emergent process. Learning must also identify the ability to create resilience by developing the capacity and ability to be creative when such “lessons learned” prove inappropriate in an emerging scenario. This has implications for policy learning processes that may be difficult to justify since public inquiries are also institutionalized events that require “legitimate” recommendations to codify learning.
Why Do Product-Market Strategies Fail? A Sociostructural Examination Under Conditions of Adherence
Authors: Hughes Paul , Hughes Mathew , Morgan Robert E.
Published: October 2010

The authors contend that structural and managerial antecedents of strategy failure exist and the extent to which these determine failure is different under conditions of high and low adherence to strategy. Our results support these arguments and demonstrate that the drivers of failure differ according to the unusual strategy process environment of both types of firms. Resource scarcity is found to be a common antecedent to strategy failure in organizations regardless of adherence. From there, managerial conditions (symbolic information use, strategy championing, and tenure) drive strategy failure in high-adherence firms. However, only structural conditions (formalization and resource scarcity) are antecedents of strategy failure in low-adherence firms, while failure is mitigated by centralized decision making.
Global exponential stabilization for a class of distributed parameter control systems with Markovian jumping parameters and time-varying delay
Authors: Linshan Wang  , Yangfan Wang
Published: October 2010

The global exponential stabilization is considered for a class of distributed parameter control systems with Markovian jumping parameters and time-varying delay. By employing a new Lyapunov-Krasovskii functional, a linear matrix inequality (LMI) approach is developed to establish some easy-to-test criteria for global exponential stabilization in the mean square for the stochastic systems. A numerical example is exploited to show the usefulness of the derived LMI-based stabilization conditions.
Modified projective synchronization of a hyperchaotic system with unknown and/or uncertain parameters
Authors: Luo Runzi  , Deng Shucheng  , Wei Zhengmin
Published: October 2010

This paper investigates the modified projective synchronization problem of two hyperchaotic systems in the presence of unknown and/or uncertain system parameters. Based on the Lyapunov stability theory two control laws are proposed to make the states of two identical hyperchaotic systems asymptotically synchronized. Numerical simulations are presented to show the effectiveness of the proposed schemes.
The Treatment of Sex Offenders
Authors: Birgden Astrid , Cucolo Heather
Published: October 2010

Public policy is necessarily a political process with the law and order issue high on the political agenda. Consequently, working with sex offenders is fraught with legal and ethical minefields, including the mandate that community protection automatically outweighs offender rights. In addressing community protection, contemporary sex offender treatment is based on management rather than rehabilitation. We argue that treatment-as-management violates offender rights because it is ineffective and unethical. The suggested alternative is to deliver treatment-as-rehabilitation underpinned by international human rights law and universal professional ethics. An effective and ethical community–offender balance is more likely when sex offenders are treated with respect and dignity that, as human beings, they have a right to claim.
“But I Didn’t Do It!”
Authors: Levenson Jill S.
Published: October 2010

This article addresses ethical questions and issues related to the treatment of sex offenders in denial, using the empirical research literature and the ethical codes of American Psychological Association (APA) and National Association of Social Workers (NASW) to guide the ethical decision-making process. The empirical literature does not provide an unequivocal link between denial and recidivism, though some studies suggest that decreased denial and increased accountability appear to be associated with greater therapeutic engagement and reduced recidivism for some offenders. The ethical codes of APA and NASW value the client’s self-determination and autonomy, and psychologists and social workers have a duty to empower individual well-being while doing no harm to clients or others. Clinicians should view denial not as a categorical construct but as a continuum of distorted cognitions requiring clinical attention. Denial might also be considered as a responsivity factor that can interfere with treatment progress. Offering a reasonable time period for therapeutic engagement might provide a better alternative than automatically refusing treatment to categorical deniers.
A Nietzschean reading of Foucauldian thinking: constructing a project of the self within an ontology of becoming
Authors: Bardon Thibaut , Josserand Emmanuel
Published: October 2010

As influential as Michel Foucault may be in organization theory, several critics have seriously questioned the epistemological foundations of the Foucauldian philosophical project (Ackroyd and Thompson, 1995, 1999; Caldwell, 2007; Habermas, 1990; Newton, 1994, 1998; Reed, 2000; Thompson, 1993). If these remain unanswered, the Foucauldian approach could be relegated to a self-contradictory, ultra-relativist and partial reading grid of ‘reality’. In this article, we develop a Nietzschean reading of Foucault’s thinking that offers answers to these criticisms, and reinstates it as an independent philosophical project grounded in epistemological assumptions that are coherent with its ontology and methodology. Finally, we suggest that, following Nietzsche, the whole Foucauldian project can be approached as a genealogy of morals. Subsequently, we call on scholars to further explore the ‘third generation’ of Foucauldian studies which would study management practices as morals understood as an ‘art de vivre’.
The Dark Night of the Soul: Causes and Resolution of Emotional Distress Among Contemplative Nuns
Authors: Durà-Vilà Glòria , Dein Simon , Littlewood Roland , Leavey Gerard
Published: October 2010

An ethnographic study was conducted in the Spanish Monastery of Santa Mónica whose community consists of ten contemplative Augustinian nuns. Through participant observation and interviews the stresses encountered by the nuns and the coping strategies they deployed are explored in depth. It was found that symptoms that otherwise might have been described as evidence of a depressive episode were understood by the nuns within the framework of the so-called Dark Night of the Soul narrative: an active process of transforming emotional distress into a process of self-reflection, attribution of religious meaning and spiritual growth. We conclude by discussing the clinical implications of this religious narrative, highlighting the importance of incorporating existential issues into clinical practice.
A Study of the Toxicity of Moulds Isolated from Dwellings
Authors: Gutarowska Beata , Sulyok Michael , Krska Rudolf
Published: October 2010

An analysis of the toxicity of moulds isolated from 34 dwellings with mould-affected walls was performed. During the analysis 74 moulds strains were isolated, 17.5% of them were toxic. Detailed analysis by high performance liquid chromatography/tandem mass spectrometry of six toxic strains proved their ability to grow on building materials and produce mycotoxins. It was confirmed that the toxins stachybotrylactam, sterigmatocystin and roquefortin were produced on gypsum board and concrete by Stachybotrys chartarum, Aspergillus versicolor and Penicillium chrysogenum, respectively. This is also the first report on the production of aflatoxin B1 and G1 by A. flavus on building materials. Extracts from A. versicolor, A. flavus, P. chrysogenum growing on building materials were found to have cytotoxic potential. It was found that some mycotoxin production may be reduced or may even vanish, when moulds grow on building materials. However, taking into consideration the appreciable amounts of some mycotoxins that were still produced on the building materials investigated, the study indicated a toxic risk in the mould-affected buildings analysed.
Gender and climate change in Australia
Authors: Alston Margaret
Published: October 2010

Debate continues to rage as to the veracity of evidence around the permanence of climate change. There is no doubt that changes are occurring across the world and that these changes are causing significant social hardship, including food and water insecurity and large-scale movements of people. What is also emerging in research across the world is that these social impacts and adaptations are highly gendered. This article draws on several years of research on the Australian drought and more recent research on declining water availability in the Murray—Darling Basin of Australia. It notes the significant social impacts, particularly in remote and irrigation areas, and draws out the gendered impacts of these changes. The article argues for more sensitive rights-based social policy to address people who are under extraordinary stress during times of unparalleled change.
The symbolic burden of homelessness
Authors: Farrugia David
Published: October 2010

Young people’s subjective experience of homelessness is constituted by particular social processes which to this point have not been explicitly theorized. This article draws on qualitative interviews with young people who have experienced or are experiencing homelessness in order to argue that homelessness carries a symbolic burden, the acknowledgement of which is crucial to understanding the process of embodied subjectivity for young people who have this experience. Popular understandings construct those who experience homelessness as irresponsible, passive and obscene. Young people are aware of this, and this knowledge has consequences for the process of subjectivity for these young people. This article draws on conceptual contributions from Bourdieu and Massumi to theorize the nature of the symbolic burden of homelessness and reflect on the issues involved in understanding the process of subjectivity in the context of this kind of inequality.
Big tree, small news: Media access, symbolic power and strategic intervention
Authors: Lester Libby
Published: October 2010

The death of El Grande — Australia’s biggest tree and the world’s largest flowering plant and hardwood tree — created a powerful symbol for environmentalists challenging the destruction of native forests across Tasmania, but only outside Tasmania. In local media, the reporting of the tree’s fate remained contained and isolated from the broader environmental conflict. Using El Grande’s discovery, burning and death as a critical case study and drawing on a range of media texts and interviews with journalists, environmentalists and public relations practitioners, this article analyses the complex dynamics operating at the interface of symbolic power and news production, particularly in terms of the contest for media access and visibility by both elite and non-elite sources; the nature and successes of strategic interventions by competing sources and media themselves to enhance or limit this power; and how these various dynamics function over time.
Weight Status and High Blood Pressure Among Low-Income African American Men
Authors: Bruce Marino A. , Beech Bettina M. , Edwards Christopher L. , Sims Mario , Scarinci Isabel , Whitfield Keith E. , Gilbert Keon , Crook Errol D.
Published: October 2010

Obesity is a biological risk factor or comorbidity that has not received much attention from scientists studying hypertension among African American men. The purpose of this study was to examine the relationship between weight status and high blood pressure among African American men with few economic resources. The authors used surveillance data collected from low-income adults attending community- and faith-based primary care clinics in West Tennessee to estimate pooled and group-specific regression models of high blood pressure. The results from group-specific logistic regression models indicate that the factors associated with hypertension varied considerably by weight status. This study provides a glimpse into the complex relationship between weight status and high blood pressure status among African American men. Additional research is needed to identify mechanisms through which excess weight affects the development and progression of high blood pressure.
Tracing the Self-Regulatory Bases of Moral Emotions
Authors: Sheikh Sana , Janoff-Bulman Ronnie
Published: October 2010

In this article we explore a self-regulatory perspective on the self-evaluative moral emotions, shame and guilt. Broadly conceived, self-regulation distinguishes between two types of motivation: approach/activation and avoidance/inhibition. We use this distinction to conceptually understand the socialization dimensions (parental restrictiveness versus nurturance), associated emotions (anxiety versus empathy), and forms of morality (proscriptive versus prescriptive) that serve as precursors to each self-evaluative moral emotion. We then examine the components of shame and guilt experiences in greater detail and conclude with more general implications of a self-regulatory perspective on moral emotions.
The Many Meanings/Aspects of Emotion: Definitions, Functions, Activation, and Regulation
Authors: Izard Carroll E.
Published: October 2010

Many psychological scientists and behavioral neuroscientists affirm that “emotion” influences thinking, decision-making, actions, social relationships, well-being, and physical and mental health. Yet there is no consensus on a definition of the word “emotion,” and the present data suggest that it cannot be defined as a unitary concept. Theorists and researchers attribute quite different yet heuristic meanings to “emotion.” They show considerable agreement about emotion activation, functions, and regulation. The central goal of this article is to alert researchers, students, and other consumers of “emotion” research to the multiple meanings or aspects that distinguished scientists attribute to ”emotion,” increase appreciation of its interesting and challenging complexity, and sharpen perspectives on “emotion” and the associated body of literature that is of critical significance to science and society.
On Emotions and on Definitions: A Response to Izard
Authors: Wierzbicka Anna
Published: October 2010

This commentary argues that the question of metalanguage is a key issue in emotion research. Izard (2010) ignores this issue (and all the earlier literature relating to it, including the debate in Emotion Review, 2009, 1[1]), and thus falls into the old traps of circularity, obscurity, and ethnocentrism. This commentary rejects Izard’s claim that “emotion” defies definition, and it offers a viable definition of “emotion” formulated in simple and universal human concepts, using the English version of the universal conceptual lingua franca called Natural Semantic Metalanguage (NSM). Once again, this commentary draws attention to the centrality of the question of language in emotion research.
Defining Emotion: A Brief History
Authors: Gendron Maria
Published: October 2010

The effort to define the term “emotion” has a long history in the discipline of psychology. Izard’s survey (2010) canvassed prominent emotion theorists and researchers on their working definitions of emotion. The particular assumptions about emotion reported, as well as the conclusion that the term “emotion” lacks a consensus definition, both have historical precedent. In this commentary, I place Izard’s findings in this historical context and discuss the implications of his survey for the future of emotion research.
Acute Osteoclast Activity following Subchondral Drilling Is Promoted by Chitosan and Associated with Improved Cartilage Repair Tissue Integration
Authors: Chen G. , Sun J. , Lascau-Coman V. , Chevrier A. , Marchand C. , Hoemann Caroline D.
Published: October 2010

Objective:

Cartilage-bone integration is an important functional end point of cartilage repair therapy, but little is known about how to promote integration. We tested the hypothesis that chitosan-stabilized blood clot implant elicits osteoclasts to drilled cartilage defects and promotes repair and cartilage-bone integration.

Design:

Bilateral trochlear defects in 15 skeletally mature rabbit knees were microdrilled and then treated with chitosan–glycerol phosphate (GP)/blood implant with fluorescent chitosan tracer and thrombin to accelerate in situ solidification or with thrombin alone. Chitosan clearance, osteoclast density, and osteochondral repair were evaluated at 1, 2, and 8 weeks at the outside, edge, and through the proximal microdrill holes.

Results:

Chitosan was retained at the top of the drill holes at 1 week as extracellular particles became internalized by granulation tissue cells at 2 weeks and was completely cleared by 8 weeks. Osteoclasts burst-accumulated at microdrill hole edges at 1 week, in new woven bone at the base of the drill holes at 2 weeks, and below endochondral cartilage repair at 8 weeks. Implants elicited 2-fold more osteoclasts relative to controls ( P < 0.001), a more complete drill hole bone repair, and improved cartilage-bone integration and histological tissue quality. Treated and control 8-week cartilage repair tissues contained 85% collagen type II. After 8 weeks of repair, subchondral osteoclast density correlated positively with bone-cartilage repair tissue integration ( P < 0.0005).

Conclusions:

Chitosan-GP/blood implant amplified the acute influx of subchondral osteoclasts through indirect mechanisms, leading to significantly improved repair and cartilage-bone integration without inducing net bone resorption. Osteoclasts are cellular mediators of marrow-derived cartilage repair integration.
Impaired angiogenesis and altered Notch signaling in mice overexpressing endothelial Egfl7
Authors: Nichol Donna , Shawber Carrie , Fitch Michael J. , Bambino Kathryn , Sharma Anshula , Kitajewski Jan , Stuhlmann Heidi
Published: October 2010

Epidermal growth factor-like domain 7 (Egfl7) is important for regulating tubulogenesis in zebrafish, but its role in mammals remains unresolved. We show here that endothelial overexpression of Egfl7 in transgenic mice leads to partial lethality, hemorrhaging, and altered cardiac morphogenesis. These defects are accompanied by abnormal vascular patterning and remodeling in both the embryonic and postnatal vasculature. Egfl7 overexpression in the neonatal retina results in a hyperangiogenic response, and EGFL7 knockdown in human primary endothelial cells suppresses endothelial cell proliferation, sprouting, and migration. These phenotypes are reminiscent of Notch inhibition. In addition, our results show that EGFL7 and endothelial-specific NOTCH physically interact in vivo and strongly suggest that Egfl7 antagonizes Notch in both the postnatal retina and in primary endothelial cells. Specifically, Egfl7 inhibits Notch reporter activity and down-regulates the level of Notch target genes when overexpressed. In conclusion, we have uncovered a critical role for Egfl7 in vascular development and have shown that some of these functions are mediated through modulation of Notch signaling.
Nature and severity of lung function abnormalities in extremely pre-term children at 11 years of age
Authors: Lum S. , Kirkby J. , Welsh L. , Marlow N. , Hennessy E. , Stocks J.
Published: October 2010

Advances in neonatal care have resulted in increased survival of children born extremely pre-term (EP). Nevertheless the incidence of bronchopulmonary dysplasia and long-term respiratory morbidity remains high. We investigated the nature of pathophysiological changes at 11 yrs of age to ascertain whether respiratory morbidity in EP children primarily reflects alterations in the lung periphery or more centralised airway function in this population.

Spirometry, plethysmography, diffusing capacity, exhaled nitric oxide, multiple-breath washout, skin tests and methacholine challenge were used during laboratory-based assessments in a subgroup of the 1995 EPICure cohort and in controls.

Results were obtained in 49 EP and 52 control children. Lung function abnormalities were found in 78% of EP children, with evidence of airway obstruction, ventilation inhomogeneity, gas trapping and airway hyperresponsiveness. Levels of atopy and exhaled nitric oxide were similar between the groups. Prior wheeze was associated with significant reductions in forced flows and volumes. By contrast, abnormalities of the lung periphery appear to be mediated primarily through EP birthper se.

The prevalence of lung function abnormalities, which is largely obstructive in nature and likely to have long-term implications, remains high among 11-yr-old children born EP. Spirometry proved an effective means of detecting these persistent abnormalities.
Association of phospholipase A2 receptor 1 polymorphisms with idiopathic membranous nephropathy in Chinese patients in Taiwan
Authors: Liu Yu-Huei , Chen Cheng-Hsu , Chen Shih-Yin , Lin Ying-Ju , Liao Wen-Ling , Tsai Chang-Hai , Wan Lei , Tsai Fuu-Jen
Published: October 2010

Background

Idiopathic membranous nephropathy (IMN) is one of the most common forms of autoimmune nephritic syndrome in adults. The purpose of this study is to evaluate whether polymorphisms of PLA2R1 affect the development of IMN.

Methods

Taiwanese-Chinese individuals (129 patients with IMN and 106 healthy controls) were enrolled in this study. The selected single nucleotide polymorphisms (SNPs) in PLA2R1 were genotyped by real-time polymerase chain reaction using TaqMan fluorescent probes, and were further confirmed by polymerase chain reaction-restriction fragment length polymorphism. The roles of the SNPs in disease progression were analyzed.

Results

Genotype distribution was significantly different between patients with IMN and controls for PLA2R1 SNP rs35771982 (p = 0.015). The frequency of G allele at rs35771982 was significantly higher in patients with IMN as compared with controls (p = 0.005). In addition, haplotypes of PLA2R1 may be used to predict the risk of IMN (p = 0.004). Haplotype H1 plays a role in an increased risk of IMN while haplotype H3 plays a protective role against this disease. None of these polymorphisms showed a significant and independent influence on the progression of IMN and the risk of end-stage renal failure and death (ESRF/death). High disease progression in patients having C/T genotype at rs6757188 and C/G genotype at rs35771982 were associated with a low rate of remission.

Conclusions

Our results provide new evidence that genetic polymorphisms of PLA2R1 may be the underlying cause of IMN, and the polymorphisms revealed by this study warrant further investigation.
Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development
Authors: Terrat Sébastien , Peyretaillade Eric , Gonçalves Olivier , Dugat-Bony Eric , Gravelat Fabrice , Moné Anne , Biderre-Petit Corinne , Boucher Delphine , Troquet Julien , Peyret Pierre
Published: October 2010

Background

Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes.

Results

First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently.

Conclusions

We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to study any group of genes. The Metabolic Design software is freely available from the authors and can be downloaded and modified under general public license.
Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis
Authors: Wu Timothy H , Chang Ian Yi-Feng , Chu Li-chieh Julie , Huang Hsuan-Cheng , Ng Wailap Victor
Published: October 2010

Background

sRNAs, which belong to the non-coding RNA family and range from approximately 50 to 400 nucleotides, serve various important gene regulatory roles. Most are believed to be trans-regulating and function by being complementary to their target mRNAs in order to inhibiting translation by ribosome occlusion. Despite this understanding of their functionality, the global properties associated with regulation by sRNAs are not yet understood. Here we use topological analysis of sRNA targets in terms of protein-protein interaction and transcription-regulatory networks in Escherichia coli to shed light on the global correlation between sRNA regulation and cellular control networks.

Results

The analysis of sRNA targets in terms of their networks showed that some specific network properties could be identified. In protein-protein interaction network, sRNA targets tend to occupy more central positions (higher closeness centrality, p-val = 0.022) and more cliquish (larger clustering coefficient, p-val = 0.037). The targets of the same sRNA tend to form a network module (shorter characteristic path length, p-val = 0.015; larger density, p-val = 0.019; higher in-degree ratio, p-val = 0.009). Using the transcription-regulatory network, sRNA targets tend to be under multiple regulation (higher indegree, p-val = 0.013) and the targets usually are important to the transfer of regulatory signals (higher betweenness, p-val = 0.012). As was found for the protein-protein interaction network, the targets that are regulated by the same sRNA also tend to be closely knit within the transcription-regulatory network (larger density, p-val = 0.036), and inward interactions between them are greater than the outward interactions (higher in-degree ratio, p-val = 0.023). However, after incorporating information on predicted sRNAs and down-stream targets, the results are not as clear-cut, but the overall network modularity is still evident.

Conclusions

Our results indicate that sRNA targeting tends to show a clustering pattern that is similar to the human microRNA regulation associated with protein-protein interaction network that was observed in a previous study. Namely, the sRNA targets show close interaction and forms a closely knit network module for both the protein-protein interaction and the transcription-regulatory networks. Thus, targets of the same sRNA work in a concerted way toward a specific goal. In addition, in the transcription-regulatory network, sRNA targets act as "multiplexor", accepting regulatory control from multiple sources and acting accordingly. Our results indicate that sRNA targeting shows different properties when compared to the proteins that form cellular networks.
Response of swine spleen to Streptococcus suis infection revealed by transcription analysis
Authors: Li Ran , Zhang Anding , Chen Bo , Teng Liu , Wang Ya , Chen Huanchun , Jin Meilin
Published: October 2010

Astract

Background

Streptococcus suis serotype 2 (SS2), a major swine pathogen and an emerging zoonotic agent, has greatly challenged global public health. Systematical information about host immune response to the infection is important for understanding the molecular mechanism of diseases.

Results

104 and 129 unique genes were significantly up-regulated and down-regulated in the spleens of pigs infected with SS2 (WT). The up-regulated genes were principally related to immune response, such as genes involved in inflammatory response; acute-phase/immune response; cell adhesion and response to stress. The down-regulated genes were mainly involved in transcription, transport, material and energy metabolism which were representative of the reduced vital activity of SS2-influenced cells. Only a few genes showed significantly differential expression when comparing avirulent isogenic strain (ΔHP0197) with mock-infected samples.

Conclusions

Our findings indicated that highly pathogenic SS2 could persistently induce cytokines mainly by Toll-like receptor 2 (TLR2) pathway, and the phagocytosis-resistant bacteria could induce high level of cytokines and secrete toxins to destroy deep tissues, and cause meningitis, septicaemia, pneumonia, endocarditis, and arthritis.
Primary transcriptomes of Mycobacterium avium subsp. paratuberculosis reveal proprietary pathways in tissue and macrophages
Authors: Janagama Harish K , Lamont Elise A , George Sajan , Bannantine John P , Xu Wayne W , Tu Zheng J , Wells Scott J , Schefers Jeremy , Sreevatsan Srinand
Published: October 2010

Background

Mycobacterium avium subsp. paratuberculosis (MAP) persistently infects intestines and mesenteric lymph nodes leading to a prolonged subclinical disease. The MAP genome sequence was published in 2005, yet its transcriptional organization in natural infection is unknown. While prior research analyzed regulated gene sets utilizing defined, in vitro stress related or advanced surgical methods with various animal species, we investigated the intracellular lifestyle of MAP in the intestines and lymph nodes to understand the MAP pathways that function to govern this persistence.

Results

Our transcriptional analysis shows that 21%, 8% and 3% of the entire MAP genome was represented either inside tissues, macrophages or both, respectively. Transcripts belonging to latency and cell envelope biogenesis were upregulated in the intestinal tissues whereas those belonging to intracellular trafficking and secretion were upregulated inside the macrophages. Transcriptomes of natural infection and in vitro macrophage infection shared genes involved in transcription and inorganic ion transport and metabolism. MAP specific genes within large sequence polymorphisms of ancestral M. avium complex were downregulated exclusively in natural infection.

Conclusions

We have unveiled common and unique MAP pathways associated with persistence, cell wall biogenesis and virulence in naturally infected cow intestines, lymph nodes and in vitro infected macrophages. This dichotomy also suggests that in vitro macrophage models may be insufficient in providing accurate information on the events that transpire during natural infection. This is the first report to examine the primary transcriptome of MAP at the local infection site (i.e. intestinal tissue). Regulatory pathways that govern the lifecycle of MAP appear to be specified by tissue and cell type. While tissues show a "shut-down" of major MAP metabolic genes, infected macrophages upregulate several MAP specific genes along with a putative pathogenicity island responsible for iron acquisition. Many of these regulatory pathways rely on the advanced interplay of host and pathogen and in order to decipher their message, an interactome must be established using a systems biology approach. Identified MAP pathways place current research into direct alignment in meeting the future challenge of creating a MAP-host interactome.
Low hospital admission rates for respiratory diseases in children
Authors: Uijen Johannes HJM , Schellevis François G , Bindels Patrick JE , Willemsen Sten P , van der Wouden Johannes C
Published: October 2010

Background

Population-based data on hospital admissions for children aged 0-17 years concerning all respiratory diseases are scarce. This study examined hospital admissions in relation to the preceding consultations in general practice in this age group.

Methods

Data on children aged 0-17 years with respiratory diseases included in the Second Dutch National Survey of General Practice (DNSGP-2) were linked to all hospital admissions in the Dutch National Medical Registration. Admission rates for respiratory diseases were calculated. Data were analysed using multivariate logistic regression.

Results

Of all 79,272 children within the DNSGP-2, 1.8% were admitted to hospital for any respiratory diagnosis. The highest admission rates per 1000 children were for chronic disease of tonsils and adenoids (12.9); pneumonia and influenza (0.97); and asthma (0.92). Children aged 0-4 years and boys were admitted more frequently. Of children with asthma, 2.3% were admitted for respiratory diseases. For asthma, admission rates varied by urbanisation level: 0.47/1000 children/year in cities with ≤ 30,000 inhabitants, 1.12 for cities with ≥ 50,000 inhabitants, and 1.73 for the three largest cities (p = 0.002). Multivariate logistic regression showed that within two weeks after a GP consultation, younger age (OR 0.81, 95% CI 0.76-0.88) and more severe respiratory diseases (5.55, 95% CI 2.99-8.11) predicted hospital admission.

Conclusions

Children in the general population with respiratory diseases (especially asthma) had very low hospital admission rates. In urban regions children were more frequently admitted due to respiratory morbidity. For effectiveness studies in a primary care setting, hospital admission rates should not be used as quality end-point.
Enhanced chlorhexidine skin penetration with eucalyptus oil
Authors: Karpanen Tarja J , Conway Barbara R , Worthington Tony , Hilton Anthony C , Elliott Tom SJ , Lambert Peter A
Published: October 2010

Background

Chlorhexidine digluconate (CHG) is a widely used skin antiseptic, however it poorly penetrates the skin, limiting its efficacy against microorganisms residing beneath the surface layers of skin. The aim of the current study was to improve the delivery of chlorhexidine digluconate (CHG) when used as a skin antiseptic.

Method

Chlorhexidine was applied to the surface of donor skin and its penetration and retention under different conditions was evaluated. Skin penetration studies were performed on full-thickness donor human skin using a Franz diffusion cell system. Skin was exposed to 2% (w/v) CHG in various concentrations of eucalyptus oil (EO) and 70% (v/v) isopropyl alcohol (IPA). The concentration of CHG (μg/mg of skin) was determined to a skin depth of 1500 μm by high performance liquid chromatography (HPLC).

Results

The 2% (w/v) CHG penetration into the lower layers of skin was significantly enhanced in the presence of EO. Ten percent (v/v) EO in combination with 2% (w/v) CHG in 70% (v/v) IPA significantly increased the amount of CHG which penetrated into the skin within 2 min.

Conclusion

The delivery of CHG into the epidermis and dermis can be enhanced by combination with EO, which in turn may improve biocide contact with additional microorganisms present in the skin, thereby enhancing antisepsis.
Effect of duration of postherpetic neuralgia on efficacy analyses in a multicenter, randomized, controlled study of NGX-4010, an 8% capsaicin patch evaluated for the treatment of postherpetic neuralgia
Authors: Webster Lynn R , Tark Marvin , Rauck Richard , Tobias Jeffrey K , Vanhove Geertrui F
Published: October 2010

Background

Postherpetic neuralgia (PHN) is a painful and difficult to treat complication of acute herpes zoster. Current treatment options provide only partial relief and are often limited by poor tolerability. We evaluated the safety and efficacy of a single 60-minute application of NGX-4010, an 8% capsaicin patch, in patients with PHN.

Methods

This multicenter, double-blind, controlled study randomized 155 patients 2:1 to receive either NGX-4010 or a 0.04% capsaicin control patch. Patients were at least 18 years old with PHN for at least 3 months, and an average Numeric Pain Rating Scale (NPRS) score of 3 to 9. The primary efficacy endpoint was the percentage change in NPRS score from baseline to weeks 2-8.

Results

The mean percent reduction in "average pain for the past 24 hours" NPRS scores from baseline to weeks 2-8 was greater in the NGX-4010 group (36.5%) compared with control (29.9%) although the difference was not significant (p = 0.296). PGIC analysis demonstrated that more NGX-4010 recipients considered themselves improved (much, or very much) compared with control at weeks 8 and 12, but the differences did not reach statistical significance. Post hoc analyses of patients with PHN for at least 6 months showed significantly greater reductions in "average pain for the past 24 hours" NPRS scores from baseline to weeks 2-8 in NGX-4010 patients compared to controls (37.6% versus 23.4%; p = 0.0291). PGIC analysis in this subgroup demonstrated that significantly more NGX-4010 recipients considered themselves much or very much improved compared with control at week 12 (40% versus 20%; p = 0.0403;).

Conclusions

Although treatment appeared to be safe and well tolerated, a single 60-minute application of NGX-4010 failed to show efficacy in this study which included patients with PHN for less than 6 months. Large reductions in pain observed among control patients with pain for less than 6 months may have been due to spontaneous resolution of PHN, may have confounded the results of the prespecified analyses, and should be taken into account when designing PHN studies.

Trial Registration

NCT00068081
Screening of the DNA mismatch repair genes MLH1, MSH2 and MSH6in a Greek cohort of Lynch syndrome suspected families
Authors: Thodi Georgia , Fostira Florentia , Sandaltzopoulos Raphael , Nasioulas George , Grivas Anastasios , Boukovinas Ioannis , Mylonaki Maria , Panopoulos Christos , Magic Mirjana Brankovic , Fountzilas George , Yannoukakos Drakoulis
Published: October 2010

Background

Germline mutations in the DNA mismatch repair genes predispose to Lynch syndrome, thus conferring a high relative risk of colorectal and endometrial cancer. The MLH1, MSH2 and MSH6 mutational spectrum reported so far involves minor alterations scattered throughout their coding regions as well as large genomic rearrangements. Therefore, a combination of complete sequencing and a specialized technique for the detection of genomic rearrangements should be conducted during a proper DNA-testing procedure. Our main goal was to successfully identify Lynch syndrome families and determine the spectrum of MLH1, MSH2 and MSH6 mutations in Greek Lynch families in order to develop an efficient screening protocol for the Greek colorectal cancer patients' cohort.

Methods

Forty-two samples from twenty-four families, out of which twenty two of Greek, one of Cypriot and one of Serbian origin, were screened for the presence of germline mutations in the major mismatch repair genes through direct sequencing and MLPA. Families were selected upon Amsterdam criteria or revised Bethesda guidelines.

Results

Ten deleterious alterations were detected in twelve out of the twenty-four families subjected to genetic testing, thus our detection rate is 50%. Four of the pathogenic point mutations, namely two nonsense, one missense and one splice site change, are novel, whereas the detected genomic deletion encompassing exon 6 of the MLH1 gene has been described repeatedly in the LOVD database. The average age of onset for the development of both colorectal and endometrial cancer among mutation positive families is 43.2 years.

Conclusion

The mutational spectrum of the MMR genes investigated as it has been shaped by our analysis is quite heterogeneous without any strong indication for the presence of a founder effect.