bluuebunny/crossref_metadata_2025 huggingface dataset:
Lenin in Allah’s court: Iqbal’s critique of Western capitalism and the opening up of the postcolonial imagination in critical management studies
Authors: Farzad Rafi Khan  , Basit Bilal Koshul
Published: May 2011

One manifestation of the Eurocentrism present in postcolonial critical management studies is its failure to engage with Muslim critiques of Western capitalism on their own terms. In this article we seek to address this deficiency by introducing the thought of Muhammad Iqbal (d. 1938)— one of the most influential thinkers in the postcolonial Muslim world. We do a close reading of three of Iqbal’s poems that are considered among his most representative and poignant critical reflections on Western capitalism and its imperialistic presence in the Global South. This close reading generates the major contribution of this article which is an alternative critical narrative on Western capitalism that is characterized by theocentrism and embodied love. We argue that this is a distinct way of critiquing Western capitalism which allows us to better recognize the provincial (i.e. Western) character of postcolonial critical management studies.
Defining and measuring niche parties
Authors: Wagner Markus
Published: May 2011

Various scholars have recently argued that niche parties are to be distinguished from mainstream parties, in particular because the two party types differ in their programmes, behaviour and strategies. However, so far there has been no attempt to provide a concise, measureable definition of the niche-party concept. In this article I argue that niche parties are best defined as parties that compete primarily on a small number of non-economic issues. The occurrence of niche parties is then operationalized and measured using issue salience information provided by expert surveys and manifesto data. After comparing the findings with existing definitions, the main characteristics of the niche parties identified are examined in a final step.
To See and Be Seen: Celebrity Practice on Twitter
Authors: Marwick Alice , boyd danah
Published: May 2011

Social media technologies let people connect by creating and sharing content. We examine the use of Twitter by famous people to conceptualize celebrity as a practice. On Twitter, celebrity is practiced through the appearance and performance of ‘backstage’ access. Celebrity practitioners reveal what appears to be personal information to create a sense of intimacy between participant and follower, publicly acknowledge fans, and use language and cultural references to create affiliations with followers. Interactions with other celebrity practitioners and personalities give the impression of candid, uncensored looks at the people behind the personas. But the indeterminate ‘authenticity’ of these performances appeals to some audiences, who enjoy the game playing intrinsic to gossip consumption. While celebrity practice is theoretically open to all, it is not an equalizer or democratizing discourse. Indeed, in order to successfully practice celebrity, fans must recognize the power differentials intrinsic to the relationship.
The Changing Nature of Public Service Radio: A Case Study of iCat fm
Authors: Bonet Montse , Fernández-Quijada David , Ribes Xavier
Published: May 2011

In an openly hostile environment in which public service broadcasting (PSB) has to justify its mere existence, its relationship with new technologies and its transformation into Public Service Media (PSM) have been the subject of controversy in Europe, with respect to the legitimate use of new technologies by a public broadcasting service. Making use of qualitative techniques with a case study, this article illustrates how the Catalan public broadcaster iCat fm uses diverse technological distribution platforms in order to successfully achieve its public service remit proposals and provides an example of a successful public service radio that uses diverse technological distribution platforms.
Invisible Whispers: Accounts of SMS Communication in Shared Physical Space
Authors: Tjora Aksel H.
Published: May 2011

The use of short message services (SMS) on mobile phones has gained huge popularity in most western and many developing countries — so much so that it has become established as the preferred medium for mobile communication especially among young people. This article explores SMS as used for discreet communication between people in the same physical space (‘shared physical space SMS’ — or ‘SPS-SMS’). Drawing from semi-structured interviews with young people in Norway, 10 different scenarios of SPS-SMS use are explored and analysed within an interactionist framework. These sites of SPS-SMS are presented here as ‘communicative affordances’. It is concluded that the mobile phone, by the application of SPS-SMS, affords communicative layers of transparency, by which various SMS users maintain semi-synchronous communication, both for care and coordination. Although a qualitative study of this nature does not lend itself to generalizations about SPS-SMS communication, it does demonstrate how detailed studies of extraordinary uses of mediated communication may be used to widen analyses of social interaction.
HD Aesthetics
Authors: Flaxton Terry
Published: May 2011

Professional expertise derived from developing and handling higher resolution technologies now challenges academic convention by seeking to reinscribe digital image making as a material process. In this article and an accompanying online resource, I propose to examine the technology behind High Definition (HD), identifying key areas of understanding to enable an enquiry into those aesthetics that might derive from the technical imperatives within the medium. (This article is accompanied by a series of online interviews entitled A Verbatim History of the Aesthetics, Technology and Techniques of Digital Cinematography. To access this please go to http://www.flaxton.btinternet. co.uk/KTV.htm. This resource seeks to circumscribe and circumlocute the wide variety of interests and usages of incoming digital media with specific relation to the effects of increased definition being offered by incoming digital technologies). Having discussed the aesthetics of HD I will then proceed to look at the consequent artistic and cultural implications. The article concludes by challenging the current academic position of the digital as being inherently immaterial.
Taking personal responsibility for well-being increases birth satisfaction of first time mothers
Authors: Howarth Anne M. , Swain Nicola , Treharne Gareth J.
Published: May 2011

Birth satisfaction has been found to enhance a mother’s capacity to develop a sense of maternal identity. This study used a phenomenological form of thematic analysis to gain in-depth insights into the birth experiences of first-time New Zealand mothers. Taking personal responsibility (the choices participants made in relation to being in control of and accountable for their own birth processes) was a core theme. Those participants who described the neoliberalist ideal of taking personal responsibility to be well informed and well prepared for any birth experience felt more confident that they would be able to work with whatever labour and birth event eventuated.
Lead in PM10 and in Indoor Dust Around Schools and Preschools in Selangor, Malaysia
Authors: Mohd Talib Latif  , Nor Hafizah Baharudin  , Zafirah Mohamad Nor  , Mazlin Bin Mokhtar
Published: May 2011

A study of possible exposure to indoor lead by school and preschool children was conducted around Selangor, Malaysia. For collecting suspended particulates less than 10 micrometer in diameter (PM10) inside and outside the school and preschool buildings, a low-volume sampler was used. For collecting dust in the indoor environments, small brushes and Kimwipes were used. Lead in PM10 and in dust was determined using an atomic absorption spectrophotometer with a graphite furnace. The average lead concentrations in PM10 in the indoor environment were found to be higher in schools (118.85 ± 86.08 ng•m-3) than in preschools (6.97 ± 0.30 ng·m-3). Higher concentrations of lead in the indoor dust in school environments (ranging between 19.10 ±1.55 and 31.62 ± 0.98 μg·g-1) compared to lead in the indoor dust in preschool environments (ranged between 0.37 ± 0.01 and 2.74 ± 0.04 μg·g-1) suggest that indoor sources, particularly paint on indoor walls, are also capable of generating lead in indoor environments. Furthermore, in all indoor environments, the levels of lead in PM10 increased with rising levels of lead in their associated outdoor environments, thus suggesting that the local outdoor environments also add lead to the indoor environments.
Assessment of Population Exposure to Extremely Low Frequency Magnetic Fields and Its Possible Childhood Health Risk in the Czech Republic
Authors: Jirik Vitezslav , Pekarek Ludek , Janout Vladimir
Published: May 2011

The purpose of this study was to estimate exposure of children to power frequency magnetic field and its possible variability in the main types of houses. Spot measurements with a number of additional measurements were used for exposure assessment. The objective was to find out how many children in the Czech Republic are exposed to low-frequency magnetic field above 0.4 μT — level, hypothetically associated with the increased risk of childhood leukaemia.
Non-neutrality and argument in the hybrid political interview
Authors: Hutchby Ian
Published: May 2011

This article explores the nature of argumentative interaction in the hybrid political interview: a broadcast news genre whose discourse positions the journalist not just as investigator but as socio-political advocate. Such interviews offer explicit challenges to the traditionally conceived ‘neutral’ role of the broadcast news journalist. Interviewer ‘non-neutrality’ is examined in contexts where the speech exchange system shifts into the unmitigated and aggravated opposition characteristic of argument. Drawing on a sample of interviews involving different hosts, I analyse the structural features of both interviewer and interviewee turns that occur in these environments. I do this in relation both to sequential matters — that is, the types of turns taken and their relations with other turns in their immediate environment — and to matters of the substantive content of utterances — that is, what speakers are saying and/or the way they are saying it.
Formulating dispositions in coming out advice
Authors: Chirrey Deborah A.
Published: May 2011

This article considers the advice found on six internet sites written for people who are considering coming out. The article uses Edwards’ (1994, 1995, 1997) script formulation theory to examine how the grammatical choices by the writers formulate the dispositions of the main actors in the texts: the advice seeker, LGB individuals, and the people to whom they come out. The writers’ formulations are shaped by a view of coming out as the act of a reasonable, emotionally healthy, moral and loving lesbian, gay or bisexual (LGB) individual. It is argued that one of the purposes of these texts is to normalize coming out as a routine event and as a rational course of action for an LGB individual. Furthermore, the use of script formulation is seen to be characteristic of written texts and a strategy by which advice writers can legitimize themselves as qualified to give advice.
Word repeats as unit ends
Authors: Schegloff Emanuel A.
Published: May 2011

Turns-at-talk are fundamental units of participation in talk-in-interaction, and turn-constructional-units (TCUs) are the basic building blocks for turns. Possible completion of a TCU is, in principle, the possible completion of the turn, but multi-unit turns are not uncommon, and participants have practices for constructing multi-unit turns and for recognizing them in the course of their production. This article offers an account of one practice (and several of its variants) usable by speakers and recipients to convey and recognize the designed completion of a multi-TCU turn and/or a multi-turn sequence in which ‘answering’ is being done: returning to, or ‘re-using’, a word or phrase from the start of the turn or sequence, whether articulated by same or different speaker, whether used to refer to same or different referents. This practice is one of the resources by which the overall structural organization of an interactional unit and its local realization are mutually realized.
How to Generate Personal Networks: Issues and Tools for a Sociological Perspective
Authors: Bidart Claire , Charbonneau Johanne
Published: May 2011

The debate on the limits and relevance of the different name generators comes with the development of social network studies. The core questions are: What are they supposed to construct? For what research question? Some procedures tend to choose a precise target with a unique name generator; others prefer to use a series of name generators. The authors discuss here some specificities and advantages of these methods for ego-centered networks. The authors then present the ‘‘contextual’’ name generator, which was developed in longitudinal qualitative panel studies in France and Québec. This tool gives access to a great variety of information focused on sociological questions. Its original design differentiates two complementary stages to distinguish the global contexts-based network from specific resource-based networks. This tool remains flexible and may be adapted to different topics.
Athletic Scholarships in Intercollegiate Football
Authors: Pitts Joshua D. , Rezek Jon Paul
Published: May 2011

Despite the financial and cultural importance of intercollegiate athletics in the United States, there is a paucity of research into how athletic scholarships are awarded. In this article, the authors empirically examine the factors that universities use in their decision to offer athletic scholarships to high school football players. Using a Zero-Inflated Negative Binomial (ZINB) model, the authors find a player’s weight, height, body mass index (BMI), race, speed, on-the-field performance, and his high school team’s success often have large and significant impacts on the number of scholarship offers he receives. There is also evidence of a negative relationship between academic performance and scholarship offers. In addition, the authors find evidence of a scholarship premium for players from Florida and Texas. The results also show that running backs, wide receivers, and defensive backs appear to generate the most attention from college football coaches, other things equal.
Genealogy: A Tale of Two Families and a Cat
Authors: Halley Jean
Published: May 2011

In this essay, I juxtapose mundane moments in life with two other time experiences. One is the larger sweep of time expressed in a genealogy or a family history, and the other is the time-out-of-time experience of trauma. Family histories work to contain experience, to offer explanations. And, in sharp contrast, often simultaneous to such stories, trauma happens, bursting though other experience, refusing containment.
Modeling of dynamics, guidance, and control systems of air-to-surface missiles
Authors: Özkan Bülent , Özgören M Kemal , Mahmutyazıcıoğlu Gökmen
Published: May 2011

In this study, the generic dynamic models of air-to-surface missiles are given in addition to the related guidance and control schemes. In this extent, two-part missile configurations are considered as well as the traditional single-part missile geometries. The dynamic modelling part consists of the general equations of motion for both of the mentioned types of missile configurations, aerodynamic modelling and corresponding transfer functions, which are used in the design of missile autopilots. Further, the notable guidance laws applicable to such missiles are given along with the relevant autopilot, or missile control system, models. Regarding the mission profile of these munitions, the target is modelled as a surface vehicle moving on the ground. After conducting some computer simulations based on the proposed models, the study is concluded by a general evaluation section.
Failures of the RM finger prosthesis joint replacement system
Authors: Middleton A. , Lakshmipathy R. , Irwin L. R.
Published: May 2011

In our unit a high failure rate of the RM finger prosthesis joint replacement system was noted, prompting a review of cases. A series of patients underwent implantation under the care of one surgeon and the results were monitored. Twenty-one devices were implanted of which 16 were inserted for rheumatoid disease. Patients were reviewed regularly and the implant performance was assessed critically along with survival of the implant to revision, infection or death of the patient. The mean follow-up was 32 months. Unacceptable failure rates at early and medium term stages were identified, with 15 of the implants revised by 2 years. Loosening was the commonest mode of failure. The authors do not recommend the use of this implant, especially in cases of rheumatoid arthritis.
Percutaneous needle fasciotomy for primary Dupuytren’s contracture
Authors: Rahr L. , Søndergaard P. , Bisgaard T. , Baad-Hansen T.
Published: May 2011

This study evaluated the effect of percutaneous needle fasciotomy on primary Dupuytren’s contracture in 149 patients (213 rays) admitted to our clinic in 2007. Ninety-two patients (130 rays) were followed up for 2 years to compare the change in total passive extension deficit and the passive extension deficit across the individual joint and to note side effects. No tendon rupture or damage to sensory nerves was observed and the rehabilitation period was short (mean, 0.6 days). We found a significant change ( p < 0.001) in total passive extension deficit after 2 years, but the effect of the treatment was greater in Tubiana I and II stages and our best results were in correction of MCP joint contractures. Percutaneous needle fasciotomy is an alternative treatment for elderly patients with severe comorbidity or for those patients who do not want open surgery.
Effects of forearm muscles on carpal stability
Authors: Salva-Coll G. , Garcia-Elias M. , Leon-Lopez M. T. , Llusa-Perez M. , Rodríguez-Baeza A.
Published: May 2011

Thirty cadaveric forearms were tested using a wrist testing apparatus specifically designed to investigate the mechanisms of muscle stabilization of the wrist. The specimens were set in a jig allowing the distal row to migrate proximally and to rotate around the pronosupination forearm axis. Five wrist motor tendons (FCR, FCU, ECU, ECRL and APL) were loaded with specific weights. Reactive rotations of the scaphoid, triquetrum and capitate were measured by an electromagnetic motion tracking device. When all five tendons were loaded simultaneously, the capitate supinated and the proximal row predominantly supinated and flexed. By contrast, when the ECU was loaded in isolation, it caused pronation to both proximal and distal rows. The FCR exhibited a mixed effect pronating the capitate and triquetrum, whilst supinating the scaphoid. Based on this, a hypothesis is proposed linking wrist stability to the balance of wrist pronators (ECU and FCR) and supinators (FCU, ECRL and APL).
Ten years follow-up of health and disability in people with acute traumatic hand injury: pain and cold sensitivity are long-standing problems
Authors: Gustafsson M. , Hagberg L. , Holmefur M.
Published: May 2011

The aim of this study was to investigate health and disability in people with acute traumatic hand injury 10 years after the accident. A consecutive sample of patients from the Department of Hand Surgery was followed up by means of a postal questionnaire containing the instruments EQ-5D for assessment of health and DASH for assessment of disability. Questions were added about cold sensitivity, numbness and aesthetic problems. The 97 people with various acute hand injuries had greater problems with impairments of hand function than with limitations of activities and participation in daily life. Pain was more common than among the general Swedish population. Cold sensitivity was reported by 78% and was associated with both worse impairments and greater limitations on activity and participation. Despite problems with pain and cold sensitivity, they reported good health and a low degree of disability.
Accuracy of intrasheath injection techniques for de Quervain’s disease: a cadaveric study
Authors: Mirzanli C. , Ozturk K. , Esenyel C. Z. , Ayanoglu S. , Imren Y. , Aliustaoglu S.
Published: May 2011

The purpose of this study was to assess the accuracy of injections of dye into the first extensor compartment of the wrist using three different techniques in 150 wrists in 75 fresh cadavers. To compare injections, 50 wrists from 25 cadavers were used for each technique. After the injections, the first extensor compartment was dissected and the dispersion of dye around the abductor pollicis longus and extensor pollicis brevis tendons was investigated. In 72 % of all the wrists, acrylic dye was dispersed into one compartment containing both the abductor pollicis longus and extensor pollicis brevis tendons, but in 28% of the wrists there was a separate compartment for extensor pollicis brevis and dye entered only one of the compartments (14% for each compartment). For accurate injections, we think the injections should be made separately over the two tendons, to allow for the possibility of a septum within the compartment.
Fractures of the distal radius in women aged 50 to 75 years: natural course of patient-reported outcome, wrist motion and grip strength between 1 year and 2–4 years after fracture
Authors: Brogren E. , Hofer M. , Petranek M. , Dahlin L. B. , Atroshi I.
Published: May 2011

Fractures of the distal radius in postmenopausal women may cause prolonged pain and disability, but little is known about their natural course beyond the first year. In this study, women of 50–75 years of age, initially treated with cast or external fixation, were examined 1 year after distal radial fracture and then re-evaluated after a mean of 3 (range, 2–4) years. The evaluation included pain, disability (DASH) scores, grip strength and range of motion. In the 49 participating women pain scores, grip strength and range of motion improved significantly, although the mean improvement was moderate or small. In a subgroup of 13 patients with moderate or severe malunion, the 1 year DASH score was significantly worse than in the remaining patients but improved significantly together with grip strength and range of motion. After fractures of the distal radius, pain, grip strength and range of motion continued to improve beyond 1 year, up to 2–4 years. Patients with malunion had more disability at 1 year but showed significant improvement at 2–4 years.
Key questions for conducting role delineation research
Authors: Taub Alyson , Gilmore Gary D. , Olsen Larry K. , Connell Dave
Published: May 2011

Role delineation research for the verification of professional competencies is essential in many professions to promote quality assurance and support capacity building and workforce development. In this article, guidance is provided about key aspects of role delineation research. The information contained in this article focuses on 13 key questions within three selected research phases when attempting to identify and verify the roles that are inherent within any given profession. The major sections in the paper include planning the research, collecting and analyzing the data, interpreting findings, and considering the future. Recommendations and examples related to each of the important questions are provided to assist others undertaking role delineation research.
Cultures locales de vaccination : le rôle central des agents de santé en milieu rural au Burkina Faso
Authors: Sia Drissa , Fournier Pierre , Sondo Blaise K.
Published: May 2011

Problématique. Le Burkina Faso a utilisé différentes stratégies de vaccination auxquelles d’importantes ressources ont été allouées, cependant la couverture vaccinale est demeurée insuffisante. Au niveau périphérique du système de santé, à son interface avec la communauté, se développent des « cultures locales de vaccination ». Objectif. Analyser les composantes de ces cultures locales de vaccination : (i) l’étiologie attribuée aux maladies du programme élargi de vaccination (PEV), son acceptation et ses avantages perçus et ; (ii) les expériences de vaccination. Méthodes. Des focus groups (21) et des entretiens individuels semi-dirigés (13) ont été réalisés dans deux aires sanitaires (ayant les meilleurs et les moins bons résultats en matière de vaccination), d’un district sanitaire au Burkina Faso. Résultats. Les maladies cibles du PEV sont bien connues et sont classées parmi les maladies du « blanc », catégorie de maladies devant être traitées au centre de santé. Malgré leur recours à la médecine traditionnelle, les populations attribuent la régression de la fréquence et de la gravité des épidémies de rougeole, coqueluche et poliomyélite à la vaccination. La fièvre et la diarrhée post vaccinales peuvent être vues comme un succès ou une contre-indication de la vaccination. Les deux centres de santé appliquent les mêmes stratégies et font face aux mêmes barrières à l’accessibilité. A Yirtan, l’organisation de la vaccination est meilleure, le comité de gestion y est impliqué et l’agent de santé est plus disponible ; il accueille mieux les mères et est soucieux de s’intégrer à la communauté. On y note une meilleure mobilisation sociale. Conclusion. Le contraste de deux cultures locales de vaccination différentes, montre que le comportement de l’agent de santé en constitue la composante déterminante. Tant dans la sphère professionnelle que personnelle, il doit créer un climat de confiance avec la population qui acceptera de faire vacciner ses enfants, pour autant que le service soit disponible.
What should we do in China to close the implementation gap in health promotion? A response to the WHO’s Nairobi Call to Action
Authors: Yang Li  , Maoxuan Tao  , Hua Fu
Published: May 2011

In response to the WHO’s Nairobi Call to Action, the paper presents results of a SWOT analysis (Strengths, Weaknesses, Opportunities, Threats) of current health promotion activities in China, and makes recommendations for putting into practice the Call to Action, based on China’s reality and culture.
Common Herbs and Foods Used as Galactogogues
Authors: Nice Frank J.
Published: May 2011

Historically, herbs and foods have been used as galactogogues by breastfeeding women to maintain and increase milk supply. Commonly used herbs and foods used as galactogogues are reviewed. Doses, other uses for taking herbals by breastfeeding mothers, and cautions to observe when using these galactogogues are discussed. This information can be used by health care professionals as general guidelines to counsel lactating mothers who wish to use or are already using herbals or consuming foods to stimulate milk supply. A brief mention of prescription galactogogue alternatives is provided. Sources of currently available nonprescription galactogogue information are listed. This information will be useful for community, clinic, hospital, and other health care settings where consultative services are provided to breastfeeding mothers. Utilization of the information provided will allow health care professionals to counsel mothers on the use of herbals and foods as galactogogues.
Nutrition Practice in the Early Intervention System: Illinois
Authors: Baranoski Cindy , Grutza Tammy , Hagen Ginger L. , Humphrey Jeannine , Kedzierski Cindy , Schrock Kathleen
Published: May 2011

Provision of nutrition therapy for children with special needs is a necessity to ensure that they grow and develop to the best of their ability. Regulations exist at the federal and state level for the Early Intervention (EI) program, guiding professionals who can provide nutrition to eligible children. Specifics detailing the scope of a dietitian’s practice are available through the American Dietetic Association and are primary to effective and ethical care. Unfortunately, this detail is not found at the state level in the Illinois EI system, allowing for varying interpretations by all who participate or work within the program. Educating those persons in Illinois about the value of services performed by dietitians is imperative, given that potential changes and recommendations by the state are already being imposed. Ramifications exist for children who receive nutrition services in EI, when regulations are created or modified without input of registered dietitians. Ensuring that nutrition services in the EI system continue to be available to families, and performed by qualified providers, is essential. The purpose of this article is to highlight nutrition services in the state of Illinois and to demonstrate the vital role of registered dietitians in the provision of optimal nutrition care for children with special health care needs, in an effort to limit future changes that might be detrimental to the nutrition care of the children in any state who participate in the EI system.
Nutrition Management of Children With Osteosarcoma
Authors: Ringwald-Smith Karen , Surprise Harriet , Billups Catherine , Daw Najat
Published: May 2011

Children with cancer are at risk of developing nutrition deficiencies as a result of both disease progression and treatment. Providing timely and appropriate nutrition intervention is paramount to the attainment of positive outcomes, yet guidelines regarding the most effective forms of intervention are lacking. The purpose of this retrospective study was to identify the types of nutrition intervention provided during treatment and to evaluate effectiveness of each. Medical records of patients treated on an established institutional protocol for osteosarcoma between May 1999 and May 2006 were reviewed. Data collected at baseline, weeks 12 and 23, and after completion of treatment included nutrition status, change in nutrition status, type of nutrition support, and number of days on support. In total, 14 of 48 patients (29%) received nutrition support during treatment. Appetite stimulants (dronabinol, cyproheptadine, or megestrol acetate) were the most common type of support used. This form of nutrition intervention seems to be effective in maintaining nutrition status as a sole modality or in combination with parenteral nutrition. Optimizing nutrition interventions by including appetite stimulants may prove to be effective in this population.
AMP-activated protein kinase deficiency reduces ozone-induced lung injury and oxidative stress in mice
Authors: Hulo Sébastien , Tiesset Hélène , Lancel Steve , Louis Edmé Jean J , Viollet Benoit , Sobaszek Annie , Nevière Rémi
Published: May 2011

Background

Acute ozone exposure causes lung oxidative stress and inflammation leading to lung injury. At least one mechanism underlying the lung toxicity of ozone involves excessive production of reactive oxygen and nitrogen intermediates such as peroxynitrite. In addition and beyond its major prooxidant properties, peroxynitrite may nitrate tyrosine residues altering phosphorylation of many protein kinases involved in cell signalling. It was recently proposed that peroxynitrite activates 5'-AMP-activated kinase (AMPK), which regulates metabolic pathways and the response to cell stress. AMPK activation as a consequence of ozone exposure has not been previously evaluated. First, we tested whether acute ozone exposure in mice would impair alveolar fluid clearance, increase lung tissue peroxynitrite production and activate AMPK. Second, we tested whether loss of AMP-activated protein kinase alpha1 subunit in mouse would prevent enhanced oxidative stress and lung injury induced by ozone exposure.

Methods

Control and AMPKα1 deficient mice were exposed to ozone at a concentration of 2.0 ppm for 3 h in glass cages. Evaluation was performed 24 h after ozone exposure. Alveolar fluid clearance (AFC) was evaluated using fluorescein isothiocyanate tagged albumin. Differential cell counts, total protein levels, cytokine concentrations, myeloperoxidase activity and markers of oxidative stress, i.e. malondialdehyde and peroxynitrite, were determined in bronchoalveolar lavage (BAL) and lung homogenates (LH). Levels of AMPK-Thr172 phosphorylation and basolateral membrane Na(+)-K(+)-ATPase abundance were determined by Western blot.

Results

In control mice, ozone exposure induced lung inflammation as evidence by increased leukocyte count, protein concentration in BAL and myeloperoxidase activity, pro-inflammatory cytokine levels in LH. Increases in peroxynitrite levels (3 vs 4.4 nM, p = 0.02) and malondialdehyde concentrations (110 vs 230 μmole/g wet tissue) were detected in LH obtained from ozone-exposed control mice. Ozone exposure consistently increased phosphorylated AMPK-Thr172 to total AMPK ratio by 80% in control mice. Ozone exposure causes increases in AFC and basolateral membrane Na(+)-K(+)-ATPase abundance in control mice which did not occur in AMPKα1 deficient mice.

Conclusions

Our results collectively suggest that AMPK activation participates in ozone-induced increases in AFC, inflammation and oxidative stress. Further studies are needed to understand how the AMPK pathway may provide a novel approach for the prevention of ozone-induced lung injury.
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
Authors: Luna Augustin , Karac Evrim I , Sunshine Margot , Chang Lucas , Nussinov Ruth , Aladjem Mirit I , Kohn Kurt W
Published: May 2011

Background

The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation.

Results

A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification.

Conclusions

The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available athttp://discover.nci.nih.gov/mim.
TAFFEL: Independent Enrichment Analysis of gene sets
Authors: Kurki Mitja I , Paananen Jussi , Storvik Markus , Ylä-Herttuala Seppo , Jääskeläinen Juha E , von und zu Fraunberg Mikael , Wong Garry , Pehkonen Petri
Published: May 2011

Background

A major challenge in genomic research is identifying significant biological processes and generating new hypotheses from large gene sets. Gene sets often consist of multiple separate biological pathways, controlled by distinct regulatory mechanisms. Many of these pathways and the associated regulatory mechanisms might be obscured by a large number of other significant processes and thus not identified as significant by standard gene set enrichment analysis tools.

Results

We present a novel method called Independent Enrichment Analysis (IEA) and software TAFFEL that eases the task by clustering genes to subgroups using Gene Ontology categories and transcription regulators. IEA indicates transcriptional regulators putatively controlling biological functions in studied condition.

Conclusions

We demonstrate that the developed method and TAFFEL tool give new insight to the analysis of differentially expressed genes and can generate novel hypotheses. Our comparison to other popular methods showed that the IEA method implemented in TAFFEL can find important biological phenomena, which are not reported by other methods.
The Enhancer of split transcription factor Her8a is a novel dimerisation partner for Her3 that controls anterior hindbrain neurogenesis in zebrafish
Authors: Webb Katharine J , Coolen Marion , Gloeckner Christian J , Stigloher Christian , Bahn Brigitte , Topp Stefanie , Ueffing Marius , Bally-Cuif Laure
Published: May 2011

Background

Neurogenesis control and the prevention of premature differentiation in the vertebrate embryo are crucial processes, allowing the formation of late-born cell types and ensuring the correct shape and cytoarchitecture of the brain. Members of the Hairy/Enhancer of Split (Hairy/E(spl)) family of bHLH-Orange transcription factors, such as zebrafish Her3, 5, 9 and 11, are implicated in the local inhibition of neurogenesis to maintain progenitor pools within the early neural plate. To better understand how these factors exert their inhibitory function, we aimed to isolate some of their functional interactors.

Results

We used a yeast two-hybrid screen with Her5 as bait and recovered a novel zebrafish Hairy/E(spl) factor - Her8a. Using phylogenetic and synteny analyses, we demonstrate thather8aevolved from an ancient duplicate ofHes6that was recently lost in the mammalian lineage. We show thather8ais expressed across the mid- and anterior hindbrain from the start of segmentation. Through knockdown and misexpression experiments, we demonstrate that Her8a is a negative regulator of neurogenesis and plays an essential role in generating progenitor pools within rhombomeres 2 and 4 - a role resembling that of Her3. Her8a co-purifies with Her3, suggesting that Her8a-Her3 heterodimers may be relevant in this domain of the neural plate, where both proteins are co-expressed. Finally, we demonstrate thather8aexpression is independent of Notch signaling at the early neural plate stage but that SoxB factors play a role in its expression, linking patterning information to neurogenesis control. Overall, the regulation and function of Her8a differ strikingly from those of its closest relative in other vertebrates - the Hes6-like proteins.

Conclusions

Our results characterize the phylogeny, expression and functional interactions involving a new Her factor, Her8a, and highlight the complex interplay of E(spl) proteins that generates the neurogenesis pattern of the zebrafish early neural plate.
The mode and tempo of hepatitis C virus evolution within and among hosts
Authors: Gray Rebecca R , Parker Joe , Lemey Philippe , Salemi Marco , Katzourakis Aris , Pybus Oliver G
Published: May 2011

Background

Hepatitis C virus (HCV) is a rapidly-evolving RNA virus that establishes chronic infections in humans. Despite the virus' public health importance and a wealth of sequence data, basic aspects of HCV molecular evolution remain poorly understood. Here we investigate three sets of whole HCV genomes in order to directly compare the evolution of whole HCV genomes at different biological levels: within- and among-hosts. We use a powerful Bayesian inference framework that incorporates both among-lineage rate heterogeneity and phylogenetic uncertainty into estimates of evolutionary parameters.

Results

Most of the HCV genome evolves at ~0.001 substitutions/site/year, a rate typical of RNA viruses. The antigenically-important E1/E2 genome region evolves particularly quickly, with correspondingly high rates of positive selection, as inferred using two related measures. Crucially, in this region an exceptionally higher rate was observed for within-host evolution compared to among-host evolution. Conversely, higher rates of evolution were seen among-hosts for functionally relevant parts of the NS5A gene. There was also evidence for slightly higher evolutionary rate for HCV subtype 1a compared to subtype 1b.

Conclusions

Using new statistical methods and comparable whole genome datasets we have quantified, for the first time, the variation in HCV evolutionary dynamics at different scales of organisation. This confirms that differences in molecular evolution between biological scales are not restricted to HIV and may represent a common feature of chronic RNA viral infection. We conclude that the elevated rate observed in the E1/E2 region during within-host evolution more likely results from the reversion of host-specific adaptations (resulting in slower long-term among-host evolution) than from the preferential transmission of slowly-evolving lineages.
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
Authors: Gilles André , Meglécz Emese , Pech Nicolas , Ferreira Stéphanie , Malausa Thibaut , Martin Jean-François
Published: May 2011

Background

The rapid evolution of 454 GS-FLX sequencing technology has not been accompanied by a reassessment of the quality and accuracy of the sequences obtained. Current strategies for decision-making and error-correction are based on an initial analysis by Huse et al. in 2007, for the older GS20 system based on experimental sequences. We analyze here the quality of 454 sequencing data and identify factors playing a role in sequencing error, through the use of an extensive dataset for Roche control DNA fragments.

Results

We obtained a mean error rate for 454 sequences of 1.07%. More importantly, the error rate is not randomly distributed; it occasionally rose to more than 50% in certain positions, and its distribution was linked to several experimental variables. The main factors related to error are the presence of homopolymers, position in the sequence, size of the sequence and spatial localization in PT plates for insertion and deletion errors. These factors can be described by considering seven variables. No single variable can account for the error rate distribution, but most of the variation is explained by the combination of all seven variables.

Conclusions

The pattern identified here calls for the use of internal controls and error-correcting base callers, to correct for errors, when available (e.g. when sequencing amplicons). For shotgun libraries, the use of both sequencing primers and deep coverage, combined with the use of random sequencing primer sites should partly compensate for even high error rates, although it may prove more difficult than previous thought to distinguish between low-frequency alleles and errors.
BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.)
Authors: Schulte Daniela , Ariyadasa Ruvini , Shi Bujun , Fleury Delphine , Saski Chris , Atkins Michael , deJong Pieter , Wu Cheng-Cang , Graner Andreas , Langridge Peter , Stein Nils
Published: May 2011

Background

Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC) libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place.

Result

Five new BAC libraries were constructed for barley (Hordeum vulgare L.) cultivar Morex. These libraries were constructed in different cloning sites (Hind III, EcoR I, Mbo I and BstX I) of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also generated. The new BAC libraries were fully characterized in depth by scrutinizing the major quality parameters such as average insert size, degree of contamination (plate wide, neighboring, and chloroplast), empty wells and off-scale clones (clones with <30 or >250 fragments). Additionally a set of gene-based probes were hybridized to high density BAC filters and showed that genome coverage of each library is between 2.4 and 6.6 X.

Conclusion

BAC libraries representing >20 haploid genomes are available as a new resource to the barley research community. Systematic utilization of these libraries in high-throughput BAC fingerprinting should allow developing a genome-wide physical map for the barley genome, which will be instrumental for map-based gene isolation and genome sequencing.
Horizontal gene transfer in silkworm, Bombyx mori
Authors: Zhu Bo , Lou Miao-Miao , Xie Guan-Lin , Zhang Guo-Qing , Zhou Xue-Ping , Li Bin , Jin Gu-Lei
Published: May 2011

Background

The domesticated silkworm, Bombyx mori, is the model insect for the order Lepidoptera, has economically important values, and has gained some representative behavioral characteristics compared to its wild ancestor. The genome of B. mori has been fully sequenced while function analysis of BmChi-h and BmSuc1 genes revealed that horizontal gene transfer (HGT) maybe bestow a clear selective advantage to B. mori. However, the role of HGT in the evolutionary history of B. mori is largely unexplored. In this study, we compare the whole genome of B. mori with those of 382 prokaryotic and eukaryotic species to investigate the potential HGTs.

Results

Ten candidate HGT events were defined in B. mori by comprehensive sequence analysis using Maximum Likelihood and Bayesian method combining with EST checking. Phylogenetic analysis of the candidate HGT genes suggested that one HGT was plant-to- B. mori transfer while nine were bacteria-to- B. mori transfer. Furthermore, functional analysis based on expression, coexpression and related literature searching revealed that several HGT candidate genes have added important characters, such as resistance to pathogen, to B. mori.

Conclusions

Results from this study clearly demonstrated that HGTs play an important role in the evolution of B. mori although the number of HGT events in B. mori is in general smaller than those of microbes and other insects. In particular, interdomain HGTs in B. mori may give rise to functional, persistent, and possibly evolutionarily significant new genes.