bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using chemical organization theory for model checking
Authors: Kaleta Christoph , Richter Stephan , Dittrich Peter 
Published: May 2009

Abstract
Motivation: The increasing number and complexity of biomodels makes automatic procedures for checking the models' properties and quality necessary. Approaches like elementary mode analysis, flux balance analysis, deficiency analysis and chemical organization theory (OT) require only the stoichiometric structure of the reaction network for derivation of valuable information. In formalisms like Systems Biology Markup Language (SBML), however, information about the stoichiometric coefficients required for an analysis of chemical organizations can be hidden in kinetic laws.
Results: First, we introduce an algorithm that uncovers stoichiometric information that might be hidden in the kinetic laws of a reaction network. This allows us to apply OT to SBML models using modifiers. Second, using the new algorithm, we performed a large-scale analysis of the 185 models contained in the manually curated BioModels Database. We found that for 41 models (22%) the set of organizations changes when modifiers are considered correctly. We discuss one of these models in detail (BIOMD149, a combined model of the ERK- and Wnt-signaling pathways), whose set of organizations drastically changes when modifiers are considered. Third, we found inconsistencies in 5 models (3%) and identified their characteristics. Compared with flux-based methods, OT is able to identify those species and reactions more accurately [in 26 cases (14%)] that can be present in a long-term simulation of the model. We conclude that our approach is a valuable tool that helps to improve the consistency of biomodels and their repositories.
Availability: All data and a JAVA applet to check SBML-models is available from http://www.minet.uni-jena.de/csb/prj/ot/tools
Contact: dittrich@minet.uni-jena.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Systematic review: adherence to a gluten‐free diet in adult patients with coeliac disease
Authors: HALL N. J. , RUBIN G. , CHARNOCK A. 
Published: May 2009

SummaryBackground  Coeliac disease is increasingly diagnosed in adult patients who present with atypical symptoms or who are asymptomatic and detected by case screening. Its treatment, a gluten‐free diet, can have a considerable impact on daily living. Understanding the factors associated with non‐adherence is important in terms of supporting patients with their condition.Aim  To investigate factors associated with adherence to a gluten‐free diet in adults with coeliac disease.Methods  A literature search of multiple electronic databases using a pre‐determined search string for literature between 1980 and November 2007 identified a possible 611 hits. After checking for relevance, 38 studies were included in this review.Results  Rates for strict adherence range from 42% to 91% depending on definition and method of assessment and are the lowest among ethnic minorities and those diagnosed in childhood. Adherence is most strongly associated with cognitive, emotional and socio‐cultural influences, membership of an advocacy group and regular dietetic follow‐up. Screen and symptom‐detected coeliac patients do not differ in their adherence to a gluten‐free diet.Conclusions  The existing evidence for factors associated with non‐adherence to a gluten‐free diet is of variable quality. Further and more rigorous research is needed to characterize those individuals most likely to be non‐adherent to assist them better with their treatment.
Clinical predictors for biphasic reactions in children presenting with anaphylaxis
Authors: Mehr S. , Liew W. K. , Tey D. , Tang M. L. K. 
Published: May 2009

SummaryBackground
One of the main reasons for hospital admission once a child has been stabilized following anaphylaxis is to monitor for a biphasic reaction. However, only a small percentage of anaphylactic episodes involve biphasic reactions that would benefit from admission. Identification of predictive factors for a biphasic reaction would assist in determining who may benefit from prolonged observation.Objective
To determine predictive factors for biphasic reactions in children presenting with anaphylaxis.Methods
This was a retrospective study of children presenting with anaphylaxis to a major paediatric emergency department over a 5‐year period.Results
There were 95 uniphasic (87%), 12 (11%) biphasic and two protracted reactions (2%). One child with a protracted reaction died. For the management of the primary anaphylactic reaction, children developing biphasic reactions were more likely to have received >1 dose of adrenaline (58% vs. 22%, P=0.01) and/or a fluid bolus (42% vs. 8%, P=0.01) than those experiencing uniphasic reactions. The absence of either factor was strongly predictive of the absence of a biphasic reaction (negative predictive value 99%), but the presence of either factor was poorly predictive of a biphasic reaction (positive predictive value of 32%). All biphasic reactors, in which the second phase was anaphylactic, received either >1 dose of adrenaline and/or a fluid bolus.Conclusions
Children who received >1 dose of adrenaline and/or a fluid bolus for treatment of their primary anaphylactic reaction were at increased risk of developing a biphasic reaction.
Recombinant lipid transfer protein Tri a 14: a novel heat and proteolytic resistant tool for the diagnosis of baker's asthma
Authors: Palacin A. , Varela J. , Quirce S. , Del Pozo V. , Tordesillas L. , Barranco P. , Fernandez‐Nieto M. , Sastre J. , Diaz‐Perales A. , Salcedo G. 
Published: May 2009

SummaryBackground
Baker's asthma is an important occupational allergic disease. Wheat lipid transfer protein (LTP) Tri a 14 is a major allergen associated with wheat allergy. No panel of wheat recombinant allergens for component‐resolved diagnosis of baker's asthma is currently available.Objective
To evaluate the potential role of recombinant Tri a 14 as a novel tool for the diagnosis of baker's asthma, and to test the heat and proteolytic resistance of the wheat LTP allergen.Methods
A cDNA encoding Tri a 14 was isolated and sequenced, the recombinant allergen produced in Pichia pastoris and purified by chromatographic methods. Physicochemical and immunological comparison of the natural and recombinant forms of Tri a 14 was carried out by N‐terminal amino acid sequencing, matrix‐assisted laser desorption/ionization mass spectrometry, circular dichroism (CD) analysis, IgE immunodetection, and specific IgE determination and ELISA‐inhibition assays using a pool or individual sera from 26 patients with baker's asthma. Thermal denaturation and simulated gastrointestinal digestion of both Tri a 14 forms were checked by spectroscopic and electrophoretic methods, respectively, and biological activity by basophil activation test (BAT).Results
Natural and recombinant Tri a 14 were similarly folded, as indicated by their nearly identical CD spectra and heat denaturation profiles. A high interclass correlation coefficient (0.882) was found between specific IgE levels to both Tri a 14 proteins in individual sera from baker's asthma patients, but a slightly lower IgE‐binding potency of rTri a 14 was detected by ELISA‐inhibition assays. Natural and recombinant Tri a 14 elicited positive BAT in two and one out of three patients, respectively. Heat denaturation profiles and simulated gastrointestinal digestion assays indicated that Tri a 14 displayed a high heat and digestive proteolytic resistance, comparable to those of peach Pru p 3, the model food allergen of the LTP family.Conclusions
Recombinant Tri a 14 is a potential tool for baker's asthma diagnosis, based on its physicochemical and immunological similarity with its natural counterpart. Wheat Tri a 14 shows a high thermal stability and resistance to gastrointestinal digestion.
Cat sensitization according to cat window of exposure in adult asthmatics
Authors: Oryszczyn M.‐P. , Van Ree R. , Maccario J. , Nadif R. , Kauffmann F. ,   on behalf of the EGEA cooperative group
Published: May 2009

SummaryBackground
In adults, there is limited information on tolerance to cat, which may be reflected by high IgG4 without IgE sensitization. Early exposure to cat may play a critical role.Objective
The aim was to assess among adults the association of Fel d 1 IgG4, Fel d 1 IgE, skin prick test (SPT) response to cat and pet‐related symptoms in relation to exposure to cat considering the period of exposure.Methods
SPT response to cat, specific IgE and IgG4 to Fel d 1 were assessed in 167 asthmatics recruited in chest clinics (40 years of age in average) from the French Epidemiological study on the Genetics and Environment of Asthma (EGEA). Childhood and/or current exposure to cat were studied retrospectively.Results
IgG4 was higher in relation to current cat exposure (0.53 vs. 0.09 ng/mL; P<0.001) and higher in women than in men. The period of cat exposure was significantly related to Fel d 1 IgE, the IgE/IgG4 pattern and cat weal size. The lowest values of Fel d 1 IgE, cat weal size, pet‐related nasal or respiratory symptoms were observed in those with both childhood and current exposure as well as the highest proportion of the IgE−/IgG4+ pattern observed in 1.4%, 4.0%, 38.1% and 12.5% of those with −/−, +/−, +/+, −/+ childhood/current exposure, respectively.Conclusions
Adult asthmatics exposed to cats since childhood present an immunologic pattern with high IgG4 and low IgE. Continuous exposure may maintain a state of immunological tolerance to cat.
Expression of a pheromone receptor in ovipositor sensilla of the female moth (Heliothis virescens)
Authors: Widmayer P. , Heifetz Y. , Breer H. 
Published: May 2009

AbstractFemale moths release pheromones that influence various behavioral and physiological processes. The highly specific responses elicited by pheromones are mediated via specific chemosensory proteins, pheromone binding proteins and chemoreceptors, operating in the antennal sensory neurons. In Heliothis virescens, the response to the major pheromone component (Z)‐11‐hexadecenal (Z11‐16:Al) is mediated by the pheromone binding protein PBP2 and the receptor type HR13. PCR experiments revealed that transcripts for relevant chemosensory molecules are also present in the abdomen suggesting an additional role. In the female, mRNA for HR13 as well as for the related PBP2 was found in the ovipositor tip and in an immunohistochemical analysis with a specific antiserum it was possible to visualize the receptor protein in distinct sensilla types surrounding the ovipositor tip. The expression of HR13 implies a chemosensory responsiveness of these sensilla types to pheromones possibly provided by PBP2. Due to the close vicinity of sensillar HR13 cells and pheromone producing cells in the ovipositor we propose that the HR13 cells might mediate abdominal responses to the emitted pheromones.
Complex adaptive chronic care
Authors: Martin Carmel , Sturmberg Joachim 
Published: May 2009

AbstractBackground  The Chronic Care Model (CCM) is widely taken up as the universal operational framework for redesigning health systems to address the increasing chronic disease burden of an ageing population. Chronic care encompasses health promotion, prevention, self management, disease control, treatment and palliation to address ‘chronicity’ of long journeys through disease, illness and care in the varying contexts of complex health systems. Yet at an operational level, CCM activities are predominantly based on an evidence‐base of discreet chronic disease interventions in specific settings; and their demonstrable impact is limited to processes of select disease management such as diabetes in specific disease management programs.Aims  This paper proposes a framework that makes sense of the nature of chronicity and its multiple dimensions beyond disease and argues for a set of building blocks and leverage points that should constitute the starting points for ‘redesign’?Findings  Complex Adaptive Chronic Care is proposed as an idea for an explanatory and implementation framework for addressing chronicity in existing and future chronic care models. Chronicity is overtly conceptualized to encompass the phenomena of an individual journey, with simple and complicated, complex and chaotic phases, through long term asymptomatic disease to bodily dysfunction and illness, located in family and communities. Chronicity encompasses trajectories of self‐care and health care, as health, illness and disease co‐exist and co‐evolve in the setting of primary care, local care networks and at times institutions. A systems approach to individuals in their multi‐layered networks making sense of and optimizing experiences of their chronic illness would build on core values and agency around a local vision of health, empowerment of individuals and adaptive leadership, and it responds in line with the local values inherent in the community's disease‐based knowledge and the local service's history and dynamics. Complex Adaptive Chronic Care exceeds the current notions of disease management as an endpoint. Primary care team members are system adaptors in partnership with individuals constructing their care and system leadership in response to chronic illness, and enable healthy resilience as well as personal healing and support. Outcomes of complex adaptive chronic care are the emergence of health in individuals and communities through adaptability, self‐organization and empowerment.Discussion  Chronic care reform from within a complex adaptive system framework is bottom up and emergent and stands in stark contrast to (but has to co‐exist with) the prevailing protocol based disease care rewarding selective surrogate indicators of disease control. Frameworks such as the Chronic Care Model provide guidance, but do not replace individual experience, local adaptive leadership and responsiveness. The awareness of complexity means opening up problems to a different reality demanding different set of questions and approaches to answer them.
The social construction of chronicity – a key to understanding chronic care transformations
Authors: Martin Carmel M. , Peterson Chris 
Published: May 2009

AbstractPurpose  The purpose of this paper is to argue the importance of contemporary analysis of the modern social construction of chronicity – encapsulating the world views of the chronically ill, and the medical and health system constructions of chronic disease, through the nature of care for chronic conditions. It is argued that chronic diseases are themselves, socially constructed, despite widely accepted disease classification systems. Thus, there is a need to examine how different ideas have permeated our clinical and health system developments and their social context and vice versa.Methods  We examine historical ideas, theory and evidence about the tensions in social construction of chronic illness by those afflicted and the responses of society, the medical and health professions and increasingly the public and private institutions that shape health care. This is with the background of major differences in the two cultures that create knowledge: those based upon argument and intellectual logic – hermeneutic, and those based upon ‘objectivist’ empirical science, often called heuristic. Evidence‐based medicine (EBM) is the flagship of disease management, increasingly narrative‐based medicine and other similar genres are becoming the pragmatic face of social constructions, yet sit in juxtaposition without synthesis. A third culture has emerged of scientific intellectuals who straddle these cultures and in health care their public face is ‘mixed methods’.Findings  Recent cases of modern ideas about improving chronic care were reviewed. We found that despite developments of social theory, the world view of the chronically ill exerts small influence in health system redesign, apparently dominated by chronic disease models. Confusion remains within health system reforms as to the social construction of chronicity – chronic disease, chronic condition or chronic illness and chronic care transformations. The role of Primary Care remains ambiguous straddling disease and illness. Radical redesign of health systems is taking place without an understanding and discourse about the nature of their construction. Ad hoc eclectism with unquestioning adoption of the dominant EBM paradigm is driving a new health culture based on disease‐based performance incentives, which is intrusive beyond the medical model and pays little attention to narratives of illness and even less to the whole social reconstruction of illness and wellness.Conclusions  Health care systems cannot afford to avoid, and should actively embrace the critiques of social theory and analyses in the transformations of health systems to improve chronic care. Creative tensions between empirical and intellectual critique, and a synthetic middle ground are likely to lead to more realistic and innovative approaches spanning the nature of chronicity and the transformation of Primary Care.
Monitoring the performance of intensive care units using the variable life‐adjusted display: a simulation study to explore its applicability and efficiency
Authors: Foltran Francesca , Baldi Ileana , Bertolini Guido , Merletti Franco , Gregori Dario 
Published: May 2009

AbstractRationale, aims and objectives  Graphical monitoring tools are needed for real‐time quality evaluation in intensive care unit. The variable life‐adjusted display (VLAD) provides a directly interpretable assessment indicating whether the overall performance is better or worse than expected on the basis of the predicted risk of failure. The aim of this study is to quantify the ability of VLAD charts to early recognize a worsening in clinical performance.Methods  A Monte Carlo experiment simulating the sequence of successes and failures of an intensive care unit is performed; the predicted mortality is calculated by means of the Simplified Acute Physiology Score 3 admission score. From a given position in the admissions sequence, we increased the probability of death; we calculated: (i) the surveillance system delay in responding to the mortality increase; (ii) the percentage of cases where the VLAD has been able to give an alarm within the first 5, 10, 20 and 60 deaths occurred after the increase of probability of death; and (iii) the percentage of false declarations of increase (anticipated alarms).Results  The frequency distribution of the alarm delays shows VLAD was not always able to early detect mortality increase. Only a very small number of anticipated alarms were given.Conclusions  Variable life‐adjusted display ability to signal is mild and strictly correlated with the institution volume of activity. Therefore, the use of VLAD seems to be not always advisable, and an integration between VLAD and other well‐documented tools as CUSUM charts could be preferable.
Identifying patterns in primary care consultations: a cluster analysis
Authors: Sturmberg Joachim P. , Siew Eu‐gene , Churilov Leonid , Smith‐Miles Kate 
Published: May 2009

AbstractBackground  A literature review revealed that little is known about the systems context of general practice consultations and their outcomes.Objectives  To describe the systems context and resulting underlying patterns of primary care consultations in a local area.Design  Cross‐sectional multi‐practice study based on a three‐part questionnaire. Cluster analysis of data.Setting  Stratified random sample of general practices and general practitioners – NSW‐Central Coast, Australia.Participants  A total of 1104 adults attending 12 general practitioners between February and November 1999.Results and Conclusions  The study identified seven subgroups within the study population uniquely defined by variables from the health system, individual doctor and patient, consultation and consultation outcomes domains. A systems approach provides a framework in which to track and consider the important variables and their known and/or expected workings and thus offer a contextual framework to guide primary care reform.
An investigation on the Culicoides species composition at seven sites in southern Switzerland
Authors: CASATI S. , RACLOZ V. , DELÉCOLLE J. C. , KUHN M. , MATHIS A. , GRIOT C. , STÄRK K. D. C. , VANZETTI T. 
Published: May 2009

AbstractIn the past decade, there have been regular outbreaks of bluetongue (BT) in many parts of Europe. Owing to the presence of BT disease and its vectors in countries adjacent to Switzerland, an initial entomological survey was conducted in 2003, which established the presence of several midges of the genus Culicoides (Diptera: Ceratopogonidae). Subsequently, a sentinel herd monitoring system was established with the primary entomological aim being the determination and further study of Culicoides population compositions. Insects were collected in 2005 and 2006 at seven sentinel herd sites in the south of Switzerland (canton of Ticino) near the border of Italy, using Onderstepoort‐type light traps. This region is botanically and zoologically similar to the Mediterranean and is one of the warmest and most humid areas of the country, hence it is considered a potential access path for BT disease into Switzerland. Collections were made at four cattle farms, two equestrian centres and one goat farm. Sites were sampled four times per month from June to October. Traps were operated from dusk until dawn and samples were collected monthly for analysis through microscopy as well as a Culicoides imicola‐specific PCR. Results confirmed the absence of C. imicola (Kieffer) and demonstrated that the potential BT virus vectors are highly abundant, notably: Culicoides obsoletus (Meigen), Culicoides scoticus (Downes & Kettle) and Culicoides dewulfi (Goetghebuer) subgenus Avaritia and Culicoides pulicaris (Linnaeus) subgenus Culicoides. These findings expand the current knowledge of Culicoides population composition in the southern part of the Switzerland. Culicoides cataneii (Clastrier), Culicoides flavipulicaris (Dzhafarov), Culicoides indistinctus (Khalaf), Culicoides nubeculosus (Meigen) and species of the Grisescens complex were reported for the first time in Switzerland.
Adaptation of the BG‐Sentinel trap to capture male and female Aedes albopictus mosquitoes
Authors: LACROIX R. , DELATTE H. , HUE T. , DEHECQ J. S. , REITER P. 
Published: May 2009

AbstractIn recent years, the remarkable spread of Aedes albopictus (Skuse) (Diptera: Culicidae) throughout the world has drawn attention to this hitherto poorly studied species, particularly after its role in outbreaks of chikungunya fever in the western Indian Ocean and in Italy. Variants of sterile insect technique (SIT), including the release of transgenic males with a dominant lethal gene (RIDL), have been proposed in the search for new and innovative methods of control. Knowledge of male dispersal, mating behaviour and longevity will be critical to the success of this approach. We present an effective and practical method for trapping both male and female Ae. albopictus using a mouse‐baited BG‐Sentinel trap.