bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian ensemble methods for survival prediction in gene expression data
Authors: Bonato Vinicius , Baladandayuthapani Veerabhadran , Broom Bradley M. , Sulman Erik P. , Aldape Kenneth D. , Do Kim-Anh 
Published: December 2010

AbstractMotivation: We propose a Bayesian ensemble method for survival prediction in high-dimensional gene expression data. We specify a fully Bayesian hierarchical approach based on an ensemble ‘sum-of-trees’ model and illustrate our method using three popular survival models. Our non-parametric method incorporates both additive and interaction effects between genes, which results in high predictive accuracy compared with other methods. In addition, our method provides model-free variable selection of important prognostic markers based on controlling the false discovery rates; thus providing a unified procedure to select relevant genes and predict survivor functions.Results: We assess the performance of our method several simulated and real microarray datasets. We show that our method selects genes potentially related to the development of the disease as well as yields predictive performance that is very competitive to many other existing methods.Availability: http://works.bepress.com/veera/1/.Contact: veera@mdanderson.orgSupplementary Information: Supplementary data are available at Bioinformatics online.
Oral glucose tolerance testing in an outpatient heart failure clinic reveals a high proportion of undiagnosed diabetic patients with an adverse prognosis
Authors: Egstrup Michael , Schou Morten , Gustafsson Ida , Kistorp Caroline N. , Hildebrandt Per R. , Tuxen Christian D. 
Published: December 2010

AimsWe evaluated the applicability and prognostic importance of oral glucose tolerance testing (OGTT) among outpatients with systolic heart failure (SHF).Methods and resultsConsecutive patients with SHF and left ventricular ejection fraction (LVEF) ≤ 45% referred to a heart failure clinic (n= 413) were included in this study. An OGTT was conducted in patients without a history of diabetes. Information on NYHA class, aetiology of SHF, LVEF, treatment, and biochemical parameters were collected at baseline. The survival status was obtained after a median follow‐up time of 591 days. Of the 413 patients, 82 (20%) had known diabetes. Of the remaining 331 patients, 227 (69%) agreed to undergo an OGTT. Among the tested subjects, 136 (60%) were classified as having normal glucose tolerance (NGT), 51 (23%) impaired glucose tolerance (IGT), and 40 (18%) newly diagnosed diabetes. Assuming a similar prevalence of unrecognized diabetes among the patients who refused OGTT, the prevalence of diabetes in the total population was 34%. If only fasting blood glucose had been used, 16 of the 40 newly diagnosed diabetic patients would have been undiagnosed. During follow‐up, 24 (29%) patients with known diabetes, 6 (15%) of the newly diagnosed diabetic patients, 9 (18%) of those with IGT, and 13 (9%) patients with NGT died. Patients with diabetes had higher mortality rate compared with non‐diabetic patients [multivariate hazard ratio 1.89 (1.02–3.59); P = 0.047].ConclusionIt is feasible to perform diabetes screening using OGTT in outpatients with SHF. A substantial proportion of patients tested were found to have unrecognized diabetes. The presence of diabetes was associated with a higher mortality rate.
Realized habitats of early-stage North Sea herring: looking for signals of environmental change
Authors: Röckmann Christine , Dickey-Collas Mark , Payne Mark R. , van Hal Ralf 
Published: December 2010

Abstract
Röckmann, C., Dickey-Collas, M., Payne, M. R., and van Hal, R. 2011. Realized habitats of early-stage North Sea herring: looking for signals of environmental change. – ICES Journal of Marine Science, 68: . Realized habitats of North Sea herring for two larval and two juvenile stages were estimated over the past 30 years, using abundances from surveys tied to modelled estimates of temperature and salinity. Newly hatched larvae (NHL) were found mainly in water masses of 9–11°C, pre-metamorphosis larvae (PML) around 5–6°C, juveniles aged 0 in summer around 13–14°C, and juveniles aged 1 in winter around 4–5°C. The median salinity in which the NHL were distributed was 34.4–35.0 and 33.7–33.9, respectively, for PML and juveniles. Interannual variations in temperature and geographic variables in the North Sea were compared with the time-series of realized habitats. The realized temperature habitats of the NHL did not change over time, but the habitat of juveniles in summer may be associated with higher temperatures. Juveniles aged 1 in winter are found in waters colder than the average for the North Sea, a result also reflected in their geographic shift east into shallower water. The results suggest that juveniles could be limited by temperature, but may also track changes in food or predator distribution, and/or internal population dynamics. Time-series analysis of realized salinity habitats was not possible with the available data because of differences between model outputs.
Significance of Esophageal Crohn Disease in Children
Authors: Ammoury Rana F , Pfefferkorn Marian D 
Published: December 2010

ABSTRACTBackground and Aim:Esophageal Crohn disease (ECD) is more common than it was originally thought to be. Only limited information, however, is available regarding its significance and effect on clinical course in the pediatric population. The aim of the study was to determine the prevalence of ECD in our patient population and compare clinical features and severity of disease among patients with ECD and nonesophageal Crohn disease (NECD).Patients and Methods:Medical records of all patients with ECD diagnosed during a 12‐year period based on specific endoscopic and histological criteria were reviewed and compared with a random group of patients with NECD.Results:During the study period, 81 (20%) patients with ECD were identified. Mean age at diagnosis was 12 (range 4–19 years) with a male predominance of 63%. Only 29 (36%) patients had symptoms suggestive of upper gastrointestinal involvement. Endoscopic ulcers were present in 45 (56%) of patients with ECD, whereas noncaseating granulomas were found in 10 (12%) of those patients. The majority (89%) of these patients had concomitant gastric and/or duodenal involvement. When compared with 160 random patients with NECD, patients with ECD had higher mean Pediatric Crohn Disease Activity Index scores (40.2 vs 23.9; P < 0.001), more penetrating‐type disease (12% vs 2%; P = 0.001), and a greater frequency of perianal involvement (51% vs 33%; P = 0.005) at diagnosis. No differences, however, were noted between the 2 groups in terms of need for surgical resection throughout duration of follow‐up.Conclusions:Patients with ECD may represent a phenotype of Crohn disease with a more severe presentation. Patients with perianal disease at the time of initial physical examination should be considered for an upper endoscopy in addition to the colonoscopy to exclude esophageal involvement despite the absence of specific upper gastrointestinal symptoms. These observations should foster additional investigation into ECD phenotype to determine appropriate treatment and prognosis.
Methodology for Longitudinal Assessment of Nutrient Intake and Dietary Habits in Early Childhood in a Transnational Multicenter Study
Authors: Verwied‐Jorky Sabine , Schiess Sonia , Luque Verónica , Grote Veit , Scaglioni Silvia , Vecchi Fiammetta , Martin Francoise , Stolarczyk Anna , Koletzko Berthold ,   European Childhood Obesity Project
Published: December 2010

ABSTRACTObjectives:The aim of this study was to describe developed methods for repeated longitudinal assessment of feeding habits and nutrient intakes of children in a multicenter trial in different European countries and to assess feasibility.Patients and Methods:Nutrient intake and dietary habits of formula‐fed and breast‐fed infants were assessed in 5 European countries (Belgium, Germany, Italy, Poland, and Spain). Prospective age‐adapted 3‐day weighed food records were used from birth to 2 years of age (1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 18, and 24 months). Standard operating procedures were developed to check each day's food record for quality. Dietitians were trained by using standardized food records. Data entry and nutrient analyses were performed with a dedicated software developed for this project.Results:Of 1368 study participants, at least one 3‐day food record was available; of 25,367 1‐day food records, data on quality could be evaluated. Overall, between 81% and 97% (depending on the country) of the food records had been completed with high accuracy. The implementation of solid foods and regular family foods decreased the recording quality significantly during the 2‐year time course (P < 0.001). The standardized training shows coefficients of variation up to a maximum of about 41%, indicating differences in data entry.Conclusions:The experiences gathered indicate that collecting dietary and behavioral data in a large number of infants from different cultures is a challenging but feasible task in which permanent supervision and training is vital. However, we conclude that the established methodology is suitable to obtain valuable results on current infant nutrition practice in Europe.
Initial Dietary and Microbiological Environments Deviate in Normal‐weight Compared to Overweight Children at 10 Years of Age
Authors: Luoto Raakel , Kalliomäki Marko , Laitinen Kirsi , Delzenne Nathalie M , Cani Patrice D , Salminen Seppo , Isolauri Erika 
Published: December 2010

ABSTRACTObjective:The aim of the study was to characterize early nutritional and microbiological environments (maternal colostrum adiponectin concentration and early gut microbiota composition) in children subsequently becoming normal weight versus overweight.Patients and Methods:Fifteen overweight children at 10 years of age were identified from an ongoing prospective nutrition, allergy, mucosal immunology and intestinal microbiota project. Normal‐weight children (n = 15), matched for sex, gestational age and body mass index at birth, mode of delivery, probiotic intervention, and duration of breast‐feeding, were identified from the same cohort as controls. To characterize the early dietary environment we analyzed the adiponectin concentration in the maternal colostrum. With an aim to assess the initial microbiological environment, we analyzed the gut microbiota composition by fluorescent in situ hybridization in these children at the age of 3 months. Additionally, putative early markers of low‐grade inflammation, such as serum‐soluble innate microbial receptor sCD14, were analyzed at the age of 3 months.Results:The colostrum adiponectin concentration was significantly higher in mothers whose children were normal weight than in those whose children were overweight at the age of 10 years (P = 0.001). In parallel, the normal‐weight children had significantly higher sCD14 concentrations in the serum (P = 0.049) and tended to have higher bifidobacterial numbers in the gut microbiota (P = 0.087) at the age of 3 months.Conclusions:The results of the present study suggest that early dietary and gut microbiological environments have a more complex effect on the metabolic programming of a child than previously anticipated.
Supplementation of Infant Formula With Probiotics and/or Prebiotics: A Systematic Review and Comment by the ESPGHAN Committee on Nutrition
Authors:   ESPGHAN Committee on Nutrition:, Braegger Christian , Chmielewska Anna , Decsi Tamas , Kolacek Sanja , Mihatsch Walter , Moreno Luis , Pieścik Małgorzata , Puntis John , Shamir Raanan , Szajewska Hania , Turck Dominique , van Goudoever Johannes 
Published: December 2010

ABSTRACTInfant formulae are increasingly supplemented with probiotics, prebiotics, or synbiotics despite uncertainties regarding their efficacy. The present article, developed by the Committee on Nutrition of the European Society for Paediatric Gastroenterology, Hepatology, and Nutrition, systematically reviews published evidence related to the safety and health effects of the administration of formulae supplemented with probiotics and/or prebiotics compared with unsupplemented formulae. Studies in which probiotics/prebiotics were not administered during the manufacturing process, but thereafter, for example in capsules, the contents of which were supplemented to infant formula or feeds, were excluded.On the basis of this review, available scientific data suggest that the administration of currently evaluated probiotic‐ and/or prebiotic‐supplemented formula to healthy infants does not raise safety concerns with regard to growth and adverse effects. The safety and clinical effects of 1 product should not be extrapolated to other products. At present, there is insufficient data to recommend the routine use of probiotic‐ and/or prebiotic‐supplemented formulae. The Committee considers that the supplementation of formula with probiotics and/or prebiotics is an important field of research. There is a need in this field for well‐designed and carefully conducted randomised controlled trials, with relevant inclusion/exclusion criteria and adequate sample sizes. These studies should use validated clinical outcome measures to assess the effects of probiotic and/or prebiotic supplementation of formulae. Such trials should also define the optimal doses and intake durations, as well as provide more information about the long‐term safety of probiotics and/or prebiotics. Because most of the trials were company funded, independent trials, preferentially financed jointly by national/governmental/European Union bodies and other international organisations, would be desirable.
Processes controlling retention of spring‐spawned Atlantic cod (Gadus morhua) in the western Gulf of Maine and their relationship to an index of recruitment success
Authors: CHURCHILL JAMES H. , RUNGE JEFFREY , CHEN CHANGSHENG 
Published: December 2010

AbstractAtlantic cod, Gadus morhua, harvested in US waters are currently managed as a Gulf of Maine stock and as a stock comprising Georges Bank and southern New England populations. Over the past two and a half decades, success of age‐1 recruitment to the Gulf of Maine stock has varied by more than an order of magnitude. To investigate the hypothesis that this variation is related to variation in the transport of larval cod to nursery areas, we carried out model simulations of the movement of planktonic eggs and larvae spawned within the western Gulf of Maine during spring spawning events of 1995–2005. Results indicate that the retention of spring‐spawned cod, and their transport to areas suitable for early stage juvenile development, is strongly dependent on local wind conditions. Larval cod retention is favored during times of downwelling‐favorable winds and is least likely during times of upwelling‐favorable winds, during which buoyant eggs and early stage larvae tend to be advected offshore to the Western Maine Coastal Current and subsequently carried out of the Gulf of Maine. Model results also indicate that diel vertical migration of later stage larvae enhances the likelihood of retention within the western Gulf of Maine. Consistent with model results is a strong correlation between age‐1 recruitment success to the Gulf of Maine cod stock and the mean northward wind velocity measured in Massachusetts Bay during May. Based on these findings, we propose a wind index for strong recruitment success of age‐1 cod to the Gulf of Maine stock.
Evolutionary and comparative analysis of MYB and bHLH plant transcription factors
Authors: Feller Antje , Machemer Katja , Braun Edward L. , Grotewold Erich 
Published: December 2010

SummaryThe expansion of gene families encoding regulatory proteins is typically associated with the increase in complexity characteristic of multi‐cellular organisms. The MYB and basic helix‐loop‐helix (bHLH) families provide excellent examples of how gene duplication and divergence within particular groups of transcription factors are associated with, if not driven by, the morphological and metabolic diversity that characterize the higher plants. These gene families expanded dramatically in higher plants; for example, there are approximately 339 and 162 MYB and bHLH genes, respectively, in Arabidopsis, and approximately 230 and 111, respectively, in rice. In contrast, theChlamydomonasgenome has only 38 MYB genes and eight bHLH genes. In this review, we compare the MYB and bHLH gene families from structural, evolutionary and functional perspectives. The knowledge acquired on the role of many of these factors in Arabidopsis provides an excellent reference to explore sequence–function relationships in crops and other plants. The physical interaction and regulatory synergy between particular sub‐classes of MYB and bHLH factors is perhaps one of the best examples of combinatorial plant gene regulation. However, members of the MYB and bHLH families also interact with a number of other regulatory proteins, forming complexes that either activate or repress the expression of sets of target genes that are increasingly being identified through a diversity of high‐throughput genomic approaches. The next few years are likely to witness an increasing understanding of the extent to which conserved transcription factors participate at similar positions in gene regulatory networks across plant species.
Metformin improves cardiac function in rats via activation of AMP‐activated protein kinase
Authors: Wang Xiao‐Fang , Zhang Jin‐Ying , Li Ling , Zhao Xiao‐Yan , Tao Hai‐Long , Zhang Li 
Published: December 2010

Summary1. Metformin is one of the most commonly used drugs for the treatment of Type 2 diabetes. Accumulating evidence suggests that metformin also has cardioprotective effects. In the present study, we investigated the cardioprotective effects of metformin and the mechanisms involved.2. A rat model of chronic heart failure was established by permanent left coronary artery occlusion. Heart failure rats were randomly divided into four groups: (i) a saline‐treated group given 4 mL/kg day via intragastric gavage; (ii) a metformin‐treated group, given 100 mg/kg metformin once daily via intragastric gavage; (iii) a group treated with 5 mg/kg 5′‐aminoimidazole‐4‐carboxyamide‐ribonucleoside (AICAR), an AMP‐activated protein kinase (AMPK) agonist, every second day; and (iv) a group treated with 100 mg/kg per day metformin + 20 mg/kg, i.p., compound C (an AMPK antagonist). After 4 weeks treatment, echocardiography was used to assess left ventricular (LV) dimensions and function. Expression of AMPK, endothelial nitric oxide synthase (eNOS) and transforming growth factor (TGF)‐β1 was determined by reverse transcription–polymerase chain reaction and western blot analysis.3. Metformin administration significantly improved cardiac function and LV remodelling, as evidenced by increases in LV systolic pressure and LV ejection fraction and decreases in LV end‐diastolic diameter and LV end‐systolic diameter. These beneficial effects of metformin were associated with increased AMPK and eNOS phosphorylation, as well as reductions in insulin, TGF‐β1, basic fibroblast growth factor and tumour necrosis factor‐α levels in the circulation and/or myocardium.4. The results indicate that chronic low‐dose metformin confers significant cardioprotective effects against chronic heart failure by activating the AMPK–eNOS pathway.
Nursing and justice as a basic human need
Authors: Johnstone Megan‐Jane 
Published: December 2010

AbstractThis paper explores the idea that justice is a basic human need akin to those famously depicted in Maslow's hierarchy of human needs and, as such, warrants recognition as a core element in representative ideas about nursing. Early nurse theorists positioned the principles and practice of nursing as having their origins in ‘universal human needs’. The principle of deriving nursing care from human needs was thought to provide a guide not only for promoting health, but for preventing disease and illness. The nursing profession has had a longstanding commitment to social justice as a core professional value and ideal, obligating nurses to address the social conditions that undermine people's health. The idea of justice as a universal human need per se and its possible relationship to people's health outcomes has, however, not been considered. One reason for this is that justice in nursing discourse has more commonly been associated with law and ethics, and the legal and ethical responsibilities of nurses in relation to individualized patient care and, more recently, changing systems of care to improve health and health outcomes. Although this association is not incorrect, it is incomplete. A key aim of this paper is to redress this oversight and to encourage a broader conceptualization of justice as necessary for human survival, health and development, not merely as a professional value, or legal or ethical principle for guiding human conduct.
Naturalistic nursing
Authors: Hussey Trevor 
Published: December 2010

AbstractWhere nurse education aims to provide an overarching intellectual framework, this paper argues that it should be the framework of naturalism. After an exposition of the chief features of naturalism and its relationship to science and morality, the paper describes naturalistic nursing, contrasting it with some other perspectives. There follows a defence of naturalism and naturalistic nursing against several objections, including those concerning spirituality, religion, meaning, morality, and alternative sources of knowledge. The paper ends with some of the advantages of the naturalistic approach.
Bruteau's philosophy of spiritual evolution and consciousness: foundation for a nursing cosmology
Authors: McCarthy M. Patrice 
Published: December 2010

AbstractThe ontological foundation of the modern world view based on irreconcilable dichotomies has held hegemonic status since the dawn of the scientific revolution. The post‐modern critique has exposed the inadequacies of the modern perspective and challenged the potential for any narrative to adequately ground a vision for the future. This paper proposes that the philosophy of Beatrice Bruteau can support a foundation for a visionary world view consistent with nursing's respect for human dignity and societal health. The author discusses the key concepts of Bruteau's perspective on societal evolution based on an integrated study of science, mathematics, religion, and philosophy. This perspective is discussed as a foundation to move beyond the dichotomous influence of the modern world view and the deconstructive critique of the post‐modern perspective. The author suggests spiritual evolution and a participatory consciousness as an ontological foundation for a cosmology congruent with nursing's social mandate.
What do nurses know?
Authors: Luntley Michael 
Published: December 2010

AbstractThis paper defends an epistemic conservatism – propositional knowing‐that suffices for capturing all the fine details of the knowledge of experienced nurses that depends on the complex ways in which they are embedded in shared fields of activity. I argue against the proliferation of different ways of knowing associated with the work of Dreyfus and Benner. I show how propositional knowledge can capture the detail of the phenomenology that motivates the Dreyfus/Benner proliferation.