bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilevel support vector regression analysis to identify condition-specific regulatory networks
Authors: Chen Li , Xuan Jianhua , Riggins Rebecca B. , Wang Yue , Hoffman Eric P. , Clarke Robert 
Published: April 2010

AbstractMotivation: The identification of gene regulatory modules is an important yet challenging problem in computational biology. While many computational methods have been proposed to identify regulatory modules, their initial success is largely compromised by a high rate of false positives, especially when applied to human cancer studies. New strategies are needed for reliable regulatory module identification.Results: We present a new approach, namely multilevel support vector regression (ml-SVR), to systematically identify condition-specific regulatory modules. The approach is built upon a multilevel analysis strategy designed for suppressing false positive predictions. With this strategy, a regulatory module becomes ever more significant as more relevant gene sets are formed at finer levels. At each level, a two-stage support vector regression (SVR) method is utilized to help reduce false positive predictions by integrating binding motif information and gene expression data; a significant analysis procedure is followed to assess the significance of each regulatory module. To evaluate the effectiveness of the proposed strategy, we first compared the ml-SVR approach with other existing methods on simulation data and yeast cell cycle data. The resulting performance shows that the ml-SVR approach outperforms other methods in the identification of both regulators and their target genes. We then applied our method to breast cancer cell line data to identify condition-specific regulatory modules associated with estrogen treatment. Experimental results show that our method can identify biologically meaningful regulatory modules related to estrogen signaling and action in breast cancer.Availability and implementation: The ml-SVR MATLAB package can be downloaded at http://www.cbil.ece.vt.edu/software.htmContact: xuan@vt.eduSupplementary information: Supplementary data are available at Bioinformatics online.
FastEpistasis: a high performance computing solution for quantitative trait epistasis
Authors: Schüpbach Thierry , Xenarios Ioannis , Bergmann Sven , Kapur Karen 
Published: April 2010

AbstractMotivation: Genome-wide association studies have become widely used tools to study effects of genetic variants on complex diseases. While it is of great interest to extend existing analysis methods by considering interaction effects between pairs of loci, the large number of possible tests presents a significant computational challenge. The number of computations is further multiplied in the study of gene expression quantitative trait mapping, in which tests are performed for thousands of gene phenotypes simultaneously.Results: We present FastEpistasis, an efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. Our results show that the algorithm scales with the number of processors and offers a reduction in computation time when several phenotypes are analyzed simultaneously. FastEpistasis is capable of testing the association of a continuous trait with all single nucleotide polymorphism (SNP) pairs from 500 000 SNPs, totaling 125 billion tests, in a population of 5000 individuals in 29, 4 or 0.5 days using 8, 64 or 512 processors.Availability: FastEpistasis is open source and available free of charge only for non-commercial users from http://www.vital-it.ch/software/FastEpistasisContact: karen.kapur@unil.chSupplementary information: Supplementary data are available at Bioinformatics online.
Effect of Feeding a Formula Supplemented With Long‐chain Polyunsaturated Fatty Acids for 14 Weeks Improves the Ex Vivo Response to a Mitogen and Reduces the Response to a Soy Protein in Infants at Low Risk for Allergy
Authors: Field Catherine J , Van Aerde John E , Goruk Susan , Clandinin M Thomas 
Published: April 2010

ABSTRACTBackground and Objective:Feeding long‐chain polyunsaturated fatty acids (LCP) influences immunity in adults; however, less is known about their effect during development. The aim of the study was to determine the effect of feeding LCP on immunity in healthy infants during the first 4 months of life.Patients and Methods:Formula‐fed infants were randomized at ≤14 days of age to standard term formula (Formula) or formula containing LCP (Formula+LCP). Infants exclusively fed human milk (HM) were included for comparison. At 16 weeks of age, blood was collected and phenotypes, the ability to proliferate and produce cytokines (interleukin [IL]‐2, IL‐4, IL‐6, IL‐10, IL‐12, interferon [IFN]‐γ, tumor necrosis factor [TNF]‐α, TGF‐β) after incubation with phytohemaglutinin (PHA), β‐lactoglobulin, or soy protein were measured.Results:Feeding LCP resulted in a higher than and more similar proliferation rate to PHA in HM‐fed infants, possibly because of a greater TH1 type cytokine response and a higher percentage of antigen mature (CD45RO+) cells (P < 0.05). The response to β‐lactoglobulin did not differ among groups. After incubation with soy protein Formula+LCP, compared with Formula produced less IL‐2 and more TNF‐α and had a higher percentage of CD8+ and a lower percentage of CD20+ (CD20+CD54+) cells poststimulation (P < 0.05). Both formula groups produced less IL‐2 after PHA, had a lower percentage of CD80+ cells, and a higher percentage of CD54+ cells after incubation with food proteins (P < 0.05).Conclusions:Formula‐fed infants, at low risk for allergy, respond differently to mitogen and food proteins ex vivo than those fed HM. Feeding LCP altered some of these differences in the direction that is hypothesized to confer immune benefits.
Clinical and Genetic Characteristics of Meconium Ileus in Newborns With and Without Cystic Fibrosis
Authors: Gorter RR , Karimi A , Sleeboom C , Kneepkens CMF , Heij HA 
Published: April 2010

ABSTRACTThe present study compares the clinical presentation and diagnostic features of meconium ileus (MI) in newborns with and without cystic fibrosis (CF). A retrospective study of 43 patients treated in the Pediatric Surgical Center of Amsterdam was performed. Twenty‐three of the patients (53.5%) were diagnosed as having CF. Complex MI was significantly more frequent in patients without CF, and these patients had lower gestational ages and birth weights than patients with CF. All of the patients with complex MI had homozygous DF508 mutations, whereas the patients with simple MI also had other mutations. None of the patients with other mutations had complex MI. Therefore, we conclude that the clinical entity of MI represents a spectrum of underlying pathologies.
Effectiveness of Infliximab in Brazilian Children and Adolescents With Crohn Disease and Ulcerative Colitis According to Clinical Manifestations, Activity Indices of Inflammatory Bowel Disease, and Corticosteroid Use
Authors: Tiemi Juliana , Komati Saito , Sdepanian Vera Lucia 
Published: April 2010

ABSTRACTObjective:The objective of the study was to evaluate the response to infliximab in children and adolescents with Crohn disease and ulcerative colitis up to week 22.Patients and Methods:A total of 21 patients with inflammatory bowel disease (IBD) received 5 mg/kg of infliximab at weeks 0, 2, 6, and 14. The following parameters were evaluated: clinical manifestations; activity indices of IBD, including the Pediatric Crohn Disease Activity Index for Crohn disease, the Lightiger Colitis Activity Index and the Pediatric Ulcerative Colitis Activity Index for ulcerative colitis, and the modified Harvey‐Bradshaw Index for Crohn disease and ulcerative colitis; and the reduction or suspension of corticosteroid use.Results:All of the patients had improvements in clinical manifestations after the first infusion of infliximab. At week 22, 18 of 21 (85.7%) patients were categorized as being in remission, 3 of 21 (14.3%) patients were categorized as having clinical improvement, and none of the patients were categorized as having no response. There was a statistically significant difference in all of the IBD activity indices at weeks 2, 6, 14, and 22 compared with time 0. The corticosteroid use was completely discontinued in 6 of 15 patients by week 22.Conclusions:Infliximab is effective in the treatment of Crohn disease and ulcerative colitis in children and adolescents up to week 22.
European Academy of Paediatrics Research in Ambulatory Setting network (EAPRASnet): a multi‐national general paediatric research network for better child health
Authors: Del Torso S. , Van Esso D. , Gerber A. , Drabik A. , Hadjipanayis A. , Nicholson A. , Grossman Z. 
Published: April 2010

AbstractBackground  In 2008, the European Academy of Paediatrics launched a paediatric‐based research network – EAPRASnet (European Academy of Paediatrics Research in Ambulatory Setting network). The network has recruited primary care and general paediatricians from European and Mediterranean countries.Methods  Every paediatrician joining the network has been asked to complete a recruitment survey. The aims of the survey were to characterize paediatrician's demographics, practice arrangements and patient's demographics, to define main incentives for research, and to learn what paediatricians view as unsolved issues that need to be studied.Results  A total of 156 paediatricians from 19 countries were recruited with 144 completing the questionnaire (92%). Majority of respondents (89%) were general paediatricians for more than half of their time. Practice arrangement of 47% of paediatricians was solo practice, with 40% in group practice. Electronic medical records were being used by 72% of respondents. Over 70% of the paediatricians had more than 1000 patients under their clinical care, and patients younger than 6 years old contributed nearly half of the patient population. Areas of most interest for research were: quality of care indicators, communication with parents, obesity, attention deficit hyperactivity disorder and effective well child care. Main incentives for participation in a research project were interest in the topic (81%) and effort to improve quality of care (71%). Lack of time was the leading reported obstacle for research activity (72%). EAPRASnet is growing, and the network's structure, operation and funding are described. Methods for joining the network and the process of study development are presented.Conclusion  A core group of EAP general paediatricians are committed to research in their practices. The information gathered will serve for future planning of research projects in the EAPRASnet to harmonize and optimize the care given to children in the primary care setting in Europe.
Cholinergic stimulation of the immune system protects against lethal infection bySalmonella entericaserovar Typhimurium
Authors: Fernandez‐Cabezudo Maria J. , Lorke Dietrich E. , Azimullah Sheikh , Mechkarska Milena , Hasan Mohammed Y. , Petroianu Georg A. , al‐Ramadi Basel K. 
Published: April 2010

SummaryThe cholinergic nervous system has been demonstrated to attenuate the inflammatory response during sepsis via the inhibitory action of acetylcholine (ACh) on macrophages. These findings were largely based on experimental sepsis models using endotoxin as the inducing agent. Herein, however, we report that the specific inhibition of acetylcholinesterase (AChE) renders animals more resistant to infection by a virulent strain ofSalmonella entericaserovar Typhimurium, a Gram‐negative enteric pathogen. Inhibition of AChE was induced by a subchronic exposure to paraoxon, a potent anti‐cholinesterase metabolite of the organophosphorous compound parathion. Our findings indicate that inhibition of AChE enhanced survival of infected mice in a dose‐dependent fashion and this correlated with efficient control of bacterial proliferation in target organs. Immunologically, inhibition of AChE enabled the animals to mount a more effective inflammatory anti‐microbial response, and to secrete higher levels of interleukin‐12, a key T helper type 1‐promoting cytokine. The ACh‐induced enhancement in resistance to infection was abrogated by co‐administration of an oxime which can reactivate AChE. Hence, in a model of Gram‐negative bacterial infection, cholinergic stimulation is shown to enhance the anti‐microbial immune response leading to effective control of bacterial proliferation and enhanced animal survival.
Ectopic expression of an endoparasitic wasp venom protein in Drosophila melanogaster affects immune function, larval development and oviposition
Authors: Thomas P. , Yamada R. , Johnson K. N. , Asgari S. 
Published: April 2010

AbstractEndoparasitic hymenoptera inject maternal factors into the host, along with their eggs, to subvert the host immune system. The venom protein, Vn50, previously characterized from the wasp Cotesia rubecula inhibits prophenoloxidase activation in its host Pieris rapae and in another lepidopteran, Manduca sexta. We generated a stable line in the model insect, Drosophila melanogaster, which ectopically expresses Vn50. Results indicated that Vn50 expression accelerates larval development, increases oviposition and reduces melanization in the haemolymph of the transgenic flies. Since melanization is known to be an important facet of the insect immune response, we examined the impact of Vn50 expression on susceptibility to pathogens. Transgenic Vn50 flies challenged with the fungus Beauveria bassiana had increased mortality compared with control flies, but there was no significant change in survival in flies challenged with the pathogenic bacteria, Serratia marcescens. Interestingly, mortality induced by the natural pathogen Drosophila C virus was significantly delayed in Vn50 expressing flies. This indicates a wider range of potential hosts that may be affected by Vn50 and its potential for manipulation of immune system in insects.
Latitudinal variation in breeding time reaction norms in a passerine bird
Authors: Gienapp Phillip , Väisänen Risto A. , Brommer Jon E. 
Published: April 2010

Summary 1. The timing of phenological events, as flowering time in plants or migration and breeding time in animals, is related to environmental conditions, e.g. local ambient temperature, and varies considerably between years. The relationship between the relevant environmental condition(s) and phenology can be described by a reaction norm. 2. Apart from variation among years phenology also varies geographically and the timing of phenological events is generally later at higher latitudes. However, whether this latitudinal trend is caused by a single reaction norm (and locally varying conditions) or whether reaction norms differ spatially is largely unknown. 3. Avian breeding time is determined by a variety of internal and external factors, e.g. photoperiod and temperature. The corresponding reaction norms are normally described by a regression of annual mean against temperatures averaged over a certain period. We circumvented problems inherent in this approach by using proportional hazards models to describe the relationship between breeding time and local temperature and day length. 4. The proportional hazards model describes a ‘time to event’, e.g. survival or in this case time until laying of the first egg, by modelling the probability that the event will occur per unit time as a function of an unspecified baseline hazard and fixed or time‐dependent variables. Any variable that changes its value during the ‘time to event’, e.g. ambient temperature, can be included as time‐dependent variable. 5. Applying this approach to a large data set of Finnish great tit (Parus major) egg laying dates from populations spanning about 700 km in latitude, we found that temperature‐ and day length‐reaction norms vary with latitude. 6. Optimal reaction norms likely differ between populations and the observed variation in reaction norms among populations may thus reflect local adaptation. Under environmental change, local reaction norms may become suboptimal, and latitude‐specific breeding time reaction norms may represent a source of variation that could benefit a species to adapt to such changes.
Lived experience of epilepsy from the perspective of children in Taiwan
Authors: Chen Hsiu‐Jung , Chen Yueh‐Chih , Yang Hui‐Chuan , Chi Ching‐Shiang 
Published: April 2010

Aims.  The purpose of this study was to explore the lived experiences of school‐aged children with epilepsy in Taiwan.Background.  Epilepsy affects many people worldwide, especially school‐aged children, but few studies have examined children’s viewpoints of their experiences with epilepsy.Design.  An exploratory, phenomenological interview design was used.Methods.  Children (ages 7–12 years) with well‐controlled epilepsy and no developmental delay were recruited from a hospital in central Taiwan. Data were collected from 15 children using a semi‐structured interview guide. Interviews were tape‐recorded with permission from parents and children. Verbatim transcripts were analysed using Colazzi’s phenomenological method.Results.  Two themes emerged from the analysis. The first theme, ‘living with epilepsy’, had two subthemes: disease‐related experiences and school‐related issues. The second theme, ‘coping with epilepsy’, had two subthemes: developing strategies to manage or reduce seizures and seeking support from family members.Conclusions.  Taiwanese children with epilepsy had similar lived experiences as their counterparts in Western culture, e.g. unpleasant somatic symptoms, difficulty learning and troubled peer relationships. Taiwanese children also coped similarly with epilepsy by taking medications to control seizures, but they differed from their Western counterparts in trying to self‐manage seizures and seeking support from family members.Relevance to clinical practice.  Public health and school nurses can apply our findings to educate schoolteachers and parents about epilepsy and encourage activities that allow children with and without epilepsy to interact, thus improving peer relationships and reducing stigmatisation. Children with and without epilepsy would also benefit from an age‐appropriate education manual that includes causes of epilepsy, treatment, dealing with seizures and psychological and social adaptation.
Recognising our role: improved confidence of general nurses providing care to young people with a mental illness in a rural paediatric unit
Authors: Moxham Lorna , Dwyer Trudy , Happell Brenda , Reid‐Searl Kerry , Kahl Julie , Morris Jodie , Wheatland Narelle 
Published: April 2010

Objective.  To implement and evaluate strategies suggested by general nurses to improve management of children and adolescents with mental health problems admitted to a paediatric unit of a general hospital.Background.  The first phase of a study using a Participatory Action Research approach identified several concerns associated with general nurses providing care to young people with mental disorders in paediatric units of general hospitals, together with suggestions for strategies to address these issues. This paper describes the second and third phase of the Participatory Action Research study, involving the implementation and evaluation of these strategies.Design.  Participatory Action Research.Methods.  Actions that occurred during phase two of the Participatory Action Research study included revision and introduction of policies and procedures for mental health care in the unit, education and training sessions for paediatric nursing staff and opportunities to strengthen communication between existing mental health services. In phase three, two focus groups were conducted to explore current perceptions of mental health care delivery in the unit and evaluate change, following phase two.Results.  Changes in clinical practice for paediatric mental health care were acknowledged by participants. Reflection has assisted nurses to better understand their strengths and weaknesses and to acknowledge and challenge the assumptions on which their ideas, feelings and actions about patients with mental health issues are based. Participants also recognised the existing skills and expertise they possess that are relevant to the management of young people with a mental health problem, although they continue to seek ongoing education and support in this field.Conclusions.  This study demonstrates that through Participatory Action Research it is possible to enhance mental health nursing care in a rural paediatric unit.Relevance to clinical practice.  Such changes have the potential to improve the experience of young people and their families whilst receiving treatment for mental health conditions in a general paediatric unit.
An Australian investigation of emotional work, emotional well‐being and professional practice: an emancipatory inquiry
Authors: Rose Jayln , Glass Nel 
Published: April 2010

Aims and objectives.  This study set out to explore the relationship between emotional work, emotional well‐being and professional practice of generalist community health nurses who provided palliative care to clients living at home.Background.  Research suggests that palliative care practice is emotionally demanding and at times challenging. Whilst nurses find their palliative practice a source of job satisfaction the associated stresses can impact on nurses emotional well‐being.Design.  A qualitative emancipatory methodology informed this study.Methods.  Semi‐structured interviews/storytelling and reflective journaling were the two methods applied. Sixteen community health nurses including the researcher participated. Thematic analysis of the data was undertaken.Results.  The concept of emotional well‐being is associated with nurses’ feelings of being balanced or out of balance. There is a pervasive interconnectedness between emotional work, emotional well‐being and professional practice that is influenced by factors such as organisational and workplace issues; communication with health professionals, professional boundaries; education and professional development. Three major interwoven themes emerged highlighting that palliative care provision was demanding and rewarding, yet dependent on the nurse’s comfortability within practice. Self‐care is also important to the generalist nurses and strategies to enhance well‐being include healthy lifestyle choices, debriefing, self‐validation, assertiveness and emotional support.Conclusions.  Emotional well‐being is complex and multifaceted. The value of emotional well‐being to professional practice is important. Palliative care provision is associated with demands, rewards and comfortability. It is essential that attention be given to the experiences of generalist community health nurses who engage in palliative care provision.Relevance to clinical practice.  As the demand for community palliative care increases, the issues that limit and enhance the emotional well‐being of generalist palliative care nurses’ become critical. The findings have international relevance to generalist and specialist palliative care nurses, academics and researchers alike.