bluuebunny/crossref_metadata_2025_split huggingface dataset:
A quantitative genotype algorithm reflecting H5N1 Avian influenza niches
Authors: Wan Xiu-Feng , Chen Guorong , Luo Feng , Emch Michael , Donis Ruben 
Published: July 2007

AbstractMotivation: Computational genotyping analyses are critical for characterizing molecular evolutionary footprints, thus providing important information for designing the strategies of influenza prevention and control. Most of the current methods that are available are based on multiple sequence alignment and phylogenetic tree construction, which are time consuming and limited by the number of taxa. Arbitrarily defining genotypes further complicates the interpretation of genotyping results.Methods: In this study, we describe a quantitative influenza genotyping algorithm based on the theory of quasispecies. First, the complete composition vector (CCV) was utilized to calculate the pairwise evolutionary distance between genotypes. Next, Hierarchical Bayesian Modeling using the Gibbs Sampling algorithm was applied to identify the segment genotype threshold, which is used to identify influenza segment genotype through a modularity calculation. The viral genotype was defined by combining eight segment genotypes based on the genetic reassortment feature of influenza A viruses.Results: We applied this method for H5N1 avian influenza viruses and identified 107 niches among 283 viruses with a complete genome set. The diversity of viral genotypes, and their correlation with geographic locations suggests that these viruses form local niches after being introduced to a new ecological environment through poultry trade or bird migration. This novel method allows us to define genotypes in a robust, quantitative as well as hierarchical manner.Contact: wanhenry@yahoo.com or fvq7@cdc.govSupplementary information: Supplementary data are available at Bioinformatics online.
RefPlus: an R package extending the RMA Algorithm
Authors: Harbron Chris , Chang Kai-Ming , South Marie C. 
Published: July 2007

AbstractSummary: RMA has become a widely used methodology to pre-process Affymetrix gene expression microarrays. A limitation of RMA is that the calculated probeset intensities change when a set of microarrays is re-pre-processed after the inclusion of additional microarrays into the analysis set. Here we report the availability of the RefPlus package containing functions to perform the Extrapolation Strategy and Extrapolation Averaging algorithms which address these issues.Availability: The software is implemented in the R language and can be downloaded from the Bioconductor project website (http://www.bioconductor.org).Contact: Chris.Harbron@AstraZeneca.ComSupplementary information: Further details of the workings and evaluation of these functions are given in the documentation available on the Bioconductor website.
Role of UGT1A1*6, UGT1A1*28 and ABCG2 c.421C>A polymorphisms in irinotecan‐induced neutropenia in Asian cancer patients
Authors: Jada Srinivasa Rao , Lim Robert , Wong Chiung Ing , Shu Xiaochen , Lee Soo Chin , Zhou Qingyu , Goh Boon Cher , Chowbay Balram 
Published: July 2007

The objectives of the present study were (i) to study the pharmacogenetics of UGT1A1*6, UGT1A1*28 and ABCG2 c.421C>A in three distinct healthy Asian populations (Chinese, Malays and Indians), and (ii) to investigate the polygenic influence of these polymorphic variants in irinotecan‐induced neutropenia in Asian cancer patients. Pharmacokinetic and pharmacogenetic analyses were done after administration of irinotecan as a 90‐min intravenous infusion of 375 mg/m2 once every 3 weeks (n = 45). Genotypic–phenotypic correlates showed a non‐significant influence of UGT1A1*28 and ABCG2 c.421C>A polymorphisms on the pharmacokinetics of SN‐38 (P > 0.05), as well as severity of neutropenia (P > 0.05). Significantly higher exposure levels to SN‐38 (P = 0.018), lower relative extent of glucuronidation (REG; P = 0.006) and higher biliary index (BI; P = 0.003) were found in cancer patients homozygous for the UGT1A1*6 allele compared with patients harboring the reference genotype. The mean absolute neutrophil count (ANC) was 85% lower and the prevalence of grade 4 neutropenia (ANC ≤ 500/µL) was 27% in patients homozygous for UGT1A1*6 compared with the reference group. Furthermore, the presence of the UGT1A1*6 allele was associated with an approximately 3‐fold increased risk of developing severe grade 4 neutropenia compared with patients harboring the reference genotype. These exploratory findings suggest that homozygosity for UGT1A1*6 allele may be associated with altered SN‐38 disposition and may increase the risk of severe neutropenia in Asian cancer patients, particularly in the Chinese cancer patients who comprised 80% (n = 36) of the patient population in the present study. (Cancer Sci 2007; 98: 1461–1467)
CR229, a novel derivative of β‐carbolin‐1‐one, induces cell cycle arrest and apoptosis in HeLa cells via p53 activation
Authors: Kim Min Kyoung , Oh Ha Lim , Choi Bu‐Young , Lim Haeyoung , Cho Youl‐Hee , Lee Chul‐Hoon 
Published: July 2007

In the course of screening for novel anticancer compounds, CR229 (6‐Bromo‐2,3,4,9‐tetrahydro‐carbolin‐1‐one), a novel derivative of β‐carbolin‐1‐one, was generated as a new scaffold candidate. For the first time, the authors demonstrate that CR229 inhibited the growth of HeLa cells by the induction of cell cycle arrest and apoptosis. Analysis of flow cytometry and western blots of HeLa cells treated with 2.5 µM CR229 revealed an appreciable cell cycle arrest in the G1, G2/M phase and apoptotic induction via thep53‐dependent pathway. Furthermore, the release of cytochromecfrom mitochondria was detected using confocal microscopy in HeLa cells treated with CR229. Accordingly, these data demonstrate that the anticancer activity of CR229 is associated with: (i) the down‐regulation of cyclins and cyclin‐dependent kinase; (ii) the induction of p53, p21, and p16; and (iii) the activation of caspase‐3. (Cancer Sci2007; 98: 1402–1407)
Assessment of 11C‐labeled‐4‐N‐(3‐bromoanilino)‐6, 7‐dimethoxyquinazoline as a positron emission tomography agent to monitor epidermal growth factor receptor expression
Authors: Wang Hui , Yu Jinming , Yang Guoren , Song Xianrang , Sun Xiaorong , Zhao Shuqiang , Mu Dianbin 
Published: July 2007

The aim of the present study was to investigate the biodistribution of 11C‐labeled‐4‐N‐(3‐bromoanilino), 6,7‐dimethoxyquinazoline (11C‐PD153035) and the relationship between accumulation of the tracer and epidermal growth factor receptor (EGFR) expression levels. Biodistribution studies of 11C‐PD153035 were performed in tumor‐bearing nude mice. The amount of radioactivity in the lungs was small while concentrations were highest in the liver and intestine. From in vitro studies, the level of 11C‐PD153035 accumulation was detected in MDA‐MB‐468, A549, and MDA‐MB‐231 cells. The uptake of 11C‐PD153035 in cells was closely correlated with the EGFR expression level of cells (r2 = 0.85; P < 0.001), and the results obtained in excised tumors were also significantly correlated (r2 = 0.63; P = 0.003). Binding in MDA‐MB‐468, A549, and MDA‐MB‐231 tumors was reduced to background level at 60 min post injection 11C‐PD153035 by pretreatment with cold PD153035. The present study showed that whether in vitro or ex vivo the uptake of 11C‐PD153035 closely correlated with EGFR expression levels. In contrast, blocking studies revealed specific binding in the three kinds of tumors. Thus 11C‐PD153035 may be used as a positron emission tomography tracer to yield useful information about tumors, particularly for lung cancer with different EGFR expression levels. (Cancer Sci 2007; 98: 1413–1416)
Aunties and Uncles Co‐operative Family Project: the experiences of children, volunteers and parents
Authors: Beale B. , Wilkes L. , Power B. , Beale R. 
Published: July 2007

AbstractBackground This paper reports on the experiences of the children (nieces and nephews), volunteers (aunts and uncles) and parents involved in the Aunties and Uncles Co‐operative Family Project in Sydney, Australia. The project has run for 30 years as an extended family network of community volunteers and has never been evaluated.Methods A survey comprising open‐ended and closed questions relating to the service was administered to all stakeholders. Demographic data were collected on all respondents. The text from answers to open‐ended questions on the survey was coded for similarities and differences and was categorized. From the categories, the experiences of children, volunteers and parents were written with exemplars from the respondents' text.Results Three major categories emerged from the text: enjoyment/satisfaction of the experience for volunteers, children and parents; family relationships; and the difference it has made to me (children, parents and volunteers).Conclusions The long‐term benefits of a supportive ‘extended family type’ relationship were recognized by all participants. Although the children were the primary focus of the project, parents and volunteers also described the rewards they experienced. The volunteer element was integral to providing the wide‐ranging, ongoing supports which would not be possible from a paid staff basis.
Age‐related changes in the occurrence and characteristics of thymic CD4+ CD25+ T cells in mice
Authors: Kozlowska Ewa , Biernacka Marzena , Ciechomska Marzena , Drela Nadzieja 
Published: July 2007

SummaryNatural regulatory CD4+ CD25+ T cells play an important role in preventing autoimmunity by maintaining self‐tolerance. They express CD25 constitutively and are produced in the thymus as a functionally mature T‐cell population. Changes in the potential of these cells to regulate the activity of conventional effector lymphocytes may contribute to an increased susceptibility to infection, cancer and age‐associated autoimmune diseases. In this study we demonstrated that the thymi of aged mice are populated by a higher percentage of CD4+ CD25+ thymocytes than in young animals. The expression of several surface markers (CD69, CD5, CD28, CTLA‐4, CD122, FOXP3), usually used to characterize the phenotype of CD4+ CD25+ T regulatory cells, was compared between young and aged mice. We also examined the ability of sorted thymus‐deriving regulatory T cells of young and aged BALB/c mice to inhibit the proliferation of lymph node lymphocytes activated in vitro. Natural regulatory T cells isolated from the thymi of young mice suppress the proliferation of responder lymph node cells. We demonstrated that thymus‐deriving CD4+ CD25+ T cells of old mice maintain their potential to suppress the proliferation of activated responder lymphocytes of young mice. However, their potential to inhibit the proliferation of old responder T cells is abrogated. Differences in the occurrence and activity of CD4+ CD25+ thymocytes between young and old animals are discussed in relation to the expression of these surface markers.
Interleukin‐31 induces cytokine and chemokine production from human bronchial epithelial cells through activation of mitogen‐activated protein kinase signalling pathways: implications for the allergic response
Authors: Ip Wai K. , Wong Chun K. , Li Mandy L. Y. , Li Pok W. , Cheung Phyllis F. Y. , Lam Christopher W. K. 
Published: July 2007

SummaryInterleukin‐31 (IL‐31) is a novel T‐helper‐lymphocyte‐derived cytokine that plays an important role in allergic skin inflammation and atopic dermatitis. It has recently been implicated in bronchial inflammation. We investigated the functions and mechanisms of IL‐31‐induced activation of human bronchial epithelial cells. The gene and protein expressions of candidate cytokines/chemokines from IL‐31‐stimulated human bronchial epithelial BEAS‐2B cells were first quantified by quantitative real‐time polymerase chain reaction and enzyme‐linked immunosorbent assay, respectively. The activity of different mitogen‐activated protein kinases (MAPKs) in IL‐31‐stimulated BEAS‐2B cells was assessed by Western blot. The IL‐31 could significantly elevate the gene and protein expressions of epidermal growth factor (EGF), vascular endothelial growth factor (VEGF) and monocyte chemoattractant protein‐1 (MCP‐1/CCL2) of BEAS‐2B cells in both time‐dependently and dose‐dependently. Combination of IL‐31 with either IL‐4 or IL‐13 further enhanced VEGF and CCL2 production while IL‐31 could synergistically augment the release of EGF, VEGF, CCL2, IL‐6 and IL‐8 in cocultures of BEAS‐2B cells and eosinophils. In addition, IL‐31 could activate p38 MAPK, extracellular signal‐regulated kinase (ERK) and c‐Jun N‐terminal kinase (JNK) of BEAS‐2B cells. Selective inhibitors of p38 MAPK (SB203580), ERK (PD98059), and JNK (SP600125) could differentially inhibit the production of EGF, VEGF and CCL2, thereby suggesting a role for MAPKs in IL‐31 functions. In conclusion, the activation of MAPKs can be crucial for IL‐31‐mediated activation of bronchial epithelial cells, thereby providing an immunological role for IL‐31 in bronchial inflammation, at least partly, via epithelial EGF, VEGF and CCL2 production.
The Fps/Fes kinase regulates leucocyte recruitment and extravasation during inflammation
Authors: Parsons Sean A. , Mewburn Jeffrey D. , Truesdell Peter , Greer Peter A. 
Published: July 2007

SummaryFps/Fes and Fer comprise a distinct subfamily of cytoplasmic protein‐tyrosine kinases, and have both been implicated in the regulation of innate immunity. Previous studies showed that Fps/Fes‐knockout mice were hypersensitive to systemic lipopolysaccharide (LPS) challenge, and Fer‐deficient mice displayed enhanced recruitment of leucocytes in response to localized LPS challenge. We show here for the first time, a role for Fps in the regulation of leucocyte recruitment to areas of inflammation. Using the cremaster muscle intravital microscopy model, we observed increased leucocyte adherence to venules, and increased rates and degrees of transendothelial migration in Fps/Fes‐knockout mice relative to wild‐type animals subsequent to localized LPS challenge. There was also a decreased vessel wall shear rate in the post‐capillary venules of LPS‐challenged Fps/Fes‐knockout mice, and an increase in neutrophil migration into the peritoneal cavity subsequent to thioglycollate challenge. Using flow cytometry to quantify the expression of surface molecules, we observed prolonged expression of the selectin ligand PSGL‐1 on peripheral blood neutrophils from Fps/Fes‐knockout mice stimulated ex vivo with LPS. These observations provide important insights into the observed in vivo behaviour of leucocytes in LPS‐challenged Fps/Fes‐knockout mice and provide evidence that the Fps/Fes kinase plays an important role in the innate immune response.
Poverty, socio‐economic position, social capital and the health of children and adolescents with intellectual disabilities in Britain: a replication
Authors: Emerson E. , Hatton C. 
Published: July 2007

AbstractBackground  When compared with their nonintellectually disabled peers, people with intellectual disabilities (IDs) have poorer health and are more likely to be exposed to poverty during childhood. Given that exposure to child poverty has been linked to poorer health outcomes, we attempted to estimate the extent to which the health inequalities faced by children and adolescents with IDs may be accounted for by their more disadvantaged socio‐economic position.Methods  Secondary analysis of data on a nationally representative sample of 12 160 British children aged under 17 years extracted from the Department of Work and Pensions' Families and Children Study.Results  After controlling for age and sex, children with IDs were significantly more likely (corrected odds ratio = 2.49) to be reported to have less than good health than their nonintellectually disabled peers. However, 31% of the elevated risk for poorer health was accounted for by between‐group differences in socio‐economic position and social capital.Conclusions  A socially and statistically significant proportion of the increased risk of poorer health among children and adolescents with IDs may be attributed to their increased risk of socio‐economic disadvantage.
Profiles and correlates of aggressive behaviour among adults with intellectual disabilities
Authors: Crocker A. G. , Mercier C. , Allaire J.‐F. , Roy M.‐E. 
Published: July 2007

AbstractBackground Despite the heterogeneity in aggressive behaviours observed among individuals with intellectual disabilities (ID), little attention has been paid to the identification of typologies of aggression among individuals with mild or moderate ID and their associated factors.Objective The goal of the present study was to identify profiles of aggressive behaviour and their psychosocial correlates.Method In this cross‐sectional study of 296 adults with mild or moderate ID, information was gathered through interviews with the ID participants, their case manager and a significant other. Client files were also reviewed.Results Multiple correspondence analysis followed by hierarchical cluster analysis generated six distinct profiles of aggressive behaviour in this sample. The ‘violent’ group clearly stood out as lacking social and vocational involvement, having more severe mental health problems, high levels of impulsivity and antisocial tendencies compared with all other groups.Discussion The identification of distinct profiles of aggressive behaviour offers new possibilities for studying risk factors and eventually targeting specific risk prevention strategies.
Evidence of resilience in families of children with autism
Authors: Bayat M. 
Published: July 2007

AbstractBackground  Family resilience is a growing field of inquiry, investigating factors that contribute to a family's becoming stronger in spite of dealing with adversity. Despite the growing interest in studying family resilience, the topic has not been explored in families with children who have disabilities. This report, a part of a larger study – using both quantitative and qualitative methodologies – is an examination of factors of family resilience in the families of children with autism. Evidence of family resilience such as family connectedness and closeness, positive meaning‐making of the disability, and spiritual and personal growth were identified and examined in this part of the study.Method  The study uses a survey methodology, analysing responses to several rating scales and written responses to three open‐ended questions. Survey respondents consisted of 175 parents and other primary caregivers of a child with autism – ages between 2 and 18 years.Results  Results suggest identification of specific resilience processes, such as: making positive meaning of disability, mobilization of resources, and becoming united and closer as a family; finding greater appreciation of life in general, and other people in specific; and gaining spiritual strength.Conclusions  This study presents evidence that a considerable number of families of children with autism display factors of resilience – reporting having become stronger as a result of disability in the family.
Validation of the Subjective and Objective Family Burden Interview (SOFBI/ECFOS) in primary caregivers to adults with intellectual disabilities living in the community
Authors: Martorell A. , Pereda A. , Salvador‐Carulla L. , Ochoa S. , Ayuso‐Mateos J. L. 
Published: July 2007

AbstractBackground  There is little information on the psychometric properties of instruments for assessing family care burden in adults with intellectual disabilities (ID). The aim of this study is therefore to analyse the usefulness of the ‘Subjective and Objective Family Burden Interview’ (SOFBI) in the assessment of principal caregivers in Spain.Methods  The SOFBI was administered to 166 principal caregivers of adults with ID in a vocational centre. The psychometric analysis included: internal consistency, inter‐rater and test–retest reliability, construct validity, convergent validity with the World Health Organization's Disability Assessment Schedule II, and feasibility.Results  The Cronbach's alpha was 0.88 for the overall interview and always above 0.7 in the quantitative subdomains. The Kappa coefficients for test–retest were between 0.5 and 0.8, whereas inter‐rater agreement was nearly perfect. Maximum‐likelihood factor analysis showed four well‐defined factors, which fitted the previously designed domains. Feasibility was also good.Conclusions  The SOFBI is a multi‐domain, modular instrument which is feasible, reliable and valid for measuring the burden of family caregivers to adults with ID living in the community.
The impact of alleged abuse on behaviour in adults with severe intellectual disabilities
Authors: Murphy G. H. , O'Callaghan A. C. , Clare I. C. H. 
Published: July 2007

AbstractBackground  People with intellectual disabilities (ID) are particularly vulnerable to abuse, and most incidents come to light through victim disclosure. Those people with severe or profound ID are not able to describe what has happened to them. This project aimed to describe the consequences of abuse and changes in behaviour following alleged abuse in 18 adults with severe ID.Method  Family members or other carers were interviewed to collect information about the alleged abuse. They were also asked about the person's adaptive and challenging behaviours at three time points: in the 3 months immediately prior to the abuse (time 1), in the 3 months immediately after the abuse (time 2) and in the 3 months prior to interview (time 3).Results  A typical pattern emerged for both adaptive and challenging behaviours: there were few problems or difficulties at time 1, major difficulties at time 2 and some recovery by time 3.Conclusions  Evidence is mounting that clinicians considering the sequelae of abuse for people with severe or profound ID need to consider changes in adaptive and challenging behaviours, as well as the typical symptoms of post‐traumatic stress disorder.
Evolution of pathogens in a man‐made world
Authors: LEBARBENCHON CAMILLE , BROWN SAM P. , POULIN ROBERT , GAUTHIER‐CLERC MICHEL , THOMAS FRÉDÉRIC 
Published: July 2007

AbstractHuman activities have resulted in substantial, large‐scale environmental modifications, especially in the past century. Ecologists and evolutionary biologists are increasingly coming to realize that parasites and pathogens, like free‐living organisms, evolve as the consequence of these anthropogenic changes. Although this area now commands the attention of a variety of researchers, a broad predictive framework is lacking, mainly because the links between human activities, the environment and parasite evolution are complex. From empirical and theoretical examples chosen in the literature, we give an overview of the ways in which humans can directly or indirectly influence the evolution of different traits in parasites (e.g.specificity, virulence, polymorphism). We discuss the role of direct and indirect factors as diverse as habitat fragmentation, pollution, biodiversity loss, climate change, introduction of species, use of vaccines and antibiotics, ageing of the population, etc. We also present challenging questions for further research. Understanding the links between anthropogenic changes and parasite evolution needs to become a cornerstone of public health planning, economic development and conservation biology.