bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide co-expression based prediction of differential expressions
Authors: Lai Yinglei 
Published: November 2007

AbstractMotivation: Microarrays have been widely used for medical studies to detect novel disease-related genes. They enable us to study differential gene expressions at a genomic level. They also provide us with informative genome-wide co-expressions. Although many statistical methods have been proposed for identifying differentially expressed genes, genome-wide co-expressions have not been well considered for this issue. Incorporating genome-wide co-expression information in the differential expression analysis may improve the detection of disease-related genes.Results: In this study, we proposed a statistical method for predicting differential expressions through the local regression between differential expression and co-expression measures. The smoother span parameter was determined by optimizing the rank correlation between the observed and predicted differential expression measures. A mixture normal quantile-based method was used to transform data. We used the gene-specific permutation procedure to evaluate the significance of a prediction. Two published microarray data sets were analyzed for applications. For the data set collected for a prostate cancer study, the proposed method identified many genes with weak differential expressions. Several of these genes have been shown in literature to be associated with the disease. For the data set collected for a type 2 diabetes study, no significant genes could be identified by the traditional methods. However, the proposed method identified many genes with significantly low false discovery rates.Availability: The R codes are freely available at http://home.gwu.edu/~ylai/research/CoDiff, where the gene lists ranked by our method are also provided as the Supplementary Material.Contact: ylai@gwu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Gene Set Expression Comparison kit for BRB-ArrayTools
Authors: Xu Xiaojiang , Zhao Yingdong , Simon Richard 
Published: November 2007

Abstract
Summary: A Gene Set Expression Comparison kit is developed as a module of BRB-ArrayTools for discovering biologically meaningful patterns in gene expression data. The kit consists of gene sets of transcription factor (TF) targets, gene sets containing genes whose protein products share the same protein domain and gene sets of microRNA targets. Using this module of BRB-ArrayTools, researchers can efficiently analyze pre-defined sets of gene whose expression is correlated with a categorical quantitative phenotype or patient survival.
Availability: Gene Set Expression Comparison kit is freely available as a module of BRB-ArrayTools for non-commercial users. BRB-ArrayTools is available at http://linus.nci.nih.gov/BRB-ArrayTools.html.
Contact: rsimon@mail.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories
Authors: Yang Da , Li Yanhui , Xiao Hui , Liu Qing , Zhang Min , Zhu Jing , Ma Wencai , Yao Chen , Wang Jing , Wang Dong , Guo Zheng , Yang Baofeng 
Published: November 2007

AbstractMotivation: In microarray studies, numerous tools are available for functional enrichment analysis based on GO categories. Most of these tools, due to their requirement of a prior threshold for designating genes as differentially expressed genes (DEGs), are categorized as threshold-dependent methods that often suffer from a major criticism on their changing results with different thresholds.Results: In the present article, by considering the inherent correlation structure of the GO categories, a continuous measure based on semantic similarity of GO categories is proposed to investigate the functional consistence (or stability) of threshold-dependent methods. The results from several datasets show when simply counting overlapping categories between two groups, the significant category groups selected under different DEG thresholds are seemingly very different. However, based on the semantic similarity measure proposed in this article, the results are rather functionally consistent for a wide range of DEG thresholds. Moreover, we find that the functional consistence of gene lists ranked by SAM metric behaves relatively robust against changing DEG thresholds.Availability: Source code in R is available on request from the authors.Contact: guoz@ems.hrbmu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.
Using multinomial models to analyse data from Iberian sardine egg incubation experiments: a comparison with traditional techniques
Authors: Bernal Miguel , Ibaibarriaga Leire , Lago de Lanzós Ana , Lonergan Mike E. , Hernández Carmen , Franco Concha , Rasines Inmaculada , Valdés Luis , Borchers David L. 
Published: November 2007

AbstractBernal, M., Ibaibarriaga, L., Lago de Lanzós, A., Lonergan, M. E., Hernández, C., Franco, C., Rasines, I., Valdés, L., and Borchers, D. L. 2008. Using multinomial models to analyse data from Iberian sardine egg incubation experiments: a comparison with traditional techniques. – ICES Journal of Marine Science, 65: 51–59. Multinomial rather than traditional models were applied to improve data analysis of incubation experiments for Iberian sardine (Sardina pilchardus) eggs. Incubation experiments were carried out in 2002 in the Gulf of Cádiz, southwestern Spain, and data were taken from the literature for the Cantabrian Sea area. Rigorous review of the traditional models revealed shortcomings in the statistical framework for modelling the developmental progression of egg stages as well as a lack of transparency of the inherent assumptions. Multinomial model results show that egg stage duration varies for all stages, with stages 3 and 4 having the shortest duration. Comparison of the results between multinomial and traditional models shows that multinomial models provide improved insight into developmental mechanisms than that can be achieved using traditional models.
Bovine milk fat enriched in conjugated linoleic and vaccenic acids attenuates allergic airway disease in mice
Authors: Kanwar R. K. , MacGibbon A. K. , Black P. N. , Kanwar J. R. , Rowan A. , Vale M. , Krissansen G. W. 
Published: November 2007

SummaryBackground
It has been argued that a reduction in the Western diet of anti‐inflammatory unsaturated lipids, such as n‐3 polyunsaturated fatty acids, has contributed to the increase in the frequency and severity of allergic diseases.Objective
We investigated whether feeding milk fat enriched in conjugated linoleic acid and vaccenic acids (VAs) (‘enriched’ milk fat), produced by supplementing the diet of pasture‐fed cows with fish and sunflower oil, will prevent development of allergic airway responses.Methods
C57BL/6 mice were fed a control diet containing soybean oil and diets supplemented with milk lipids. They were sensitized by intraperitoneal injection of ovalbumin (OVA) on days 14 and 28, and challenged intranasally with OVA on day 42. Bronchoalveolar lavage fluid, lung tissues and serum samples were collected 6 days after the intranasal challenge.Results
Feeding of enriched milk fat led to marked suppression of airway inflammation as evidenced by reductions in eosinophilia and lymphocytosis in the airways, compared with feeding of normal milk fat and control diet. Enriched milk fat significantly reduced circulating allergen‐specific IgE and IgG1 levels, together with reductions in bronchoalveolar lavage fluid of IL‐5 and CCL11. Treatment significantly inhibited changes in the airway including airway epithelial cell hypertrophy, goblet cell metaplasia and mucus hypersecretion. The two major components of enriched milk fat, cis‐9, trans‐11 conjugated linoleic acid and VA, inhibited airway inflammation when fed together to mice, whereas alone they were not effective.Conclusion
Milk fat enriched in conjugated linoleic and VAs suppresses inflammation and changes to the airways in an animal model of allergic airway disease.
Agile requirements engineering practices and challenges: an empirical study
Authors: Ramesh Balasubramaniam , Cao Lan , Baskerville Richard 
Published: November 2007

AbstractThis paper describes empirical research into agile requirements engineering (RE) practices. Based on an analysis of data collected in 16 US software development organizations, we identify six agile practices. We also identify seven challenges that are created by the use of these practices. We further analyse how this collection of practices helps mitigate some, while exacerbating other risks in RE. We provide a framework for evaluating the impact and appropriateness of agile RE practices by relating them to RE risks. Two risks that are intractable by agile RE practices emerge from the analysis. First, problems with customer inability and a lack of concurrence among customers significantly impact agile development. Second, risks associated with the neglecting non‐functional requirements such as security and scalability are a serious concern. Developers should carefully evaluate the risk factors in their project environment to understand whether the benefits of agile RE practices outweigh the costs imposed by the challenges.
Colonization of Pacific islands by parasites of low dispersal ability: phylogeography of two monogenean species parasitizing butterflyfishes in the South Pacific Ocean
Authors: Plaisance Laetitia , Rousset Vincent , Morand Serge , Littlewood D. Timothy J. 
Published: November 2007

AbstractAim  To investigate the phylogeographical patterns of two poorly dispersing but widely distributed monogenean species, Haliotrema aurigae and Euryhaliotrematoides grandis, gill parasites of coral reef fishes from the family Chaetodontidae.Location  South Pacific Ocean (SPO).Methods  Sequence data from the mitochondrial cytochrome oxidase subunit I (COI) gene were obtained from samples from five localities of the SPO (Heron Island, Lizard Island, Moorea, Palau and Wallis) for the two parasite species. Phylogenetic and genetic diversity analyses were used to reconstruct phylogeographical patterns, and dates of cladogenetic events were estimated.Results  Overall, 50 individuals of 17 Haliotrema aurigae and 33 of Euryhaliotrematoides grandis were sequenced from five localities of the SPO for COI mtDNA (798 bp). Our results revealed a deep phylogeographical structure in the species Euryhaliotrematoides grandis. The molecular divergence between individuals from Moorea and individuals from the remaining localities (7.7%) may be related to Pleistocene sea‐level fluctuations. In contrast, Haliotrema aurigae shows no phylogeographical patterns with the presence of most of the mitochondrial haplotypes in every locality sampled.Main conclusions  Our study shows contrasting phylogeographical patterns of the two monogenean parasite species studied, despite many shared characteristics. Both parasites are found on the same host family, share the same geographical range and ecology, and are phylogenetically close. We propose two hypotheses that may help explain the diparity: the hypotheses involve differences in the evolutionary age of the parasite species and their dispersal capabilities. Additionally, the lack of phylogeographical structure in Haliotrema aurigae contrasts with its apparently restricted dispersion, which is likely to occur during the egg stage of the life cycle, inducing a passive dispersal mechanism in butterflyfish monogeneans.
Mitochondrial phylogeographic structure of the white‐browed piculet (Sasia ochracea): cryptic genetic differentiation and endemism in Indochina
Authors: Fuchs Jérôme , Ericson Per G.P. , Pasquet Eric 
Published: November 2007

AbstractAim  Our understanding of the geographic patterns of gene flow between populations of birds in the Indo‐Malayan faunal region is surprisingly poor compared with that in other parts of the world. A thorough knowledge of general patterns of phylogeographic structure is, however, of utmost importance for conservation purposes. Species with poor dispersal capabilities could serve as indicators of endemism and genetic isolation in the Indochinese subregion. From their morphology (tiny size, short tail, short and rounded wings), piculets of the genus Sasia are inferred to have poor dispersal capabilities, and thus form a suitable focal species. This study analysed the pattern of genetic variation within the White‐browed Piculet (Sasia ochracea).Location  Southeast Asia, north of the Isthmus of Kra.Methods  We sampled 43 individuals throughout the breeding range of S. ochracea. DNA was extracted both from fresh tissues (n = 15) and from toe pads from ancient museum skins (n = 28). We amplified a 801‐bp fragment of the mitochondrial ND2 gene to reconstruct the phylogeographic history of the White‐browed Piculet. The sequence data were analysed using Bayesian inference, statistical parsimony, and population genetics methods (analysis of molecular variance, mismatch distributions). We estimated the amount of ongoing gene flow between populations using the coalescent‐based method implemented in Mdiv.Results  The analysis of molecular variance indicated that the current taxonomy does not adequately reflect the amount of genetic variation within S. ochracea, as the great majority of genetic variation was nested within the nominal subspecies, which is distributed from Nepal to southern Vietnam. Bayesian inference analyses and haplotype networks suggested the occurrence of five main lineages that are strongly correlated with geography. Our coalescent‐based analyses indicated a very limited amount of ongoing gene flow between these five lineages. Our dating analyses suggested that the genetic structuring probably occurred during the last 400,000 years.Main conclusions  Our analyses revealed that S. ochracea is composed of at least five lineages: south Vietnam (South Annam and ‘Cochinchina’), India and Nepal, Myanmar and India, the remainder of Indochina, and probably southern Myanmar (Tenasserim). We strongly recommend that studies aiming to understand the phylogeographic structure within Indo‐Malayan species sample these areas.
A review of children’s decision‐making competence in health care
Authors: Mårtenson Eva K , Fägerskiöld Astrid M 
Published: November 2007

Aims and objectives.  The purpose of this literature review was to search for and review, systematically, children’s decision‐making competence in health care in the scientific literature. Findings of both quantitative and qualitative studies were analysed thematically.Background.  Most previous research in children’s decision‐making competence in health care concerns adults’ care in the best interests of the child. It is important to consider decision‐making competence from the child’s perspective because of children’s own human rights.Methods.  Systematic review including database search, manual selection, supplementary searching, management and acquisition of relevant literature, quality appraisal, literature review saturation and thematic review.Results.  Six themes emerged: measurable issues, values and beliefs, power, parent‐related communication, trust and self‐determination. Measurable issues were age, reading ability and memory. Values and beliefs as well as power and parent‐related communication were associated with healthcare professionals. Children showed trust and expressed a wish to use self‐determination.Conclusions.  Age appropriate information and participation were prerequisites for allowing children to have possibilities of making competent decisions about their own care. Children’s decision‐making competence is dependent on others, such as parents and healthcare professionals, attitudes and not only on their own capacity. Lack of competence, however, does not exclude children from the human right to have a say. It should be noted that it is a decision to leave the determination to a parent or healthcare professional.Relevance to clinical practice.  Future research from the viewpoint of children is important to reach optimal levels of participation, through respecting their integrity and to develop them into potential competent decision makers.
‘Good’ and ‘bad’ stories: decisive moments, ‘shock and awe’ and being moral
Authors: Carter Bernie 
Published: November 2007

Aim.  Within this paper I explore some of the issues related to eliciting, interpreting, choosing and re‐telling stories gathered within narrative inquiry.Background.  Most of the literature focusing on narrative inquiry and narratives makes little mention of what makes a story intrinsically ‘good’ or ‘bad’ although it is generally acknowledged that stories have moral lessons embedded within them and have a teaching/learning function. However, many of the moral issues associated with gathering, interpreting and re‐telling stories are not really addressed.Method.  Adopting a reflexive stance, I draw on Cartier‐Bresson's notion of decisive moments and link this to narratives as a way of exploring what makes a story ‘good’/compelling as well as potentially ‘bad’/morally problematic. I develop the idea that narrative researchers may act as ‘horror magnets’ attracting ‘bad news’ stories and may be overlooking some of the more ‘neutral’ and ‘good’/‘good news’ stories.Conclusion.  Narrative researchers may be adopting a ‘shock and awe’ approach to their stories without fully considering the potential impact. I propose that narrative researchers should engage in a morally proficient manner with participants/stories and conclude that a relational ethical approach can help us to ‘act well’ with people's stories.Relevance to clinical practice.  Narrative inquiry and a storied approach to practice has much to offer researchers, practitioners and patients/families. Stories can get to the heart of patients’ experiences. Stories provide practitioners with one means of ‘acting well’ and in a relational way with their patients.
Factors affecting exclusive breastfeeding of healthy babies aged zero to four months: a community‐based study of Turkish women
Authors: Karaçam Zekiye 
Published: November 2007

Aim.  The purpose of this study was to determine the factors that affect exclusive breastfeeding of healthy babies aged 0–4 months.Background.  Both the World Health Organization (WHO) and UNICEF recommend feeding babies of 0–6 months exclusively with breast milk and starting complementary foods after the sixth month. In Turkey, however, a vast majority of babies 1–5 months of age (89·4%) are given complementary foods.Methods.  This cross‐sectional study was conducted in central Ankara province, with a sampling of 514 individuals who were selected using the convenience sampling method.Results.  Of the 514 mothers who participated in my research, 260 (50·6%) were found to be feeding their babies exclusively with breast milk; 77 (15·0%), with breast milk + water; 87 (16·9%), with breast milk + baby formula; 70 (13·6%), with breast milk + baby formula + other foods; and 20 (3·9%), baby formula + other foods. Based on multivariate logistic regression analysis results, the mother's employment [odds ratio (OR) = 0·488; 95% confidence interval (CI) = 0·288–0·827) considerably reduced the incidence of complementary foods, while frequent crying of the baby (OR = 1·687; 95% CI = 1·125–2·530) significantly increased the use of supplementary foods in infant nutrition.Conclusion.  This study concluded that frequent crying of the baby increases the likelihood of giving the baby complementary foods. Midwives and nurses can encourage exclusive breastfeeding behaviour by providing individual education and counselling to women whose babies cry frequently.Relevance to clinical practice.  Exclusive breastfeeding of babies aged 0–6 months is crucial for the development and growth of the baby and instrumental in reducing infant morbidities and mortalities. One factor that increases the likelihood of provision of complementary foods is frequent crying of the baby. Midwives and nurses can encourage exclusive breastfeeding behaviour by providing individual education and counselling to women whose babies cry frequently.
A comparison of some of the cardiovascular risk factors in vegetarian and omnivorous Turkish females
Authors: Karabudak E. , Kiziltan G. , Cigerim N. 
Published: November 2007

AbstractBackground  Elevated serum total homocysteine (tHcy) is associated with an increased risk of cardiovascular disease. Homocysteine levels may be influenced by dietary habits. The aim of the present study was to determine the effects of a vegetarian diet on some of the cardiovascular risk factors in Turkish females.Method  The study was conducted on 26 vegetarian and 26 omnivore females. Serum tHcy, folate, vitamin B12 and lipids were determined and dietary data were assessed using a 4‐day food intake record at two time points.Results  Compared with omnivores, vegetarians had higher plasma tHcy, 10.8 ± 3.72 versus 12.6 ± 5.97, (P < 0.05) and folate (P < 0.05) levels. The prevalence of hyperhomocysteinaemia was higher in vegetarians than in omnivores (34.6% versus 12.0%). In addition, serum vitamin B12 levels were lower in vegetarians than in omnivores (P < 0.05). In vegetarians, significant inverse correlation was found between tHcy and serum vitamin B12 levels (r = −0.969, P = 0.001).Conclusion  The higher prevalence of mild hyperhomocysteinaemia in vegetarians indicated a diminished protective effect of vegetarian nutrition in cardiovascular disease prevention.
Evolution of serum biochemical indicators in anorexia nervosa patients: a 1‐year follow‐up study
Authors: Nova E. , Lopez‐Vidriero I. , Varela P. , Casas J. , Marcos A. 
Published: November 2007

AbstractBackground  Long‐term studies on the evolution of serum biochemical indicators in anorexia nervosa (AN) patients during treatment are lacking in the literature. Thus, a 1‐year follow‐up of serum biochemical parameters in a homogeneous group of AN patients was performed.Methods  Fourteen restricting‐type AN patients were studied on admission to hospital, after 1 month of inpatient treatment and after 6 and 12 months after admission.Results  Red blood cell count (RBC) and haemoglobin, serum glucose, total protein and the enzyme activities aspartate aminotransferase (AST), alkaline phosphatase (AlP), lactate dehydrogenase (LDH) and creatine kinase (CK) were significantly lower in patients on admission than in the control group. Total protein, high‐density lipoprotein cholesterol (HDL‐c), AST, AlP and CK showed significant changes among time points (anova, P < 0.05). Significant correlations were found between the change in RBC, haemoglobin, haematocrit, and the change in weight and body mass index (r = 0.74–0.86; P < 0.01). High cholesterol and amylase activity were found at all time points. While AST, LDH and CK reached control values within 6 months of treatment, AlP was always lower.Conclusion  Serum AlP, hypercholesterolaemia and RBC seem to need longer periods of treatment with further weight gain to fully normalize. Therefore, these parameters should be monitored in AN patients long‐term follow‐up.