bluuebunny/crossref_metadata_2025_split huggingface dataset:
Algebraic stability indicators for ranked lists in molecular profiling
Authors: Jurman Giuseppe , Merler Stefano , Barla Annalisa , Paoli Silvano , Galea Antonio , Furlanello Cesare 
Published: November 2007

Abstract
Motivation: We propose a method for studying the stability of biomarker lists obtained from functional genomics studies. It is common to adopt resampling methods to tune and evaluate marker-based diagnostic and prognostic systems in order to prevent selection bias. Such caution promotes honest estimation of class prediction, but leads to alternative sets of solutions. In microarray studies, the difference in lists may be bewildering, also due to the presence of modules of functionally related genes. Methods for assessing stability understand the dependency of the markers on the data or on the predictor's type and help selecting solutions.
Results: A computational framework for comparing sets of ranked biomarker lists is presented. Notions and algorithms are based on concepts from permutation group theory. We introduce several algebraic indicators and metric methods for symmetric groups, including the Canberra distance, a weighted version of Spearman's footrule. We also consider distances between partial lists and an aggregation of sets of lists into an optimal list based on voting theory (Borda count). The stability indicators are applied in practical situations to several synthetic, cancer microarray and proteomics datasets. The addressed issues are predictive classification, presence of modules, comparison of alternative biomarker lists, outlier removal, control of selection bias by randomization techniques and enrichment analysis.
Availability: Supplementary Material and software are available at the address http://biodcv.fbk.eu/listspy.html
Contact: furlan@fbk.eu
Supplementary information: Supplementary data are available at Bioinformatics online.
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
Authors: Langfelder Peter , Zhang Bin , Horvath Steve 
Published: November 2007

AbstractSummary: Hierarchical clustering is a widely used method for detecting clusters in genomic data. Clusters are defined by cutting branches off the dendrogram. A common but inflexible method uses a constant height cutoff value; this method exhibits suboptimal performance on complicated dendrograms. We present the Dynamic Tree Cut R package that implements novel dynamic branch cutting methods for detecting clusters in a dendrogram depending on their shape. Compared to the constant height cutoff method, our techniques offer the following advantages: (1) they are capable of identifying nested clusters; (2) they are flexible—cluster shape parameters can be tuned to suit the application at hand; (3) they are suitable for automation; and (4) they can optionally combine the advantages of hierarchical clustering and partitioning around medoids, giving better detection of outliers. We illustrate the use of these methods by applying them to protein–protein interaction network data and to a simulated gene expression data set.Availability: The Dynamic Tree Cut method is implemented in an R package available at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCuttingContact: stevitihit@yahoo.comSupplementary information: Supplementary data are available at Bioinformatics online.
PHYTOCHROME KINASE SUBSTRATE1 Regulates Root Phototropism and Gravitropism
Authors: Boccalandro Hernán E. , De Simone Silvia N. , Bergmann-Honsberger Ariane , Schepens Isabelle , Fankhauser Christian , Casal Jorge J. 
Published: November 2007

Abstract
Light promotes the expression of PHYTOCHROME KINASE SUBSTRATE1 (PKS1) in the root of Arabidopsis thaliana, but the function of PKS1 in this organ is unknown. Unilateral blue light induced a negative root phototropic response mediated by phototropin 1 in wild-type seedlings. This response was absent in pks1 mutants. In the wild type, unilateral blue light enhanced PKS1 expression in the subapical region of the root several hours before bending was detectable. The negative phototropism and the enhanced PKS1 expression in response to blue light required phytochrome A (phyA). In addition, the pks1 mutation enhanced the root gravitropic response when vertically oriented seedlings were placed horizontally. The negative regulation of gravitropism by PKS1 occurred even in dark-grown seedlings and did not require phyA. Blue light also failed to induce negative phototropism in pks1 under reduced gravitational stimulation, indicating that the effect of pks1 on phototropism is not simply the consequence of the counteracting effect of enhanced gravitropism. We propose a model where the background level of PKS1 reduces gravitropism. After a phyA-dependent increase in its expression, PKS1 positively affects root phototropism and both effects contribute to negative curvature in response to unilateral blue light.
Physiological Roles of the β-Substituted Alanine Synthase Gene Family in Arabidopsis
Authors: Watanabe Mutsumi , Kusano Miyako , Oikawa Akira , Fukushima Atsushi , Noji Masaaki , Saito Kazuki 
Published: November 2007

Abstract
The β-substituted alanine (Ala) synthase (Bsas) family in the large superfamily of pyridoxal 5′-phosphate-dependent enzymes comprises cysteine (Cys) synthase (CSase) [O-acetyl-serine (thiol) lyase] and β-cyano-Ala synthase (CASase) in plants. Nine genomic sequences encode putative Bsas proteins in Arabidopsis thaliana. The physiological roles of these Bsas isoforms in vivo were investigated by the characterization of T-DNA insertion mutants. Analyses of gene expression, activities of CSase and CASase, and levels of Cys and glutathione in the bsas mutants indicated that cytosolic Bsas1;1, plastidic Bsas2;1, and mitochondrial Bsas2;2 play major roles in Cys biosynthesis. Cytosolic Bsas1;1 has the most dominant contribution both in leaf and root, and mitochondrial Bsas2;2 plays a significant role in root. Mitochondrial Bsas3;1 is a genuine CASase. Nontargeted metabolome analyses of knockout mutants were carried out by a combination of gas chromatography time-of-flight mass spectrometry and capillary electrophoresis time-of-flight mass spectrometry. The level of γ-glutamyl-β-cyano-Ala decreased in the mutant bsas3;1, indicating the crucial role of Bsas3;1 in β-cyano-Ala metabolism in vivo.
Genome-Wide Analysis of mRNA Decay Rates and Their Determinants inArabidopsis thaliana
Authors: Narsai Reena , Howell Katharine A. , Millar A. Harvey , O'Toole Nicholas , Small Ian , Whelan James 
Published: November 2007

AbstractTo gain a global view of mRNA decay in Arabidopsis thaliana, suspension cell cultures were treated with a transcriptional inhibitor, and microarrays were used to measure transcript abundance over time. The deduced mRNA half-lives varied widely, from minutes to &gt;24 h. Three features of the transcript displayed a correlation with decay rates: (1) genes possessing at least one intron produce mRNA transcripts significantly more stable than those of intronless genes, and this was not related to overall length, sequence composition, or number of introns; (2) various sequence elements in the 3′ untranslated region are enriched among short- and long-lived transcripts, and their multiple occurrence suggests combinatorial control of transcript decay; and (3) transcripts that are microRNA targets generally have short half-lives. The decay rate of transcripts correlated with subcellular localization and function of the encoded proteins. Analysis of transcript decay rates for genes encoding orthologous proteins between Arabidopsis, yeast, and humans indicated that yeast and humans had a higher percentage of transcripts with shorter half-lives and that the relative stability of transcripts from genes encoding proteins involved in cell cycle, transcription, translation, and energy metabolism is conserved. Comparison of decay rates with changes in transcript abundance under a variety of abiotic stresses reveal that a set of transcription factors are downregulated with similar kinetics to decay rates, suggesting that inhibition of their transcription is an important early response to abiotic stress.
Comparison ofPetunia inflata S-Locus F-Box Protein (Pi SLF) with Pi SLF–Like Proteins Reveals Its Unique Function in S-RNase–Based Self-Incompatibility
Authors: Hua Zhihua , Meng Xiaoying , Kao Teh-hui 
Published: November 2007

AbstractPetunia inflata possesses S-RNase–based self-incompatibility (SI), which prevents inbreeding and promotes outcrossing. Two polymorphic genes at the S-locus, S-RNase and P. inflata S-locus F-box (Pi SLF), determine the pistil and pollen specificity, respectively. To understand how the interactions between Pi SLF and S-RNase result in SI responses, we identified four Pi SLF–like (Pi SLFL) genes and used them, along with two previously identified Pi SLFLs, for comparative studies with Pi SLF2. We examined the in vivo functions of three of these Pi SLFLs and found that none functions in SI. These three Pi SLFLs and two other Pi SLFs either failed to interact with S3-RNase (a non-self S-RNase for all of them) or interacted much more weakly than did Pi SLF2 in vitro. We divided Pi SLF2 into FD1 (for Functional Domain1), FD2, and FD3, each containing one of the Pi SLF–specific regions, and used truncated Pi SLF2, chimeric proteins between Pi SLF2 and one of the Pi SLFLs that did not interact with S3-RNase, and chimeric proteins between Pi SLF1 and Pi SLF2 to address the biochemical roles of these three domains. The results suggest that FD2, conserved among three allelic variants of Pi SLF, plays a major role in the strong interaction with S-RNase; additionally, FD1 and FD3 (each containing one of the two variable regions of Pi SLF) together negatively modulate this interaction, with a greater effect on interactions with self S-RNase than with non-self S-RNases. A model for how an allelic product of Pi SLF determines the fate of its self and non-self S-RNases in the pollen tube is presented.
The role of dynamic cultural theories in explaining the viability of international strategic alliances
Authors: Patel Taran 
Published: November 2007

PurposeMany managers of Indo‐French alliances consider culture to be a failure, rather than a success factor because they address the national or corporate level for cross‐cultural comparisons. In contrast, this study proposes using the Douglasian Cultural Theory (CT) to address the transactional level of culture. In so doing, it aims to overcome some of the limitations of the national, corporate and transactional approaches and provide a systematic framework for discussing the viability of international alliances.Design/methodology/approachAn analysis of 48 ethnographic interviews and field studies was conducted in 25 Indo‐French alliances.FindingsThrough an analysis of the ethnographic interviews and field studies conducted, the paper offers the following guidelines to managers for the design of viable alliances: the commonly‐cited interdependence of the hierarchical and competitive solidarities is not sufficient to ensure the viability of international alliances; the presence of a third solidarity seems essential; an analysis of failed alliances reveals that fatalism is not the third solidarity we are looking for; and an analysis of viable alliances shows that the egalitarian solidarity plays a role in ensuring the viability of international alliances by building a bridge between the hierarchical and competitive solidarity, thereby preventing gridlocks.Research limitations/implicationsMajor methodological limitations of this study include over‐emphasis on ethnographic interviews for data and use of unsystematic criteria for identifying solidarities in Indo‐French alliancesOriginality/valueUnlike the paper's predecessors, it recommends that cultural plurality, not cultural domination, leads to viable alliances. International managers often tend to impose their own thought styles on others, thereby neglecting the inherent wisdom of other thought styles. The paper stresses that cultural diversity without duality leads to viability.
Reference theory: strategic groups and competitive benchmarking
Authors: Panagiotou George 
Published: November 2007

PurposeThe concept of strategic groups is a central theme in the field of strategic management, and over time it has been used by a considerable body of theoretical and empirical literature to examine different aspects of competitive strategy. However, to date, there has been little systematic investigation that examines aspects associated with competitive benchmarking and the impact and effect that this has on strategy development. Thus despite the level of knowledge that has been accumulated over the years regarding the dynamics of competitive landscapes, our understanding of the impact and effect of this particular matter on decision making is limited. More importantly, studies that have addressed the topic are either theoretical alone in contents or have only used secondary data. Equally, these studies have approached the subject mostly from an impersonal mathematical perspective and practitioners' views on the issue have been overlooked. This paper aims to address these weaknesses in the literature. In doing so, it seeks to place attention on the individual, which has been overlooked by previous examinations.Design/methodology/approachThe research is cross‐sectional and it is based on primary methodology, having employed qualitative techniques for analysis. It involves face‐to‐face semi‐structured interviews combined with the repertory grid technique. The industry investigated is the UK mainstream leisure foreign package holidays. The sample size is near to the sampling frame of the research and the investigation took place between March and August 2003.FindingsIt was found that managers of firms from the same strategic group consider their group as a reference point in their decision‐making process and as a result of their benchmarking observations they adjust their firms' competitive strategies to reflect their group's strategic behaviour. It was also found that firms of the same strategic group are more likely to respond to market conditions and events in a similar manner.Originality/valueThis paper examined issues associated with benchmarking, in the context of strategic groups, having employed primary qualitative research strategies in order to add “fresh” data on a topic that so far has merely been investigated quantitatively through secondary sources alone. As such, it has initiated a much needed contents dimension on the topic to complement the activity and process‐oriented only studies in the area. The research not only tested earlier propositions in order to accumulate more evidence in the field and enable better generalisations on the subject but it has also expanded current theories in the area.
Innovation in Learning
Authors: Thorsell Jørgen 
Published: November 2007

PurposeThe paper aims to look at how the Danish Leadership Institute facilitated the programme Innovation in Learning in Fujitsu Services during a three‐year period.Design/methodology/approachThe paper examines how the Danish Leadership Institute developed 2,200 managers from Fujitsu Services from 13 different countries.FindingsThis case story reveals: how highly focused one‐day interventions can create immediate impact in managers' performance; the effect of a management development initiative for 2,200 managers throughout Europe; how multinational development initiatives can be implemented to address directly both global and local issues; and, finally, how 100 per cent tailored learning solutions were used.Originality/valueThe paper provides useful information for those wanting to improve managers' performance.
Dietary habits of Mauritian school adolescents
Authors: Oogarah‐Pratap Brinda 
Published: November 2007

PurposeThere is a strong need for nutrition education strategies that foster healthy eating from a young age in Mauritius, as the island has one of the highest rates of diet‐related diseases such as obesity, diabetes and cardio‐vascular diseases in the world. In order to be effective, the strategies should focus on current eating habits of adolescents. However, there is limited up‐to‐date information on the eating habits of Mauritian adolescents. This study, thus, aims to provide up‐to‐date data on the dietary habits of Mauritian adolescents.Design/methodology/approachA cross‐sectional study on the dietary habits of school adolescents (13‐16 years old) was conducted in 2003/2004. Stratified random sampling was used to select study participants (n = 315) from 12 secondary schools across the island. Data were collected using a self‐administered questionnaire.FindingsFoods that are high in fats, sugar or salt and low in dietary fibre were commonly consumed by adolescents. The most popular sources of nutrition information were parents, the Science and Home Economics teachers and print materials. More than half of the adolescents (54 per cent) regularly gave dietary advice to their friends and relatives, and 41.2 per cent prepared foods at home on their own. The majority of adolescents (81.2 per cent) expressed their interest in learning more about nutrition at school.Practical implicationsFindings should provide a sound basis for local nutrition educators to identify priority areas, and thereafter develop appropriate health promotion strategies in collaboration with health and education authorities.Originality/valueThis study provides up‐to‐date baseline data on the eating habits of young adolescents in Mauritius. Moreover, it is the first study of its kind to focus on the food skills of Mauritian adolescents.
Hypocholesterolemic effect of diet supplemented with Indian bean (Dolichos lablab L. var lignosus) seeds
Authors: Ramakrishna Vadde , Jhansi Rani Pochana , Ramakrishna Rao Pillutla 
Published: November 2007

PurposeLegume seeds provide one of the most concentrated sources of nutrients rich in fibre and high‐quality protein in the diet. The present work aims to investigate the hypocholesterolemic effect of germinated Indian bean (Dolichos lablab L. var lignosus) by feeding albino rats with a hypercholesterolemic diet.Design/methodology/approachMale albino rats of Wistar strain were divided into five groups (each group consisting of ten rats) according to randomized block design, housed in individual cages and fed with one of the five diets over an eight‐week period. At the end of eight weeks, the body weights were recorded and the rats put down. Samples of blood and liver were collected and used for analysis of liver and plasma cholesterol.FindingsSupplementation of the diet with dried powder of soaked bean almost brought the plasma cholesterol to 72.5 ± 0.75 from 178 ± 1.85 compared with that of the control (61.5 ± 0.70), although the liver cholesterol was still three times higher compared with the control. The 24h germinated Indian bean cotyledons could effectively counteract the effects of added cholesterol on liver and plasma by their high fibre content coupled with enormous increase in ascorbic acid levels.Originality/valueResults suggest germination to be a simple biochemical tool to effectively lower the cholesterol levels in liver and plasma by virtue of its higher contents of ascorbic acid and dietary fibre in ischemic heart disease patients.
The effect of some Lactobacillus strains on deoxynivalenol biodegradation
Authors: Štyriak I. , Čonkova´ E. , Bořutová R. , Mojžišova´ J. 
Published: November 2007

PurposeSome useful bacteria could be used regularly in mycotoxins biodegradation. It is a very good and ecological method, which was tested in experiments when lactobacilli were used. The paper aims to describe this.Design/methodology/approachFive strains of lactobacilli in experiments were shown, by direct enzyme‐linked immunosorbent assay (CD‐ELISA) test after their growth in MRS broth, to have decreased in the amount of deoxynivalenol (DON) measured by spectrophotometer. Free DON in the samples and control is allowed to compete with enzyme‐labeled DON (conjugate) for the antibody binding sites. The test was read in a microwell reader to yield optical densities.FindingsIt was found that Lactobacillus plantarum, Lactobacillus rhamnosus and Lactobacillus fermentum were more active than human strain Lactobacillus casei Shirota.Originality/valueThe paper suggests that other lactobacilli should be tested in this research field and could be used for detoxification of some feed kinds contaminated minimally by DON.
Chemical and sensory properties of yam (Discorea alata) flour substituted with grain amaranth (Amaranthus cruentus) flour
Authors: Babalola S.O. , Taylor O. , Babalola A.O. , Ashaye O.A. 
Published: November 2007

PurposeYam flour (YMF) is an important staple food in the tropics but its utilization is limited by low nutrient and consumer acceptability. The aim of this paper is to investigate the effect of substituting yam flour with grain amaranth on chemical and sensory properties.Design/methodology/approachYMF and grain amaranth flour (GAF) were prepared on a dry matter basis; GAF was mixed with YMF at ratio 1:3. All flour samples were subjected to chemical (moisture, protein, fat, ash, crude fibre, carbohydrate and minerals) evaluation and sensory evaluation of the stiff gel was conducted by a ten‐member panel consisting of five adult males and five females.FindingsGAF increased the protein content of YMF significantly atp < 0.05 from 1.8 to 9.63 per cent. There was a decrease in carbohydrate content of YAF when substituted with GAF. There was a significant increase (atp < 0.05) in phosphorus and sodium elements when YMF was substituted with GAF. There was no significant difference in acceptability of gel from grain amaranth and yam flour (GAF–YMF) compared with whole YMF gel on colour, texture, flavour and overall acceptability.Originality/valueIt was apparent that substitution of YMF with GAF improved nutrient composition without affecting the acceptability. This will further improve the nutritional status of people in YMF‐consuming areas.
Social interaction and adolescent's learning in enterprise education
Authors: Wing Yan Man Thomas , Wai Mui Yu Christina 
Published: November 2007

PurposeThe purpose of this study is to investigate the impact of social interaction on participants' learning experience in enterprise education.Design/methodology/approachOn a sample of 420 high school students who participated in an enterprise activity in Hong Kong, two questionnaires surveys were conducted to collect data on them at the beginning of and after the enterprise activity. Hypotheses were tested on the impacts of two particular aspects of interactive learning – interaction with facilitator and interaction with team members in the enterprise activity.FindingsThe results support the hypotheses that both types of social interaction are positively correlated to students' affection on the enterprise activity and the change in their perceived level of personal competencies before and after the activity.Research limitations/implicationsAlthough two types of interaction are identified in this study, it is possible to extend the scope of interactive learning toward a broader range of social interaction. Also, the impacts of social interaction on other learning outcomes may be considered in further studies.Practical implicationsIt is necessary to maximise social interaction and develop participants' interpersonal skills for achieving effective enterprise education. More guidance and supervision on social interaction should also be provided in enterprise programmes and activities.Originality/valueThe studies help to address the importance of the social interaction aspect in enterprise education, as the majority of the focus has been centred on the uses of experiential learning approaches.