bluuebunny/crossref_metadata_2025 huggingface dataset:
Note. Modelling the Rheological Properties of the Solution of Konjac Glucomannan and Milk Powder
Authors: Yang X. H. , Zhu W. L.
Published: April 2006

Shear storage and loss moduli (G″ and G ′) of a solution of konjac glucomannan (KGM) and milk powder were measured while varying angular frequency and temperature. Results showed that both G′ and G″ increased with the angular frequency sweeping from 0.1 rad/s to 100 rad/s, in a variety of temperatures and KGM concentrations. However, they decrease with temperature sweeping from 10°C to 50°C. These recorded curves were satisfactorily fitted to a multi-element Maxwell model. The angular sweep and temperature ramp data sitting along a sole line on the G″ –G′ diagram demonstrates the solution of KGM and milk powder obeys the time–temperature superposition principle. Furthermore, the fitted magnitude of G1 of the first multi-element Maxwell model is proportional to the concentration of the solution. These results are valuable for the optimising production of the functional KGM-milk food.
Attributions to Discrimination and Self-Esteem: The Role of Group Identification and Appraisals
Authors: Eccleston Collette P. , Major Brenda N.
Published: April 2006

This study tested the hypothesis that appraisals of discrimination (i.e. its perceived severity, global aspects, stability, and uncontrollability) mediate the relationship between attributions to discrimination and personal self-esteem. It also tested three models of how ethnic group identification is related to discrimination attributions, discrimination appraisals, and personal self-esteem. In a cross-sectional study of 160 Latino-American students, group identification was positively related to attributing ambiguous negative events to discrimination. Discrimination attributions were related to appraising discrimination as more global and severe. These latter appraisals, in turn, were related to lower self-esteem. No direct relationships were observed between self-esteem and either group identification or discrimination attributions. Results illustrate the importance of appraisals in understanding the relationship between perceived discrimination and self-esteem.
Collective Guilt as Distress over Illegitimate Intergroup Inequality
Authors: Miron Anca M. , Branscombe Nyla R. , Schmitt Michael T.
Published: April 2006

We examine how appraisals of the legitimacy of gender inequality affect men's experience of collective guilt. We tested two potential routes by which perceiving intergroup inequality as legitimate might undermine collective guilt: via reductions in empathy for the disadvantaged outgroup or via reductions in the distress experienced when confronted with the suffering of the outgroup. In the first study ( N= 52), we measured legitimacy appraisals, and in the second experimental study ( N= 73) we manipulated the legitimacy of gender inequality. In both studies, reductions in self-focused distress mediated the effect of legitimacy appraisals on collective guilt, while other-oriented empathy did not. These effects suggest that collective guilt is a self-focused emotion that emerges when members of a dominant group perceive their relationship with a disadvantaged outgroup to be illegitimate.
Effects of Threat to a Valued Social Identity on Implicit Self-Esteem and Discrimination
Authors: Smurda Julie D. , Wittig Michele A. , Gokalp Gokce
Published: April 2006

This research provides an experimental test of the self-esteem hypothesis that avoids potential hypothesis guessing and self-presentational concerns associated with previous research by including subtle measures of both social self-esteem and intergroup discrimination. The role of group identification and social self-esteem as determinants of ingroup bias was examined under high and low identity-threatening conditions utilizing an implicit measure of social self-esteem. Participants read a fictitious statement indicating whether their university received a good or bad evaluation relative to a rival university and then made attributions for this situation. High group identifiers had a greater decrease in implicit social self-esteem after a threat than low group identifiers did and they displayed the greatest ingroup favoritism. Greater ingroup-serving bias was associated with a subsequent increase in implicit social self-esteem.
Weighing the Prospects of War
Authors: Pratto Felicia , Glasford Demis E. , Hegarty Peter
Published: April 2006

Prospect theory (Kahneman & Tversky, 1979) predictions were examined in light of ethnocentrism and intergroup conflict. An experiment conducted at the outset of the 2003 invasion of Iraq by the US, UK and their allies explored American and British participants' preferences for certain versus uncertain gains and losses concerning Iraqi, American, and British lives. In four conditions, participants showed the usual loss-aversion when deciding between options that only affected Iraqi lives. Six other conditions examined choices between the lives of Americans, Britons, or Iraqis. Strong ethnocentric biases rather than risk-aversion occurred. Participants preferred policies that prioritized their own nationals' and allies' lives over Iraqi lives. War-related and other attitudes corresponded to participants' decisions. The need to expand prospect theory to address intergroup relations is discussed.
Temporal Causal Links Between Outgroup Attitudes and Social Categorization: The Case of Hong Kong 1997 Transition
Authors: Hong Ying-yi , Liao Hsin-ya , Chan Gloria , Wong Rosanna Y. M. , Chiu Chi-yue , Ip Grace Wai-man , Fu Ho-ying , Hansen Ian G.
Published: April 2006

Social identity theories have posited that people's social categorization renders ingroup favoritism and outgroup discrimination. However, studies conducted during political transitions (South Africa's democratic election and East-West German unification) have revealed mixed directions of the causal links between social categorization and intergroup attitudes. To further address this issue, we conducted two longitudinal studies during the handover of Hong Kong in 1997. Study 1 revealed mixed temporal causal links between Hong Kong participants' social categorization and their attitudes toward Chinese Mainlanders across four waves. In Study 2, we conducted a summer camp in which Hong Kong participants came into contact with new immigrants from Mainland China. In this condition, Hong Kong participants' prior attitudes toward Mainlanders predicted their subsequent social categorization. These findings were interpreted in terms of intergroup relations during political transitions.
A blurring of categorization: the Japanese connective de in spontaneous conversation
Authors: Sadler Misumi
Published: April 2006

The Japanese connective de has been found to be the most frequently occurring connective in spontaneous conversation. Yet, studies on de have been rather scarce compared to other connectives such as demo ‘but’ and dakara ‘so; therefore’. The current study examines the occurrence of this highly frequent connective (as well as its variants, sorede and nde) and demonstrates its very distinctive characteristics in on-line interaction. The results reveal a unique and ambiguous status of de, which behaves like an independent word at times but also shows prefix-like usage at other times. That is, de seems to have some properties that clitics have, in that it is not like a typical independent word, and is not like a typical bound morpheme, either. An examination of de in naturally occurring conversation supports and calls into question the notion of ‘categorization’.
The other side of the story: towards a narrative analysis of narratives-in-interaction
Authors: Georgakopoulou Alexandra
Published: April 2006

The starting point of this article is what will be identified as the ‘narrative canon’ comprising a specific type of narrative (past events personal experience elicited in research interviews) that mutually feeds into a specific analytic vocabulary, an interpretive idiom, and a research agenda (normally identity analysis) within conventional narrative analysis. The aim here is to give voice to, and advance understanding for, stories that do not fit this canon and are thus in the fringes of narrative research. Examples of such stories are brought in from two communication contexts (adolescents’ conversations - private email messages) and their interactional features of ongoing-ness, intertextuality and recontextualization are documented. The issues that are then addressed on their basis involve the ways in which mainstream conceptualization of narrative analysis (e.g. tellership, tellability, embeddedness) can be revised and stretched to reach out to those cases; also, the implications for narrative cum identity research.
The Effect of Music on Cognitive Performance: Insight From Neurobiological and Animal Studies
Authors: Rickard Nikki S. , Toukhsati Samia R. , Field Simone E.
Published: April 2006

The past 50 years have seen numerous claims that music exposure enhances human cognitive performance. Critical evaluation of studies across a variety of contexts, however, reveals important methodological weaknesses. The current article argues that an interdisciplinary approach is required to advance this research. A case is made for the use of appropriate animal models to avoid many confounds associated with human music research. Although such research has validity limitations for humans, reductionist methodology enables a more controlled exploration of music's elementary effects. This article also explores candidate mechanisms for this putative effect. A review of neurobiological evidence from human and comparative animal studies confirms that musical stimuli modify autonomic and neurochemical arousal indices, and may also modify synaptic plasticity. It is proposed that understanding how music affects animals provides a valuable conjunct to human research and may be vital in uncovering how music might be used to enhance cognitive performance.
The Endophenotype of Impulsivity: Reaching Consilience Through Behavioral, Genetic, and Neuroimaging Approaches
Authors: Congdon Eliza , Canli Turhan
Published: April 2006

Impulsivity is a multidimensional construct with implications for understanding the etiology and treatment of multiple forms of psychopathology. As a multidimensional construct, however, the processes underlying impulsivity, particularly behavioral inhibition, must be separated to allow for investigations into its neurogenetic bases. Evidence from both animal and human studies supports the role of dopamine in impulsivity, and neuroimaging research is elucidating brain regions involved in behavioral inhibition. Evidence is now emerging that suggests an interaction between dopamine system genes and frontal brain regions in underlying individual differences in behavioral inhibition. However, to reach a comprehensive understanding of the neurogenetic bases of behavioral inhibition, an appropriate framework is required. Therefore, it is proposed that by identifying intervening variables more sensitive to the effects of genetic variation, known as an endophenotype approach, we will be able to overcome many of the methodological limitations that prevent a better understanding at present.
Preliminary studies on friction welding of sintered P/M steel preforms to wrought mild steel
Authors: Shashank Rao S. , Jayabharath K. , Ashfaq M. , Vamsi Krishna B.
Published: April 2006

Continuous drive friction welding studies on sintered powder metallurgical (P/M) steel preforms–wrought mild steel combination are reported in the present study. The work is a preliminary study to optimise the friction welding parameters and data generated by the present work is expected to contribute to friction welding of dissimilar and similar sintered P/M preforms to wrought metals or sintered P/M preforms – a planned future research work. Sound welds were obtained with all welding parameter combinations studied. The mechanical properties of welds were comparable to those of sintered P/M steel. Sintered P/M preforms deformed to a greater extent than wrought mild steel due to their low flow stress and thermal conductivity. The sintered density and other properties of the P/M preforms were found to dictate the deformation at the interface and consequently the weld strength. The results indicate that the current approach can be extended to other combinations of sintered P/M preforms.
Microhardness prediction in friction stir welding of 2014 aluminium alloy
Authors: Zhao Y.-H. , Lin S.-B. , He Z.-Q. , Wu L.
Published: April 2006

Steady-state friction stir welding of 2014 Al alloy has been modelled using an Eulerian formulation that considers coupled viscoplastic flow and heat transfer near the tool. The model equations are solved using the finite element method to determine the velocity field and temperature distribution. The grain size is related to the strain rate and temperature of the friction stir welding process in 2014 Al alloy, and the hardness is found to be essentially related to grain size through the Hall–Petch relationship in the stir zone. Using the simulation results of strain rate and temperature, the microhardness in friction stir processing of 2014 Al alloy was predicted. It was found that the microhardness prediction distribution along the friction stir zone agrees well with experimental results.
Multimaterial car body design: Challenge for welding and joining
Authors: Dilthey U. , Stein L.
Published: April 2006

High safety and low weight are requested for modern automobiles. Both demands are met best by tailored application of different materials. Multimaterial car body design is a challenge for joining and welding.
Finite element modelling: A solution to seam end cracking?
Authors: McPherson N. A. , McGibbon K. , Wen S. W.
Published: April 2006

Seam end cracking has been a common feature of many single sided seam welding installations. The crack tends to be located about 140 mm in from the plate end, but this distance has been found to be related to plate thickness. In addition, the longer cracks tend to be more prevalent in thicker plates. The incidence of cracking in this particular case was typically 38%, which incurred significant inspection and rectification costs. The present study presents a detailed FEM study of a slot run-off plate configuration that was carried out using a thermo-mechanical model. The outcome of this investigation was that the run-off plate slot angle had an effect on the potential for cracking but the slot width did not. When the slot run-off plate was used in practice, over a wide range in thickness, the transverse cracking was eliminated.
Hormonal regulation of alveolarization: structure-function correlation
Authors: Garber Samuel J , Zhang Huayan , Foley Joseph P , Zhao Hengjiang , Butler Stephan J , Godinez Rodolfo I , Godinez Marye H , Gow Andrew J , Savani Rashmin C
Published: April 2006

Background

Dexamethasone (Dex) limits and all-trans-retinoic acid (RA) promotes alveolarization. While structural changes resulting from such hormonal exposures are known, their functional consequences are unclear.

Methods

Neonatal rats were treated with Dex and/or RA during the first two weeks of life or were given RA after previous exposure to Dex. Morphology was assessed by light microscopy and radial alveolar counts. Function was evaluated by plethysmography at d13, pressure volume curves at d30, and exercise swim testing and arterial blood gases at both d15 and d30.

Results

Dex-treated animals had simplified lung architecture without secondary septation. Animals given RA alone had smaller, more numerous alveoli. Concomitant treatment with Dex + RA prevented the Dex-induced changes in septation. While the results of exposure to Dex + RA were sustained, the effects of RA alone were reversed two weeks after treatment was stopped. At d13, Dex-treated animals had increased lung volume, respiratory rate, tidal volume, and minute ventilation. On d15, both RA- and Dex-treated animals had hypercarbia and low arterial pH. By d30, the RA-treated animals resolved this respiratory acidosis, but Dex-treated animals continued to demonstrate blood gas and lung volume abnormalities. Concomitant RA treatment improved respiratory acidosis, but failed to normalize Dex-induced changes in pulmonary function and lung volumes. No differences in exercise tolerance were noted at either d15 or d30. RA treatment after the period of alveolarization also corrected the effects of earlier Dex exposure, but the structural changes due to RA alone were again lost two weeks after treatment.

Conclusion

We conclude that both RA- and corticosteroid-treatments are associated with respiratory acidosis at d15. While RA alone-induced changes in structure andrespiratory function are reversed, Dex-treated animals continue to demonstrate increased respiratory rate, minute ventilation, tidal and total lung volumes at d30. Concomitant treatment with Dex + RA prevents decreased septation induced by Dex alone and results in correction of hypercarbia. However, these animals continue to have abnormal pulmonary function and lung volumes. Increased septation as a result of RA treatment alone is reversed upon discontinuation of treatment. These data suggest that Dex + RA treatment results in improved gas exchange likely secondary to normalized septation.
Exploring supervised and unsupervised methods to detect topics in biomedical text
Authors: Lee Minsuk , Wang Weiqing , Yu Hong
Published: April 2006

Background

Topic detection is a task that automatically identifies topics (e.g., "biochemistry" and "protein structure") in scientific articles based on information content. Topic detection will benefit many other natural language processing tasks including information retrieval, text summarization and question answering; and is a necessary step towards the building of an information system that provides an efficient way for biologists to seek information from an ocean of literature.

Results

We have explored the methods of Topic Spotting, a task of text categorization that applies the supervised machine-learning technique naïve Bayes to assign automatically a document into one or more predefined topics; and Topic Clustering, which apply unsupervised hierarchical clustering algorithms to aggregate documents into clusters such that each cluster represents a topic. We have applied our methods to detect topics of more than fifteen thousand of articles that represent over sixteen thousand entries in the Online Mendelian Inheritance in Man (OMIM) database. We have explored bag of words as the features. Additionally, we have explored semantic features; namely, the Medical Subject Headings (MeSH) that are assigned to the MEDLINE records, and the Unified Medical Language System (UMLS) semantic types that correspond to the MeSH terms, in addition to bag of words, to facilitate the tasks of topic detection. Our results indicate that incorporating the MeSH terms and the UMLS semantic types as additional features enhances the performance of topic detection and the naïve Bayes has the highest accuracy, 66.4%, for predicting the topic of an OMIM article as one of the total twenty-five topics.

Conclusion

Our results indicate that the supervised topic spotting methods outperformed the unsupervised topic clustering; on the other hand, the unsupervised topic clustering methods have the advantages of being robust and applicable in real world settings.
More robust detection of motifs in coexpressed genes by using phylogenetic information
Authors: Monsieurs Pieter , Thijs Gert , Fadda Abeer A , De Keersmaecker Sigrid CJ , Vanderleyden Jozef , De Moor Bart , Marchal Kathleen
Published: April 2006

Background

Several motif detection algorithms have been developed to discover overrepresented motifs in sets of coexpressed genes. However, in a noisy gene list, the number of genes containing the motif versus the number lacking the motif might not be sufficiently high to allow detection by classical motif detection tools. To still recover motifs which are not significantly enriched but still present, we developed a procedure in which we use phylogenetic footprinting to first delineate all potential motifs in each gene. Then we mutually compare all detected motifs and identify the ones that are shared by at least a few genes in the data set as potential candidates.

Results

We applied our methodology to a compiled test data set containing known regulatory motifs and to two biological data sets derived from genome wide expression studies. By executing four consecutive steps of 1) identifying conserved regions in orthologous intergenic regions, 2) aligning these conserved regions, 3) clustering the conserved regions containing similar regulatory regions followed by extraction of the regulatory motifs and 4) screening the input intergenic sequences with detected regulatory motif models, our methodology proves to be a powerful tool for detecting regulatory motifs when a low signal to noise ratio is present in the input data set. Comparing our results with two other motif detection algorithms points out the robustness of our algorithm.

Conclusion

We developed an approach that can reliably identify multiple regulatory motifs lacking a high degree of overrepresentation in a set of coexpressed genes (motifs belonging to sparsely connected hubs in the regulatory network) by exploiting the advantages of using both coexpression and phylogenetic information.
GOPET: A tool for automated predictions of Gene Ontology terms
Authors: Vinayagam Arunachalam , del Val Coral , Schubert Falk , Eils Roland , Glatting Karl-Heinz , Suhai Sándor , König Rainer
Published: April 2006

Background

Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for their predictions.

Description

We recently established a learning system for automated annotation, trained with a broad variety of different organisms to predict the standardised annotation terms from Gene Ontology (GO). Now, this method has been made available to the public via our web-service GOPET (Gene Ontology term Prediction and Evaluation Tool). It supplies annotation for sequences of any organism. For each predicted term an appropriate confidence value is provided. The basic method had been developed for predicting molecular function GO-terms. It is now expanded to predict biological process terms. This web service is available via http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar

Conclusion

Our web service gives experimental researchers as well as the bioinformatics community a valuable sequence annotation device. Additionally, GOPET also provides less significant annotation data which may serve as an extended discovery platform for the user.
AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation
Authors: Le Texier Vincent , Riethoven Jean-Jack , Kumanduri Vasudev , Gopalakrishnan Chellappa , Lopez Fabrice , Gautheret Daniel , Thanaraj Thangavel Alphonse
Published: April 2006

Background

The three major mechanisms that regulate transcript formation involve the selection of alternative sites for transcription start (TS), splicing, and polyadenylation. Currently there are efforts that collect data & annotation individually for each of these variants. It is important to take an integrated view of these data sets and to derive a data set of alternate transcripts along with consolidated annotation. We have been developing in the past computational pipelines that generate value-added data at genome-scale on individual variant types; these include AltSplice on splicing and AltPAS on polyadenylation. We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants.

Description

The AltSplice pipeline examines gene-transcript alignments and delineates alternative splice events and splice patterns; this pipeline is extended as AltTrans to delineate isoform transcript patterns for each of which both introns/exons and 'terminating' polyA site are delineated; EST/mRNA sequences that qualify the transcript pattern confirm both the underlying splicing and polyadenylation. The AltPAS pipeline examines gene-transcript alignments and delineates all potential polyA sites irrespective of underlying splicing patterns. Resultant polyA sites from both AltTrans and AltPAS are merged. The generated database reports data on alternative splicing, alternative polyadenylation and the resultant alternate transcript patterns; the basal data is annotated for various biological features. The data (named as integrated AltTrans data) generated for both the organisms of human and mouse is made available through the Alternate Transcript Diversity web site at http://www.ebi.ac.uk/atd/.

Conclusion

The reported data set presents alternate transcript patterns that are annotated for both alternative splicing and alternative polyadenylation. Results based on current transcriptome data indicate that the contribution of alternative splicing is larger than that of alternative polyadenylation.
Automatic pathway building in biological association networks
Authors: Yuryev Anton , Mulyukov Zufar , Kotelnikova Ekaterina , Maslov Sergei , Egorov Sergei , Nikitin Alexander , Daraselia Nikolai , Mazo Ilya
Published: April 2006

Background

Scientific literature is a source of the most reliable and comprehensive knowledge about molecular interaction networks. Formalization of this knowledge is necessary for computational analysis and is achieved by automatic fact extraction using various text-mining algorithms. Most of these techniques suffer from high false positive rates and redundancy of the extracted information. The extracted facts form a large network with no pathways defined.

Results

We describe the methodology for automatic curation of Biological Association Networks (BANs) derived by a natural language processing technology called Medscan. The curated data is used for automatic pathway reconstruction. The algorithm for the reconstruction of signaling pathways is also described and validated by comparison with manually curated pathways and tissue-specific gene expression profiles.

Conclusion

Biological Association Networks extracted by MedScan technology contain sufficient information for constructing thousands of mammalian signaling pathways for multiple tissues. The automatically curated MedScan data is adequate for automatic generation of good quality signaling networks. The automatically generated Regulome pathways and manually curated pathways used for their validation are available free in the ResNetCore database from Ariadne Genomics, Inc. [1]. The pathways can be viewed and analyzed through the use of a free demo version of PathwayStudio software. The Medscan technology is also available for evaluation using the free demo version of PathwayStudio software.
The Gaggle: An open-source software system for integrating bioinformatics software and data sources
Authors: Shannon Paul T , Reiss David J , Bonneau Richard , Baliga Nitin S
Published: April 2006

Background

Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing.

Results

In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy ofseparation of concernsand a policy ofsemantic flexibility, it integrates existing popular programs and web resources into a user-friendly, easily-extended environment.

We demonstrate that four simple data types (names, matrices, networks, and associative arrays) are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration ofHelicobacter pyloripathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous data exploration using a wide range of publicly available data and a variety of popular bioinformatics software tools.

Conclusion

We have integrated diverse databases (for example, KEGG, BioCyc, String) and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer). Through this loose coupling of diverse software and databases the Gaggle enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions), functional associations (operon, chromosomal proximity, phylogenetic pattern), metabolic pathways (KEGG) and Pubmed abstracts (STRING web resource), creating an exploratory environment useful to 'web browser and spreadsheet biologists', to statistically savvy computational biologists, and those in between. The Gaggle uses Java RMI and Java Web Start technologies and can be found athttp://gaggle.systemsbiology.net.
Highly sensitive and specific bioassay for measuring bioactive TGF-β
Authors: Tesseur Ina , Zou Kun , Berber Elisabeth , Zhang Hui , Wyss-Coray Tony
Published: April 2006

Background

Transforming Growth Factor-β (TGF-β) regulates key biological processes during development and in adult tissues and has been implicated in many diseases. To study the biological functions of TGF-β, sensitive, specific, and convenient bioassays are necessary. Here we describe a new cell-based bioassay that fulfills these requirements.

Results

Embryonic fibroblasts fromTgfb1-/-mice were stably transfected with a reporter plasmid consisting of TGF-β responsive Smad-binding elements coupled to a secreted alkaline phosphatase reporter gene (SBE-SEAP). Clone MFB-F11 showed more than 1000-fold induction after stimulation with 1 ng/ml TGF-β1, and detected as little as 1 pg/ml TGF-β1. MFB-F11 cells were highly induced by TGF-β1, TGF-β2 and TGF-β3, but did not show induction with related family members activin, nodal, BMP-2 and BMP-6 or with trophic factors bFGF and BDNF. MFB-F11 cells can detect and quantify TGF-β in biological samples without prior enrichment of TGF-βs, and can detect biologically activated TGF-β in a cell co-culture system.

Conclusion

MFB-F11 cells can be used to rapidly and specifically measure TGF-β with high sensitivity.
Notch signaling through Tramtrack bypasses the mitosis promoting activity of the JNK pathway in the mitotic-to-endocycle transition of Drosophila follicle cells
Authors: Jordan Katherine C , Schaeffer Valerie , Fischer Karin A , Gray Elizabeth E , Ruohola-Baker Hannele
Published: April 2006

Background

The follicle cells of the Drosophila egg chamber provide an excellent model in which to study modulation of the cell cycle. During mid-oogenesis, the follicle cells undergo a variation of the cell cycle, endocycle, in which the cells replicate their DNA, but do not go through mitosis. Previously, we showed that Notch signaling is required for the mitotic-to-endocycle transition, through downregulating String/Cdc25, and Dacapo/p21 and upregulating Fizzy-related/Cdh1.

Results

In this paper, we show that Notch signaling is modulated by Shaggy and temporally induced by the ligand Delta, at the mitotic-to-endocycle transition. In addition, a downstream target of Notch, tramtrack, acts at the mitotic-to-endocycle transition. We also demonstrate that the JNK pathway is required to promote mitosis prior to the transition, independent of the cell cycle components acted on by the Notch pathway.

Conclusion

This work reveals new insights into the regulation of Notch-dependent mitotic-to-endocycle switch.
Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes
Authors: Andersson Jan O , Hirt Robert P , Foster Peter G , Roger Andrew J
Published: April 2006

Background

Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the hybrid-cluster protein, A-type flavoprotein, glucosamine-6-phosphate isomerase, and alcohol dehydrogenase E. These four genes have a limited distribution among sequenced prokaryotic and eukaryotic genomes and were previously implicated in gene transfer events affecting eukaryotes. If our previous contention that these genes were introduced by LGT independently into the diplomonad and Entamoeba lineages were true, we expect that the number of putative transfers and the phylogenetic signal supporting LGT should be stable or increase, rather than decrease, when novel eukaryotic and prokaryotic homologs are added to the analyses.

Results

The addition of homologs from phagotrophic protists, including several Entamoeba species, the pelobiont Mastigamoeba balamuthi, and the parabasalid Trichomonas vaginalis, and a large quantity of sequences from genome projects resulted in an apparent increase in the number of putative transfer events affecting all three domains of life. Some of the eukaryotic transfers affect a wide range of protists, such as three divergent lineages of Amoebozoa, represented by Entamoeba, Mastigamoeba, and Dictyostelium, while other transfers only affect a limited diversity, for example only the Entamoeba lineage. These observations are consistent with a model where these genes have been introduced into protist genomes independently from various sources over a long evolutionary time.

Conclusion

Phylogenetic analyses of the updated datasets using more sophisticated phylogenetic methods, in combination with the gene distribution analyses, strengthened, rather than weakened, the support for LGT as an important mechanism affecting the evolution of these gene families. Thus, gene transfer seems to be an on-going evolutionary mechanism by which genes are spread between unrelated lineages of all three domains of life, further indicating the importance of LGT from non-organellar sources into eukaryotic genomes.
A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage
Authors: Kramer Elena M , Su Huei-Jiun , Wu Cheng-Chiang , Hu Jer-Ming
Published: April 2006

Background

The evolution of type II MADS box genes has been extensively studied in angiosperms. One of the best-understood subfamilies is that of the Arabidopsis gene APETALA3 (AP3). Previous work has demonstrated that the ancestral paleoAP3 lineage was duplicated at some point within the basal eudicots to give rise to the paralogous TM6 and euAP3 lineages. This event was followed in euAP3 orthologs by the replacement of the C-terminal paleoAP3 motif with the derived euAP3 motif. It has been suggested that the new motif was created by an eight-nucleotide insertion that produced a translational frameshift.

Results

The addition of 25 eudicot AP3 homologs to the existing dataset has allowed us to clarify the process by which the euAP3 motif evolved. Phylogenetic analysis indicates that the euAP3/TM6 duplication maps very close to the base of the core eudicots, associated with the families Trochodendraceae and Buxaceae. We demonstrate that although the transformation of paleoAP3 into euAP3 was due to a frameshift mutation, this was the result of a single nucleotide deletion. The use of ancestral character state reconstructions has allowed us to demonstrate that the frameshift was accompanied by few other nucleotide changes. We further confirm that the sequence is evolving as coding region.

Conclusion

This study demonstrates that the simplest of genetic changes can result in the remodeling of protein sequence to produce a kind of molecular 'hopeful monster.' Moreover, such a novel protein motif can become conserved almost immediately on the basis of what appears to be a rapidly generated new function. Given that the existing data on the function of such C-terminal motifs are somewhat disparate and contradictory, we have sought to synthesize previous findings within the context of the current analysis and thereby highlight specific hypotheses that require further investigation before the significance of the euAP3 frameshift event can be fully understood.
"Per cell" normalization method for mRNA measurement by quantitative PCR and microarrays
Authors: Kanno Jun , Aisaki Ken-ichi , Igarashi Katsuhide , Nakatsu Noriyuki , Ono Atsushi , Kodama Yukio , Nagao Taku
Published: April 2006

Background

Transcriptome data from quantitative PCR (Q-PCR) and DNA microarrays are typically obtained from a fixed amount of RNA collected per sample. Therefore, variations in tissue cellularity and RNA yield across samples in an experimental series compromise accurate determination of the absolute level of each mRNA species per cell in any sample. Since mRNAs are copied from genomic DNA, the simplest way to express mRNA level would be as copy number per template DNA, or more practically, as copy number per cell.

Results

Here we report a method (designated the "Percellome" method) for normalizing the expression of mRNA values in biological samples. It provides a "per cell" readout in mRNA copy number and is applicable to both quantitative PCR (Q-PCR) and DNA microarray studies. The genomic DNA content of each sample homogenate was measured from a small aliquot to derive the number of cells in the sample. A cocktail of five external spike RNAs admixed in a dose-graded manner (dose-graded spike cocktail; GSC) was prepared and added to each homogenate in proportion to its DNA content. In this way, the spike mRNAs represented absolute copy numbers per cell in the sample. The signals from the five spike mRNAs were used as a dose-response standard curve for each sample, enabling us to convert all the signals measured to copy numbers per cell in an expression profile-independent manner. A series of samples was measured by Q-PCR and Affymetrix GeneChip microarrays using this Percellome method, and the results showed up to 90 % concordance.

Conclusion

Percellome data can be compared directly among samples and among different studies, and between different platforms, without further normalization. Therefore, "percellome" normalization can serve as a standard method for exchanging and comparing data across different platforms and among different laboratories.
A cross sectional survey of urban Canadian family physicians' provision of minor office procedures
Authors: Sempowski Ian P , Rungi Arne A , Seguin Rachelle
Published: April 2006

Background

A discordance exists between the proportion of Canadian family physicians that we expect should be able to perform minor office procedures and the actual provision of care. This pattern has not been extensively studied. The objective of this study was to determine the current patterns and obstacles relating to the provision of four minor office procedures by GP/FPs in a small city in Ontario, Canada. An additional goal was to determine the impact of the remuneration method on the provision of such services.

Methods

A survey was mailed to all GP/FPs practising in Kingston, Ontario. The main outcomes measured in the study were work setting and remuneration method, current procedural practices with respect to four procedures, reasons for not performing procedures, current skill levels, and desire to upgrade.

Results

Surveys were mailed to all 108 GP/FPs in the City of Kingston. Completed surveys were collected for 82 percent (89/108) and 10 were excluded leaving 79 eligible participants. The percentages of GP/FPs who reported performing the procedure were as follows: dermatological excision (63.3%), endometrial biopsy (35.4%), shoulder injection (31.6%), and knee injection (43.0%). The majority of GP/FPs who would not do the procedure themselves would refer to a specialist colleague rather than to another GP/FP. The top reason cited for not performing a specific procedure was "lack of up to date skills" followed by "lack of time". The latter was the only statistically significant difference reported between GP/FPs working in Family Health Networks and GP/FPs working in fee for service settings (26.7% vs 47.0%, χ2 = 4.191 p = 0.041).

Conclusion

A large number of Kingston, Ontario GP/FPs refer patients who require one of four minor office-based procedures for specialist consultation. Referral to other GP/FP colleagues appears underutilized. A perceived lack of up to date skills and a lack of time appear to be concerns. GP/FPs working in Family Health Networks were more likely to perform these procedures themselves. Further studies would clarify the role of changes in medical education, the role of continuing education, and the impact of different remuneration models.
Herpes encephalitis presenting as mild aphasia: Case report
Authors: Khan Omar A , Ramsay Allan
Published: April 2006

Background

Encephalitis presenting as a change in mental status can be challenging to recognize in the primary care setting. However, early detection via a low threshold of suspicion can be useful, leading in turn to early treatment and improved survival.

Case presentation

We present a case which we consider relevant to primary care practitioners. The patient in question presented with relatively mild mental status changes, progressing to confusion, dysnomia and delirium over a period of three days. While infection did not appear to be the leading cause on her differential diagnosis, she was found on extensive workup to have encephalitis caused by Herpes Simplex Virus type 1.

Conclusion

The case is instructive for general practitioners and other clinicians to maintain vigilance for central nervous system (CNS) infections which may present atypically.
Characteristics and prevalence of hardcore smokers attending UK general practitioners
Authors: MacIntosh Hannah , Coleman Tim
Published: April 2006

Background

Smoking remains a public health problem and although unsolicited GPs' advice against smoking causes between one and three percent of smokers to stop, a significant proportion of smokers are particularly resistant to the notion of stopping smoking. These resistant smokers have been called "hardcore smokers" and although 16% of smokers in the community are hardcore, little is known about hardcore smokers presenting to primary care physicians. Consequently, this study reports the characteristics and prevalence of hardcore smokers attending UK GPs.

Methods

A cross-sectional survey using data from two different research projects was conducted. Data for this analysis had been collected from surgery consultation sessions with 73 GPs in Leicestershire, England, (42 GPs from one project). Research assistants distributed pre-consultation questionnaires to 4147 adults attending GPs' surgery sessions. Questionnaires identified regular smokers, the proportion of hardcore smokers and their characteristics. Non-hardcore and hardcore smokers' ages, gender and nicotine addiction levels were compared.

Results

1170 regular smokers attended surgery sessions and, 16.1% (95% CI, 14.1 to 18.4) were hardcore smokers. Hardcore smokers had higher levels of nicotine addiction than others (p = 0.000), measured by the Heaviness of Smoking Index and were more likely to be male [50.5% hardcore versus 35.3% non-hardcore, (OR = 1.88, 95% CI = 1.4 to 2.6)] but no age differences were observed between groups.

Conclusion

A significant minority of the smokers who present in general practice are resistant to the notion of smoking cessation and these smokers are more heavily nicotine addicted than others. Although clinical guidelines suggest that GPs should regularly advise all smokers against smoking, it is probable that hardcore smokers do not respond positively to this and help to make up the 97%–99% of smokers who do not quit after being advised to stop smoking by GPs. General practitioners need to find approaches for raising the issue of smoking during consultations in ways that do not reinforce the negative opinions of hardcore smokers concerning smoking cessation.
Analysis of Bordetella pertussis pertactin and pertussis toxin types from Queensland, Australia, 1999–2003
Authors: Byrne Shane , Slack Andrew T
Published: April 2006

Background

In Australia two acellular Bordetella pertussis vaccines have replaced the use of a whole cell vaccine. Both of the licensed acellular vaccines contain the following three components; pertussis toxoid, pertussis filamentous haemagglutinin and the 69 kDa pertactin adhesin. One vaccine also contains pertussis fimbriae 2 and 3. Various researchers have postulated that herd immunity due to high levels of pertussis vaccination might be influencing the makeup of endemic B. pertussis populations by selective pressure for strains possessing variants of these genes, in particular the pertactin gene type. Some publications have suggested that B. pertussis variants may be contributing to a reduced efficacy of the existing vaccines and a concomitant re-emergence of pertussis within vaccinated populations. This study was conducted to survey the pertactin and pertussis toxin subunit 1 types from B. pertussis isolates in Queensland, Australia following the introduction of acellular vaccines.

Methods

Forty-six B. pertussis isolates recovered from Queensland patients between 1999 and 2003 were examined by both DNA sequencing and LightCycler™ real time PCR to determine their pertactin and pertussis toxin subunit 1 genotypes.

Results

Pertactin typing showed that 38 isolates possessed the prn1 allele, 3 possessed the prn2 allele and 5 possessed the prn3 allele. All forty-six isolates possessed the pertussis toxin ptxS1A genotype. Amongst the circulating B. pertussis population in Queensland, 82.5% of the recovered clinical isolates therefore possessed the prn1/ptxS1A genotype.

Conclusion

The results of this study compared to historical research on Queensland isolates suggest that B. pertussis pertactin and pertussis toxin variants are not becoming more prevalent in Queensland since the introduction of the acellular vaccines. Current prevalences of pertactin variants are significantly different to that described in a number of other countries with high vaccine coverage. Relative paucity of recovered isolates compared to notified infections, due primarily to non culture based pertussis diagnostics is however a confounding factor in the assessment of variant prevalence.